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Osuna-Prieto FJ, Xu H, Ortiz-Alvarez L, Di X, Kohler I, Jurado-Fasoli L, Rubio-Lopez J, Plaza-Díaz J, Vilchez-Vargas R, Link A, Gil A, Ruiz JR, Rensen PCN, Martinez-Tellez B. The relative abundance of fecal bacterial species belonging to the Firmicutes and Bacteroidetes phyla is related to plasma levels of bile acids in young adults. Metabolomics 2023; 19:54. [PMID: 37278866 DOI: 10.1007/s11306-023-02016-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 05/05/2023] [Indexed: 06/07/2023]
Abstract
BACKGROUND Gut bacteria play a crucial role in the metabolism of bile acids (BA). Whether an association exists between the fecal microbiota composition and circulating BA levels in humans is poorly understood. Here, we investigated the relationship between fecal microbiota diversity and composition with plasma levels of BA in young adults. METHODS Fecal microbiota diversity/composition was analyzed with 16S rRNA sequencing in 80 young adults (74% women; 21.9 ± 2.2 years old). Plasma levels of BA were measured using liquid chromatography-tandem mass spectrometry. PERMANOVA and Spearman correlation analyses were used to investigate the association between fecal microbiota parameters and plasma levels of BA. RESULTS Fecal microbiota beta (P = 0.025) and alpha diversity indexes of evenness (rho = 0.237, P = 0.033), Shannon (rho = 0.313, P = 0.004), and inverse Simpson (rho = 0.283, P = 0.010) were positively associated with plasma levels of the secondary BA glycolithocholic acid (GLCA). The relative abundance of genera belonging to the Firmicutes and Bacteroidetes phyla was positively correlated with plasma levels of GLCA (all rho ≥ 0.225, P ≤ 0.049). However, the relative abundance of species from Firmicutes and Bacteroidetes phyla were negatively correlated with plasma levels of primary and secondary BA (all rho ≤ - 0.220, P ≤ 0.045), except for the relative abundance of Bacteroides vulgatus, Alistipes onderdonkii, and Bacteroides xylanisolvens species (Bacteroidetes phylum) that were positively correlated with the plasma levels of GLCA. CONCLUSIONS The relative abundance of specific fecal bacteria species is associated with plasma levels of BA in young adults. However, further investigations are required to validate whether the composition of the gut microbiota can regulate the plasma concentrations of BA in humans.
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Affiliation(s)
- Francisco J Osuna-Prieto
- Department of Physical Education and Sports, Faculty of Sport Sciences, PROmoting FITness and Health through Physical Activity Research Group (PROFITH), Sport and Health University Research Institute (iMUDS), University of Granada, Granada, Spain.
- Department of Analytical Chemistry, University of Granada, 18071, Granada, Spain.
| | - Huiwen Xu
- Department of Physical Education and Sports, Faculty of Sport Sciences, PROmoting FITness and Health through Physical Activity Research Group (PROFITH), Sport and Health University Research Institute (iMUDS), University of Granada, Granada, Spain
- Department of Biochemistry and Molecular Biology II, Institute of Nutrition and Food Technology, Center for Biomedical Research, University of Granada, Granada, Spain
| | - Lourdes Ortiz-Alvarez
- Department of Physical Education and Sports, Faculty of Sport Sciences, PROmoting FITness and Health through Physical Activity Research Group (PROFITH), Sport and Health University Research Institute (iMUDS), University of Granada, Granada, Spain
- Department of Biochemistry and Molecular Biology II, Institute of Nutrition and Food Technology, Center for Biomedical Research, University of Granada, Granada, Spain
| | - Xinyu Di
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | - Isabelle Kohler
- Division of BioAnalytical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Center for Analytical Sciences Amsterdam, Amsterdam, The Netherlands
| | - Lucas Jurado-Fasoli
- Department of Physical Education and Sports, Faculty of Sport Sciences, PROmoting FITness and Health through Physical Activity Research Group (PROFITH), Sport and Health University Research Institute (iMUDS), University of Granada, Granada, Spain
- Department of Physiology. Faculty of Medicine, University of Granada, Av.Conocimiento S/N, 18011, Granada, Spain
| | - Jose Rubio-Lopez
- Department of Physical Education and Sports, Faculty of Sport Sciences, PROmoting FITness and Health through Physical Activity Research Group (PROFITH), Sport and Health University Research Institute (iMUDS), University of Granada, Granada, Spain
- Cirugía General Y del Aparato Digestivo, Complejo Hospitalario de Jaen, Jaén, Spain
| | - Julio Plaza-Díaz
- Department of Biochemistry and Molecular Biology II, Institute of Nutrition and Food Technology, Center for Biomedical Research, University of Granada, Granada, Spain
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, K1H 8L1, Canada
| | - Ramiro Vilchez-Vargas
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
| | - Alexander Link
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
| | - Angel Gil
- Department of Biochemistry and Molecular Biology II, Institute of Nutrition and Food Technology, Center for Biomedical Research, University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria, ibs. Granada, Granada, Spain
- CIBEROBN, Biomedical Research Networking Center for Physiopathology of Obesity and Nutrition, Carlos III Health Institute, Madrid, Spain
| | - Jonatan R Ruiz
- Department of Physical Education and Sports, Faculty of Sport Sciences, PROmoting FITness and Health through Physical Activity Research Group (PROFITH), Sport and Health University Research Institute (iMUDS), University of Granada, Granada, Spain.
- Instituto de Investigación Biosanitaria, ibs. Granada, Granada, Spain.
- CIBEROBN, Biomedical Research Networking Center for Physiopathology of Obesity and Nutrition, Carlos III Health Institute, Madrid, Spain.
| | - Patrick C N Rensen
- Department of Medicine, Division of Endocrinology, and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Borja Martinez-Tellez
- Department of Physical Education and Sports, Faculty of Sport Sciences, PROmoting FITness and Health through Physical Activity Research Group (PROFITH), Sport and Health University Research Institute (iMUDS), University of Granada, Granada, Spain.
- CIBEROBN, Biomedical Research Networking Center for Physiopathology of Obesity and Nutrition, Carlos III Health Institute, Madrid, Spain.
- Department of Medicine, Division of Endocrinology, and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, The Netherlands.
- Department of Education, Faculty of Education Sciences and SPORT Research Group (CTS-1024), CERNEP Research Center, University of Almería, Almería, Spain.
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Lehr K, Nikitina D, Vilchez-Vargas R, Steponaitiene R, Thon C, Skieceviciene J, Schanze D, Zenker M, Malfertheiner P, Kupcinskas J, Link A. Microbial composition of tumorous and adjacent gastric tissue is associated with prognosis of gastric cancer. Sci Rep 2023; 13:4640. [PMID: 36944721 PMCID: PMC10030820 DOI: 10.1038/s41598-023-31740-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 03/16/2023] [Indexed: 03/23/2023] Open
Abstract
Helicobacter pylori (H. pylori) infection has been considered as the main causal factor in gastric carcinogenesis, but other bacterial species may also play an important role in pathophysiology of gastric cancer. The aim of the study was to explore the link between gastric cancer prognosis and the mucosal microbial community in tumorous and adjacent gastric tissue. The bacterial profile was analysed using 16S sequencing (V1-V2 region). Microbial differences were mostly characterized by lower relative abundances of H. pylori in tumorous gastric tissues. Bacterial community and outcome data analysis revealed the genus Fusobacterium and Prevotella significantly associated with worse overall survival in gastric cancer patients. In particular, Fusobacterium was associated with significant increase in hazard ratio in both univariable and multivariable analysis and independently validated using TCMA data. Phylogenetic biodiversity of Fusobacterium species in the stomach revealed F. periodonticum as the most prevalent in healthy subjects, while F. nucleatum was most abundant in patients with gastric cancer. Bacterial community network analysis in gastric cancer suggests substantial complexity and a strong interplay between F. nucleatum and Prevotella. In summary, mucosal microbial community in the stomach was associated with worse overall survival in gastric cancer patients. Strongest negative impact on prognosis was linked to the abundance of F. nucleatum in tumorous specimens, suggesting its translational relevance in management of gastric cancer patients.
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Affiliation(s)
- Konrad Lehr
- Department of Gastroenterology, Hepatology and Infectious Diseases, Section of Molecular Gastroenterology and Microbiota-associated Diseases, Otto-von-Guericke University Magdeburg, Magdeburg, Germany.
| | - Darja Nikitina
- Institute for Digestive Research, Lithuanian University of Health Sciences Kaunas, Kaunas, Lithuania
| | - Ramiro Vilchez-Vargas
- Department of Gastroenterology, Hepatology and Infectious Diseases, Section of Molecular Gastroenterology and Microbiota-associated Diseases, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Ruta Steponaitiene
- Institute for Digestive Research, Lithuanian University of Health Sciences Kaunas, Kaunas, Lithuania
| | - Cosima Thon
- Department of Gastroenterology, Hepatology and Infectious Diseases, Section of Molecular Gastroenterology and Microbiota-associated Diseases, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Jurgita Skieceviciene
- Institute for Digestive Research, Lithuanian University of Health Sciences Kaunas, Kaunas, Lithuania
| | - Denny Schanze
- Institute of Human Genetics, Otto-Von-Guericke University, Magdeburg, Germany
| | - Martin Zenker
- Institute of Human Genetics, Otto-Von-Guericke University, Magdeburg, Germany
| | - Peter Malfertheiner
- Department of Gastroenterology, Hepatology and Infectious Diseases, Section of Molecular Gastroenterology and Microbiota-associated Diseases, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
- Department of Internal Medicine 2, University Hospital, LMU Munich, Munich, Germany
| | - Juozas Kupcinskas
- Institute for Digestive Research, Lithuanian University of Health Sciences Kaunas, Kaunas, Lithuania
- Department of Gastroenterology, Lithuanian University of Health Sciences Kaunas, Kaunas, Lithuania
| | - Alexander Link
- Department of Gastroenterology, Hepatology and Infectious Diseases, Section of Molecular Gastroenterology and Microbiota-associated Diseases, Otto-von-Guericke University Magdeburg, Magdeburg, Germany.
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Povedano-Priego C, Jroundi F, Solari PL, Guerra-Tschuschke I, Abad-Ortega MDM, Link A, Vilchez-Vargas R, Merroun ML. Unlocking the bentonite microbial diversity and its implications in selenium bioreduction and biotransformation: Advances in deep geological repositories. J Hazard Mater 2023; 445:130557. [PMID: 36502723 DOI: 10.1016/j.jhazmat.2022.130557] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/28/2022] [Accepted: 12/03/2022] [Indexed: 06/17/2023]
Abstract
Selenium, 79Se, is one of the most critical radionuclides in radioactive waste disposed in future deep geological repositories (DGRs). Here, we investigate the impact of bentonite microbial communities on the allotropic transformation of Se(IV) bioreduction products under DGR relevant conditions. In addition, Se amendment-dependent shifts in the bentonite microbial populations are assessed. Microcosms of water-saturated bentonites were spiked with a bacterial consortium, treated with selenite and incubated anaerobically for six months. A combination of X-Ray Absorption Spectroscopy, Electron Microscopy, and Raman Spectroscopy was used to track the allotropic changes of the Se bioreduction products. Interestingly, the color of bentonite shifted from orange to black in the selenite-treated microcosms. In the orange layers, amorphous or monoclinic Se(0) were identified, whilst black precipitates consisted of stable trigonal Se(0) form. Illumina DNA sequencing indicated the distribution of strains with Se(IV) reducing and Se(0) allotropic biotransformation potential, like Pseudomonas, Stenotrophomonas, Desulfosporosinus, and unclassified-Desulfuromonadaceae. The archaea Methanosarcina decreased its abundance in the presence of Se(IV), probably caused by this oxyanion toxicity. These findings provide an understanding of the bentonite microbial strategies involved in the immobilization of Se(IV) by reduction processes, and prove their implication in the allotropic biotransformation from amorphous to trigonal Se(0) under DGR relevant conditions.
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Affiliation(s)
| | - Fadwa Jroundi
- Department of Microbiology, Faculty of Sciences, University of Granada, Granada, Spain.
| | - Pier L Solari
- MARS Beamline, Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, Gif-sur-Yvette Cedex, France.
| | | | | | - Alexander Link
- Department of Gastroenterology, Hepatology and Infectious Diseases, University of Magdeburg, Magdeburg, Germany.
| | - Ramiro Vilchez-Vargas
- Department of Gastroenterology, Hepatology and Infectious Diseases, University of Magdeburg, Magdeburg, Germany.
| | - Mohamed L Merroun
- Department of Microbiology, Faculty of Sciences, University of Granada, Granada, Spain.
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4
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Ortiz-Alvarez L, Acosta FM, Xu H, Sanchez-Delgado G, Vilchez-Vargas R, Link A, Plaza-Díaz J, Llamas JM, Gil A, Labayen I, Rensen PCN, Ruiz JR, Martinez-Tellez B. Fecal microbiota composition is related to brown adipose tissue 18F-fluorodeoxyglucose uptake in young adults. J Endocrinol Invest 2023; 46:567-576. [PMID: 36242744 PMCID: PMC9938059 DOI: 10.1007/s40618-022-01936-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 10/07/2022] [Indexed: 10/17/2022]
Abstract
OBJECTIVE Human brown adipose tissue (BAT) has gained considerable attention as a potential therapeutic target for obesity and its related cardiometabolic diseases; however, whether the gut microbiota might be an efficient stimulus to activate BAT metabolism remains to be ascertained. We aimed to investigate the association of fecal microbiota composition with BAT volume and activity and mean radiodensity in young adults. METHODS 82 young adults (58 women, 21.8 ± 2.2 years old) participated in this cross-sectional study. DNA was extracted from fecal samples and 16S rRNA sequencing was performed to analyse the fecal microbiota composition. BAT was determined via a static 18F-fluorodeoxyglucose (18F-FDG) positron emission tomography-computed tomography scan (PET/CT) after a 2 h personalized cooling protocol. 18F-FDG uptake was also quantified in white adipose tissue (WAT) and skeletal muscles. RESULTS The relative abundance of Akkermansia, Lachnospiraceae sp. and Ruminococcus genera was negatively correlated with BAT volume, BAT SUVmean and BAT SUVpeak (all rho ≤ - 0.232, P ≤ 0.027), whereas the relative abundance of Bifidobacterium genus was positively correlated with BAT SUVmean and BAT SUVpeak (all rho ≥ 0.262, P ≤ 0.012). On the other hand, the relative abundance of Sutterellaceae and Bifidobacteriaceae families was positively correlated with 18F-FDG uptake by WAT and skeletal muscles (all rho ≥ 0.213, P ≤ 0.042). All the analyses were adjusted for the PET/CT scan date as a proxy of seasonality. CONCLUSION Our results suggest that fecal microbiota composition is involved in the regulation of BAT and glucose uptake by other tissues in young adults. Further studies are needed to confirm these findings. CLINICAL TRIAL INFORMATION ClinicalTrials.gov no. NCT02365129 (registered 18 February 2015).
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Affiliation(s)
- L Ortiz-Alvarez
- PROFITH (PROmoting FITness and Health Through Physical Activity) Research Group, Sport and Health University Research Institute (iMUDS), University of Granada, Granada, Spain.
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, Granada, Spain.
| | - F M Acosta
- PROFITH (PROmoting FITness and Health Through Physical Activity) Research Group, Sport and Health University Research Institute (iMUDS), University of Granada, Granada, Spain
- Turku PET Centre, University of Turku, Turku, Finland
- Turku PET Centre, Turku University Hospital, Turku, Finland
- InFLAMES Research Flagship Centre, University of Turku, Turku, Finland
- Department of Physical and Sports Education, School of Sports Science, University of Granada, Granada, Spain
| | - H Xu
- PROFITH (PROmoting FITness and Health Through Physical Activity) Research Group, Sport and Health University Research Institute (iMUDS), University of Granada, Granada, Spain
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, Granada, Spain
| | - G Sanchez-Delgado
- Department of Physical and Sports Education, School of Sports Science, University of Granada, Granada, Spain
- Pennington Biomedical Research Center, Baton Rouge, LA, 70808, USA
| | - R Vilchez-Vargas
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-Von-Guericke-University Magdeburg, Magdeburg, Germany
| | - A Link
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-Von-Guericke-University Magdeburg, Magdeburg, Germany
| | - J Plaza-Díaz
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, Granada, Spain
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, K1H 8L1, Canada
| | - J M Llamas
- Instituto de Investigación Biosanitaria Ibs Granada, 18014, Granada, Spain
- Servicio de Medicina Nuclear, Hospital Universitario Virgen de las Nieves, Granada, Spain
| | - A Gil
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria Ibs Granada, 18014, Granada, Spain
- Centro de Investigación Biomédica En Red (CIBER) Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III (ISCIII), Málaga, Spain
- Institute of Nutrition and Food Technology "José Mataix", Biomedical Research Center, Parque Tecnológico Ciencias de la Salud, University of Granada, Armilla, Granada, Spain
- Instituto de Investigación Biosanitaria, Ibs.Granada, Granada, Spain
| | - I Labayen
- Institute for Innovation and Sustainable Development in Food Chain (IS-FOOD), Public University of Navarra, Campus de Arrosadía, Pamplona, Spain
| | - P C N Rensen
- Department of Medicine, Division of Endocrinology, and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - J R Ruiz
- PROFITH (PROmoting FITness and Health Through Physical Activity) Research Group, Sport and Health University Research Institute (iMUDS), University of Granada, Granada, Spain
- Department of Physical and Sports Education, School of Sports Science, University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria, Ibs.Granada, Granada, Spain
| | - B Martinez-Tellez
- PROFITH (PROmoting FITness and Health Through Physical Activity) Research Group, Sport and Health University Research Institute (iMUDS), University of Granada, Granada, Spain.
- Department of Medicine, Division of Endocrinology, and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, The Netherlands.
- Department of Education, Faculty of Education Sciences, SPORT Research Group (CTS-1024), CERNEP Research Center, University of Almería, Almería, Spain.
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5
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Pinel-Cabello M, Jauregui R, Jroundi F, Geffers R, Jarek M, Link A, Vilchez-Vargas R, Merroun ML. Genetic mechanisms for Se(VI) reduction and synthesis of trigonal 1-D nanostructures in Stenotrophomonas bentonitica: Perspectives in eco-friendly nanomaterial production and bioremediation. Sci Total Environ 2023; 862:160635. [PMID: 36476772 DOI: 10.1016/j.scitotenv.2022.160635] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/15/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Selenate (Se(VI)) is one of the most soluble and toxic species of Se. Microbial Se(VI) reduction is an efficient tool for bioremediation strategies. However, this process is limited to a few microorganisms, and its molecular basis remains unknown. We present detailed Se(VI)-resistance mechanisms under 50 and 200 mM, in Stenotrophomonas bentonitica BII-R7, coupling enzymatic reduction of Se(VI) to formation of less toxic trigonal Se (t-Se). The results reveal a concentration-dependent response. Despite the lack of evidence of Se(VI)-reduction to Se(0) under 50 mM Se(VI), many genes were highly induced, indicating that Se(VI)-resistance could be based on intracellular reduction to Se(IV), mainly through molybdenum-dependent enzymes (e.g. respiratory nitrate reductase), and antioxidant activity by enzymes like glutathione peroxidase. Although exposure to 200 mM provoked a sharp drop in gene expression, a time-dependent process of reduction and formation of amorphous (a), monoclinic (m) and t-Se nanostructures was unravelled: a-Se nanospheres were initially synthesized intracellularly, which would transform into m-Se and finally into t-Se nanostructures during the following phases. This is the first work describing an intracellular Se(VI) reduction and biotransformation process to long-term stable and insoluble t-Se nanomaterials. These results expand the fundamental understanding of Se biogeochemical cycling, and the effectiveness of BII-R7 for bioremediation purposes.
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Affiliation(s)
| | - Ruy Jauregui
- AgResearch Grasslands Research Centre, Tennent Drive, Palmerston North, New Zealand
| | - Fadwa Jroundi
- Department of Microbiology, University of Granada, Granada, Spain
| | - Robert Geffers
- Genome Analytics, Helmholtz Centre for Infection Research (HZI), 38124 Braunschweig, Germany
| | - Michael Jarek
- Genome Analytics, Helmholtz Centre for Infection Research (HZI), 38124 Braunschweig, Germany
| | - Alexander Link
- Department of Gastroenterology, Hepatology and Infectious Diseases, University of Magdeburg, Leipziger Str. 44, 39120 Magdeburg, Germany
| | - Ramiro Vilchez-Vargas
- Department of Gastroenterology, Hepatology and Infectious Diseases, University of Magdeburg, Leipziger Str. 44, 39120 Magdeburg, Germany
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6
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Nikitina D, Lehr K, Vilchez-Vargas R, Jonaitis LV, Urba M, Kupcinskas J, Skieceviciene J, Link A. Comparison of genomic and transcriptional microbiome analysis in gastric cancer patients and healthy individuals. World J Gastroenterol 2023; 29:1202-1218. [PMID: 36926663 PMCID: PMC10011954 DOI: 10.3748/wjg.v29.i7.1202] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/19/2022] [Accepted: 12/21/2022] [Indexed: 02/21/2023] Open
Abstract
BACKGROUND Helicobacter pylori and the stomach microbiome play a crucial role in gastric carcinogenesis, and detailed characterization of the microbiome is necessary for a better understanding of the pathophysiology of the disease. There are two common modalities for microbiome analysis: DNA (16S rRNA gene) and RNA (16S rRNA transcript) sequencing. The implications from the use of one or another sequencing approach on the characterization and comparability of the mucosal microbiome in gastric cancer (GC) are poorly studied.
AIM To characterize the microbiota of GC using 16S rRNA gene and its transcript and determine difference in the bacterial composition.
METHODS In this study, 316 DNA and RNA samples extracted from 105 individual stomach biopsies were included. The study cohort consisted of 29 healthy control individuals and 76 patients with GC. Gastric tissue biopsy samples were collected from damaged mucosa and healthy mucosa at least 5 cm from the tumor tissue. From the controls, healthy stomach mucosa biopsies were collected. From all biopsies RNA and DNA were extracted. RNA was reverse transcribed into cDNA. V1-V2 region of bacterial 16S rRNA gene from all samples were amplified and sequenced on an Illumina MiSeq platform. Bray-Curtis algorithm was used to construct sample-similarity matrices abundances of taxonomic ranks in each sample type. For significant differences between groups permutational multivariate analysis of variance and Mann-Whitney test followed by false-discovery rate test were used.
RESULTS Microbial analysis revealed that only a portion of phylotypes (18%-30%) overlapped between microbial profiles obtained from DNA and RNA samples. Detailed analysis revealed differences between GC and controls depending on the chosen modality, identifying 17 genera at the DNA level and 27 genera at the RNA level. Ten of those bacteria were found to be different from the control group at both levels. The key taxa showed congruent results in various tests used; however, differences in 7 bacteria taxa were found uniquely only at the DNA level, and 17 uniquely only at the RNA level. Furthermore, RNA sequencing was more sensitive for detecting differences in bacterial richness, as well as differences in the relative abundance of Reyranella and Sediminibacterium according to the type of GC. In each study group (control, tumor, and tumor adjacent) were found differences between DNA and RNA bacterial profiles.
CONCLUSION Comprehensive microbial study provides evidence for the effect of choice of sequencing modality on the microbiota profile, as well as on the identified differences between case and control.
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Affiliation(s)
- Darja Nikitina
- Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas 44307, Lithuania
| | - Konrad Lehr
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke University Hospital, Magdeburg 39120, Germany
| | - Ramiro Vilchez-Vargas
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke University Hospital, Magdeburg 39120, Germany
| | | | - Mindaugas Urba
- Department of Gastroenterology, Lithuanian University of Health Sciences, Kaunas 44307, Lithuania
| | - Juozas Kupcinskas
- Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas 44307, Lithuania
- Department of Gastroenterology, Lithuanian University of Health Sciences, Kaunas 44307, Lithuania
| | - Jurgita Skieceviciene
- Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas 44307, Lithuania
| | - Alexander Link
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke University Hospital, Magdeburg 39120, Germany
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7
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Xu H, Jurado-Fasoli L, Ortiz-Alvarez L, Osuna-Prieto FJ, Kohler I, Di X, Vilchez-Vargas R, Link A, Plaza-Díaz J, Gil A, Rensen PCN, Ruiz JR, Martinez-Tellez B. Plasma Levels of Omega-3 and Omega-6 Derived Oxylipins Are Associated with Fecal Microbiota Composition in Young Adults. Nutrients 2022; 14:nu14234991. [PMID: 36501021 PMCID: PMC9736377 DOI: 10.3390/nu14234991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/16/2022] [Accepted: 11/21/2022] [Indexed: 11/25/2022] Open
Abstract
Pre-clinical studies suggest that circulating oxylipins, i.e., the oxidation products of polyunsaturated fatty acids (PUFAs), modulate gut microbiota composition in mice, but there is no information available in humans. Therefore, this study aimed to investigate the relationship between omega-3 and omega-6 derived oxylipins plasma levels and fecal microbiota composition in a cohort of young adults. 80 young adults (74% women; 21.9 ± 2.2 years old) were included in this cross-sectional study. Plasma levels of oxylipins were measured using liquid chromatography-tandem mass spectrometry. Fecal microbiota composition was analyzed by V3-V4 16S rRNA gene sequencing. We observed that plasma levels of omega-3 derived oxylipins were positively associated with the relative abundance of Clostridium cluster IV genus (Firmicutes phylum; rho ≥ 0.415, p ≤ 0.009) and negatively associated with the relative abundance of Sutterella genus (Proteobacteria phylum; rho ≥ -0.270, p ≤ 0.041), respectively. Moreover, plasma levels of omega-6 derived oxylipins were negatively associated with the relative abundance of Acidaminococcus and Phascolarctobacterium genera (Firmicutes phylum; all rho ≥ -0.263, p ≤ 0.024), as well as Sutterella, Succinivibrio, and Gemmiger genera (Proteobacteria phylum; all rho ≥ -0.263, p ≤ 0.024). Lastly, the ratio between omega-6 and omega-3 oxylipins plasma levels was negatively associated with the relative abundance of Clostridium cluster IV genus (Firmicutes phylum; rho = -0.334, p = 0.004) and Butyricimonas genus (Bacteroidetes phylum; rho = -0.292, p = 0.014). In conclusion, our results show that the plasma levels of omega-3 and omega-6 derived oxylipins are associated with the relative abundance of specific fecal bacteria genera.
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Affiliation(s)
- Huiwen Xu
- PROFITH (PROmoting FITness and Health through Physical Activity) Research Group, Sport and Health University Research Institute (iMUDS), Department of Physical and Sports Education, Faculty of Sport Sciences, University of Granada, 18071 Granada, Spain
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, 18071 Granada, Spain
| | - Lucas Jurado-Fasoli
- PROFITH (PROmoting FITness and Health through Physical Activity) Research Group, Sport and Health University Research Institute (iMUDS), Department of Physical and Sports Education, Faculty of Sport Sciences, University of Granada, 18071 Granada, Spain
- Department of Physiology, Faculty of Medicine, University of Granada, 18071 Granada, Spain
| | - Lourdes Ortiz-Alvarez
- PROFITH (PROmoting FITness and Health through Physical Activity) Research Group, Sport and Health University Research Institute (iMUDS), Department of Physical and Sports Education, Faculty of Sport Sciences, University of Granada, 18071 Granada, Spain
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, 18071 Granada, Spain
| | - Francisco J. Osuna-Prieto
- PROFITH (PROmoting FITness and Health through Physical Activity) Research Group, Sport and Health University Research Institute (iMUDS), Department of Physical and Sports Education, Faculty of Sport Sciences, University of Granada, 18071 Granada, Spain
- Department of Analytical Chemistry, Faculty of Sciences, University of Granada, 18071 Granada, Spain
| | - Isabelle Kohler
- Division of BioAnalytical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, 1081 Amsterdam, The Netherlands
- Center for Analytical Sciences Amsterdam, 1081 Amsterdam, The Netherlands
| | - Xinyu Di
- Department of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research (LACDR), Leiden University, 2300 Leiden, The Netherlands
| | - Ramiro Vilchez-Vargas
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke-University Magdeburg, 39106 Magdeburg, Germany
| | - Alexander Link
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke-University Magdeburg, 39106 Magdeburg, Germany
| | - Julio Plaza-Díaz
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, 18071 Granada, Spain
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada
- Instituto de Investigación Biosanitaria, ibs.Granada, 18014 Granada, Spain
| | - Angel Gil
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, 18071 Granada, Spain
- Instituto de Investigación Biosanitaria, ibs.Granada, 18014 Granada, Spain
- CIBEROBN, Biomedical Research Networking Center for Physiopathology of Obesity and Nutrition, Carlos III Health Institute, 28029 Madrid, Spain
- Institute of Nutrition and Food Technology, Center of Biomedical Research, University of Granada, 18071 Granada, Spain
| | - Patrick C. N. Rensen
- Department of Medicine, Division of Endocrinology, and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2300 Leiden, The Netherlands
| | - Jonatan R. Ruiz
- PROFITH (PROmoting FITness and Health through Physical Activity) Research Group, Sport and Health University Research Institute (iMUDS), Department of Physical and Sports Education, Faculty of Sport Sciences, University of Granada, 18071 Granada, Spain
- Instituto de Investigación Biosanitaria, ibs.Granada, 18014 Granada, Spain
- Correspondence: (J.R.R.); (B.M.-T.)
| | - Borja Martinez-Tellez
- PROFITH (PROmoting FITness and Health through Physical Activity) Research Group, Sport and Health University Research Institute (iMUDS), Department of Physical and Sports Education, Faculty of Sport Sciences, University of Granada, 18071 Granada, Spain
- Department of Medicine, Division of Endocrinology, and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2300 Leiden, The Netherlands
- Department of Education, Faculty of Education Sciences and SPORT Research Group (CTS-1024), CERNEP Research Center, University of Almería, 04120 Almería, Spain
- Correspondence: (J.R.R.); (B.M.-T.)
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8
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Abstract
Microbiota research has received an increasing attention for its role in disease development and fungi are considered as one of the key players in the microbial niche. Various sequencing approaches have been applied to uncover the role of fungal community in health and disease; however, little is known on the performance of various primers and comparability between the studies. Motivated by the recent publications, we performed a systematic comparison of the 18S and ITS regions to identify the impact of various primers on the sequencing results. Using four pairs of primers extensively used in literature, fungal community was retrieve from 25 fecal samples, and applying high throughput sequencing; and the results were compared in order to select the most suitable primers for fungal detection in human fecal samples. Considering the high variability between samples, primers described in the Earth microbiome project detected the broadest fungal spectrum suggesting its superior performance in mycobiome research.
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Affiliation(s)
- Crispin Wiesmann
- Department of Gastroenterology, Hepatology, and Infectious Diseases, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Konrad Lehr
- Department of Gastroenterology, Hepatology, and Infectious Diseases, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Juozas Kupcinskas
- Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania,Department of Gastroenterology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Ramiro Vilchez-Vargas
- Department of Gastroenterology, Hepatology, and Infectious Diseases, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Alexander Link
- Department of Gastroenterology, Hepatology, and Infectious Diseases, Otto-von-Guericke University Magdeburg, Magdeburg, Germany,CONTACT Alexander Link Department of Gastroenterology, Hepatology and Infectious Diseases Otto-von-Guericke University Magdeburg, Leipziger Straße 44 39120Magdeburg, Germany
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9
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Gelmez E, Lehr K, Kershaw O, Frentzel S, Vilchez-Vargas R, Bank U, Link A, Schüler T, Jeron A, Bruder D. Characterization of Maladaptive Processes in Acute, Chronic and Remission Phases of Experimental Colitis in C57BL/6 Mice. Biomedicines 2022; 10:biomedicines10081903. [PMID: 36009449 PMCID: PMC9405850 DOI: 10.3390/biomedicines10081903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/01/2022] [Accepted: 08/02/2022] [Indexed: 11/20/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic recurrent inflammatory disease with unknown etiology. Dextran sulfate sodium (DSS) induced colitis is a widely used mouse model in IBD research. DSS colitis involves activation of the submucosal immune system and can be used to study IBD-like disease characteristics in acute, chronic, remission and transition phases. Insight into colon inflammatory parameters is needed to understand potentially irreversible adaptations to the chronification of colitis, determining the baseline and impact of further inflammatory episodes. We performed analyses of non-invasive and invasive colitis parameters in acute, chronic and remission phases of the DSS colitis in C57BL/6 mice. Non-invasive colitis parameters poorly reflected inflammatory aspects of colitis in chronic remission phase. We found invasive inflammatory parameters, positively linked to repeated DSS-episodes, such as specific colon weight, inflamed colon area, spleen weight, absolute cell numbers of CD4+ and CD8+ T cells as well as B cells, blood IFN-γ level, colonic chemokines BLC and MDC as well as the prevalence of Turicibacter species in feces. Moreover, microbial Lactobacillus species decreased with chronification of disease. Our data point out indicative parameters of recurrent gut inflammation in context of DSS colitis.
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Affiliation(s)
- Elif Gelmez
- Infection Immunology Group, Institute of Medical Microbiology and Hospital Hygiene, Otto-von-Guericke University, 39120 Magdeburg, Germany
| | - Konrad Lehr
- Department of Gastroenterology, Hepatology and Infectious Diseases, Section of Molecular Gastroenterology and Microbiota-Associated Diseases, Otto-von-Guericke University, 39120 Magdeburg, Germany
| | - Olivia Kershaw
- Institute of Veterinary Pathology, Freie Universität Berlin, 14163 Berlin, Germany
| | - Sarah Frentzel
- Infection Immunology Group, Institute of Medical Microbiology and Hospital Hygiene, Otto-von-Guericke University, 39120 Magdeburg, Germany
| | - Ramiro Vilchez-Vargas
- Department of Gastroenterology, Hepatology and Infectious Diseases, Section of Molecular Gastroenterology and Microbiota-Associated Diseases, Otto-von-Guericke University, 39120 Magdeburg, Germany
| | - Ute Bank
- Institute of Molecular and Clinical Immunology, Medical Faculty, Otto-von-Guericke University, 39120 Magdeburg, Germany
| | - Alexander Link
- Department of Gastroenterology, Hepatology and Infectious Diseases, Section of Molecular Gastroenterology and Microbiota-Associated Diseases, Otto-von-Guericke University, 39120 Magdeburg, Germany
| | - Thomas Schüler
- Institute of Molecular and Clinical Immunology, Medical Faculty, Otto-von-Guericke University, 39120 Magdeburg, Germany
| | - Andreas Jeron
- Infection Immunology Group, Institute of Medical Microbiology and Hospital Hygiene, Otto-von-Guericke University, 39120 Magdeburg, Germany
- Immune Regulation Group, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Dunja Bruder
- Infection Immunology Group, Institute of Medical Microbiology and Hospital Hygiene, Otto-von-Guericke University, 39120 Magdeburg, Germany
- Immune Regulation Group, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
- Correspondence: ; Tel.: +49-391-67-13374
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10
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Ortiz-Alvarez L, Xu H, Di X, Kohler I, Osuna-Prieto FJ, Acosta FM, Vilchez-Vargas R, Link A, Plaza-Díaz J, van der Stelt M, Hankemeier T, Clemente-Postigo M, Tinahones FJ, Gil A, Rensen PCN, Ruiz JR, Martinez-Tellez B. Plasma Levels of Endocannabinoids and Their Analogues Are Related to Specific Fecal Bacterial Genera in Young Adults: Role in Gut Barrier Integrity. Nutrients 2022; 14:2143. [PMID: 35631284 PMCID: PMC9143287 DOI: 10.3390/nu14102143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 05/12/2022] [Accepted: 05/18/2022] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVE To investigate the association of plasma levels of endocannabinoids with fecal microbiota. METHODS Plasma levels of endocannabinoids, anandamide (AEA) and 2-arachidonoylglycerol (2-AG), as well as their eleven analogues, and arachidonic acid (AA), were measured using liquid chromatography-tandem mass spectrometry in 92 young adults. DNA extracted from stool samples was analyzed using 16S rRNA gene sequencing. Lipopolysaccharide levels were measured in plasma samples. RESULTS Plasma levels of endocannabinoids and their analogues were not related to beta or alpha diversity indexes. Plasma levels of AEA and related N-acylethanolamines correlated positively with the relative abundance of Faecalibacterium genus (all rho ≥ 0.26, p ≤ 0.012) and Akkermansia genus (all rho ≥ 0.22, p ≤ 0.036), and negatively with the relative abundance of Bilophila genus (all rho ≤ -0.23, p ≤ 0.031). Moreover, plasma levels of 2-AG and other acylglycerols correlated positively with the relative abundance of Parasutterella (all rho ≥ 0.24, p ≤ 0.020) and Odoribacter genera (all rho ≥ 0.27, p ≤ 0.011), and negatively with the relative abundance of Prevotella genus (all rho ≤ -0.24, p ≤ 0.023). In participants with high lipopolysaccharide values, the plasma levels of AEA and related N-acylethanolamines, as well as AA and 2-AG, were negatively correlated with plasma levels of lipopolysaccharide (all rho ≤ -0.24, p ≤ 0.020). CONCLUSION Plasma levels of endocannabinoids and their analogues are correlated to specific fecal bacterial genera involved in maintaining gut barrier integrity in young adults. This suggests that plasma levels of endocannabinoids and their analogues may play a role in the gut barrier integrity in young adults.
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Affiliation(s)
- Lourdes Ortiz-Alvarez
- PROFITH (PROmoting FITness and Health through Physical Activity) Research Group, Sport and Health University Research Institute (iMUDS), University of Granada, 18071 Granada, Spain; (L.O.-A.); (H.X.); (F.J.O.-P.); (F.M.A.); (B.M.-T.)
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, 18071 Granada, Spain; (J.P.-D.); (A.G.)
| | - Huiwen Xu
- PROFITH (PROmoting FITness and Health through Physical Activity) Research Group, Sport and Health University Research Institute (iMUDS), University of Granada, 18071 Granada, Spain; (L.O.-A.); (H.X.); (F.J.O.-P.); (F.M.A.); (B.M.-T.)
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, 18071 Granada, Spain; (J.P.-D.); (A.G.)
| | - Xinyu Di
- Leiden Academic Centre for Drug Research, Division of Systems Biomedicine and Pharmacology, Leiden University, 2300 Leiden, The Netherlands;
| | - Isabelle Kohler
- Division of BioAnalytical Chemistry, Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, 1081 Amsterdam, The Netherlands;
- Center for Analytical Sciences Amsterdam, 1098 Amsterdam, The Netherlands
| | - Francisco J. Osuna-Prieto
- PROFITH (PROmoting FITness and Health through Physical Activity) Research Group, Sport and Health University Research Institute (iMUDS), University of Granada, 18071 Granada, Spain; (L.O.-A.); (H.X.); (F.J.O.-P.); (F.M.A.); (B.M.-T.)
- Center for Biomedical Research, Department of Analytical Chemistry, Institute of Nutrition and Food Technology, University of Granada, 18071 Granada, Spain
- Research and Development of Functional Food Center (CIDAF), Health Sciences Technology Park, 18071 Granada, Spain
| | - Francisco M. Acosta
- PROFITH (PROmoting FITness and Health through Physical Activity) Research Group, Sport and Health University Research Institute (iMUDS), University of Granada, 18071 Granada, Spain; (L.O.-A.); (H.X.); (F.J.O.-P.); (F.M.A.); (B.M.-T.)
- Turku PET Centre, University of Turku, 20014 Turku, Finland
- Turku PET Centre, Turku University Hospital, 20521 Turku, Finland
- InFLAMES Research Flagship Centre, University of Turku, 20014 Turku, Finland
| | - Ramiro Vilchez-Vargas
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto von Guericke University Magdeburg, 39106 Magdeburg, Germany; (R.V.-V.); (A.L.)
| | - Alexander Link
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto von Guericke University Magdeburg, 39106 Magdeburg, Germany; (R.V.-V.); (A.L.)
| | - Julio Plaza-Díaz
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, 18071 Granada, Spain; (J.P.-D.); (A.G.)
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada
| | - Mario van der Stelt
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, 2300 Leiden, The Netherlands;
| | - Thomas Hankemeier
- Leiden Academic Centre for Drug Research (LACDR), Department of Systems Biomedicine and Pharmacology, Leiden University, 2300 Leiden, The Netherlands;
| | - Mercedes Clemente-Postigo
- Department of Cell Biology, Physiology and Immunology, Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Reina Sofia University Hospital, University of Córdoba, 14004 Córdoba, Spain;
- Unidad de Gestión Clínica Endocrinología y Nutrición, Instituto de Investigación Biomédica de Málaga-IBIMA, Hospital Universitario Virgen de la Victoria, Universidad de Málaga, 29016 Malaga, Spain;
- Centro de Investigación Biomédica En Red (CIBER), Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III (ISCIII), 28029 Malaga, Spain
| | - Francisco J. Tinahones
- Unidad de Gestión Clínica Endocrinología y Nutrición, Instituto de Investigación Biomédica de Málaga-IBIMA, Hospital Universitario Virgen de la Victoria, Universidad de Málaga, 29016 Malaga, Spain;
- Centro de Investigación Biomédica En Red (CIBER), Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III (ISCIII), 28029 Malaga, Spain
| | - Angel Gil
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, 18071 Granada, Spain; (J.P.-D.); (A.G.)
- Centro de Investigación Biomédica En Red (CIBER), Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III (ISCIII), 28029 Malaga, Spain
- Biomedical Research Center, Institute of Nutrition and Food Technology “José Mataix”, University of Granada, Parque Tecnológico Ciencias de la Salud, 18071 Granada, Spain
- Instituto de Investigación Biosanitaria, 18014 Granada, Spain
| | - Patrick C. N. Rensen
- Einthoven Laboratory for Experimental Vascular Medicine, Department of Medicine, Division of Endocrinology, Leiden University Medical Center, 2300 Leiden, The Netherlands;
| | - Jonatan R. Ruiz
- PROFITH (PROmoting FITness and Health through Physical Activity) Research Group, Sport and Health University Research Institute (iMUDS), University of Granada, 18071 Granada, Spain; (L.O.-A.); (H.X.); (F.J.O.-P.); (F.M.A.); (B.M.-T.)
- Instituto de Investigación Biosanitaria, 18014 Granada, Spain
- Department of Physical and Sports Education, School of Sports Science, University of Granada, 18071 Granada, Spain
| | - Borja Martinez-Tellez
- PROFITH (PROmoting FITness and Health through Physical Activity) Research Group, Sport and Health University Research Institute (iMUDS), University of Granada, 18071 Granada, Spain; (L.O.-A.); (H.X.); (F.J.O.-P.); (F.M.A.); (B.M.-T.)
- Einthoven Laboratory for Experimental Vascular Medicine, Department of Medicine, Division of Endocrinology, Leiden University Medical Center, 2300 Leiden, The Netherlands;
- CERNEP Research Center, Department of Education, Faculty of Education Sciences and SPORT Research Group (CTS-1024), University of Almería, 04120 Almeria, Spain
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11
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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, Malfertheiner P. Impact of healthy aging on active bacterial assemblages throughout the gastrointestinal tract. Gut Microbes 2022; 13:1966261. [PMID: 34455919 PMCID: PMC8409759 DOI: 10.1080/19490976.2021.1966261] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
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.
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Affiliation(s)
- Kerstin Schütte
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke University Magdeburg, Magdeburg, Germany,Department of Internal Medicine and Gastroenterology, Niels-Stensen-Kliniken Marienhospital Osnabrück, Bischofsstr. 1, Osnabrück, Germany
| | - Christian Schulz
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke University Magdeburg, Magdeburg, Germany,Department of Internal Medicine 2, University Hospital, Munich, Germany
| | - Ramiro Vilchez-Vargas
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Riccardo Vasapolli
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke University Magdeburg, Magdeburg, Germany,Department of Internal Medicine 2, University Hospital, Munich, Germany
| | - Frederike Palm
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Bianca Simon
- Department of Internal Medicine and Gastroenterology, Niels-Stensen-Kliniken Marienhospital Osnabrück, Bischofsstr. 1, Osnabrück, Germany
| | - Dirk Schomburg
- Institute of Biometry and Medical Informatics, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Anke Lux
- Institute of Biometry and Medical Informatics, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Robert Geffers
- GMAK Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Dietmar H. Pieper
- Microbial Interactions and Processes (MINP) Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Alexander Link
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Peter Malfertheiner
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke University Magdeburg, Magdeburg, Germany,Department of Internal Medicine 2, University Hospital, Munich, Germany,CONTACT Peter Malfertheiner Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke University Hospital, 39120Magdeburg, Germany
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12
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Manka P, Sydor S, Wase N, Best J, Brandenburg M, Hellbeck A, Schänzer J, Vilchez-Vargas R, Link A, Figge A, Jähnert A, von Arnim U, Coombes JD, Cubero FJ, Kahraman A, Kim MS, Kälsch J, Kinner S, Faber KN, Moshage H, Gerken G, Syn WK, Friedman SL, Canbay A, Bechmann LP. Anti-TNFα treatment in Crohn's disease: Impact on hepatic steatosis, gut-derived hormones and metabolic status. Liver Int 2021; 41:2646-2658. [PMID: 34219348 DOI: 10.1111/liv.15003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 06/04/2021] [Accepted: 06/21/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND AND AIMS An association between Crohn's disease (CD) and hepatic steatosis has been reported. However, the underlying mechanisms of steatosis progression in CD are not clear. Among the most effective CD treatments are agents that inhibit Tumor-Necrosis-Factor (TNF) activity, yet it is unclear why anti-TNFα agents would affect steatosis in CD. Recent studies suggest that microbiome can affect both, CD and steatosis pathogenesis. Therefore, we here analysed a potential relationship between anti-TNF treatment and hepatic steatosis in CD, focusing on the gut-liver axis. METHODS This cross-sectional study evaluated patients with established CD, with and without anti-TNFα treatment, analysing serum markers of liver injury, measurement of transient elastography, controlled attenuation parameter (CAP) and MRI for fat detection. Changes in lipid and metabolic profiles were assessed by serum and stool lipidomics and metabolimics. Additionally, we analysed gut microbiota composition and mediators of bile acid (BA) signalling via stool and serum analysis. RESULTS Patients on anti-TNFα treatment had less hepatic steatosis as assessed by CAP and MRI. Serum FGF19 levels were significantly higher in patients on anti-TNFα therapy and associate with reduced steatosis and increased bowel motility. Neutral lipids including triglycerides were reduced in the serum of patients on anti-TNF treatment. Bacteria involved in BA metabolism and FGF19 regulation, including Firmicutes, showed group-specific alterations with low levels in patients without anti-TNFα treatment. Low abundance of Firmicutes was associated with higher triglyceride levels. CONCLUSIONS Anti-TNFα treatment is associated with reduced steatosis, lower triglyceride levels, alterations in FXR-signalling (eg FGF19) and microbiota composition in CD.
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Affiliation(s)
- Paul Manka
- Department of Internal Medicine, University Hospital Knappschaftskrankenhaus, Ruhr-University Bochum, Bochum, Germany.,Department of Gastroenterology and Hepatology, University Hospital Essen, Essen, Germany
| | - Svenja Sydor
- Department of Internal Medicine, University Hospital Knappschaftskrankenhaus, Ruhr-University Bochum, Bochum, Germany
| | - Nishikant Wase
- Biomolecular Analysis Facility, University of Virginia, School of Medicine, Charlottesville, VA, USA
| | - Jan Best
- Department of Internal Medicine, University Hospital Knappschaftskrankenhaus, Ruhr-University Bochum, Bochum, Germany
| | - Malte Brandenburg
- Department of Gastroenterology and Hepatology, University Hospital Essen, Essen, Germany
| | - Annika Hellbeck
- Department of Gastroenterology and Hepatology, University Hospital Essen, Essen, Germany
| | - Julia Schänzer
- Department of Gastroenterology and Hepatology, University Hospital Essen, Essen, Germany
| | - Ramiro Vilchez-Vargas
- Department of Gastroenterology, Hepatology, and Infectious Diseases, Otto-von-Guericke-University Hospital Magdeburg, Magdeburg, Germany
| | - Alexander Link
- Department of Gastroenterology, Hepatology, and Infectious Diseases, Otto-von-Guericke-University Hospital Magdeburg, Magdeburg, Germany
| | - Anja Figge
- Department of Internal Medicine, University Hospital Knappschaftskrankenhaus, Ruhr-University Bochum, Bochum, Germany
| | - Andreas Jähnert
- Department of Internal Medicine, University Hospital Knappschaftskrankenhaus, Ruhr-University Bochum, Bochum, Germany
| | - Ulrike von Arnim
- Department of Gastroenterology, Hepatology, and Infectious Diseases, Otto-von-Guericke-University Hospital Magdeburg, Magdeburg, Germany
| | - Jason D Coombes
- Inflammation Biology, School of Immunology and Microbial Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Francisco-Javier Cubero
- Department of Immunology, Ophthalmology and ORL, Complutense University School of Medicine, Madrid, Spain.,12 de Octubre Health Research Institute (imas 12), Madrid, Spain
| | - Alisan Kahraman
- Department of Gastroenterology and Hepatology, University Hospital Essen, Essen, Germany
| | - Moon-Sung Kim
- Department of Diagnostic and Interventional Radiology and Neuroradiology, University Hospital Essen, Essen, Germany
| | - Julia Kälsch
- Department of Gastroenterology and Hepatology, University Hospital Essen, Essen, Germany
| | - Sonja Kinner
- Department of Diagnostic and Interventional Radiology and Neuroradiology, University Hospital Essen, Essen, Germany
| | - Klaas-Nico Faber
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Han Moshage
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Guido Gerken
- Department of Gastroenterology and Hepatology, University Hospital Essen, Essen, Germany
| | - Wing-Kin Syn
- Division of Gastroenterology and Hepatology, Department of Medicine, Medical University of South Carolina, Charleston, SC, USA.,Section of Gastroenterology, Ralph H. Johnson Veterans Affairs Medical Center, Charleston, SC, USA.,Department of Physiology, Faculty of Medicine and Nursing, University of Basque Country UPV/EHU, Vizcaya, Spain
| | - Scott L Friedman
- Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ali Canbay
- Department of Internal Medicine, University Hospital Knappschaftskrankenhaus, Ruhr-University Bochum, Bochum, Germany
| | - Lars P Bechmann
- Department of Internal Medicine, University Hospital Knappschaftskrankenhaus, Ruhr-University Bochum, Bochum, Germany
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13
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Molina NM, Plaza-Díaz J, Vilchez-Vargas R, Sola-Leyva A, Vargas E, Mendoza-Tesarik R, Galán-Lázaro M, Mendoza-Ladrón de Guevara N, Tesarik J, Altmäe S. Assessing the testicular sperm microbiome: a low-biomass site with abundant contamination. Reprod Biomed Online 2021; 43:523-531. [PMID: 34344601 DOI: 10.1016/j.rbmo.2021.06.021] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 05/19/2021] [Accepted: 06/22/2021] [Indexed: 12/31/2022]
Abstract
RESEARCH QUESTION The semen harbours a diverse range of microorganisms. The origin of the seminal microbes, however, has not yet been established. Do testicular spermatozoa harbour microbes and could they potentially contribute to the seminal microbiome composition? DESIGN The study included 24 samples, comprising a total of 307 testicular maturing spermatozoa. A high-throughput sequencing method targeting V3 and V4 regions of 16S rRNA gene was applied. A series of negative controls together with stringent in-silico decontamination methods were analysed. RESULTS Between 50 and 70% of all the detected bacterial reads accounted for contamination in the testicular sperm samples. After stringent decontamination, Blautia (P = 0.04), Cellulosibacter (P = 0.02), Clostridium XIVa (P = 0.01), Clostridium XIVb (P = 0.04), Clostridium XVIII (P = 0.02), Collinsella (P = 0.005), Prevotella (P = 0.04), Prolixibacter (P = 0.02), Robinsoniella (P = 0.04), and Wandonia (P = 0.04) genera demonstrated statistically significant abundance among immature spermatozoa. CONCLUSIONS Our results indicate that the human testicle harbours potential bacterial signature, though in a low-biomass, and could contribute to the seminal microbiome composition. Further, applying stringent decontamination methods is crucial for analysing microbiome in low-biomass site.
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Affiliation(s)
- Nerea M Molina
- University of Granada, Department of Biochemistry and Molecular Biology I, Faculty of Sciences, Granada 18071, Spain; Instituto de Investigación Biosanitaria ibs.GRANADA, Granada 18014, Spain
| | - Julio Plaza-Díaz
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada 18014, Spain; University of Granada, Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, Granada 18071, Spain; Institute of Nutrition and Food Technology (INYTA), 'José Mataix Verdú' Biomedical Research Centre (CIBM), University of Granada, Granada 18016, Spain; Children's Hospital of Eastern Ontario Research Institute, Ottawa ON K1H 8L1, Canada
| | - Ramiro Vilchez-Vargas
- Department of Gastroenterology, Hepatology, and Infectious Diseases, Otto von Guericke University Hospital Magdeburg, Magdeburg 39120, Germany
| | - Alberto Sola-Leyva
- University of Granada, Department of Biochemistry and Molecular Biology I, Faculty of Sciences, Granada 18071, Spain; Instituto de Investigación Biosanitaria ibs.GRANADA, Granada 18014, Spain
| | - Eva Vargas
- Systems Biology Unit, Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaen, Jaen 23071, Spain
| | | | - Maribel Galán-Lázaro
- MARGen Clinic, Molecular Assisted Reproduction and Genetics, Granada 18006, Spain
| | | | - Jan Tesarik
- MARGen Clinic, Molecular Assisted Reproduction and Genetics, Granada 18006, Spain
| | - Signe Altmäe
- University of Granada, Department of Biochemistry and Molecular Biology I, Faculty of Sciences, Granada 18071, Spain; Instituto de Investigación Biosanitaria ibs.GRANADA, Granada 18014, Spain; Competence Centre on Health Technologies, Tartu 50410, Estonia.
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14
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Muñoz-Palazon B, Rosa-Masegosa A, Hurtado-Martinez M, Rodriguez-Sanchez A, Link A, Vilchez-Vargas R, Gonzalez-Martinez A, Lopez JG. Total and Metabolically Active Microbial Community of Aerobic Granular Sludge Systems Operated in Sequential Batch Reactors: Effect of Pharmaceutical Compounds. Toxics 2021; 9:93. [PMID: 33922816 PMCID: PMC8146427 DOI: 10.3390/toxics9050093] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 04/13/2021] [Accepted: 04/21/2021] [Indexed: 12/30/2022]
Abstract
Two aerobic granular sludge (AGS) sequential batch reactors were operated at a mild (15 °C) temperature for 180 days. One of those bioreactors was exposed to a mixture of diclofenac, naproxen, trimethoprim, and carbamazepine. The AGS system, operating under pressure from emerging contaminants, showed a decrease in COD, BOD5, and TN removal capacity, mainly observed during the first 100 days, in comparison with the removal ratios detected in the control bioreactor. After an acclimatisation period, the removal reached high-quality effluent for COD and TN, close to 95% and 90%, respectively. In the steady-state period, trimethoprim and diclofenac were successfully removed with values around 50%, while carbamazepine and naproxen were more recalcitrant. The dominant bacterial OTUs were affected by the presence of a mixture of pharmaceutical compounds, under which the dominant phylotypes changed to OTUs classified among the Pseudomonas, Gemmobacter, and Comamonadaceae. The RT-qPCR and qPCR results showed the deep effects of pharmaceutical compounds on the number of copies of target genes. Statistical analyses allowed for linking the total and active microbial communities with the physico-chemical performance, describing the effects of pharmaceutical compounds in pollution degradation, as well as the successful adaptation of the system to treat wastewater in the presence of toxic compounds.
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Affiliation(s)
- Barbara Muñoz-Palazon
- Faculty of Pharmacy, University of Granada, Campus de Cartuja, s/n, 18071 Granada, Spain; (A.R.-M.); (M.H.-M.); (J.G.L.)
- Institute of Water Research, University of Granada, C/Ramón y Cajal, 4, 18071 Granada, Spain
| | - Aurora Rosa-Masegosa
- Faculty of Pharmacy, University of Granada, Campus de Cartuja, s/n, 18071 Granada, Spain; (A.R.-M.); (M.H.-M.); (J.G.L.)
- Institute of Water Research, University of Granada, C/Ramón y Cajal, 4, 18071 Granada, Spain
| | - Miguel Hurtado-Martinez
- Faculty of Pharmacy, University of Granada, Campus de Cartuja, s/n, 18071 Granada, Spain; (A.R.-M.); (M.H.-M.); (J.G.L.)
- Institute of Water Research, University of Granada, C/Ramón y Cajal, 4, 18071 Granada, Spain
| | - Alejandro Rodriguez-Sanchez
- Department of Horticulture and Landscape Architecture, Purdue University, 625 Agriculture Mall Drive, West Lafayette, IN 47907, USA;
| | - Alexander Link
- Department of Gastroenterology, Hepatology, and Infectious Diseases, Otto von Guericke University Hospital Magdeburg, 39120 Magdeburg, Germany; (A.L.); (R.V.-V.)
| | - Ramiro Vilchez-Vargas
- Department of Gastroenterology, Hepatology, and Infectious Diseases, Otto von Guericke University Hospital Magdeburg, 39120 Magdeburg, Germany; (A.L.); (R.V.-V.)
| | - Alejandro Gonzalez-Martinez
- Faculty of Pharmacy, University of Granada, Campus de Cartuja, s/n, 18071 Granada, Spain; (A.R.-M.); (M.H.-M.); (J.G.L.)
- Institute of Water Research, University of Granada, C/Ramón y Cajal, 4, 18071 Granada, Spain
| | - Jesus Gonzalez Lopez
- Faculty of Pharmacy, University of Granada, Campus de Cartuja, s/n, 18071 Granada, Spain; (A.R.-M.); (M.H.-M.); (J.G.L.)
- Institute of Water Research, University of Granada, C/Ramón y Cajal, 4, 18071 Granada, Spain
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15
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Figge A, Sydor S, Wenning C, Manka P, Assmuth S, Vilchez-Vargas R, Link A, Jähnert A, Brodesser S, Lucas C, Nevzorova YA, Faber KN, Moshage H, Porsch-Özcürümez M, Gerken G, Cubero FJ, Canbay A, Bechmann LP. Gender and gut microbiota composition determine hepatic bile acid, metabolic and inflammatory response to a single fast-food meal in healthy adults. Clin Nutr 2021; 40:2609-2619. [PMID: 33933727 DOI: 10.1016/j.clnu.2021.04.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 03/16/2021] [Accepted: 04/02/2021] [Indexed: 12/31/2022]
Abstract
BACKGROUND & AIMS Regular consumption of fast-food (FF) as a form of typical Western style diet is associated with obesity and the metabolic syndrome, including its hepatic manifestation nonalcoholic fatty liver disease. Currently, it remains unclear how intermittent excess FF consumption may influence liver metabolism. The study aimed to characterize the effects of a single FF binge on hepatic steatosis, inflammation, bile acid (BA), glucose and lipid metabolism. METHODS Twenty-five healthy individuals received a FF meal and were asked to continue eating either for a two-hour period or until fully saturated. Serum levels of transaminases, fasting BA, lipid profile, glucose and cytokine levels as well as transient elastography and controlled attenuation parameter (CAP; to assess hepatic steatosis) were analyzed before (day 0) and the day after FF binge (day 1). Feces was collected prior and after the FF challenge for microbiota analysis. RESULTS The FF meal induced a modest increase in CAP, which was accompanied by a robust increase of fasting serum BA levels. Surprisingly, levels of cholesterol and bilirubin were significantly lower after the FF meal. Differentiating individuals with a relevant delta BA (>1 μmol/l) increase vs. individuals without (delta BA ≤1 μmol/l), identified several gut microbiota, as well as gender to be associated with the BA increase and the observed alterations in liver function, metabolism and inflammation. CONCLUSION A single binge FF meal leads to a robust increase in serum BA levels and alterations in parameters of liver injury and metabolism, indicating a novel metabolic aspect of the gut-liver axis.
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Affiliation(s)
- A Figge
- Department of Internal Medicine, University Hospital Knappschaftskrankenhaus, Ruhr-University Bochum, In der Schornau 23-25, 44892 Bochum, Germany
| | - S Sydor
- Department of Internal Medicine, University Hospital Knappschaftskrankenhaus, Ruhr-University Bochum, In der Schornau 23-25, 44892 Bochum, Germany
| | - C Wenning
- Department of Gastroenterology and Hepatology, University Hospital Essen, Hufelandstrasse 55, 45147 Essen, Germany
| | - P Manka
- Department of Internal Medicine, University Hospital Knappschaftskrankenhaus, Ruhr-University Bochum, In der Schornau 23-25, 44892 Bochum, Germany; Department of Gastroenterology and Hepatology, University Hospital Essen, Hufelandstrasse 55, 45147 Essen, Germany
| | - S Assmuth
- Department of Gastroenterology and Hepatology, University Hospital Essen, Hufelandstrasse 55, 45147 Essen, Germany
| | - R Vilchez-Vargas
- Department of Gastroenterology, Hepatology, and Infectious Diseases, Otto-von-Guericke-University Hospital Magdeburg, Leipziger Strasse 44, 39120 Magdeburg, Germany
| | - A Link
- Department of Gastroenterology, Hepatology, and Infectious Diseases, Otto-von-Guericke-University Hospital Magdeburg, Leipziger Strasse 44, 39120 Magdeburg, Germany
| | - A Jähnert
- Department of Internal Medicine, University Hospital Knappschaftskrankenhaus, Ruhr-University Bochum, In der Schornau 23-25, 44892 Bochum, Germany
| | - S Brodesser
- CECAD Research Center, CECAD Lipidomics Facility, University of Cologne Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - C Lucas
- CECAD Research Center, CECAD Lipidomics Facility, University of Cologne Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Y A Nevzorova
- Department of Immunology, Opthalmology and ORL, Complutense University School of Medicine, Avenida de Séneca 2, 28040 Madrid, Spain; 12 de Octubre Health Research Institute (imas 12), Madrid, Spain
| | - K N Faber
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, the Netherlands; Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, the Netherlands
| | - H Moshage
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, the Netherlands; Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, the Netherlands
| | - M Porsch-Özcürümez
- Department of Internal Medicine, University Hospital Knappschaftskrankenhaus, Ruhr-University Bochum, In der Schornau 23-25, 44892 Bochum, Germany
| | - G Gerken
- Department of Gastroenterology and Hepatology, University Hospital Essen, Hufelandstrasse 55, 45147 Essen, Germany
| | - F J Cubero
- Department of Immunology, Opthalmology and ORL, Complutense University School of Medicine, Avenida de Séneca 2, 28040 Madrid, Spain; 12 de Octubre Health Research Institute (imas 12), Madrid, Spain
| | - A Canbay
- Department of Internal Medicine, University Hospital Knappschaftskrankenhaus, Ruhr-University Bochum, In der Schornau 23-25, 44892 Bochum, Germany
| | - L P Bechmann
- Department of Internal Medicine, University Hospital Knappschaftskrankenhaus, Ruhr-University Bochum, In der Schornau 23-25, 44892 Bochum, Germany.
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16
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Lamas-Paz A, Morán L, Peng J, Salinas B, López-Alcántara N, Sydor S, Vilchez-Vargas R, Asensio I, Hao F, Zheng K, Martín-Adrados B, Moreno L, Cogolludo A, Gómez Del Moral M, Bechmann L, Martínez-Naves E, Vaquero J, Bañares R, Nevzorova YA, Cubero FJ. Intestinal Epithelial Cell-Derived Extracellular Vesicles Modulate Hepatic Injury via the Gut-Liver Axis During Acute Alcohol Injury. Front Pharmacol 2020; 11:603771. [PMID: 33408632 PMCID: PMC7779758 DOI: 10.3389/fphar.2020.603771] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 10/05/2020] [Indexed: 12/12/2022] Open
Abstract
Binge drinking, i.e., heavy episodic drinking in a short time, has recently become an alarming societal problem with negative health impact. However, the harmful effects of acute alcohol injury in the gut-liver axis remain elusive. Hence, we focused on the physiological and pathological changes and the underlying mechanisms of experimental binge drinking in the context of the gut-liver axis. Eight-week-old mice with a C57BL/6 background received a single dose (p.o.) of ethanol (EtOH) [6 g/kg b.w.] as a preclinical model of acute alcohol injury. Controls received a single dose of PBS. Mice were sacrificed 8 h later. In parallel, HepaRGs and Caco-2 cells, human cell lines of differentiated hepatocytes and intestinal epithelial cells intestinal epithelial cells (IECs), respectively, were challenged in the presence or absence of EtOH [0–100 mM]. Extracellular vesicles (EVs) isolated by ultracentrifugation from culture media of IECs were added to hepatocyte cell cultures. Increased intestinal permeability, loss of zonula occludens-1 (ZO-1) and MUCIN-2 expression, and alterations in microbiota—increased Lactobacillus and decreased Lachnospiraceae species—were found in the large intestine of mice exposed to EtOH. Increased TUNEL-positive cells, infiltration of CD11b-positive immune cells, pro-inflammatory cytokines (e.g., tlr4, tnf, il1β), and markers of lipid accumulation (Oil Red O, srbep1) were evident in livers of mice exposed to EtOH, particularly in females. In vitro experiments indicated that EVs released by IECs in response to ethanol exerted a deleterious effect on hepatocyte viability and lipid accumulation. Overall, our data identified a novel mechanism responsible for driving hepatic injury in the gut-liver axis, opening novel avenues for therapy.
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Affiliation(s)
- Arantza Lamas-Paz
- Department of Immunology, Ophthalmology and ENT, Complutense University School of Medicine, Madrid, Spain.,12 de Octubre Health Research Institute (imas12), Madrid, Spain
| | - Laura Morán
- Department of Immunology, Ophthalmology and ENT, Complutense University School of Medicine, Madrid, Spain.,Servicio de Aparato Digestivo del Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Jin Peng
- Department of Hepatobiliary Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Beatriz Salinas
- Servicio de Aparato Digestivo del Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain.,Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain.,Bioengineering and Aerospace Engineering Department, Universidad Carlos III de Madrid, Madrid, Spain.,Centro de Investigación Biomédico en Red de Salud Mental (CIBERSAM), Madrid, Spain
| | - Nuria López-Alcántara
- Department of Immunology, Ophthalmology and ENT, Complutense University School of Medicine, Madrid, Spain
| | - Svenja Sydor
- Department of Internal Medicine, University Hospital Knappschaftskrankenhaus, Ruhr-University Bochum, Bochum, Germany
| | - Ramiro Vilchez-Vargas
- Department of Gastroenterology, Hepatology, and Infectious Diseases, Otto von Guericke University Hospital Magdeburg, Magdeburg, Germany
| | - Iris Asensio
- Servicio de Aparato Digestivo del Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain.,Centre for Biomedical Research, Network on Liver and Digestive Diseases (CIBEREHD), Madrid, Spain
| | - Fengjie Hao
- Department of Immunology, Ophthalmology and ENT, Complutense University School of Medicine, Madrid, Spain.,12 de Octubre Health Research Institute (imas12), Madrid, Spain.,Department of General Surgery, Hepatobiliary Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Kang Zheng
- Department of Immunology, Ophthalmology and ENT, Complutense University School of Medicine, Madrid, Spain.,12 de Octubre Health Research Institute (imas12), Madrid, Spain.,Department of Anesthesiology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
| | - Beatriz Martín-Adrados
- Department of Immunology, Ophthalmology and ENT, Complutense University School of Medicine, Madrid, Spain.,12 de Octubre Health Research Institute (imas12), Madrid, Spain
| | - Laura Moreno
- Department of Internal Medicine, University Hospital Knappschaftskrankenhaus, Ruhr-University Bochum, Bochum, Germany.,Department of Pharmacology and Toxicology, Complutense University School of Medicine and Centre for Biomedical Research, Network on Respiratory Diseases (CIBERES), Madrid, Spain
| | - Angel Cogolludo
- Department of Internal Medicine, University Hospital Knappschaftskrankenhaus, Ruhr-University Bochum, Bochum, Germany.,Department of Pharmacology and Toxicology, Complutense University School of Medicine and Centre for Biomedical Research, Network on Respiratory Diseases (CIBERES), Madrid, Spain
| | - Manuel Gómez Del Moral
- 12 de Octubre Health Research Institute (imas12), Madrid, Spain.,Department of Cell Biology, Complutense University School of Medicine, Madrid, Spain
| | - Lars Bechmann
- Department of Internal Medicine, University Hospital Knappschaftskrankenhaus, Ruhr-University Bochum, Bochum, Germany
| | - Eduardo Martínez-Naves
- Department of Immunology, Ophthalmology and ENT, Complutense University School of Medicine, Madrid, Spain.,12 de Octubre Health Research Institute (imas12), Madrid, Spain
| | - Javier Vaquero
- Servicio de Aparato Digestivo del Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain.,Centre for Biomedical Research, Network on Liver and Digestive Diseases (CIBEREHD), Madrid, Spain
| | - Rafael Bañares
- Servicio de Aparato Digestivo del Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain.,Centre for Biomedical Research, Network on Liver and Digestive Diseases (CIBEREHD), Madrid, Spain
| | - Yulia A Nevzorova
- Department of Immunology, Ophthalmology and ENT, Complutense University School of Medicine, Madrid, Spain.,12 de Octubre Health Research Institute (imas12), Madrid, Spain.,Department of Internal Medicine III, University Hospital RWTH Aachen, Aachen, Germany
| | - Francisco Javier Cubero
- Department of Immunology, Ophthalmology and ENT, Complutense University School of Medicine, Madrid, Spain.,12 de Octubre Health Research Institute (imas12), Madrid, Spain
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17
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Vasapolli R, Schütte K, Schulz C, Vital M, Schomburg D, Pieper DH, Vilchez-Vargas R, Malfertheiner P. Analysis of Transcriptionally Active Bacteria Throughout the Gastrointestinal Tract of Healthy Individuals. Gastroenterology 2019; 157:1081-1092.e3. [PMID: 31175864 DOI: 10.1053/j.gastro.2019.05.068] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 05/26/2019] [Accepted: 05/30/2019] [Indexed: 12/17/2022]
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.
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Affiliation(s)
- Riccardo Vasapolli
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke-University of Magdeburg, Magdeburg, Germany; Department of Internal Medicine II, Hospital of the Ludwig Maximilians University of Munich, Munich, Germany
| | - Kerstin Schütte
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke-University of Magdeburg, Magdeburg, Germany; Department of Internal Medicine and Gastroenterology, Niels-Stensen-Kliniken, Marienhospital, Osnabrück, Germany
| | - Christian Schulz
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke-University of Magdeburg, Magdeburg, Germany; Department of Internal Medicine II, Hospital of the Ludwig Maximilians University of Munich, Munich, Germany
| | - Marius Vital
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany; Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
| | - Dirk Schomburg
- Department for Biometrics and Medical Informatics, Otto-von-Guericke-University of Magdeburg, Magdeburg, Germany
| | - Dietmar H Pieper
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Ramiro Vilchez-Vargas
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke-University of Magdeburg, Magdeburg, Germany
| | - Peter Malfertheiner
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke-University of Magdeburg, Magdeburg, Germany; Department of Internal Medicine II, Hospital of the Ludwig Maximilians University of Munich, Munich, Germany.
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18
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Schulz C, Schütte K, Vilchez-Vargas R, Vasapolli R, Malfertheiner P. Long-Term Effect of Rifaximin with and without Lactulose on the Active Bacterial Assemblages in the Proximal Small Bowel and Faeces in Patients with Minimal Hepatic Encephalopathy. Dig Dis 2018; 37:161-169. [PMID: 30428474 DOI: 10.1159/000494216] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 10/01/2018] [Indexed: 02/02/2023]
Abstract
BACKGROUND Gut microbiota play an essential role in the pathogenesis of hepatic encephalopathy (HE). Treatment strategies are directed to modulate intestinal microbiota profiles and their function by the administration of the non-absorbable disaccharide lactulose and the non-absorbable antibiotic rifaximin, which are required for long terms, but little is known on their long-term effect on gut microbiota composition and function. AIM To characterize the active bacterial assemblages in duodenum and faeces in patients with minimal HE (MHE) before, during and after long-term therapy with rifaximin. METHODS We analysed the microbiota composition in 5 patients with liver cirrhosis and MHE treated either with rifaximin 550 mg bid alone continuously for a period of 3 months or combined with lactulose 30-60 mL daily for 3 months. In addition to clinical assessments of HE, biopsies from duodenum and stool samples were analysed for their specific bacterial community applying NGS after RNA isolation before treatment, after 3 months of treatment and 3 months after the end of treatment. RESULTS All 5 patients had a significant improvement of their MHE. Bacterial communities were different and distinct in duodenal samples and faeces. No statistically significant changes were found in the bacterial community profile at the different time points. CONCLUSION Rifaximin therapy with and without lactulose over a period of 3 months does not affect the bacterial community composition. The improvement of HE with rifaximin is lasting also after the end of treatment and therefore a prolonged effect on microbiota metabolic function is suggested.
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Affiliation(s)
- Christian Schulz
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-Von-Guericke University Magdeburg, Magdeburg, Germany.,Klinikum der LMU München-Grosshadern, Medizinische Klinik 2, München, Germany
| | - Kerstin Schütte
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-Von-Guericke University Magdeburg, Magdeburg, Germany.,Niels-Stensen-Kliniken Marienhospital Osnabrück, Klinik für Innere Medizin und Gastroenterologie, Osnabrück, Germany
| | - Ramiro Vilchez-Vargas
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-Von-Guericke University Magdeburg, Magdeburg, Germany
| | - Riccardo Vasapolli
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-Von-Guericke University Magdeburg, Magdeburg, Germany
| | - Peter Malfertheiner
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-Von-Guericke University Magdeburg, Magdeburg, Germany, .,Klinikum der LMU München-Grosshadern, Medizinische Klinik 2, München, Germany,
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19
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Giuliani C, Marzorati M, Innocenti M, Vilchez-Vargas R, Vital M, Pieper DH, Van de Wiele T, Mulinacci N. Dietary supplement based on stilbenes: a focus on gut microbial metabolism by the in vitro simulator M-SHIME®. Food Funct 2018; 7:4564-4575. [PMID: 27713962 DOI: 10.1039/c6fo00784h] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Polyphenols and intestinal microbiota can influence each other, modifying metabolism and gut wellness. Data on this mutual effect need to be improved. Several studies on the biological activities of resveratrol and derivatives have been carried out, but the effects of a continuous administration of stilbenes on gut microbiota have not yet been investigated. This study evaluated the effects of an extract from Vitis vinifera, containing a combination of t-resveratrol and ε-viniferin, on intestinal microbiota, using the advanced gastrointestinal simulator M-SHIME®. A triple M-SHIME® experiment was performed using two concentrations of the extract (i.e. 1 and 2 g L-1), simulating a continuous daily intake. The effects were evaluated in terms of microbial functionality (SCFA and NH4+) and composition (DGGE and Illumina sequencing), since the microbiological aspect has been less considered so far. The treatment induced changes in microbial functionality and composition. In fact, the levels of SCFA and NH4+ suffered a strong decrease (i.e. inhibition of the saccharolytic and proteolytic activity), while DGGE and Illumina showed important modifications of the microbiota composition, associated with an imbalance of the colonic microbiota (i.e. increase in the relative abundance of Enterobacteriaceae). HPLC-DAD-TOF-MS analyses demonstrated that the metabolism of t-resveratrol and other stilbenes was inhibited by continuous administration. Our results suggest M-SHIME® as an explorative tool to define the dosage of food supplements, in particular to simulate effective continuous administration in humans.
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Affiliation(s)
- Camilla Giuliani
- Department of Neurofarba- Pharmaceutical and Nutraceutical Division, University of Florence, Via Ugo Schiff 6, Sesto Fiorentino, FI, Italy.
| | - Massimo Marzorati
- Center of Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Marzia Innocenti
- Department of Neurofarba- Pharmaceutical and Nutraceutical Division, University of Florence, Via Ugo Schiff 6, Sesto Fiorentino, FI, Italy.
| | - Ramiro Vilchez-Vargas
- Center of Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Marius Vital
- Microbial Interactions and Processes Research Group, Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Inhoffenstraße 7, D-38124, Braunschweig, Germany
| | - Dietmar H Pieper
- Microbial Interactions and Processes Research Group, Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Inhoffenstraße 7, D-38124, Braunschweig, Germany
| | - Tom Van de Wiele
- Center of Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Nadia Mulinacci
- Department of Neurofarba- Pharmaceutical and Nutraceutical Division, University of Florence, Via Ugo Schiff 6, Sesto Fiorentino, FI, Italy.
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20
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Schulz C, Schütte K, Koch N, Vilchez-Vargas R, Wos-Oxley ML, Oxley APA, Vital M, Malfertheiner P, Pieper DH. The active bacterial assemblages of the upper GI tract in individuals with and without Helicobacter infection. Gut 2018; 67:216-225. [PMID: 27920199 DOI: 10.1136/gutjnl-2016-312904] [Citation(s) in RCA: 122] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 11/15/2016] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Patients infected with Helicobacter pylori develop chronic gastritis with a subgroup progressing to further complications. The role of microbiota from the oral cavity swallowed with saliva and either transiting the stomach or persisting in the gastric mucosa is uncertain. It is also not known whether the bacterial community differs in luminal and mucosal niches. A key question is whether H. pylori influences the bacterial communities of gastroduodenal niches. DESIGN Saliva, gastric and duodenal aspirates as well as gastric and duodenal biopsies were collected during oesophagogastroduodenoscopy from 24 patients (m:9, f:15, mean age 52.2±SD 14.5 years). RNA was extracted and the V1-V2 region of the retrotranscribed bacterial 16S rRNA amplified and sequenced on the Illumina MiSeq platform. RESULTS Overall, 687 bacterial phylotypes that belonged to 95 genera and 11 phyla were observed. Each individual comprised a unique microbiota composition that was consistent across the different niches. However, the stomach fluid enriched for specific microbiota components. Helicobacter spp were shown to dominate the mucosa-associated community in the stomach, and to significantly influence duodenal and oral communities. CONCLUSIONS The detailed analysis of the active global bacterial communities from the five distinct sites of the upper GI tract allowed for the first time the differentiation between host effects and the influence of sampling region on the bacterial community. The influence of Helicobacter spp on the global community structures is striking.
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Affiliation(s)
- Christian Schulz
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany.,Microbial Interactions and Processes (MINP) Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Kerstin Schütte
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany.,Department of Internal Medicine and Gastroenterology, Niels-Stensen-Kliniken, Marienhospital, Osnabrück, Germany
| | - Nadine Koch
- Microbial Interactions and Processes (MINP) Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Ramiro Vilchez-Vargas
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
| | - Melissa L Wos-Oxley
- Microbial Interactions and Processes (MINP) Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Andrew P A Oxley
- Microbial Interactions and Processes (MINP) Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Molecular Sciences Laboratory, SARDI Aquatic Sciences, West Beach, South Australia, Australia
| | - Marius Vital
- Microbial Interactions and Processes (MINP) Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Peter Malfertheiner
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
| | - Dietmar H Pieper
- Microbial Interactions and Processes (MINP) Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
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21
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Ehsani E, Hernandez-Sanabria E, Kerckhof FM, Props R, Vilchez-Vargas R, Vital M, Pieper DH, Boon N. Initial evenness determines diversity and cell density dynamics in synthetic microbial ecosystems. Sci Rep 2018; 8:340. [PMID: 29321640 PMCID: PMC5762898 DOI: 10.1038/s41598-017-18668-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 12/15/2017] [Indexed: 12/30/2022] Open
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.
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Affiliation(s)
- Elham Ehsani
- Center for Microbial Ecology and Technology (CMET), Coupure Links 653, 9000, Ghent, Belgium
| | | | | | - Ruben Props
- Center for Microbial Ecology and Technology (CMET), Coupure Links 653, 9000, Ghent, Belgium
| | - Ramiro Vilchez-Vargas
- Center for Microbial Ecology and Technology (CMET), Coupure Links 653, 9000, Ghent, Belgium
| | - Marius Vital
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Inhoffenstr. 7, Braunschweig, 38124, Germany
| | - Dietmar H Pieper
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Inhoffenstr. 7, Braunschweig, 38124, Germany
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Coupure Links 653, 9000, Ghent, Belgium.
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22
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Duarte M, Nielsen A, Camarinha-Silva A, Vilchez-Vargas R, Bruls T, Wos-Oxley ML, Jauregui R, Pieper DH. Functional soil metagenomics: elucidation of polycyclic aromatic hydrocarbon degradation potential following 12 years of in situ bioremediation. Environ Microbiol 2017; 19:2992-3011. [PMID: 28401633 DOI: 10.1111/1462-2920.13756] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 03/29/2017] [Accepted: 04/06/2017] [Indexed: 11/27/2022]
Abstract
A culture-independent function-based screening approach was used to assess the microbial aerobic catabolome for polycyclic aromatic hydrocarbons degradation of a soil subjected to 12 years of in situ bioremediation. A total of 422 750 fosmid clones were screened for key aromatic ring-cleavage activities using 2,3-dihydroxybiphenyl as substrate. Most of the genes encoding ring-cleavage enzymes on the 768 retrieved positive fosmids could not be identified using primer-based approaches and, thus, 205 fosmid inserts were sequenced. Nearly two hundred extradiol dioxygenase encoding genes of three different superfamilies could be identified. Additional key genes of aromatic metabolic pathways were identified, including a high abundance of Rieske non-heme iron oxygenases that provided detailed information on enzymes activating aromatic compounds and enzymes involved in activation of the side chain of methylsubstituted aromatics. The gained insights indicated a complex microbial network acting at the site under study, which comprises organisms similar to recently identified Immundisolibacter cernigliae TR3.2 and Rugosibacter aromaticivorans Ca6 and underlined the great potential of an approach that combines an activity-screening, a cost-effective high-throughput sequencing of fosmid clones and a phylogenomic-routed and manually curated database to carefully identify key proteins dedicated to aerobic degradation of aromatic compounds.
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Affiliation(s)
- Márcia Duarte
- Microbial Interactions and Processes Research Group, HZI - Helmholtz Centre for Infection Research, Inhoffenstr. 7, Braunschweig, D-38124, Germany
| | - Agnes Nielsen
- Microbial Interactions and Processes Research Group, HZI - Helmholtz Centre for Infection Research, Inhoffenstr. 7, Braunschweig, D-38124, Germany
| | - Amélia Camarinha-Silva
- Microbial Interactions and Processes Research Group, HZI - Helmholtz Centre for Infection Research, Inhoffenstr. 7, Braunschweig, D-38124, Germany
| | - Ramiro Vilchez-Vargas
- Microbial Interactions and Processes Research Group, HZI - Helmholtz Centre for Infection Research, Inhoffenstr. 7, Braunschweig, D-38124, Germany.,Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke-University, Magdeburg, Germany
| | - Thomas Bruls
- Institut de Génomique, Genoscope, UMR8030 (CNRS, CEA, Université d'Evry), Evry, France
| | - Melissa L Wos-Oxley
- Microbial Interactions and Processes Research Group, HZI - Helmholtz Centre for Infection Research, Inhoffenstr. 7, Braunschweig, D-38124, Germany
| | - Ruy Jauregui
- Microbial Interactions and Processes Research Group, HZI - Helmholtz Centre for Infection Research, Inhoffenstr. 7, Braunschweig, D-38124, Germany.,AgResearch Grasslands, Tennent drive, Palmerston North, New Zealand
| | - Dietmar H Pieper
- Microbial Interactions and Processes Research Group, HZI - Helmholtz Centre for Infection Research, Inhoffenstr. 7, Braunschweig, D-38124, Germany
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23
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Truchado P, Hernandez-Sanabria E, Salden BN, Van den Abbeele P, Vilchez-Vargas R, Jauregui R, Pieper DH, Possemiers S, Van de Wiele T. Long chain arabinoxylans shift the mucosa-associated microbiota in the proximal colon of the simulator of the human intestinal microbial ecosystem (M-SHIME). J Funct Foods 2017. [DOI: 10.1016/j.jff.2017.02.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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24
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Salden BN, Troost FJ, Wilms E, Truchado P, Vilchez-Vargas R, Pieper DH, Jáuregui R, Marzorati M, van de Wiele T, Possemiers S, Masclee AA. Reinforcement of intestinal epithelial barrier by arabinoxylans in overweight and obese subjects: A randomized controlled trial: Arabinoxylans in gut barrier. Clin Nutr 2017; 37:471-480. [PMID: 28214040 DOI: 10.1016/j.clnu.2017.01.024] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 11/21/2016] [Accepted: 01/26/2017] [Indexed: 11/28/2022]
Abstract
BACKGROUND & AIMS Obesity and metabolic diseases are associated with alterations in microbial composition and impaired gut barrier. Previous in vitro and animal studies have shown that arabinoxylans (AX) have the potential to modulate gut microbiota and gut barrier and therefore could have a protective role. Primary aim of the study was to investigate the effect of AX on intestinal permeability. Secondary aims included the effect of AX on gene transcription and protein expression of tight junctions (TJ), intestinal microbiota composition and activity, immune response and metabolic markers in overweight and obese individuals. METHODS In this randomized, double-blind, placebo-controlled trial, 47 overweight subjects were randomly assigned to groups receiving 7.5 g/d AX (n = 16), 15 g/d AX (n = 17) or 15 g/d placebo (n = 14) for 6 wks. Intestinal permeability was investigated using a multi-sugar test. Sigmoid colon tissue was obtained from a subgroup (n = 26) for analyzing gene transcription and mucosal expression of TJ proteins. Fecal samples were collected to assess microbial composition and activity. Furthermore, the production of cytokines by stimulated peripheral blood mononuclear cells (PBMCs) was examined. Blood was also sampled for measuring metabolic markers. RESULTS No significant changes in gastrointestinal permeability and TJ protein expression were observed after 6 wks AX supplementation compared to placebo. However, gene transcription of occludin was upregulated in the 7.5 g AX group, and transcription of claudin-3 and claudin-4 were upregulated in the 15 g AX group compared to placebo. Furthermore, fecal microbiota diversity was decreased after 6 wks 15 g AX treatment, but no change in relative abundance of dominant phyla was observed. AX intake significantly decreased fecal pH and increased fecal concentrations of total SCFAs, acetate, propionate and butyrate, compared to placebo. Additionally, a decreased TNFα production by stimulated PBMCs was observed after 15 g AX treatment. No changes in metabolic markers were detected. CONCLUSIONS Regular consumption of AX resulted in a more beneficial fermentation profile in overweight and obese individuals. Further studies are required to assess whether such fermentation profile will translate into improved gut barrier function and immune health. The trial has been registered at ClinicalTrials.gov with study ID number NCT01877044.
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Affiliation(s)
- Bouke N Salden
- Department of Internal Medicine, Division of Gastroenterology-Hepatology, School of Nutrition & Translational Research in Metabolism, Maastricht University Medical Center, Maastricht, The Netherlands.
| | - Freddy J Troost
- Department of Internal Medicine, Division of Gastroenterology-Hepatology, School of Nutrition & Translational Research in Metabolism, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Ellen Wilms
- Department of Internal Medicine, Division of Gastroenterology-Hepatology, School of Nutrition & Translational Research in Metabolism, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Pilar Truchado
- Laboratory of Microbial Ecology and Technology, Ghent University, Ghent, Belgium
| | - Ramiro Vilchez-Vargas
- Department of Gastroenterology, Hepatology and Infection Diseases, Otto von Guericke University, Magdeburg, Germany
| | - Dietmar H Pieper
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Ruy Jáuregui
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Massimo Marzorati
- Laboratory of Microbial Ecology and Technology, Ghent University, Ghent, Belgium
| | - Tom van de Wiele
- Laboratory of Microbial Ecology and Technology, Ghent University, Ghent, Belgium
| | - Sam Possemiers
- Laboratory of Microbial Ecology and Technology, Ghent University, Ghent, Belgium
| | - Ad A Masclee
- Department of Internal Medicine, Division of Gastroenterology-Hepatology, School of Nutrition & Translational Research in Metabolism, Maastricht University Medical Center, Maastricht, The Netherlands
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25
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De Weirdt R, Hernandez-Sanabria E, Fievez V, Mees E, Geirnaert A, Van Herreweghen F, Vilchez-Vargas R, Van den Abbeele P, Jauregui R, Pieper DH, Vlaeminck B, Van de Wiele T. Mucosa-associated biohydrogenating microbes protect the simulated colon microbiome from stress associated with high concentrations of poly-unsaturated fat. Environ Microbiol 2017; 19:722-739. [DOI: 10.1111/1462-2920.13622] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Rosemarie De Weirdt
- Center for Microbial Ecology and Technology (CMET), Ghent University; Coupure Links 653 Ghent BE-9000 Belgium
| | - Emma Hernandez-Sanabria
- Center for Microbial Ecology and Technology (CMET), Ghent University; Coupure Links 653 Ghent BE-9000 Belgium
| | - Veerle Fievez
- Laboratory for Animal Nutrition and Product Quality (Lanupro); Ghent University; Proefhoevestraat 10 Melle BE-9090 Belgium
| | - Eva Mees
- Center for Microbial Ecology and Technology (CMET), Ghent University; Coupure Links 653 Ghent BE-9000 Belgium
| | - Annelies Geirnaert
- Center for Microbial Ecology and Technology (CMET), Ghent University; Coupure Links 653 Ghent BE-9000 Belgium
| | - Florence Van Herreweghen
- Center for Microbial Ecology and Technology (CMET), Ghent University; Coupure Links 653 Ghent BE-9000 Belgium
| | - Ramiro Vilchez-Vargas
- Center for Microbial Ecology and Technology (CMET), Ghent University; Coupure Links 653 Ghent BE-9000 Belgium
| | - Pieter Van den Abbeele
- Center for Microbial Ecology and Technology (CMET), Ghent University; Coupure Links 653 Ghent BE-9000 Belgium
| | - Ruy Jauregui
- Microbial Interactions and Processes Research Group, Department of Molecular Infection Biology; Helmholtz Centre for Infection Research; Inhoffenstraβe 7 Braunschweig D-38124 Germany
| | - Dietmar H. Pieper
- Microbial Interactions and Processes Research Group, Department of Molecular Infection Biology; Helmholtz Centre for Infection Research; Inhoffenstraβe 7 Braunschweig D-38124 Germany
| | - Bruno Vlaeminck
- Laboratory for Animal Nutrition and Product Quality (Lanupro); Ghent University; Proefhoevestraat 10 Melle BE-9090 Belgium
| | - Tom Van de Wiele
- Center for Microbial Ecology and Technology (CMET), Ghent University; Coupure Links 653 Ghent BE-9000 Belgium
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26
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Maza-Márquez P, Vilchez-Vargas R, Kerckhof FM, Aranda E, González-López J, Rodelas B. Community structure, population dynamics and diversity of fungi in a full-scale membrane bioreactor (MBR) for urban wastewater treatment. Water Res 2016; 105:507-519. [PMID: 27668995 DOI: 10.1016/j.watres.2016.09.021] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Revised: 09/05/2016] [Accepted: 09/14/2016] [Indexed: 06/06/2023]
Abstract
Community structure, population dynamics and diversity of fungi were monitored in a full-scale membrane bioreactor (MBR) operated throughout four experimental phases (Summer 2009, Autumn 2009, Summer 2010 and Winter, 2012) under different conditions, using the 18S-rRNA gene and the intergenic transcribed spacer (ITS2-region) as molecular markers, and a combination of temperature-gradient gel electrophoresis and 454-pyrosequencing. Both total and metabolically-active fungal populations were fingerprinted, by amplification of molecular markers from community DNA and retrotranscribed RNA, respectively. Fingerprinting and 454-pyrosequencing evidenced that the MBR sheltered a dynamic fungal community composed of a low number of species, in accordance with the knowledge of fungal diversity in freshwater environments, and displaying a medium-high level of functional organization with few numerically dominant phylotypes. Population shifts were experienced in strong correlation with the changes of environmental variables and operation parameters, with pH contributing the highest level of explanation. Phylotypes assigned to nine different fungal Phyla were detected, although the community was mainly composed of Ascomycota, Basidiomycota and Chytridiomycota/Blastocladiomycota. Prevailing fungal phylotypes were affiliated to Saccharomycetes and Chytridiomycetes/Blastocladiomycetes, which displayed antagonistic trends in their relative abundance throughout the experimental period. Fungi identified in the activated sludge were closely related to genera of relevance for the degradation of organic matter and trace-organic contaminants, as well as genera of dimorphic fungi potentially able to produce plant operational issues such as foaming or biofouling. Phylotypes closely related to genera of human and plant pathogenic fungi were also detected.
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Affiliation(s)
- P Maza-Márquez
- Department of Microbiology and Institute of Water Research, University of Granada, Granada, Spain.
| | - R Vilchez-Vargas
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke University, Magdeburg, Germany
| | - F M Kerckhof
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Ghent, Belgium
| | - E Aranda
- Department of Microbiology and Institute of Water Research, University of Granada, Granada, Spain
| | - J González-López
- Department of Microbiology and Institute of Water Research, University of Granada, Granada, Spain
| | - B Rodelas
- Department of Microbiology and Institute of Water Research, University of Granada, Granada, Spain
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27
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Van Herreweghen F, Van den Abbeele P, De Mulder T, De Weirdt R, Geirnaert A, Hernandez-Sanabria E, Vilchez-Vargas R, Jauregui R, Pieper DH, Belzer C, De Vos WM, Van de Wiele T. In vitro colonisation of the distal colon by Akkermansia muciniphila is largely mucin and pH dependent. Benef Microbes 2016; 8:81-96. [PMID: 27824274 DOI: 10.3920/bm2016.0013] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Host mucin is the main constituent of the mucus layer that covers the gut epithelium of the host, and an important source of glycans for the bacteria colonising the intestine. Akkermansia muciniphila is a mucin-degrading bacterium, abundant in the human gut, that is able to produce acetate and propionate during this degradation process. A. muciniphila has been correlated with human health in previous studies, but a mechanistic explanation is lacking. In this study, the main site of colonisation was characterised alongside additional conditions, such as differences in colon pH, prebiotic supplementation and variable mucin supply. To overcome the limitations of in vivo studies concerning variations in mucin availability and difficult access to proximal regions of the colon, a dynamic in vitro gut model (SHIME) was used. In this model, A. muciniphila was found to colonise the distal colon compartment more abundantly than the proximal colon ((±8 log copies/ml compared to ±4 log copies/ml) and the preference for the distal compartment was found to be pH-dependent. The addition of mucin caused a specific increase of A. muciniphila (±4.5 log increase over two days), far exceeding the response of other bacteria present, together with an increase in propionate. These findings suggest that colonisation and mucin degradation by A. muciniphila is dependent on pH and the concentration of mucin. Our results revealed the preference of A. muciniphila for the distal colon environment due to its higher pH and uncovered the quick and stable response of A. muciniphila to mucin supplementation.
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Affiliation(s)
- F Van Herreweghen
- 1 Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - P Van den Abbeele
- 1 Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium.,4 ProDigest BVBA, Technologiepark 3, 9052 Zwijnaarde (Ghent), Belgium
| | - T De Mulder
- 1 Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - R De Weirdt
- 1 Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - A Geirnaert
- 1 Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - E Hernandez-Sanabria
- 1 Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - R Vilchez-Vargas
- 1 Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - R Jauregui
- 3 Microbial Interactions and Processes Research Group, Department of Medical Microbiology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - D H Pieper
- 3 Microbial Interactions and Processes Research Group, Department of Medical Microbiology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - C Belzer
- 2 Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands
| | - W M De Vos
- 2 Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands
| | - T Van de Wiele
- 1 Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium
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28
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De Vrieze J, Raport L, Roume H, Vilchez-Vargas R, Jáuregui R, Pieper DH, Boon N. The full-scale anaerobic digestion microbiome is represented by specific marker populations. Water Res 2016; 104:101-110. [PMID: 27522020 DOI: 10.1016/j.watres.2016.08.008] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 08/01/2016] [Accepted: 08/04/2016] [Indexed: 05/20/2023]
Abstract
Anaerobic digestion is a well-established microbial-based technology for the treatment of organic waste streams and subsequent biogas recovery. A robust and versatile microbial community to ensure overall stability of the process is essential. Four full-scale anaerobic digestion plants were followed for one year to link operational characteristics with microbial community composition and structure. Similarities between digesters, community dynamics and co-occurrence between bacteria and archaea within each digester were analysed. Free ammonia concentration (>200 mg N L-1) and conductivity (>30 mS cm-1) hindered acetoclastic methanogenesis by Methanosaetaceae. Thus, methanogenesis was pushed to the hydrogenotrophic pathway carried out by Methanobacteriales and Methanomicrobiales. Firmicutes dominated the overall bacterial community in each of the digesters (>50%), however, principal coordinate analysis of Bray-Curtis indices showed that each of the four digesters hosted a unique microbial community. The uniqueness of this community was related to two phylotypes belonging to the Syntrophomonas genus (Phy32 and Phy34) and to one unclassified bacterium (Phy2), which could both be considered marker populations in the community. A clear differentiation in co-occurrence of methanogens with several bacteria was observed between the different digesters. Our results demonstrated that full-scale anaerobic digestion plants show constant dynamics and co-occurrence patterns in function of time, but are unique in terms of composition, related to the presence of marker populations.
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Affiliation(s)
- Jo De Vrieze
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000, Gent, Belgium
| | - Linde Raport
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000, Gent, Belgium; Innolab, Derbystraat 223, 9051, Sint-Denijs-Westrem, Belgium
| | - Hugo Roume
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000, Gent, Belgium
| | - Ramiro Vilchez-Vargas
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000, Gent, Belgium
| | - Ruy Jáuregui
- Microbial Interactions and Processes Research Group, Department of Medical Microbiology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Dietmar H Pieper
- Microbial Interactions and Processes Research Group, Department of Medical Microbiology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000, Gent, Belgium.
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Meerburg FA, Vlaeminck SE, Roume H, Seuntjens D, Pieper DH, Jauregui R, Vilchez-Vargas R, Boon N. High-rate activated sludge communities have a distinctly different structure compared to low-rate sludge communities, and are less sensitive towards environmental and operational variables. Water Res 2016; 100:137-145. [PMID: 27183209 DOI: 10.1016/j.watres.2016.04.076] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Revised: 03/14/2016] [Accepted: 04/28/2016] [Indexed: 06/05/2023]
Abstract
High-rate activated sludge processes allow for the recovery of organics and energy from wastewaters. These systems are operated at a short sludge retention time and high sludge-specific loading rates, which results in a higher sludge yield and better digestibility than conventional, low-rate activated sludge. Little is known about the microbial ecology of high-rate systems. In this work, we address the need for a fundamental understanding of how high-rate microbial communities differ from low-rate communities. We investigated the high-rate and low-rate communities in a sewage treatment plant in relation to environmental and operational variables over a period of ten months. We demonstrated that (1) high-rate and low-rate communities are distinctly different in terms of richness, evenness and composition, (2) high-rate community dynamics are more variable and less shaped by deterministic factors compared to low-rate communities, (3) sub-communities of continuously core and transitional members are more shaped by deterministic factors than the continuously rare members, both in high-rate and low-rate communities, and (4) high-rate community members showed a co-occurrence pattern similar to that of low-rate community members, but were less likely to be correlated to environmental and operational variables. These findings provide a basis for further optimization of high-rate systems, in order to facilitate resource recovery from wastewater.
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Affiliation(s)
- Francis A Meerburg
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Siegfried E Vlaeminck
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Ghent, Belgium; Research Group of Sustainable Energy, Air and Water Technology, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerpen, Belgium
| | - Hugo Roume
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Dries Seuntjens
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Dietmar H Pieper
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Ruy Jauregui
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Ramiro Vilchez-Vargas
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
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Marzorati M, Vilchez-Vargas R, Bussche JV, Truchado P, Jauregui R, El Hage RA, Pieper DH, Vanhaecke L, Van de Wiele T. High-fiber and high-protein diets shape different gut microbial communities, which ecologically behave similarly under stress conditions, as shown in a gastrointestinal simulator. Mol Nutr Food Res 2016; 61. [DOI: 10.1002/mnfr.201600150] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 05/29/2016] [Accepted: 06/16/2016] [Indexed: 01/29/2023]
Affiliation(s)
- Massimo Marzorati
- Center of Microbial Ecology and Technology (CMET); Ghent University, Coupure Links 653; Ghent Belgium
| | - Ramiro Vilchez-Vargas
- Center of Microbial Ecology and Technology (CMET); Ghent University, Coupure Links 653; Ghent Belgium
| | - Julie Vanden Bussche
- Laboratory of Chemical Analysis; Department of Veterinary Public Health and Food Safety; Ghent University; Merelbeke Belgium
| | - Pilar Truchado
- Center of Microbial Ecology and Technology (CMET); Ghent University, Coupure Links 653; Ghent Belgium
| | - Ruy Jauregui
- Microbial Interactions and Processes Research Group; Department of Molecular Infection Biology; Helmholtz Centre for Infection Research; Braunschweig Germany
| | - Racha Ahmad El Hage
- Center of Microbial Ecology and Technology (CMET); Ghent University, Coupure Links 653; Ghent Belgium
| | - Dietmar H. Pieper
- Microbial Interactions and Processes Research Group; Department of Molecular Infection Biology; Helmholtz Centre for Infection Research; Braunschweig Germany
| | - Lynn Vanhaecke
- Laboratory of Chemical Analysis; Department of Veterinary Public Health and Food Safety; Ghent University; Merelbeke Belgium
| | - Tom Van de Wiele
- Center of Microbial Ecology and Technology (CMET); Ghent University, Coupure Links 653; Ghent Belgium
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Coma M, Vilchez-Vargas R, Roume H, Jauregui R, Pieper DH, Rabaey K. Product Diversity Linked to Substrate Usage in Chain Elongation by Mixed-Culture Fermentation. Environ Sci Technol 2016; 50:6467-76. [PMID: 27162101 DOI: 10.1021/acs.est.5b06021] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Acetate and ethanol can be converted to caproic acid by microorganisms through reverse β-oxidation. There is limited insight into the versatility of chain elongation in view of different starting substrates, including even- and odd-carbon carboxylates and alcohols other than ethanol. Thermodynamic analyses show that most elongation pathways are energetically feasible. Through incubations of microbial communities with different substrate-pair combinations, we established that ethanol and propanol were both highly suitable for chain elongation. As an electron acceptor, acetate, propionate, and butyrate readily elongated with ethanol, whereas an adaptation period was necessary for formate. Isobutyrate and longer-chained fatty acids above butyrate were not elongated. The microbial communities converged, and consistent enrichment of Clostridium spp. was observed, independent of the supplied alcohol or carboxylate, with a strain related to Clostridium kluyveri dominating the enrichments. Community analysis also showed phylotypes related to Bacteroidaceae and Microbacteriaceae families in all tests that are capable of converting the base substrates to useful intermediates. These organisms were mainly enriched with methanol or formate. Our overall conclusion is thus that multiple substrates can be used for chain elongation and that this process is carried out by highly similar organisms for direct chain elongation irrespective of the substrate.
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Affiliation(s)
- Marta Coma
- Center for Microbial Ecology and Technology, Ghent University , Coupure Links 653, 9000 Ghent, Belgium
| | - Ramiro Vilchez-Vargas
- Center for Microbial Ecology and Technology, Ghent University , Coupure Links 653, 9000 Ghent, Belgium
| | - Hugo Roume
- Center for Microbial Ecology and Technology, Ghent University , Coupure Links 653, 9000 Ghent, Belgium
| | - Ruy Jauregui
- Microbial Interactions and Processes Group, Department of Molecular Infection Biology, Helmholtz Centre for Infection Research , Inhoffenstraße 7, D-38124 Braunschweig, Germany
| | - Dietmar H Pieper
- Microbial Interactions and Processes Group, Department of Molecular Infection Biology, Helmholtz Centre for Infection Research , Inhoffenstraße 7, D-38124 Braunschweig, Germany
| | - Korneel Rabaey
- Center for Microbial Ecology and Technology, Ghent University , Coupure Links 653, 9000 Ghent, Belgium
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Courtens ENP, Vandekerckhove T, Prat D, Vilchez-Vargas R, Vital M, Pieper DH, Meerbergen K, Lievens B, Boon N, Vlaeminck SE. Empowering a mesophilic inoculum for thermophilic nitrification: Growth mode and temperature pattern as critical proliferation factors for archaeal ammonia oxidizers. Water Res 2016; 92:94-103. [PMID: 26841233 DOI: 10.1016/j.watres.2016.01.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 12/29/2015] [Accepted: 01/11/2016] [Indexed: 06/05/2023]
Abstract
Cost-efficient biological treatment of warm nitrogenous wastewaters requires the development of thermophilic nitrogen removal processes. Only one thermophilic nitrifying bioreactor was described so far, achieving 200 mg N L(-1) d(-1) after more than 300 days of enrichment from compost samples. From the practical point of view in which existing plants would be upgraded, however, a more time-efficient development strategy based on mesophilic nitrifying sludge is preferred. This study evaluated the adaptive capacities of mesophilic nitrifying sludge for two linear temperature increase patterns (non-oscillating vs. oscillating), two different slopes (0.25 vs. 0.08 °C d(-1)) and two different reactor types (floc vs. biofilm growth). The oscillating temperature pattern (0.25 °C d(-1)) and the moving bed biofilm reactor (0.08 °C d(-1)) could not reach nitrification at temperatures higher than 46 °C. However, nitrification rates up to 800 mg N L(-1) d(-1) and 150 mg N g(-1) volatile suspended solids d(-1) were achieved at a temperature as high as 49 °C by imposing the slowest linear temperature increase to floccular sludge. Microbial community analysis revealed that this successful transition was related with a shift in ammonium oxidizing archaea dominating ammonia oxidizing bacteria, while for nitrite oxidation Nitrospira spp. was constantly more abundant than Nitrobacter spp.. This observation was accompanied with an increase in observed sludge yield and a shift in maximal optimum temperature, determined with ex-situ temperature sensitivity measurements, predicting an upcoming reactor failure at higher temperature. Overall, this study achieved nitrification at 49 °C within 150 days by gradual adaptation of mesophilic sludge, and showed that ex-situ temperature sensitivity screening can be used to monitor and steer the transition process.
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Affiliation(s)
- Emilie N P Courtens
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, 9000 Gent, Belgium
| | - Tom Vandekerckhove
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, 9000 Gent, Belgium
| | - Delphine Prat
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, 9000 Gent, Belgium
| | - Ramiro Vilchez-Vargas
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, 9000 Gent, Belgium
| | - Marius Vital
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Dietmar H Pieper
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Ken Meerbergen
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), KU Leuven, Campus De Nayer, Fortsesteenweg 30A, 2860 Sint-Katelijne-Waver, Belgium
| | - Bart Lievens
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), KU Leuven, Campus De Nayer, Fortsesteenweg 30A, 2860 Sint-Katelijne-Waver, Belgium
| | - Nico Boon
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, 9000 Gent, Belgium
| | - Siegfried E Vlaeminck
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, 9000 Gent, Belgium; Research Group of Sustainable Energy, Air and Water Technology, Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerpen, Belgium.
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Maes S, Props R, Fitts JP, Smet RD, Vilchez-Vargas R, Vital M, Pieper DH, Vanhaecke F, Boon N, Hennebel T. Platinum Recovery from Synthetic Extreme Environments by Halophilic Bacteria. Environ Sci Technol 2016; 50:2619-2626. [PMID: 26854514 DOI: 10.1021/acs.est.5b05355] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Metal recycling based on urban mining needs to be established to tackle the increasing supply risk of critical metals such as platinum. Presently, efficient strategies are missing for the recovery of platinum from diluted industrial process streams, often characterized by extremely low pHs and high salt concentrations. In this research, halophilic mixed cultures were employed for the biological recovery of platinum (Pt). Halophilic bacteria were enriched from Artemia cysts, living in salt lakes, in different salt matrices (sea salt mixture and NH4Cl; 20-210 g L(-1) salts) and at low to neutral pH (pH 3-7). The main taxonomic families present in the halophilic cultures were Halomonadaceae, Bacillaceae, and Idiomarinaceae. The halophilic cultures were able to recover >98% Pt(II) and >97% Pt(IV) at pH 2 within 3-21 h (4-453 mg Ptrecovered h(-1) g(-1) biomass). X-ray absorption spectroscopy confirmed the reduction to Pt(0) and transmission electron microscopy revealed both intra- and extracellular Pt precipitates, with median diameters of 9-30 nm and 11-13 nm, for Pt(II) and Pt(IV), respectively. Flow cytometric membrane integrity staining demonstrated the preservation of cell viability during platinum recovery. This study demonstrates the Pt recovery potential of halophilic mixed cultures in acidic saline conditions.
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Affiliation(s)
- Synthia Maes
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University , Coupure Links 653, B-9000 Gent, Belgium
| | - Ruben Props
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University , Coupure Links 653, B-9000 Gent, Belgium
| | - Jeffrey P Fitts
- Department of Civil and Environmental Engineering, Princeton University , Princeton, New York 08544, United States
| | - Rebecca De Smet
- Department of Medical and Forensic Pathology, Ghent University , De Pintelaan 185, B-9000 Gent, Belgium
| | - Ramiro Vilchez-Vargas
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University , Coupure Links 653, B-9000 Gent, Belgium
| | - Marius Vital
- Microbial Interactions and Processes Research Group, Department of Medical Microbiology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Dietmar H Pieper
- Microbial Interactions and Processes Research Group, Department of Medical Microbiology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Frank Vanhaecke
- Department of Analytical Chemistry, Ghent University , Krijgslaan 281 (S12), B-9000 Gent, Belgium
| | - Nico Boon
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University , Coupure Links 653, B-9000 Gent, Belgium
| | - Tom Hennebel
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University , Coupure Links 653, B-9000 Gent, Belgium
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Verstraelen H, Vilchez-Vargas R, Desimpel F, Jauregui R, Vankeirsbilck N, Weyers S, Verhelst R, De Sutter P, Pieper DH, Van De Wiele T. Characterisation of the human uterine microbiome in non-pregnant women through deep sequencing of the V1-2 region of the 16S rRNA gene. PeerJ 2016; 4:e1602. [PMID: 26823997 PMCID: PMC4730988 DOI: 10.7717/peerj.1602] [Citation(s) in RCA: 170] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 12/23/2015] [Indexed: 12/16/2022] Open
Abstract
Background. It is widely assumed that the uterine cavity in non-pregnant women is physiologically sterile, also as a premise to the long-held view that human infants develop in a sterile uterine environment, though likely reflecting under-appraisal of the extent of the human bacterial metacommunity. In an exploratory study, we aimed to investigate the putative presence of a uterine microbiome in a selected series of non-pregnant women through deep sequencing of the V1-2 hypervariable region of the 16S ribosomal RNA (rRNA) gene. Methods. Nineteen women with various reproductive conditions, including subfertility, scheduled for hysteroscopy and not showing uterine anomalies were recruited. Subjects were highly diverse with regard to demographic and medical history and included nulliparous and parous women. Endometrial tissue and mucus harvesting was performed by use of a transcervical device designed to obtain endometrial biopsy, while avoiding cervicovaginal contamination. Bacteria were targeted by use of a barcoded Illumina MiSeq paired-end sequencing method targeting the 16S rRNA gene V1-2 region, yielding an average of 41,194 reads per sample after quality filtering. Taxonomic annotation was pursued by comparison with sequences available through the Ribosomal Database Project and the NCBI database. Results. Out of 183 unique 16S rRNA gene amplicon sequences, 15 phylotypes were present in all samples. In some 90% of the women included, community architecture was fairly similar inasmuch B. xylanisolvens, B. thetaiotaomicron, B. fragilis and an undetermined Pelomonas taxon constituted over one third of the endometrial bacterial community. On the singular phylotype level, six women showed predominance of L. crispatus or L. iners in the presence of the Bacteroides core. Two endometrial communities were highly dissimilar, largely lacking the Bacteroides core, one dominated by L. crispatus and another consisting of a highly diverse community, including Prevotella spp., Atopobium vaginae, and Mobiluncus curtisii. Discussion. Our findings are, albeit not necessarily generalizable, consistent with the presence of a unique microbiota dominated by Bacteroides residing on the endometrium of the human non-pregnant uterus. The transcervical sampling approach may be influenced to an unknown extent by endocervical microbiota, which remain uncharacterised, and therefore warrants further validation. Nonetheless, consistent with our understanding of the human microbiome, the uterine microbiota are likely to have a previously unrecognized role in uterine physiology and human reproduction. Further study is therefore warranted to document community ecology and dynamics of the uterine microbiota, as well as the role of the uterine microbiome in health and disease.
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Affiliation(s)
- Hans Verstraelen
- Department of Obstetrics and Gynaecology, Ghent University , Ghent , Belgium
| | - Ramiro Vilchez-Vargas
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University , Ghent , Belgium
| | - Fabian Desimpel
- Faculty of Medicine and Health Sciences, Ghent University , Ghent , Belgium
| | - Ruy Jauregui
- Microbial Interactions and Processes (MINP) Research Group, Helmholtz Centre for Infection Research , Braunschweig , Germany
| | - Nele Vankeirsbilck
- Department of Obstetrics and Gynaecology, Ghent University , Ghent , Belgium
| | - Steven Weyers
- Department of Obstetrics and Gynaecology, Ghent University , Ghent , Belgium
| | - Rita Verhelst
- Department of Obstetrics and Gynaecology, Ghent University , Ghent , Belgium
| | - Petra De Sutter
- Department of Obstetrics and Gynaecology, Ghent University , Ghent , Belgium
| | - Dietmar H Pieper
- Microbial Interactions and Processes (MINP) Research Group, Helmholtz Centre for Infection Research , Braunschweig , Germany
| | - Tom Van De Wiele
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University , Ghent , Belgium
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Grunert O, Hernandez-Sanabria E, Vilchez-Vargas R, Jauregui R, Pieper DH, Perneel M, Van Labeke MC, Reheul D, Boon N. Mineral and organic growing media have distinct community structure, stability and functionality in soilless culture systems. Sci Rep 2016; 6:18837. [PMID: 26728128 PMCID: PMC4700413 DOI: 10.1038/srep18837] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 11/25/2015] [Indexed: 11/11/2022] Open
Abstract
The choice of soilless growing medium for plant nutrition, growth and support is crucial for improving the eco-sustainability of the production in horticultural systems. As our current understanding of the functional microbial communities inhabiting this ecosystem is still limited, we examined the microbial community development of the two most important growing media (organic and mineral) used in open soilless horticultural systems. We aimed to identify factors that influence community composition over time, and to compare the distribution of individual taxa across growing media, and their potential functionality. High throughput sequencing analysis revealed a distinctive and stable microbial community in the organic growing medium. Humidity, pH, nitrate-N, ammonium-N and conductivity were uncovered as the main factors associated with the resident bacterial communities. Ammonium-N was correlated with Rhizobiaceae abundance, while potential competitive interactions among both Methylophilaceae and Actinobacteridae with Rhizobiaceae were suggested. Our results revealed that soilless growing media are unique niches for diverse bacterial communities with temporal functional stability, which may possibly impact the resistance to external forces. These differences in communities can be used to develop strategies to move towards a sustainable horticulture with increased productivity and quality.
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Affiliation(s)
- Oliver Grunert
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, B-9000 Gent, Belgium
- Peltracom NV, Skaldenstraat 7a, B-9042 Ghent-Desteldonk, Belgium
| | - Emma Hernandez-Sanabria
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, B-9000 Gent, Belgium
| | - Ramiro Vilchez-Vargas
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, B-9000 Gent, Belgium
| | - Ruy Jauregui
- Microbial Interactions and Processes Research Group, Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Inhoffenstraße 7, D-38124, Braunschweig, Germany
| | - Dietmar H. Pieper
- Microbial Interactions and Processes Research Group, Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Inhoffenstraße 7, D-38124, Braunschweig, Germany
| | - Maaike Perneel
- Peltracom NV, Skaldenstraat 7a, B-9042 Ghent-Desteldonk, Belgium
| | | | - Dirk Reheul
- Department of Plant Production, Ghent University, Coupure Links 653, B-9000 Gent, Belgium
| | - Nico Boon
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, B-9000 Gent, Belgium
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De Vrieze J, Regueiro L, Props R, Vilchez-Vargas R, Jáuregui R, Pieper DH, Lema JM, Carballa M. Presence does not imply activity: DNA and RNA patterns differ in response to salt perturbation in anaerobic digestion. Biotechnol Biofuels 2016; 9:244. [PMID: 27843490 PMCID: PMC5103597 DOI: 10.1186/s13068-016-0652-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 10/20/2016] [Indexed: 05/11/2023]
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.
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Affiliation(s)
- Jo De Vrieze
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
- Department of Chemical Engineering, School of Engineering, University of Santiago de Compostela, Rúa Lope Gomez de Marzoa s/n, E-15782 Santiago de Compostela, Spain
| | - Leticia Regueiro
- Department of Chemical Engineering, School of Engineering, University of Santiago de Compostela, Rúa Lope Gomez de Marzoa s/n, E-15782 Santiago de Compostela, Spain
| | - Ruben Props
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Ramiro Vilchez-Vargas
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Ruy Jáuregui
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research (HZI), Brunswick, Germany
- AgResearch, Tennent Drive, Palmerston North, 4442 New Zealand
| | - Dietmar H. Pieper
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research (HZI), Brunswick, Germany
| | - Juan M. Lema
- Department of Chemical Engineering, School of Engineering, University of Santiago de Compostela, Rúa Lope Gomez de Marzoa s/n, E-15782 Santiago de Compostela, Spain
| | - Marta Carballa
- Department of Chemical Engineering, School of Engineering, University of Santiago de Compostela, Rúa Lope Gomez de Marzoa s/n, E-15782 Santiago de Compostela, Spain
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Kerckhof FM, Vekeman B, Geirnaert A, Courtens EN, Vilchez-Vargas R, Ho A, Heyle K, Boon N. Enhancing microbial cryopreservation: From fastidious microbes to mixed communities. Cryobiology 2015. [DOI: 10.1016/j.cryobiol.2015.10.054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Lopez-Fernandez M, Cherkouk A, Vilchez-Vargas R, Jauregui R, Pieper D, Boon N, Sanchez-Castro I, Merroun ML. Bacterial Diversity in Bentonites, Engineered Barrier for Deep Geological Disposal of Radioactive Wastes. Microb Ecol 2015; 70:922-935. [PMID: 26024740 DOI: 10.1007/s00248-015-0630-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 05/15/2015] [Indexed: 06/04/2023]
Abstract
The long-term disposal of radioactive wastes in a deep geological repository is the accepted international solution for the treatment and management of these special residues. The microbial community of the selected host rocks and engineered barriers for the deep geological repository may affect the performance and the safety of the radioactive waste disposal. In this work, the bacterial population of bentonite formations of Almeria (Spain), selected as a reference material for bentonite-engineered barriers in the disposal of radioactive wastes, was studied. 16S ribosomal RNA (rRNA) gene-based approaches were used to study the bacterial community of the bentonite samples by traditional clone libraries and Illumina sequencing. Using both techniques, the bacterial diversity analysis revealed similar results, with phylotypes belonging to 14 different bacterial phyla: Acidobacteria, Actinobacteria, Armatimonadetes, Bacteroidetes, Chloroflexi, Cyanobacteria, Deinococcus-Thermus, Firmicutes, Gemmatimonadetes, Planctomycetes, Proteobacteria, Nitrospirae, Verrucomicrobia and an unknown phylum. The dominant groups of the community were represented by Proteobacteria and Bacteroidetes. A high diversity was found in three of the studied samples. However, two samples were less diverse and dominated by Betaproteobacteria.
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Affiliation(s)
| | - Andrea Cherkouk
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource Ecology, Bautzner Landstrasse 400, 01328, Dresden, Germany
| | | | - Ruy Jauregui
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Dietmar Pieper
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Nico Boon
- Laboratory of Microbial Ecology and Technology, Ghent University, Ghent, Belgium
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Geirnaert A, Wang J, Tinck M, Steyaert A, Van den Abbeele P, Eeckhaut V, Vilchez-Vargas R, Falony G, Laukens D, De Vos M, Van Immerseel F, Raes J, Boon N, Van de Wiele T. Interindividual differences in response to treatment with butyrate-producing Butyricicoccus pullicaecorum 25–3T studied in an in vitro gut model. FEMS Microbiol Ecol 2015; 91:fiv054. [DOI: 10.1093/femsec/fiv054] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/12/2015] [Indexed: 12/13/2022] Open
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Szafranski SP, Wos-Oxley ML, Vilchez-Vargas R, Jáuregui R, Plumeier I, Klawonn F, Tomasch J, Meisinger C, Kühnisch J, Sztajer H, Pieper DH, Wagner-Döbler I. High-resolution taxonomic profiling of the subgingival microbiome for biomarker discovery and periodontitis diagnosis. Appl Environ Microbiol 2015; 81:1047-58. [PMID: 25452281 PMCID: PMC4292489 DOI: 10.1128/aem.03534-14] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 11/17/2014] [Indexed: 01/19/2023] Open
Abstract
The oral microbiome plays a key role for caries, periodontitis, and systemic diseases. A method for rapid, high-resolution, robust taxonomic profiling of subgingival bacterial communities for early detection of periodontitis biomarkers would therefore be a useful tool for individualized medicine. Here, we used Illumina sequencing of the V1-V2 and V5-V6 hypervariable regions of the 16S rRNA gene. A sample stratification pipeline was developed in a pilot study of 19 individuals, 9 of whom had been diagnosed with chronic periodontitis. Five hundred twenty-three operational taxonomic units (OTUs) were obtained from the V1-V2 region and 432 from the V5-V6 region. Key periodontal pathogens like Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia could be identified at the species level with both primer sets. Principal coordinate analysis identified two outliers that were consistently independent of the hypervariable region and method of DNA extraction used. The linear discriminant analysis (LDA) effect size algorithm (LEfSe) identified 80 OTU-level biomarkers of periodontitis and 17 of health. Health- and periodontitis-related clusters of OTUs were identified using a connectivity analysis, and the results confirmed previous studies with several thousands of samples. A machine learning algorithm was developed which was trained on all but one sample and then predicted the diagnosis of the left-out sample (jackknife method). Using a combination of the 10 best biomarkers, 15 of 17 samples were correctly diagnosed. Training the algorithm on time-resolved community profiles might provide a highly sensitive tool to detect the onset of periodontitis.
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Affiliation(s)
- Szymon P Szafranski
- Microbial Communication Research Group, Department of Molecular Infection Biology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Melissa L Wos-Oxley
- Microbial Interactions and Processes Research Group, Department of Medical Microbiology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Ramiro Vilchez-Vargas
- Microbial Interactions and Processes Research Group, Department of Medical Microbiology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Ruy Jáuregui
- Microbial Interactions and Processes Research Group, Department of Medical Microbiology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Iris Plumeier
- Microbial Interactions and Processes Research Group, Department of Medical Microbiology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Frank Klawonn
- Bioinformatics and Statistics Research Group, Department of Cellular Proteomics, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany Department of Computer Science, Ostfalia University of Applied Sciences, Wolfenbüttel, Germany
| | - Jürgen Tomasch
- Microbial Communication Research Group, Department of Molecular Infection Biology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Christa Meisinger
- National Cohort Study Center Augsburg, Helmholtz Centre Munich, Germany
| | - Jan Kühnisch
- Department of Conservative Dentistry, Ludwig-Maximilians-University, Munich, Germany
| | - Helena Sztajer
- Microbial Communication Research Group, Department of Molecular Infection Biology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Dietmar H Pieper
- Microbial Interactions and Processes Research Group, Department of Medical Microbiology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Irene Wagner-Döbler
- Microbial Communication Research Group, Department of Molecular Infection Biology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
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Duarte M, Jauregui R, Vilchez-Vargas R, Junca H, Pieper DH. AromaDeg, a novel database for phylogenomics of aerobic bacterial degradation of aromatics. Database (Oxford) 2014; 2014:bau118. [PMID: 25468931 PMCID: PMC4250580 DOI: 10.1093/database/bau118] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Understanding prokaryotic transformation of recalcitrant pollutants and the in-situ metabolic nets require the integration of massive amounts of biological data. Decades of biochemical studies together with novel next-generation sequencing data have exponentially increased information on aerobic aromatic degradation pathways. However, the majority of protein sequences in public databases have not been experimentally characterized and homology-based methods are still the most routinely used approach to assign protein function, allowing the propagation of misannotations. AromaDeg is a web-based resource targeting aerobic degradation of aromatics that comprises recently updated (September 2013) and manually curated databases constructed based on a phylogenomic approach. Grounded in phylogenetic analyses of protein sequences of key catabolic protein families and of proteins of documented function, AromaDeg allows query and data mining of novel genomic, metagenomic or metatranscriptomic data sets. Essentially, each query sequence that match a given protein family of AromaDeg is associated to a specific cluster of a given phylogenetic tree and further function annotation and/or substrate specificity may be inferred from the neighboring cluster members with experimentally validated function. This allows a detailed characterization of individual protein superfamilies as well as high-throughput functional classifications. Thus, AromaDeg addresses the deficiencies of homology-based protein function prediction, combining phylogenetic tree construction and integration of experimental data to obtain more accurate annotations of new biological data related to aerobic aromatic biodegradation pathways. We pursue in future the expansion of AromaDeg to other enzyme families involved in aromatic degradation and its regular update. Database URL:http://aromadeg.siona.helmholtz-hzi.de
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Affiliation(s)
- Márcia Duarte
- Microbial Interactions and Processes Research Group, HZI-Helmholtz Centre for Infection Research, Inhoffenstr. 7, D-38124 Braunschweig, Germany, Research Group Microbial Ecology, Metabolism, Genomics and Evolution of Communities of Environmental Microorganisms, CorpoGen. Carrera 5 No. 66A-35, Bogotá, Colombia and Faculty of Basic and Applied Sciences, Universidad Militar Nueva Granada-UMNG, Campus Cajicá, Bogotá DC, Colombia
| | - Ruy Jauregui
- Microbial Interactions and Processes Research Group, HZI-Helmholtz Centre for Infection Research, Inhoffenstr. 7, D-38124 Braunschweig, Germany, Research Group Microbial Ecology, Metabolism, Genomics and Evolution of Communities of Environmental Microorganisms, CorpoGen. Carrera 5 No. 66A-35, Bogotá, Colombia and Faculty of Basic and Applied Sciences, Universidad Militar Nueva Granada-UMNG, Campus Cajicá, Bogotá DC, Colombia Microbial Interactions and Processes Research Group, HZI-Helmholtz Centre for Infection Research, Inhoffenstr. 7, D-38124 Braunschweig, Germany, Research Group Microbial Ecology, Metabolism, Genomics and Evolution of Communities of Environmental Microorganisms, CorpoGen. Carrera 5 No. 66A-35, Bogotá, Colombia and Faculty of Basic and Applied Sciences, Universidad Militar Nueva Granada-UMNG, Campus Cajicá, Bogotá DC, Colombia
| | - Ramiro Vilchez-Vargas
- Microbial Interactions and Processes Research Group, HZI-Helmholtz Centre for Infection Research, Inhoffenstr. 7, D-38124 Braunschweig, Germany, Research Group Microbial Ecology, Metabolism, Genomics and Evolution of Communities of Environmental Microorganisms, CorpoGen. Carrera 5 No. 66A-35, Bogotá, Colombia and Faculty of Basic and Applied Sciences, Universidad Militar Nueva Granada-UMNG, Campus Cajicá, Bogotá DC, Colombia
| | - Howard Junca
- Microbial Interactions and Processes Research Group, HZI-Helmholtz Centre for Infection Research, Inhoffenstr. 7, D-38124 Braunschweig, Germany, Research Group Microbial Ecology, Metabolism, Genomics and Evolution of Communities of Environmental Microorganisms, CorpoGen. Carrera 5 No. 66A-35, Bogotá, Colombia and Faculty of Basic and Applied Sciences, Universidad Militar Nueva Granada-UMNG, Campus Cajicá, Bogotá DC, Colombia Microbial Interactions and Processes Research Group, HZI-Helmholtz Centre for Infection Research, Inhoffenstr. 7, D-38124 Braunschweig, Germany, Research Group Microbial Ecology, Metabolism, Genomics and Evolution of Communities of Environmental Microorganisms, CorpoGen. Carrera 5 No. 66A-35, Bogotá, Colombia and Faculty of Basic and Applied Sciences, Universidad Militar Nueva Granada-UMNG, Campus Cajicá, Bogotá DC, Colombia
| | - Dietmar H Pieper
- Microbial Interactions and Processes Research Group, HZI-Helmholtz Centre for Infection Research, Inhoffenstr. 7, D-38124 Braunschweig, Germany, Research Group Microbial Ecology, Metabolism, Genomics and Evolution of Communities of Environmental Microorganisms, CorpoGen. Carrera 5 No. 66A-35, Bogotá, Colombia and Faculty of Basic and Applied Sciences, Universidad Militar Nueva Granada-UMNG, Campus Cajicá, Bogotá DC, Colombia
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Courtens ENP, Vlaeminck SE, Vilchez-Vargas R, Verliefde A, Jauregui R, Pieper DH, Boon N. Trade-off between mesophilic and thermophilic denitrification: rates vs. sludge production, settleability and stability. Water Res 2014; 63:234-244. [PMID: 25007305 DOI: 10.1016/j.watres.2014.06.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 06/05/2014] [Accepted: 06/16/2014] [Indexed: 06/03/2023]
Abstract
The development of thermophilic nitrogen removal strategies will facilitate sustainable biological treatment of warm nitrogenous wastewaters. Thermophilic denitrification was extensively compared to mesophilic denitrification for the first time in this study. Two sequential batch reactors (SBR) at 34 °C and 55 °C were inoculated with mesophilic activated sludge (26 °C), fed with synthetic influent in a first phase. Subsequently, the carbon source was switched from acetate to molasses, whereas in a third phase, the nitrate source was fertilizer industry wastewater. The denitrifying sludge maintained its activity at 55 °C, resulting in an immediate process start-up, obtaining nitrogen removal rates higher than 500 mg N g(-1) VSS d(-1) in less than one week. Although the mesophilic SBR showed twice as high specific nitrogen removal rates, the maximum thermophilic denitrifying activity in this study was nearly 10 times higher than the activities reported thus far. The thermophilic SBR moreover had a 73% lower sludge volume index, a 45% lower sludge production and a higher resilience towards a change in carbon source compared with the mesophilic SBR. The higher resilience was potentially related to a higher microbial diversity and evenness of the thermophilic community at the end of the synthetic feeding period. The thermophilic microbial community showed a higher similarity over the different feeding periods implying a more stable community. Overall, this study showed the capability of mesophilic denitrifiers to maintain their activity after a large temperature increase. Existing mesophilic process systems with cooling for the treatment of warm wastewaters could thus efficiently be converted to thermophilic systems with low sludge production and good settling properties.
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Affiliation(s)
- Emilie N P Courtens
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, 9000 Gent, Belgium
| | - Siegfried E Vlaeminck
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, 9000 Gent, Belgium
| | - Ramiro Vilchez-Vargas
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, 9000 Gent, Belgium
| | - Arne Verliefde
- The Particle and Interfacial Technology Group (PaInT), Ghent University, Coupure Links 653, 9000 Gent, Belgium
| | - Ruy Jauregui
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Dietmar H Pieper
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Nico Boon
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, 9000 Gent, Belgium.
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Kerckhof FM, Courtens ENP, Geirnaert A, Hoefman S, Ho A, Vilchez-Vargas R, Pieper DH, Jauregui R, Vlaeminck SE, Van de Wiele T, Vandamme P, Heylen K, Boon N. Optimized cryopreservation of mixed microbial communities for conserved functionality and diversity. PLoS One 2014; 9:e99517. [PMID: 24937032 PMCID: PMC4061060 DOI: 10.1371/journal.pone.0099517] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 05/15/2014] [Indexed: 12/26/2022] Open
Abstract
The use of mixed microbial communities (microbiomes) for biotechnological applications has steadily increased over the past decades. However, these microbiomes are not readily available from public culture collections, hampering their potential for widespread use. The main reason for this lack of availability is the lack of an effective cryopreservation protocol. Due to this critical need, we evaluated the functionality as well as the community structure of three different types of microbiomes before and after cryopreservation with two cryoprotective agents (CPA). Microbiomes were selected based upon relevance towards applications: (1) a methanotrophic co-culture (MOB), with potential for mitigation of greenhouse gas emissions, environmental pollutants removal and bioplastics production; (2) an oxygen limited autotrophic nitrification/denitrification (OLAND) biofilm, with enhanced economic and ecological benefits for wastewater treatment, and (3) fecal material from a human donor, with potential applications for fecal transplants and pre/probiotics research. After three months of cryopreservation at −80°C, we found that metabolic activity, in terms of the specific activity recovery of MOB, aerobic ammonium oxidizing bacteria (AerAOB) and anaerobic AOB (AnAOB, anammox) in the OLAND mixed culture, resumes sooner when one of our selected CPA [dimethyl sulfoxide (DMSO) and DMSO plus trehalose and tryptic soy broth (DMSO+TT)] was added. However, the activity of the fecal community was not influenced by the CPA addition, although the preservation of the community structure (as determined by 16S rRNA gene sequencing) was enhanced by addition of CPA. In summary, we have evaluated a cryopreservation protocol that succeeded in preserving both community structure and functionality of value-added microbiomes. This will allow individual laboratories and culture collections to boost the use of microbiomes in biotechnological applications.
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Affiliation(s)
- Frederiek-Maarten Kerckhof
- Laboratory of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Emilie N. P. Courtens
- Laboratory of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Annelies Geirnaert
- Laboratory of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Sven Hoefman
- Laboratory of Microbiology, Faculty of Sciences, Ghent University, Gent, Belgium
| | - Adrian Ho
- Laboratory of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Ramiro Vilchez-Vargas
- Laboratory of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Dietmar H. Pieper
- Microbial Interactions and Processes Research Group, Department of Medical Microbiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Ruy Jauregui
- Microbial Interactions and Processes Research Group, Department of Medical Microbiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Siegfried E. Vlaeminck
- Laboratory of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Tom Van de Wiele
- Laboratory of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Faculty of Sciences, Ghent University, Gent, Belgium
| | - Kim Heylen
- Laboratory of Microbiology, Faculty of Sciences, Ghent University, Gent, Belgium
| | - Nico Boon
- Laboratory of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
- * E-mail:
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Vilchez-Vargas R, Geffers R, Suárez-Diez M, Conte I, Waliczek A, Kaser VS, Kralova M, Junca H, Pieper DH. Analysis of the microbial gene landscape and transcriptome for aromatic pollutants and alkane degradation using a novel internally calibrated microarray system. Environ Microbiol 2013. [PMID: 22515215 DOI: 10.1111/j.14622920.2012.02752.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Despite various efforts to develop tools to detect and compare the catabolic potential and activity for pollutant degradation in environmental samples, there is still a need for an open-source, curated and reliable array method. We developed a custom array system including a novel normalization strategy that can be applied to any microarray design, allowing the calculation of the reliability of signals and make cross-experimental comparisons. Array probes, which are fully available to the scientific community, were designed from knowledge-based curated databases for key aromatic catabolic gene families and key alkane degradation genes. This design assigns signals to the respective protein subfamilies, thus directly inferring function and substrate specificity. Experimental procedures were optimized using DNA of four genome sequenced biodegradation strains and reliability of signals assessed through a novel normalization procedure, where a plasmid containing four artificial targets in increased copy numbers and co-amplified with the environmental DNA served as an internal calibration curve. The array system was applied to assess the catabolic gene landscape and transcriptome of aromatic contaminated environmental samples, confirming the abundance of catabolic gene subfamilies previously detected by functional metagenomics but also revealing the presence of previously undetected catabolic groups and specifically their expression under pollutant stress.
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Affiliation(s)
- Ramiro Vilchez-Vargas
- Microbial Interactions and Processes Research Group, HZI - Helmholtz Centre for Infection Research, Inhoffenstraße 7, D-38124 Braunschweig, Germany
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Vilchez-Vargas R, Geffers R, Suárez-Diez M, Conte I, Waliczek A, Kaser VS, Kralova M, Junca H, Pieper DH. Analysis of the microbial gene landscape and transcriptome for aromatic pollutants and alkane degradation using a novel internally calibrated microarray system. Environ Microbiol 2012; 15:1016-39. [PMID: 22515215 DOI: 10.1111/j.1462-2920.2012.02752.x] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Despite various efforts to develop tools to detect and compare the catabolic potential and activity for pollutant degradation in environmental samples, there is still a need for an open-source, curated and reliable array method. We developed a custom array system including a novel normalization strategy that can be applied to any microarray design, allowing the calculation of the reliability of signals and make cross-experimental comparisons. Array probes, which are fully available to the scientific community, were designed from knowledge-based curated databases for key aromatic catabolic gene families and key alkane degradation genes. This design assigns signals to the respective protein subfamilies, thus directly inferring function and substrate specificity. Experimental procedures were optimized using DNA of four genome sequenced biodegradation strains and reliability of signals assessed through a novel normalization procedure, where a plasmid containing four artificial targets in increased copy numbers and co-amplified with the environmental DNA served as an internal calibration curve. The array system was applied to assess the catabolic gene landscape and transcriptome of aromatic contaminated environmental samples, confirming the abundance of catabolic gene subfamilies previously detected by functional metagenomics but also revealing the presence of previously undetected catabolic groups and specifically their expression under pollutant stress.
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Affiliation(s)
- Ramiro Vilchez-Vargas
- Microbial Interactions and Processes Research Group, HZI - Helmholtz Centre for Infection Research, Inhoffenstraße 7, D-38124 Braunschweig, Germany
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Vilchez-Vargas R, Junca H, Pieper DH. Metabolic networks, microbial ecology and ‘omics’ technologies: towards understanding in situ biodegradation processes. Environ Microbiol 2010; 12:3089-104. [DOI: 10.1111/j.1462-2920.2010.02340.x] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Wos-Oxley ML, Plumeier I, von Eiff C, Taudien S, Platzer M, Vilchez-Vargas R, Becker K, Pieper DH. A poke into the diversity and associations within human anterior nare microbial communities. ISME J 2010; 4:839-51. [DOI: 10.1038/ismej.2010.15] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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Kunze M, Zerlin KF, Retzlaff A, Pohl JO, Schmidt E, Janssen DB, Vilchez-Vargas R, Pieper DH, Reineke W. Degradation of chloroaromatics by Pseudomonas putida GJ31: assembled route for chlorobenzene degradation encoded by clusters on plasmid pKW1 and the chromosome. Microbiology (Reading) 2009; 155:4069-4083. [PMID: 19744988 DOI: 10.1099/mic.0.032110-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Pseudomonas putida GJ31 has been reported to grow on chlorobenzene using a meta-cleavage pathway with chlorocatechol 2,3-dioxygenase (CbzE) as a key enzyme. The CbzE-encoding gene was found to be localized on the 180 kb plasmid pKW1 in a cbzTEXGS cluster, which is flanked by transposases and encodes only a partial (chloro)catechol meta-cleavage pathway comprising ferredoxin reductase, chlorocatechol 2,3-dioxygenase, an unknown protein, 2-hydroxymuconic semialdehyde dehydrogenase and glutathione S-transferase. Downstream of cbzTEXGS are located cbzJ, encoding a novel type of 2-hydroxypent-2,4-dienoate hydratase, and a transposon region highly similar to Tn5501. Upstream of cbzTEXGS, traNEOFG transfer genes were found. The search for gene clusters possibly completing the (chloro)catechol metabolic pathway of GJ31 revealed the presence of two additional catabolic gene clusters on pKW1. The mhpRBCDFETP cluster encodes enzymes for the dissimilation of 2,3-dihydroxyphenylpropionate in a novel arrangement characterized by the absence of a gene encoding 3-(3-hydroxyphenyl)propionate monooxygenase and the presence of a GntR-type regulator, whereas the nahINLOMKJ cluster encodes part of the naphthalene metabolic pathway. Transcription studies supported their possible involvement in chlorobenzene degradation. The upper pathway cluster, comprising genes encoding a chlorobenzene dioxygenase and a chlorobenzene dihydrodiol dehydrogenase, was localized on the chromosome. A high level of transcription in response to chlorobenzene revealed it to be crucial for chlorobenzene degradation. The chlorobenzene degradation pathway in strain GJ31 is thus a mosaic encoded by four gene clusters.
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Affiliation(s)
- Markus Kunze
- Bergische Universität Wuppertal, Chemical Microbiology, D-42097 Wuppertal, Germany
| | - Kay F Zerlin
- Bergische Universität Wuppertal, Chemical Microbiology, D-42097 Wuppertal, Germany
| | - Alexander Retzlaff
- Bergische Universität Wuppertal, Chemical Microbiology, D-42097 Wuppertal, Germany
| | - Jens O Pohl
- Bergische Universität Wuppertal, Chemical Microbiology, D-42097 Wuppertal, Germany
| | - Eberhard Schmidt
- Bergische Universität Wuppertal, Chemical Microbiology, D-42097 Wuppertal, Germany
| | - Dick B Janssen
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Ramiro Vilchez-Vargas
- Department of Microbial Pathogenesis, Helmholtz Centre for Infection Research, D-38124 Braunschweig, Germany
| | - Dietmar H Pieper
- Department of Microbial Pathogenesis, Helmholtz Centre for Infection Research, D-38124 Braunschweig, Germany
| | - Walter Reineke
- Bergische Universität Wuppertal, Chemical Microbiology, D-42097 Wuppertal, Germany
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