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Agamennone V, van den Broek TJ, de Kat Angelino-Bart A, Hoevenaars FPM, van der Kamp JW, Schuren FHJ. Individual and Group-Based Effects of In Vitro Fiber Interventions on the Fecal Microbiota. Microorganisms 2023; 11:2001. [PMID: 37630561 PMCID: PMC10459671 DOI: 10.3390/microorganisms11082001] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 07/27/2023] [Accepted: 07/31/2023] [Indexed: 08/27/2023] Open
Abstract
The development of microbiome-targeted strategies is limited by individual differences in gut microbiome composition and metabolic responses to interventions. In vitro models that can replicate this variation allow us to conduct pre-clinical studies and assess efficacy. This study describes the exposure of 16 individual fecal microbiota samples to 5 different fibers using an in vitro system for the anaerobic cultivation of bacteria. The individual microbiota differed in composition and metabolite profiles (short-chain fatty acids and branched-chain fatty acids) after incubation with the fibers. Furthermore, microbiota composition after fiber incubation was significantly different between subjects with good intestinal health and subjects with Inflammatory Bowel Disease (IBD). α-diversity was differently affected by dietary fibers; for example, exposure to psyllium resulted in increased diversity in the healthy group and in decreased diversity in the IBD group. Instead, the functional metabolic profile did not differ between the two groups. Finally, the combination of all fibers, tested on the microbiota from IBD subjects, resulted in stronger overall effects on both microbiota composition and metabolite production compared to the single fibers. These results confirm that incubation with dietary fiber results in different compositional and functional effects on individual microbiota and that in vitro models represent successful tools for studying individual fiber effects.
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Affiliation(s)
| | | | | | | | | | - Frank H. J. Schuren
- Microbiology and Systems Biology Group, TNO, 2333 BE Leiden, The Netherlands
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van der Veer C, Hertzberger RY, Bruisten SM, Tytgat HLP, Swanenburg J, de Kat Angelino-Bart A, Schuren F, Molenaar D, Reid G, de Vries H, Kort R. Comparative genomics of human Lactobacillus crispatus isolates reveals genes for glycosylation and glycogen degradation: implications for in vivo dominance of the vaginal microbiota. Microbiome 2019; 7:49. [PMID: 30925932 PMCID: PMC6441167 DOI: 10.1186/s40168-019-0667-9] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 03/15/2019] [Indexed: 05/17/2023]
Abstract
BACKGROUND A vaginal microbiota dominated by lactobacilli (particularly Lactobacillus crispatus) is associated with vaginal health, whereas a vaginal microbiota not dominated by lactobacilli is considered dysbiotic. Here we investigated whether L. crispatus strains isolated from the vaginal tract of women with Lactobacillus-dominated vaginal microbiota (LVM) are pheno- or genotypically distinct from L. crispatus strains isolated from vaginal samples with dysbiotic vaginal microbiota (DVM). RESULTS We studied 33 L. crispatus strains (n = 16 from LVM; n = 17 from DVM). Comparison of these two groups of strains showed that, although strain differences existed, both groups degraded various carbohydrates, produced similar amounts of organic acids, inhibited Neisseria gonorrhoeae growth, and did not produce biofilms. Comparative genomics analyses of 28 strains (n = 12 LVM; n = 16 DVM) revealed a novel, 3-fragmented glycosyltransferase gene that was more prevalent among strains isolated from DVM. Most L. crispatus strains showed growth on glycogen-supplemented growth media. Strains that showed less-efficient (n = 6) or no (n = 1) growth on glycogen all carried N-terminal deletions (respectively, 29 and 37 amino acid deletions) in a putative pullulanase type I protein. DISCUSSION L. crispatus strains isolated from LVM were not phenotypically distinct from L. crispatus strains isolated from DVM; however, the finding that the latter were more likely to carry a 3-fragmented glycosyltransferase gene may indicate a role for cell surface glycoconjugates, which may shape vaginal microbiota-host interactions. Furthermore, the observation that variation in the pullulanase type I gene is associated with growth on glycogen discourages previous claims that L. crispatus cannot directly utilize glycogen.
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Affiliation(s)
- Charlotte van der Veer
- Department of Infectious Diseases, Public Health Service, GGD, Amsterdam, The Netherlands
| | - Rosanne Y Hertzberger
- Department of Molecular Cell Biology, Faculty of Science, O|2 Lab Building, VU University, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Sylvia M Bruisten
- Department of Infectious Diseases, Public Health Service, GGD, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam UMC, Amsterdam, The Netherlands
| | | | - Jorne Swanenburg
- Department of Molecular Cell Biology, Faculty of Science, O|2 Lab Building, VU University, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
- Netherlands Organization for Applied Scientific Research (TNO), Microbiology and Systems Biology, Zeist, The Netherlands
| | - Alie de Kat Angelino-Bart
- Netherlands Organization for Applied Scientific Research (TNO), Microbiology and Systems Biology, Zeist, The Netherlands
| | - Frank Schuren
- Netherlands Organization for Applied Scientific Research (TNO), Microbiology and Systems Biology, Zeist, The Netherlands
| | - Douwe Molenaar
- Department of Molecular Cell Biology, Faculty of Science, O|2 Lab Building, VU University, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Gregor Reid
- Canadian R&D Centre for Human Microbiome and Probiotics, Lawson Health Research Institute, London, Canada
- Departments of Microbiology and Immunology, and Surgery, Western University, London, Ontario, Canada
| | - Henry de Vries
- Department of Infectious Diseases, Public Health Service, GGD, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam UMC, Amsterdam, The Netherlands
| | - Remco Kort
- Department of Molecular Cell Biology, Faculty of Science, O|2 Lab Building, VU University, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands.
- Netherlands Organization for Applied Scientific Research (TNO), Microbiology and Systems Biology, Zeist, The Netherlands.
- ARTIS-Micropia, Amsterdam, The Netherlands.
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Dols JAM, Molenaar D, van der Helm JJ, Caspers MPM, de Kat Angelino-Bart A, Schuren FHJ, Speksnijder AGCL, Westerhoff HV, Richardus JH, Boon ME, Reid G, de Vries HJC, Kort R. Molecular assessment of bacterial vaginosis by Lactobacillus abundance and species diversity. BMC Infect Dis 2016; 16:180. [PMID: 27107961 PMCID: PMC4841971 DOI: 10.1186/s12879-016-1513-3] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [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: 08/25/2015] [Accepted: 04/13/2016] [Indexed: 01/08/2023] Open
Abstract
Background To date, women are most often diagnosed with bacterial vaginosis (BV) using microscopy based Nugent scoring or Amsel criteria. However, the accuracy is less than optimal. The aim of the present study was to confirm the identity of known BV-associated composition profiles and evaluate indicators for BV using three molecular methods. Methods Evaluation of indicators for BV was carried out by 16S rRNA amplicon sequencing of the V5-V7 region, a tailor-made 16S rRNA oligonucleotide-based microarray, and a PCR-based profiling technique termed IS-profiling, which is based on fragment variability of the 16S-23S rRNA intergenic spacer region. An inventory of vaginal bacterial species was obtained from 40 females attending a Dutch sexually transmitted infection outpatient clinic, of which 20 diagnosed with BV (Nugent score 7–10), and 20 BV negative (Nugent score 0–3). Results Analysis of the bacterial communities by 16S rRNA amplicon sequencing revealed two clusters in the BV negative women, dominated by either Lactobacillus iners or Lactobacillus crispatus and three distinct clusters in the BV positive women. In the former, there was a virtually complete, negative correlation between L. crispatus and L. iners. BV positive subjects showed cluster profiles that were relatively high in bacterial species diversity and dominated by anaerobic species, including Gardnerella vaginalis, and those belonging to the Families of Lachnospiraceae and Leptotrichiaceae. Accordingly, the Gini-Simpson index of species diversity, and the relative abundance Lactobacillus species appeared consistent indicators for BV. Under the conditions used, only the 16S rRNA amplicon sequencing method was suitable to assess species diversity, while all three molecular composition profiling methods were able to indicate Lactobacillus abundance in the vaginal microbiota. Conclusion An affordable and simple molecular test showing a depletion of the genus Lactobacillus in combination with an increased species diversity of vaginal microbiota could serve as an alternative and practical diagnostic method for the assessment of BV. Electronic supplementary material The online version of this article (doi:10.1186/s12879-016-1513-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joke A M Dols
- Molecular Cell Physiology, Faculty of Earth and Life Sciences, VU University, Amsterdam, The Netherlands.,Department of Public Health, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Douwe Molenaar
- Molecular Cell Physiology, Faculty of Earth and Life Sciences, VU University, Amsterdam, The Netherlands
| | - Jannie J van der Helm
- STI Outpatient Clinic, Public Health Service of Amsterdam (GGD Amsterdam), Amsterdam, The Netherlands
| | - Martien P M Caspers
- Netherlands Organisation for Applied Scientific Research (TNO), Microbiology and Systems Biology, Utrechtseweg 48, 3704HE, Zeist, The Netherlands
| | - Alie de Kat Angelino-Bart
- Netherlands Organisation for Applied Scientific Research (TNO), Microbiology and Systems Biology, Utrechtseweg 48, 3704HE, Zeist, The Netherlands
| | - Frank H J Schuren
- Netherlands Organisation for Applied Scientific Research (TNO), Microbiology and Systems Biology, Utrechtseweg 48, 3704HE, Zeist, The Netherlands
| | - Adrianus G C L Speksnijder
- STI Outpatient Clinic, Public Health Service of Amsterdam (GGD Amsterdam), Amsterdam, The Netherlands.,Naturalis Biodiversity Center, Darwinweg 2, Leiden, The Netherlands
| | - Hans V Westerhoff
- Molecular Cell Physiology, Faculty of Earth and Life Sciences, VU University, Amsterdam, The Netherlands.,Synthetic Systems Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands.,Manchester Centre for Integrative Systems Biology, University of Manchester, Manchester, UK
| | - Jan Hendrik Richardus
- Department of Public Health, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Mathilde E Boon
- Leiden Cytology and Pathology Laboratory, Leiden, The Netherlands.,, Present address: Achter de Hor 2, 9304 TN, Lieveren, The Netherlands
| | - Gregor Reid
- Canadian Center for Human Microbiome and Probiotic Research, Lawson Health Research Institute, London, Ontorio, Canada; Department of Microbiology and Immunology, Division of Urology, Department of Surgery, Western University, London, Ontario, Canada
| | - Henry J C de Vries
- STI Outpatient Clinic, Public Health Service of Amsterdam (GGD Amsterdam), Amsterdam, The Netherlands.,Amsterdam Centre for Infection and Immunity (CINIMA), Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands.,Department of Dermatology, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Remco Kort
- Molecular Cell Physiology, Faculty of Earth and Life Sciences, VU University, Amsterdam, The Netherlands. .,Netherlands Organisation for Applied Scientific Research (TNO), Microbiology and Systems Biology, Utrechtseweg 48, 3704HE, Zeist, The Netherlands. .,Micropia, Natura Artis Magistra, Plantage Kerklaan 38-40, 1018 CZ, Amsterdam, The Netherlands.
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Kort R, Nocker A, de Kat Angelino-Bart A, van Veen S, Verheij H, Schuren F, Montijn R. Real-time detection of viable microorganisms by intracellular phototautomerism. BMC Biotechnol 2010; 10:45. [PMID: 20565844 PMCID: PMC2906424 DOI: 10.1186/1472-6750-10-45] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [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: 12/16/2009] [Accepted: 06/18/2010] [Indexed: 11/23/2022] Open
Abstract
Background To date, the detection of live microorganisms present in the environment or involved in infections is carried out by enumeration of colony forming units on agar plates, which is time consuming, laborious and limited to readily cultivable microorganisms. Although cultivation-independent methods are available, they involve multiple incubation steps and do mostly not discriminate between dead or live microorganisms. We present a novel generic method that is able to specifically monitor living microorganisms in a real-time manner. Results The developed method includes exposure of cells to a weak acid probe at low pH. The neutral probe rapidly permeates the membrane and enters the cytosol. In dead cells no signal is obtained, as the cytosolic pH reflects that of the acidic extracellular environment. In live cells with a neutral internal pH, the probe dissociates into a fluorescent phototautomeric anion. After reaching peak fluorescence, the population of live cells decays. This decay can be followed real-time as cell death coincides with intracellular acidification and return of the probe to its uncharged non-fluorescent state. The rise and decay of the fluorescence signal depends on the probe structure and appears discriminative for bacteria, fungi, and spores. We identified 13 unique probes, which can be applied in the real-time viability method described here. Under the experimental conditions used in a microplate reader, the reported method shows a detection limit of 106 bacteria ml-1, while the frequently used LIVE/DEAD BacLight™ Syto9 and propidium iodide stains show detection down to 106 and 107 bacteria ml-1, respectively. Conclusions We present a novel fluorescence-based method for viability assessment, which is applicable to all bacteria and eukaryotic cell types tested so far. The RTV method will have a significant impact in many areas of applied microbiology including research on biocidal activity, improvement of preservation strategies and membrane permeation and stability. The assay allows for high-throughput applications and has great potential for rapid monitoring of microbial content in air, liquids or on surfaces.
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Affiliation(s)
- Remco Kort
- Business Unit Food and Biotechnology Innovations, Microbial Genomics Group, TNO Quality of Life, Zeist, The Netherlands.
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