1
|
Kundra P, Greppi A, Duppenthaler M, Plüss S, Pugin B, Lacroix C, Geirnaert A. Vitamin B12 analogues from gut microbes and diet differentially impact commensal propionate producers of the human gut. Front Nutr 2024; 11:1360199. [PMID: 38389799 PMCID: PMC10881866 DOI: 10.3389/fnut.2024.1360199] [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: 12/22/2023] [Accepted: 01/29/2024] [Indexed: 02/24/2024] Open
Abstract
To produce the health-associated metabolite propionate, gut microbes require vitamin B12 as a cofactor to convert succinate to propionate. B12 is sourced in the human gut from the unabsorbed dietary fraction and in situ microbial production. However, experimental data for B12 production by gut microbes is scarce, especially on their produced B12-analogues. Further, the promotion of propionate production by microbially-produced and dietary B12 is not yet fully understood. Here, we demonstrated B12 production in 6 out of 8 in silico predicted B12-producing bacteria from the human gut. Next, we showed in vitro that B12 produced by Blautia hydrogenotrophica, Marvinbryantia formatexigens, and Blautia producta promoted succinate to propionate conversion of two prevalent B12-auxotrophic gut bacteria, Akkermansia muciniphila and Bacteroides thetaiotaomicron. Finally, we examined the propiogenic effect of commercially available B12-analogues present in the human diet (cyano-B12, adenosyl-B12 and hydroxy-B12) at two doses. The low dose resulted in partial conversion of succinate to propionate for A. muciniphila when grown with adenosyl-B12 (14.6 ± 2.4 mM succinate and 18.7 ± 0.6 mM propionate) and hydroxy-B12 (13.0 ± 1.1 mM and 21.9 ± 1.2 mM), in comparison to cyano-B12 (0.7 ± 0.1 mM and 34.1 ± 0.1 mM). Higher doses of adenosyl-B12 and hydroxy-B12 resulted in significantly more conversion of succinate to propionate in both propionate-producing species, compared to the low dose. B12 analogues have different potential to impact the propionate metabolism of prevalent propionate producers in the gut. These results could contribute to strategies for managing gut disorders associated with decreased propionate production.
Collapse
Affiliation(s)
- Palni Kundra
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, Zurich, Switzerland
| | - Anna Greppi
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, Zurich, Switzerland
| | - Monica Duppenthaler
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, Zurich, Switzerland
| | - Serafina Plüss
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, Zurich, Switzerland
| | - Benoit Pugin
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, Zurich, Switzerland
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, Zurich, Switzerland
| | - Annelies Geirnaert
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, Zurich, Switzerland
| |
Collapse
|
2
|
Momo Cabrera P, Rachmühl C, Derrien M, Bourdet-Sicard R, Lacroix C, Geirnaert A. Comparative prebiotic potential of galacto- and fructo-oligosaccharides, native inulin, and acacia gum in Kenyan infant gut microbiota during iron supplementation. ISME Commun 2024; 4:ycae033. [PMID: 38774131 PMCID: PMC11107946 DOI: 10.1093/ismeco/ycae033] [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] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 03/10/2024] [Indexed: 05/24/2024]
Abstract
Iron fortification to prevent anemia in African infants increases colonic iron levels, favoring the growth of enteropathogens. The use of prebiotics may be an effective strategy to reduce these detrimental effects. Using the African infant PolyFermS gut model, we compared the effect of the prebiotics short-chain galacto- with long-chain fructo-oligosaccharides (scGOS/lcFOS) and native inulin, and the emerging prebiotic acacia gum, a branched-polysaccharide-protein complex consisting of arabinose and galactose, during iron supplementation on four Kenyan infant gut microbiota. Iron supplementation did not alter the microbiota but promoted Clostridioides difficile in one microbiota. The prebiotic effect of scGOS/lcFOS and inulin was confirmed during iron supplementation in all investigated Kenyan infant gut microbiota, leading to higher abundance of bifidobacteria, increased production of acetate, propionate, and butyrate, and a significant shift in microbiota composition compared to non-supplemented microbiota. The abundance of the pathogens Clostridium difficile and Clostridium perfringens was also inhibited upon addition of the prebiotic fibers. Acacia gum had no effect on any of the microbiota. In conclusion, scGOS/lcFOS and inulin, but not acacia gum, showed a donor-independent strong prebiotic potential in Kenyan infant gut microbiota. This study demonstrates the relevance of comparing fibers in vitro prior to clinical studies.
Collapse
Affiliation(s)
- Paula Momo Cabrera
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland
| | - Carole Rachmühl
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland
| | - Muriel Derrien
- Danone Global Research & Innovation Center, 91190 Gif sur Yvette, France
- Present address: Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, Rega Institute KU, 3000 Leuven, Belgium
| | | | - Christophe Lacroix
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland
| | - Annelies Geirnaert
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland
| |
Collapse
|
3
|
Bircher L, Sourabié AM, Paurevic M, Hochuli J, Geirnaert A, Navas C, Drogue B, Lacroix C. Faecalibacterium duncaniae A2-165 growth is strongly promoted by yeast extract and vitamin B5 in cGMP medium. Microb Biotechnol 2024; 17:e14374. [PMID: 38019136 PMCID: PMC10832529 DOI: 10.1111/1751-7915.14374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 10/31/2023] [Accepted: 11/07/2023] [Indexed: 11/30/2023] Open
Abstract
Several gut microbial species within the Faecalibacterium genus have emerged as promising next-generation probiotics (NGP) due to their multifunctional protective effects against gastrointestinal and systemic disorders. To enable clinical studies and further applications, improved methods for cultivating Faecalibacterium must be developed in compliance with current Good Manufacturing Practice regulations, which is complicated by its oxygen sensitivity and complex nutritional requirements. Different yeast-based nutrients (YBNs), including yeast extracts (YEs) and yeast peptones (YPs), are ubiquitously used when cultivating microbes to supply a broad range of macro- and micronutrients. In this study, we evaluated six experimental YBNs, namely three YEs, two YPs and a yeast cell wall product (YCW), and eight B-vitamins in the cultivation of Faecalibacterium duncaniae A2-165, former Faecalibacterium prausnitzii, using growth assays in microtitre plates, dose-effect studies in Hungate tube fermentations and fully controlled bioreactor experiments. We demonstrated that YEs promote F. duncaniae A2-165 growth in a nutritionally limited medium, while YPs and YCW lacked essential growth factors for enabling cell propagation. High cell density was obtained in controlled bioreactors using a medium containing 2-4% of a selected YE and 1% casein peptone (3.4 ± 1.7 × 109 -5.1 ± 1.3 × 109 cells mL-1 ). Among all tested B-vitamins, we identified B5 as a strong growth promoter. Replacing casein peptone with YP and supplementing with vitamin B5 further increased biomass by approximately 50% (6.8 ± 1.7 × 109 cells mL-1 ). Hence, empirical selection of YE, YP and B5 allowed formulation of a high-yielding animal allergen-free nutritive medium to produce F. duncaniae A2-165. Selecting nutritionally suitable YBNs and combining these with other key nutrients are important steps for optimizing production of NGP with high yields and lower cost.
Collapse
Affiliation(s)
- Lea Bircher
- Department Health Science and Technology, Laboratory of Food Biotechnology, Institute of Food, Nutrition and HealthETH ZurichZürichSwitzerland
| | - Alain M. Sourabié
- Science Technology and Innovation DepartmentProcelys by LeSaffreMaisons‐AlfortFrance
| | - Marijana Paurevic
- Department Health Science and Technology, Laboratory of Food Biotechnology, Institute of Food, Nutrition and HealthETH ZurichZürichSwitzerland
| | - Janina Hochuli
- Department Health Science and Technology, Laboratory of Food Biotechnology, Institute of Food, Nutrition and HealthETH ZurichZürichSwitzerland
| | - Annelies Geirnaert
- Department Health Science and Technology, Laboratory of Food Biotechnology, Institute of Food, Nutrition and HealthETH ZurichZürichSwitzerland
| | - Chloé Navas
- Science Technology and Innovation DepartmentProcelys by LeSaffreMaisons‐AlfortFrance
| | - Benoît Drogue
- Science Technology and Innovation DepartmentProcelys by LeSaffreMaisons‐AlfortFrance
| | - Christophe Lacroix
- Department Health Science and Technology, Laboratory of Food Biotechnology, Institute of Food, Nutrition and HealthETH ZurichZürichSwitzerland
| |
Collapse
|
4
|
Asare PT, Greppi A, Geirnaert A, Pennacchia A, Babst A, Lacroix C. Glycerol and reuterin-producing Limosilactobacillus reuteri enhance butyrate production and inhibit Enterobacteriaceae in broiler chicken cecal microbiota PolyFermS model. BMC Microbiol 2023; 23:384. [PMID: 38053034 DOI: 10.1186/s12866-023-03091-6] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 10/26/2023] [Indexed: 12/07/2023] Open
Abstract
BACKGROUND Administering probiotic strains of Limosilactobacillus reuteri to poultry has been shown to improve poultry performance and health. Some strains of L. reuteri taxa can produce reuterin, a broad-spectrum antimicrobial compound from glycerol conversion, with high inhibitory activity against enterobacteria. However, little is known about the metabolism of glycerol in the complex chicken cecal microbiota nor the effect of glycerol, either alone or combined with L. reuteri on the microbiota. In this study, we investigated the effect of L. reuteri PTA5_F13, a high-reuterin-producing chicken strain and glycerol, alone or combined, on broiler chicken cecal microbiota composition and activity using the continuous PolyFermS model recently developed to mimic chicken cecal fermentation. METHODS Three independent PolyFermS chicken cecal microbiota models were inoculated with immobilized cecal microbiota from different animals and operated continuously. The effects of two additional levels of glycerol (50 and 100 mM) with or without daily supplementation of chicken-derived L. reuteri PTA5_F13 (107 CFU/mL final concentration) were tested in parallel second-stage reactors continuously inoculated with the same microbiota. We analyzed the complex chicken gut microbiota structure and dynamics upon treatment using 16S rRNA metabarcoding and qPCR. Microbiota metabolites, short-chain and branched-chain fatty acids, and glycerol and reuterin products were analyzed by HPLC in effluent samples from stabilized reactors. RESULTS Supplementation with 100 mM glycerol alone and combined with L. reuteri PTA5_F13 resulted in a reproducible increase in butyrate production in the three modelled microbiota (increases of 18 to 25%). Glycerol alone resulted also in a reduction of Enterobacteriaceae in two of the three microbiota, but no effect was detected for L. reuteri alone. When both treatments were combined, all microbiota quantitatively inhibited Enterobacteriaceae, including in the last model that had very high initial concentrations of Enterobacteriaceae. Furthermore, a significant 1,3-PDO accumulation was measured in the effluent of the combined treatment, confirming the conversion of glycerol via the reuterin pathway. Glycerol supplementation, independent of L. reuteri addition, did not affect the microbial community diversity. CONCLUSIONS Glycerol induced a stable and reproducible butyrogenic activity for all tested microbiota and induced an inhibitory effect against Enterobacteriaceae that was strengthened when reuterin-producing L. reuteri was spiked daily. Our in vitro study suggests that co-application of L. reuteri PTA5_F13 and glycerol could be a useful approach to promote chicken gut health by enhancing metabolism and protection against Enterobacteriaceae.
Collapse
Affiliation(s)
- Paul Tetteh Asare
- Department of Health Sciences and Technology, Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, LFV D 20, Schmelzbergstrasse 7, CH-8042, Zurich, Switzerland
- Present address: Gnubiotics Sciences SA, Epalinges, Switzerland
| | - Anna Greppi
- Department of Health Sciences and Technology, Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, LFV D 20, Schmelzbergstrasse 7, CH-8042, Zurich, Switzerland
| | - Annelies Geirnaert
- Department of Health Sciences and Technology, Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, LFV D 20, Schmelzbergstrasse 7, CH-8042, Zurich, Switzerland
| | - Alessia Pennacchia
- Department of Health Sciences and Technology, Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, LFV D 20, Schmelzbergstrasse 7, CH-8042, Zurich, Switzerland
| | - Angela Babst
- Department of Health Sciences and Technology, Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, LFV D 20, Schmelzbergstrasse 7, CH-8042, Zurich, Switzerland
| | - Christophe Lacroix
- Department of Health Sciences and Technology, Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, LFV D 20, Schmelzbergstrasse 7, CH-8042, Zurich, Switzerland.
| |
Collapse
|
5
|
Rachmühl C, Lacroix C, Cabrera PM, Geirnaert A. Long-term continuous cultivation of Kenyan infant fecal microbiota using the host adapted PolyFermS model. Sci Rep 2023; 13:20563. [PMID: 37996456 PMCID: PMC10667343 DOI: 10.1038/s41598-023-47131-7] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 11/09/2023] [Indexed: 11/25/2023] Open
Abstract
Appropriate in vitro models to investigate the impact of novel nutritional strategies on the gut microbiota of infants living in rural Africa are scarce. Here, we aimed to develop such a continuous gut fermentation model based on the PolyFermS platform, which allows controlled and stable long-term cultivation of colon microbiota in conditions akin the host. Nine immobilized Kenyan infant fecal microbiota were used as inoculum for continuous PolyFermS colon models fed with medium mimicking the weaning infant diet. Fructo-oligosaccharides (FOS) supplementation (1, 4 and 8 g/L) and cultivation pH (5.8 and 6.3) were investigated stepwise. Conditions providing a close match between fecal and in vitro microbiota (pH 5.8 with 1 g/L FOS) were selected for investigating long-term stability of four Kenyan infant PolyFermS microbiota. The shared fraction of top bacterial genera between fecal and in vitro microbiota was high (74-89%) and stable during 107 days of continuous cultivation. Community diversity was maintained and two distinct fermentation metabolite profiles of infant fecal microbiota were observed. Three propiogenic and one butyrogenic metabolite profile of infant fecal microbiota established from day 8 onwards and stayed stable. We present here the first rationally designed continuous cultivation model of African infant gut microbiota. This model will be important to assess the effect of dietary or environmental factors on the gut microbiota of African infants with high enteropathogen exposure.
Collapse
Affiliation(s)
- Carole Rachmühl
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland.
| | - Paula Momo Cabrera
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Annelies Geirnaert
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland.
| |
Collapse
|
6
|
Liu B, Garza DR, Gonze D, Krzynowek A, Simoens K, Bernaerts K, Geirnaert A, Faust K. Starvation responses impact interaction dynamics of human gut bacteria Bacteroides thetaiotaomicron and Roseburia intestinalis. ISME J 2023; 17:1940-1952. [PMID: 37670028 PMCID: PMC10579405 DOI: 10.1038/s41396-023-01501-1] [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] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 09/07/2023]
Abstract
Bacterial growth often alters the environment, which in turn can impact interspecies interactions among bacteria. Here, we used an in vitro batch system containing mucin beads to emulate the dynamic host environment and to study its impact on the interactions between two abundant and prevalent human gut bacteria, the primary fermenter Bacteroides thetaiotaomicron and the butyrate producer Roseburia intestinalis. By combining machine learning and flow cytometry, we found that the number of viable B. thetaiotaomicron cells decreases with glucose consumption due to acid production, while R. intestinalis survives post-glucose depletion by entering a slow growth mode. Both species attach to mucin beads, but only viable cell counts of B. thetaiotaomicron increase significantly. The number of viable co-culture cells varies significantly over time compared to those of monocultures. A combination of targeted metabolomics and RNA-seq showed that the slow growth mode of R. intestinalis represents a diauxic shift towards acetate and lactate consumption, whereas B. thetaiotaomicron survives glucose depletion and low pH by foraging on mucin sugars. In addition, most of the mucin monosaccharides we tested inhibited the growth of R. intestinalis but not B. thetaiotaomicron. We encoded these causal relationships in a kinetic model, which reproduced the observed dynamics. In summary, we explored how R. intestinalis and B. thetaiotaomicron respond to nutrient scarcity and how this affects their dynamics. We highlight the importance of understanding bacterial metabolic strategies to effectively modulate microbial dynamics in changing conditions.
Collapse
Affiliation(s)
- Bin Liu
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, B-3000, Leuven, Belgium
| | - Daniel Rios Garza
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, B-3000, Leuven, Belgium
| | - Didier Gonze
- Unité de Chronobiologie Théorique, Faculté des Sciences, CP 231, Université Libre de Bruxelles, Bvd du Triomphe, B-1050, Bruxelles, Belgium
| | - Anna Krzynowek
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, B-3000, Leuven, Belgium
| | - Kenneth Simoens
- Department of Chemical Engineering, Chemical and Biochemical Reactor Engineering and Safety (CREaS), KU Leuven, B-3001, Leuven, Belgium
| | - Kristel Bernaerts
- Department of Chemical Engineering, Chemical and Biochemical Reactor Engineering and Safety (CREaS), KU Leuven, B-3001, Leuven, Belgium
| | - Annelies Geirnaert
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zürich, CH-8092, Zürich, Switzerland
| | - Karoline Faust
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, B-3000, Leuven, Belgium.
| |
Collapse
|
7
|
Chauveau A, Geirnaert A, Babst A, Treyer A, Lacroix C, Hamburger M, Potterat O. Erratum to alkaloids in commercial preparations of California poppy - Quantification, intestinal permeability and microbiota interactions [Biomed. Pharmacother. 166 (2023) 115420]. Biomed Pharmacother 2023; 167:115615. [PMID: 37778907 DOI: 10.1016/j.biopha.2023.115615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2023] Open
Affiliation(s)
- Antoine Chauveau
- Division of Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Annelies Geirnaert
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Science and Technology, ETH Zurich, Zurich, Switzerland
| | - Angela Babst
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Science and Technology, ETH Zurich, Zurich, Switzerland
| | - Andrea Treyer
- Division of Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Science and Technology, ETH Zurich, Zurich, Switzerland
| | - Matthias Hamburger
- Division of Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Olivier Potterat
- Division of Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland.
| |
Collapse
|
8
|
Chauveau A, Geirnaert A, Babst A, Treyer A, Lacroix C, Hamburger M, Potterat O. Alkaloids in commercial preparations of California poppy - Quantification, intestinal permeability and microbiota interactions. Biomed Pharmacother 2023; 166:115420. [PMID: 37673017 DOI: 10.1016/j.biopha.2023.115420] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/25/2023] [Accepted: 08/30/2023] [Indexed: 09/08/2023] Open
Abstract
California poppy products are commonly used for the treatment of nervousness, anxiety and sleeping disorders. Pharmacologically relevant constituents include the main alkaloids californidine, escholtzine and protopine. However, only limited information is available about the alkaloid content in commercial preparations and their intestinal absorption. Moreover, a possible metabolization of these alkaloids by the gut microbiota, and their impact on microbial activity and viability have not been investigated. Californidine, escholtzine and protopine were quantified by UHPLC-MS/MS in eight commercial California poppy products. The intestinal permeability of alkaloids was studied in Caco-2 cell as a model for absorption in the small intestine. The gut microbial biotransformation was explored in artificial gut microbiota from the in vitro PolyFermS model. In addition, the impact of these alkaloids and a California poppy extract on the microbial production of short-chain fatty acids (SCFAs) and the viability of microbiota was investigated. Contents of californidine, escholtzine and protopine in California poppy products were in the ranges of 0.13-2.55, 0.05-0.63 and 0.008-0.200 mg/g, respectively. In the Caco-2 cell model, californidine was low-to-moderately permeable while escholtzine and protopine were highly permeable. An active transport process was potentially involved in the transfer of the three alkaloids. The three compounds were not metabolized by the artificial gut microbiota over 24 h. Neither the California poppy extract nor the alkaloids markedly impacted microbial SCFA production and bacterial viability.
Collapse
Affiliation(s)
- Antoine Chauveau
- Division of Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Annelies Geirnaert
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Science and Technology, ETH Zurich, Zurich, Switzerland
| | - Angela Babst
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Science and Technology, ETH Zurich, Zurich, Switzerland
| | - Andrea Treyer
- Division of Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Science and Technology, ETH Zurich, Zurich, Switzerland
| | - Matthias Hamburger
- Division of Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland.
| | - Olivier Potterat
- Division of Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland.
| |
Collapse
|
9
|
Rachmühl C, Lacroix C, Cabrera PM, Geirnaert A. Long-term continuous cultivation of Kenyan infant fecal microbiota using the host adapted PolyFermS model. Res Sq 2023:rs.3.rs-3101157. [PMID: 37461546 PMCID: PMC10350169 DOI: 10.21203/rs.3.rs-3101157/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
Appropriate in vitro models to investigate the impact of novel nutritional strategies on the gut microbiota of infants living in rural Africa are scarce. Here, we aimed to develop such a continuous gut fermentation model based on the PolyFermS platform. Eight immobilized Kenyan infant fecal microbiota were used as inoculum for continuous PolyFermS colon models fed with medium mimicking the weaning infant diet. Fructo-oligosaccharides (FOS) supplementation (1, 4 and 8 g/L) and cultivation pH (5.8 and 6.3) were stepwise investigated. Conditions providing a close match between fecal and in vitro microbiota (pH 5.8 with 1 g/L FOS) were selected for investigating long-term stability of four Kenyan infant PolyFermS microbiota. The shared fraction of top bacterial genera between fecal and in vitro microbiota was high (74-89%) and stable during 107 days of continuous cultivation. Community diversity was maintained, and two distinct fermentation metabolite profiles, propiogenic and butyrogenic, of infant fecal microbiota established from day 8 onwards and stayed stable. We present here the first rationally designed and accurate continuous cultivation model of African infant gut microbiota. This model will be important to assess the effect of dietary or environmental factors on the gut microbiota of African infants with high enteropathogen exposure.
Collapse
|
10
|
Rachmühl C, Lacroix C, Giorgetti A, Stoffel NU, Zimmermann MB, Brittenham GM, Geirnaert A. Validation of a batch cultivation protocol for fecal microbiota of Kenyan infants. BMC Microbiol 2023; 23:174. [PMID: 37403024 DOI: 10.1186/s12866-023-02915-9] [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: 02/03/2023] [Accepted: 06/27/2023] [Indexed: 07/06/2023] Open
Abstract
BACKGROUND The combination of cultivation studies with molecular analysis approaches allows characterization of the complex human gut microbiota in depth. In vitro cultivation studies of infants living in rural sub-Saharan Africa are scarce. In this study, a batch cultivation protocol for Kenyan infant fecal microbiota was validated. METHODS Fresh fecal samples were collected from 10 infants living in a rural area of Kenya. Samples were transported under protective conditions and subsequently prepared for inoculation within less than 30 h for batch cultivation. A diet-adapted cultivation medium was used that mimicked the daily intake of human milk and maize porridge in Kenyan infants during weaning. 16 S rRNA gene amplicon sequencing and HPLC analyses were performed to assess the composition and metabolic activity, respectively, of the fecal microbiota after 24 h of batch cultivation. RESULTS High abundance of Bifidobacterium (53.4 ± 11.1%) and high proportions of acetate (56 ± 11% of total metabolites) and lactate (24 ± 22% of total metabolites) were detected in the Kenyan infant fecal microbiota. After cultivation started at an initial pH 7.6, the fraction of top bacterial genera (≥ 1% abundant) shared between fermentation and fecal samples was high at 97 ± 5%. However, Escherichia-Shigella, Clostridium sensu stricto 1, Bacteroides and Enterococcus were enriched concomitant with decreased Bifidobacterium abundance. Decreasing the initial pH to 6.9 lead to higher abundance of Bifidobacterium after incubation and increased the compositional similarity of fermentation and fecal samples. Despite similar total metabolite production of all fecal microbiota after cultivation, inter-individual differences in metabolite profiles were apparent. CONCLUSIONS Protected transport and batch cultivation in host and diet adapted conditions allowed regrowth of the top abundant genera and reproduction of the metabolic activity of fresh Kenyan infant fecal microbiota. The validated batch cultivation protocol can be used to study the composition and functional potential of Kenyan infant fecal microbiota in vitro.
Collapse
Affiliation(s)
- Carole Rachmühl
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zürich, Zurich, Switzerland
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zürich, Zurich, Switzerland.
| | - Ambra Giorgetti
- Laboratory of Human Nutrition, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zürich, Zurich, Switzerland
| | - Nicole U Stoffel
- Laboratory of Human Nutrition, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zürich, Zurich, Switzerland
| | - Michael B Zimmermann
- Laboratory of Human Nutrition, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zürich, Zurich, Switzerland
| | - Gary M Brittenham
- Department of Pediatrics, College of Physicians and Surgeons, Columbia University, New York, USA
| | - Annelies Geirnaert
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zürich, Zurich, Switzerland.
| |
Collapse
|
11
|
Chauveau A, Treyer A, Geirnaert A, Bircher L, Babst A, Abegg VF, Simões-Wüst AP, Lacroix C, Potterat O, Hamburger M. Intestinal permeability and gut microbiota interactions of pharmacologically active compounds in valerian and St. John's wort. Biomed Pharmacother 2023; 162:114652. [PMID: 37027987 DOI: 10.1016/j.biopha.2023.114652] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/31/2023] [Accepted: 03/31/2023] [Indexed: 04/09/2023] Open
Abstract
Phytomedicines such as valerian and St. John's wort are widely used for the treatment of sleeping disorders, anxiety and mild depression. They are perceived as safe alternatives to synthetic drugs, but limited information is available on the intestinal absorption and interaction with human intestinal microbiota of pharmacologically relevant constituents valerenic acid in valerian, and hyperforin and hypericin in St. John's wort. The intestinal permeability of these compounds and the antidepressant and anxiolytic drugs citalopram and diazepam was investigated in the Caco-2 cell model with bidirectional transport experiments. In addition, interaction of compounds and herbal extracts with intestinal microbiota was evaluated in artificial human gut microbiota. Microbiota-mediated metabolisation of compounds was assessed, and bacterial viability and short-chain fatty acids (SCFA) production were measured in the presence of compounds or herbal extracts. Valerenic acid and hyperforin were highly permeable in Caco-2 cell monolayers. Hypericin showed low-to-moderate permeability. An active transport process was potentially involved in the transfer of valerenic acid. Hyperforin and hypericin were mainly transported through passive transcellular diffusion. All compounds were not metabolized over 24 h in the artificial gut microbiota. Microbial SCFA production and bacterial viability was not substantially impaired nor promoted by exposure to the compounds or herbal extracts.
Collapse
Affiliation(s)
- Antoine Chauveau
- Division of Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Andrea Treyer
- Division of Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Annelies Geirnaert
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Science and Technology, ETH Zurich, Zurich, Switzerland
| | - Lea Bircher
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Science and Technology, ETH Zurich, Zurich, Switzerland
| | - Angela Babst
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Science and Technology, ETH Zurich, Zurich, Switzerland
| | - Vanessa Fabienne Abegg
- Division of Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Ana Paula Simões-Wüst
- Department of Obstetrics, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Science and Technology, ETH Zurich, Zurich, Switzerland
| | - Olivier Potterat
- Division of Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland.
| | - Matthias Hamburger
- Division of Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland.
| |
Collapse
|
12
|
Isenring J, Bircher L, Geirnaert A, Lacroix C. In vitro human gut microbiota fermentation models: opportunities, challenges, and pitfalls. Microbiome Res Rep 2023; 2:2. [PMID: 38045607 PMCID: PMC10688811 DOI: 10.20517/mrr.2022.15] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/12/2022] [Accepted: 01/09/2023] [Indexed: 12/05/2023]
Abstract
The human gut microbiota (HGM) plays a pivotal role in health and disease. Consequently, nutritional and medical research focusing on HGM modulation strategies as a means of improving host health is steadily increasing. In vitro HGM fermentation models offer a valid complement to human and animal studies when it comes to the mechanistic exploration of novel modulation approaches and their direct effects on HGM composition and activity, while excluding interfering host effects. However, in vitro cultivation of HGM can be challenging due to its high oxygen sensitivity and the difficulties of accurately modeling the physio-chemical complexity of the gut environment. Despite the increased use of in vitro HGM models, there is no consensus about appropriate model selection and operation, sometimes leading to major deficiencies in study design and result interpretation. In this review paper, we aim to analyze crucial aspects of the application, setup and operation, data validation and result interpretation of in vitro HGM models. When carefully designed and implemented, in vitro HGM modeling is a powerful strategy for isolating and investigating biotic and abiotic factors in the HGM, as well as evaluating their effects in a controlled environment akin to the gut. Furthermore, complementary approaches combining different in vitro and in vivo models can strengthen the design and interpretation of human studies.
Collapse
Affiliation(s)
| | | | | | - Christophe Lacroix
- Department of Health Sciences and Technology, ETH Zurich, Zürich 8092, Switzerland
| |
Collapse
|
13
|
Kundra P, Geirnaert A, Pugin B, Morales Martinez P, Lacroix C, Greppi A. Healthy adult gut microbiota sustains its own vitamin B12 requirement in an in vitro batch fermentation model. Front Nutr 2022; 9:1070155. [PMID: 36532531 PMCID: PMC9751363 DOI: 10.3389/fnut.2022.1070155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 10/14/2022] [Accepted: 11/14/2022] [Indexed: 12/05/2023] Open
Abstract
Vitamin B12 (cobalamin) is present in the human lower gastrointestinal tract either coming from the unabsorbed dietary fraction or from in situ production of the gut microbiota. However, it is unclear whether the gut microbial communities need exogenous B12 for growth and metabolism, or whether B12 in low and high levels could affect gut community composition and metabolite production. Here, we investigated in vitro B12 production of human fecal microbiota and the effects of different levels of B12 (as cyanocobalamin) on composition and activity. Eight fecal communities from healthy human adults distributed over three enterotypes, dominated by Firmicutes (n = 5), Bacteroides (n = 1) or Prevotella (n = 2) were used to perform batch fermentations in Macfarlane medium supplemented with low B12 medium (Control, 5 ng/ml, within the tested fecal range), no B12 addition (NB12), and high B12 addition (ExtraB12, 2500 ng/ml). The microbiota community composition (qPCR, 16S rRNA metabarcoding), metabolic activity (HPLC-RI), and B12 levels (UHPLC-DAD) were measured after 24 h incubation at 37°C under strict anaerobic conditions. All fecal microbial communities produced B12 in the NB12 condition after 24 h, in the range from 152 ± 4 to 564 ± 25 ng/ml. None of the B12 treatments had an impact on total bacterial growth, community richness, diversity and total metabolite production, compared to the low B12 control. However, a significant increase of propionate was measured in ExtraB12 compared to NB12. Most taxonomic and metabolite changes compared to control incubations were donor-dependent, implying donor-microbiota-specific changes upon B12 treatments. Our in vitro data suggest that healthy human adult gut microbial communities have the capacity to produce B12 at levels fulfilling their own requirements, independently of the initial B12 content tested in the donor's feces. Further, supplementation of exogenous dietary B12 may have limited impact on the healthy human gut microbial community composition and function.
Collapse
Affiliation(s)
| | | | | | | | | | - Anna Greppi
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zürich, Zurich, Switzerland
| |
Collapse
|
14
|
Isenring J, Stevens MJA, Jans C, Lacroix C, Geirnaert A. Identification of Valerate as Carrying Capacity Modulator by Analyzing Lactiplantibacillus plantarum Colonization of Colonic Microbiota in vitro. Front Microbiol 2022; 13:910609. [PMID: 35722334 PMCID: PMC9197689 DOI: 10.3389/fmicb.2022.910609] [Citation(s) in RCA: 2] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/02/2022] [Indexed: 11/13/2022] Open
Abstract
Humans ingest many microorganisms, which may colonize and interact with the resident gut microbiota. However, extensive knowledge about host-independent microbe-microbe interactions is lacking. Here, we investigated such colonization process using a derivative of the model probiotic Lactiplantibacillus plantarum WCFS1 into continuously cultivated gut microbiota in the intestinal PolyFermS fermentation model inoculated with five independently immobilized human adult fecal microbiota. L. plantarum successfully colonized and organized itself spatially in the planktonic, that is, the reactor effluent, and sessile, that is, reactor biofilm, fractions of distinct human adult microbiota. The microbiota carrying capacity for L. plantarum was independent of L. plantarum introduction dose and second supplementation. Adult microbiota (n = 3) dominated by Prevotella and Ruminoccocus exhibited a higher carrying capacity than microbiota (n = 2) dominated by Bacteroides with 105 and 103 CFU/ml of L. plantarum, respectively. Cultivation of human adult microbiota over 3 months resulted in decreased carrying capacity and correlated positively with richness and evenness, suggesting enhanced resistance toward colonizers. Our analyses ultimately allowed us to identify the fermentation metabolite valerate as a modulator to increase the carrying capacity in a microbiota-independent manner. In conclusion, by uncoupling microbe-microbe interactions from host factors, we showed that L. plantarum colonizes the in vitro colonic community in a microbiota-dependent manner. We were further able to demonstrate that L. plantarum colonization levels were not susceptible to the introduction parameters dose and repeated administration but to microbiota features. Such knowledge is relevant in gaining a deeper ecological understanding of colonizer-microbiota interactions and developing robust probiotic strategies.
Collapse
Affiliation(s)
- Julia Isenring
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | - Marc J A Stevens
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland.,Institute for Food Hygiene and Safety, University of Zürich, Zürich, Switzerland
| | - Christoph Jans
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | - Annelies Geirnaert
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| |
Collapse
|
15
|
Asare PT, Greppi A, Pennacchia A, Brenig K, Geirnaert A, Schwab C, Stephan R, Lacroix C. In vitro Modeling of Chicken Cecal Microbiota Ecology and Metabolism Using the PolyFermS Platform. Front Microbiol 2022; 12:780092. [PMID: 34987487 PMCID: PMC8721126 DOI: 10.3389/fmicb.2021.780092] [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] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 11/15/2021] [Indexed: 12/30/2022] Open
Abstract
Continuous in vitro fermentation models provide a useful tool for a fast, reproducible, and direct assessment of treatment-related changes in microbiota metabolism and composition independent of the host. In this study, we used the PolyFermS model to mimic the conditions of the chicken cecum and evaluated three nutritive media for in vitro modeling of the chicken cecal microbiota ecology and metabolism. We observed that our model inoculated with immobilized cecal microbiota and fed with a modified Viande Levure medium (mVL-3) reached a high bacterial cell density of up to approximately 10.5 log cells per mL and stable microbiota composition, akin to the host, during 82 days of continuous operation. Relevant bacterial functional groups containing primary fibrolytic (Bacteroides, Bifidobacteriaceae, Ruminococcaceae), glycolytic (Enterococcus), mucolytic (Bacteroides), proteolytic (Bacteroides), and secondary acetate-utilizing butyrate-producing and propionate-producing (Lachnospiraceae) taxa were preserved in vitro. Besides, conserved metabolic and functional Kyoto Encyclopedia of Genes and Genomes pathways were observed between in vitro microbiota and cecal inoculum microbiota as predicted by functional metagenomics analysis. Furthermore, we demonstrated that the continuous inoculation provided by the inoculum reactor generated reproducible metabolic profiles in second-stage reactors comparable to the chicken cecum, allowing for the simultaneous investigation and direct comparison of different treatments with a control. In conclusion, we showed that PolyFermS is a suitable model for mimicking chicken cecal microbiota fermentation allowing ethical and ex vivo screening of environmental factors, such as dietary additives, on chicken cecal fermentation. We report here for the first time a fermentation medium (mVL-3) that closely mimics the substrate conditions in the chicken cecum and supports the growth and metabolic activity of the cecal bacterial akin to the host. Our PolyFermS chicken cecum model is a useful tool to study microbiota functionality and structure ex vivo.
Collapse
Affiliation(s)
- Paul Tetteh Asare
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zürich, Zurich, Switzerland
| | - Anna Greppi
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zürich, Zurich, Switzerland
| | - Alessia Pennacchia
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zürich, Zurich, Switzerland
| | - Katharina Brenig
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zürich, Zurich, Switzerland
| | - Annelies Geirnaert
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zürich, Zurich, Switzerland
| | - Clarissa Schwab
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zürich, Zurich, Switzerland
| | - Roger Stephan
- Institute for Food Hygiene and Safety, University of Zurich, Zurich, Switzerland
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zürich, Zurich, Switzerland
| |
Collapse
|
16
|
Isenring J, Geirnaert A, Lacroix C, Stevens MJA. Bistable auto-aggregation phenotype in Lactiplantibacillus plantarum emerges after cultivation in in vitro colonic microbiota. BMC Microbiol 2021; 21:268. [PMID: 34610822 PMCID: PMC8493755 DOI: 10.1186/s12866-021-02331-x] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 09/24/2021] [Indexed: 11/28/2022] Open
Abstract
Background Auto-aggregation is a desired property for probiotic strains because it is suggested to promote colonization of the human intestine, to prevent pathogen infections and to modulate the colonic mucosa. We recently reported the generation of adapted mutants of Lactiplantibacillus plantarum NZ3400, a derivative of the model strain WCFS1, for colonization under adult colonic conditions of PolyFermS continuous intestinal fermentation models. Here we describe and characterize the emerge of an auto-aggregating phenotype in L. plantarum NZ3400 derivatives recovered from the modelled gut microbiota. Results L. plantarum isolates were recovered from reactor effluent of four different adult microbiota and from spontaneously formed reactor biofilms. Auto-aggregation was observed in L. plantarum recovered from all microbiota and at higher percentage when recovered from biofilm than from effluent. Further, auto-aggregation percentage increased over time of cultivation in the microbiota. Starvation of the gut microbiota by interrupting the inflow of nutritive medium enhanced auto-aggregation, suggesting a link to nutrient availability. Auto-aggregation was lost under standard cultivation conditions for lactobacilli in MRS medium. However, it was reestablished during growth on sucrose and maltose and in a medium that simulates the abiotic gut environment. Remarkably, none of these conditions resulted in an auto-aggregation phenotype in the wild type strain NZ3400 nor other non-aggregating L. plantarum, indicating that auto-aggregation depends on the strain history. Whole genome sequencing analysis did not reveal any mutation responsible for the auto-aggregation phenotype. Transcriptome analysis showed highly significant upregulation of LP_RS05225 (msa) at 4.1–4.4 log2-fold-change and LP_RS05230 (marR) at 4.5–5.4 log2-fold-change in all auto-aggregating strains compared to non-aggregating. These co-expressed genes encode a mannose-specific adhesin protein and transcriptional regulator, respectively. Mapping of the RNA-sequence reads to the promoter region of the msa-marR operon reveled a DNA inversion in this region that is predominant in auto-aggregating but not in non-aggregating strains. This strongly suggests a role of this inversion in the auto-aggregation phenotype. Conclusions L. plantarum NZ3400 adapts to the in vitro colonic environment by developing an auto-aggregation phenotype. Similar aggregation phenotypes may promote gut colonization and efficacy of other probiotics and should be further investigated by using validated continuous models of gut fermentation such as PolyFermS. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02331-x.
Collapse
Affiliation(s)
- Julia Isenring
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092, Zürich, Switzerland
| | - Annelies Geirnaert
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092, Zürich, Switzerland
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092, Zürich, Switzerland.
| | - Marc J A Stevens
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092, Zürich, Switzerland.,Institute for Food Hygiene and Safety, University of Zürich, Zurich, Switzerland
| |
Collapse
|
17
|
Demuth T, Edwards V, Bircher L, Lacroix C, Nyström L, Geirnaert A. In vitro Colon Fermentation of Soluble Arabinoxylan Is Modified Through Milling and Extrusion. Front Nutr 2021; 8:707763. [PMID: 34513901 PMCID: PMC8424098 DOI: 10.3389/fnut.2021.707763] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 05/10/2021] [Accepted: 07/28/2021] [Indexed: 12/13/2022] Open
Abstract
Dietary fibers such as arabinoxylan (AX) are promising food constituents to prevent particular diet-related chronic diseases because of their prebiotic properties. Arabinoxylan fermentation by the gut microbiota depends on the structural architecture of AX, which can be modified during food processing and consequently affect its prebiotic potential, but it is little investigated. Therefore, the aim of this study was to evaluate the effects of naturally occurring and processing-induced structural alterations of the soluble AX of wheat bran and rye flour on the in vitro human colon fermentation. It was found that fermentation behavior is strongly linked to the AX fine structure and their processing-induced modifications. The short-chain fatty acid (SCFA) metabolism, acidification kinetics, bacterial growth, and bacterial composition revealed that wheat bran AX (WBAX) was fermented faster than rye flour AX. Increased levels of bound phenolic acids resulting from processing were identified as the inhibiting factor for AX fermentation kinetics. Bacterial genera promoted by AX varied between AX source and processing type, but also between microbiota. Extruded WBAX promoted butyrate production and growth of butyrate-producing Faecalibacterium in the butyrogenic microbiota while it did not enhance fermentation and inhibited the growth of Prevotella in the propiogenic microbiota. We anticipate that the findings of this study are a starting point for further investigation on the impact of processing-induced changes on the prebiotic potential of dietary fibers prior to human studies.
Collapse
Affiliation(s)
- Teresa Demuth
- Laboratory of Food Biochemistry, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Veronica Edwards
- Laboratory of Food Biochemistry, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Lea Bircher
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Laura Nyström
- Laboratory of Food Biochemistry, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Annelies Geirnaert
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| |
Collapse
|
18
|
Kundra P, Rachmühl C, Lacroix C, Geirnaert A. Role of Dietary Micronutrients on Gut Microbial Dysbiosis and Modulation in Inflammatory Bowel Disease. Mol Nutr Food Res 2021. [DOI: 10.1002/mnfr.201901271] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Palni Kundra
- Laboratory of Food Biotechnology Institute of Food Nutrition and Health Schmelzbergstrasse 7 Zürich 8092 Switzerland
| | - Carole Rachmühl
- Laboratory of Food Biotechnology Institute of Food Nutrition and Health Schmelzbergstrasse 7 Zürich 8092 Switzerland
| | - Christophe Lacroix
- Laboratory of Food Biotechnology Institute of Food Nutrition and Health Schmelzbergstrasse 7 Zürich 8092 Switzerland
| | - Annelies Geirnaert
- Laboratory of Food Biotechnology Institute of Food Nutrition and Health Schmelzbergstrasse 7 Zürich 8092 Switzerland
| |
Collapse
|
19
|
Rocha Martin VN, Schwab C, Krych L, Voney E, Geirnaert A, Braegger C, Lacroix C. Colonization of Cutibacterium avidum during infant gut microbiota establishment. FEMS Microbiol Ecol 2019; 95:5154911. [PMID: 30388209 DOI: 10.1093/femsec/fiy215] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 10/31/2018] [Indexed: 01/07/2023] Open
Abstract
Establishment of the infant gut microbiota affects gut maturation and influences long-term health. Cutibacterium (formerly Propionibacterium) have been identified as early colonizers, but little is known about their function. Using a cultivation-dependent and -independent approach, we determined Cutibacterium prevalence, diversity and functional potential. In feces from a Swiss infant cohort (n = 38), prevalence of Propionibacterium/Cutibacterium decreased from 84% at 2 weeks, to 65% at 4 weeks, 47% at 8 weeks and 41% at 12 weeks of age. Abundance varied among individuals, and persistence depended on the colonization levels at 2 weeks. Cutibacterium isolates (n = 87) were obtained from 10 infants from a smaller cohort (n = 12); restriction fragment length polymorphism clustered isolates in four groups, and all identified as Cutibacterium avidum. Colonization potential and metabolic effects of C. avidum addition were tested in an in vitro continuous intestinal fermentation model mimicking infant proximal colon conditions. Cutibacterium avidum spiked daily at 108 or 109 cells mL-1 colonized, decreased formate and persisted during the washout period. Significant correlations were observed between Propionibacterium/Cutibacterium and lactate-producers and protein-degraders in both reactors and infant feces. Our findings highlight the natural presence of C. avidum and its role as a lactate-consumer and propionate-producer in infants younger than 3 months.
Collapse
Affiliation(s)
- Vanesa Natalin Rocha Martin
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH-Zurich, 8092 Zurich, Switzerland.,Division of Gastroenterology and Nutrition, University Children's Hospital Zurich, 8032 Zurich, Switzerland
| | - Clarissa Schwab
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH-Zurich, 8092 Zurich, Switzerland
| | - Lukasz Krych
- Department of Food Science, Faculty of Science, University of Copenhagen, Copenhagen 1958, Denmark
| | - Evelyn Voney
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH-Zurich, 8092 Zurich, Switzerland
| | - Annelies Geirnaert
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH-Zurich, 8092 Zurich, Switzerland
| | - Christian Braegger
- Division of Gastroenterology and Nutrition, University Children's Hospital Zurich, 8032 Zurich, Switzerland
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH-Zurich, 8092 Zurich, Switzerland
| |
Collapse
|
20
|
Grabinger T, Glaus Garzon JF, Hausmann M, Geirnaert A, Lacroix C, Hennet T. Alleviation of Intestinal Inflammation by Oral Supplementation With 2-Fucosyllactose in Mice. Front Microbiol 2019; 10:1385. [PMID: 31275292 PMCID: PMC6593069 DOI: 10.3389/fmicb.2019.01385] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [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: 03/04/2019] [Accepted: 06/03/2019] [Indexed: 12/30/2022] Open
Abstract
Milk oligosaccharides exert a prebiotic action that contributes to the development of the infant gut microbiota during lactation. Given that milk oligosaccharides remain intact after passage through stomach and small intestine, they can potentially influence the composition of the gut microbiota when ingested as dietary supplements after weaning. To address the regulatory effects of specific oligosaccharides in colitis linked to the microbiota composition, we have supplemented interleukin-10 null (Il10 -/-) mice with four fucosylated and sialylated oligosaccharides. We found that oral supplementation with 2-fucosyllactose significantly decreased the severity of colitis as displayed by reduced inflammatory marker expression, histological and diarrhea scores, an increased epithelial integrity and less pronounced colon shortening. Oral supplementation with 2-fucosyllactose led to a marked expansion of the commensal Ruminococcus gnavus, which was accompanied by an enhanced cecal concentration of propionate. Decreased activation of immune cells by R. gnavus was confirmed by reconstitution of antibiotic-treated Il10 -/- mice and by stimulation of dendritic cells in vitro. This study demonstrates that post-weaning administration of specific oligosaccharides can shift the composition of the gut microbiota to lessen chronic inflammation as observed in Il10 -/- mice. The expansion of R. gnavus sets a positive microbial environment at the cost of pro-inflammatory Gram-negative bacteria, thereby lowering intestinal inflammation.
Collapse
Affiliation(s)
- Thomas Grabinger
- Institute of Physiology, University of Zurich, Zurich, Switzerland
| | | | - Martin Hausmann
- Department of Gastroenterology and Hepatology, University Hospital Zurich - University of Zurich, Zurich, Switzerland
| | - Annelies Geirnaert
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Thierry Hennet
- Institute of Physiology, University of Zurich, Zurich, Switzerland
| |
Collapse
|
21
|
Poeker SA, Lacroix C, de Wouters T, Spalinger MR, Scharl M, Geirnaert A. Stepwise Development of an in vitro Continuous Fermentation Model for the Murine Caecal Microbiota. Front Microbiol 2019; 10:1166. [PMID: 31191488 PMCID: PMC6548829 DOI: 10.3389/fmicb.2019.01166] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [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: 01/15/2019] [Accepted: 05/07/2019] [Indexed: 12/24/2022] Open
Abstract
Murine models are valuable tools to study the role of gut microbiota in health or disease. However, murine and human microbiota differ in species composition, so further investigation of the murine gut microbiota is important to gain a better mechanistic understanding. Continuous in vitro fermentation models are powerful tools to investigate microbe-microbe interactions while circumventing animal testing and host confounding factors, but are lacking for murine gut microbiota. We therefore developed a novel continuous fermentation model based on the PolyFermS platform adapted to the murine caecum and inoculated with immobilized caecal microbiota. We followed a stepwise model development approach by adjusting parameters [pH, retention time (RT), growth medium] to reach fermentation metabolite profiles and marker bacterial levels similar to the inoculum. The final model had a stable and inoculum-alike fermentation profile during continuous operation. A lower pH during startup and continuous operation stimulated bacterial fermentation (115 mM short-chain fatty acids at pH 7 to 159 mM at pH 6.5). Adjustments to nutritive medium, a decreased pH and increased RT helped control the in vitro Enterobacteriaceae levels, which often bloom in fermentation models, to 6.6 log gene copies/mL in final model. In parallel, the Lactobacillus, Lachnospiraceae, and Ruminococcaceae levels were better maintained in vitro with concentrations of 8.5 log gene copies/mL, 8.8 log gene copies/mL and 7.5 log gene copies/mL, respectively, in the final model. An independent repetition with final model parameters showed reproducible results in maintaining the inoculum fermentation metabolite profile and its marker bacterial levels. Microbiota community analysis of the final model showed a decreased bacterial diversity and compositional differences compared to caecal inoculum microbiota. Most of the caecal bacterial families were represented in vitro, but taxa of the Muribaculaceae family were not maintained. Functional metagenomics prediction showed conserved metabolic and functional KEGG pathways between in vitro and caecal inoculum microbiota. To conclude, we showed that a rational and stepwise approach allowed us to model in vitro the murine caecal microbiota and functions. Our model is a first step to develop murine microbiota model systems and offers the potential to study microbiota functionality and structure ex vivo.
Collapse
Affiliation(s)
- Sophie A Poeker
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Tomas de Wouters
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Marianne R Spalinger
- Department of Gastroenterology and Hepatology, University Hospital Zurich, Zurich, Switzerland
| | - Michael Scharl
- Department of Gastroenterology and Hepatology, University Hospital Zurich, Zurich, Switzerland
| | - Annelies Geirnaert
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| |
Collapse
|
22
|
Spalinger MR, Schmidt TS, Schwarzfischer M, Hering L, Atrott K, Lang S, Gottier C, Geirnaert A, Lacroix C, Dai X, Rawlings DJ, Chan AC, von Mering C, Rogler G, Scharl M. Protein tyrosine phosphatase non-receptor type 22 modulates colitis in a microbiota-dependent manner. J Clin Invest 2019; 129:2527-2541. [PMID: 31107248 DOI: 10.1172/jci123263] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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: 06/28/2018] [Accepted: 04/02/2019] [Indexed: 12/16/2022] Open
Abstract
The gut microbiota is crucial for our health, and well-balanced interactions between the host's immune system and the microbiota are essential to prevent chronic intestinal inflammation, as observed in inflammatory bowel diseases (IBD). A variant in protein tyrosine phosphatase non-receptor type 22 (PTPN22) is associated with reduced risk of developing IBD, but promotes the onset of autoimmune disorders. While the role of PTPN22 in modulating molecular pathways involved in IBD pathogenesis is well studied, its impact on shaping the intestinal microbiota has not been addressed in depth. Here, we demonstrate that mice carrying the PTPN22 variant (619W mice) were protected from acute dextran sulfate sodium (DSS) colitis, but suffered from pronounced inflammation upon chronic DSS treatment. The basal microbiota composition was distinct between genotypes, and DSS-induced dysbiosis was milder in 619W mice than in WT littermates. Transfer of microbiota from 619W mice after the first DSS cycle into treatment-naive 619W mice promoted colitis, indicating that changes in microbial composition enhanced chronic colitis in those animals. This indicates that presence of the PTPN22 variant affects intestinal inflammation by modulating the host's response to the intestinal microbiota.
Collapse
Affiliation(s)
- Marianne R Spalinger
- Department of Gastroenterology and Hepatology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Thomas Sb Schmidt
- Institute of Molecular Life Science and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland.,European Molecular Biology Laboratory, Heidelberg, Germany
| | - Marlene Schwarzfischer
- Department of Gastroenterology and Hepatology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Larissa Hering
- Department of Gastroenterology and Hepatology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Kirstin Atrott
- Department of Gastroenterology and Hepatology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Silvia Lang
- Department of Gastroenterology and Hepatology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Claudia Gottier
- Department of Gastroenterology and Hepatology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Annelies Geirnaert
- Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Christophe Lacroix
- Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Xuezhi Dai
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, Washington, USA
| | - David J Rawlings
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Andrew C Chan
- Research, Genentech Inc., South San Francisco, California, USA
| | - Christian von Mering
- Institute of Molecular Life Science and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Gerhard Rogler
- Department of Gastroenterology and Hepatology, University Hospital Zurich and University of Zurich, Zurich, Switzerland.,Zurich Institute for Human Physiology, University of Zurich, Zurich, Switzerland
| | - Michael Scharl
- Department of Gastroenterology and Hepatology, University Hospital Zurich and University of Zurich, Zurich, Switzerland.,Zurich Institute for Human Physiology, University of Zurich, Zurich, Switzerland
| |
Collapse
|
23
|
Tovaglieri A, Sontheimer-Phelps A, Geirnaert A, Prantil-Baun R, Camacho DM, Chou DB, Jalili-Firoozinezhad S, de Wouters T, Kasendra M, Super M, Cartwright MJ, Richmond CA, Breault DT, Lacroix C, Ingber DE. Species-specific enhancement of enterohemorrhagic E. coli pathogenesis mediated by microbiome metabolites. Microbiome 2019; 7:43. [PMID: 30890187 PMCID: PMC6425591 DOI: 10.1186/s40168-019-0650-5] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 02/21/2019] [Indexed: 05/24/2023]
Abstract
BACKGROUND Species-specific differences in tolerance to infection are exemplified by the high susceptibility of humans to enterohemorrhagic Escherichia coli (EHEC) infection, whereas mice are relatively resistant to this pathogen. This intrinsic species-specific difference in EHEC infection limits the translation of murine research to human. Furthermore, studying the mechanisms underlying this differential susceptibility is a difficult problem due to complex in vivo interactions between the host, pathogen, and disparate commensal microbial communities. RESULTS We utilize organ-on-a-chip (Organ Chip) microfluidic culture technology to model damage of the human colonic epithelium induced by EHEC infection, and show that epithelial injury is greater when exposed to metabolites derived from the human gut microbiome compared to mouse. Using a multi-omics approach, we discovered four human microbiome metabolites-4-methyl benzoic acid, 3,4-dimethylbenzoic acid, hexanoic acid, and heptanoic acid-that are sufficient to mediate this effect. The active human microbiome metabolites preferentially induce expression of flagellin, a bacterial protein associated with motility of EHEC and increased epithelial injury. Thus, the decreased tolerance to infection observed in humans versus other species may be due in part to the presence of compounds produced by the human intestinal microbiome that actively promote bacterial pathogenicity. CONCLUSION Organ-on-chip technology allowed the identification of specific human microbiome metabolites modulating EHEC pathogenesis. These identified metabolites are sufficient to increase susceptibility to EHEC in our human Colon Chip model and they contribute to species-specific tolerance. This work suggests that higher concentrations of these metabolites could be the reason for higher susceptibility to EHEC infection in certain human populations, such as children. Furthermore, this research lays the foundation for therapeutic-modulation of microbe products in order to prevent and treat human bacterial infection.
Collapse
Affiliation(s)
- Alessio Tovaglieri
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
- Department of Health Sciences and Technology, ETH Zurich, 8092, Zurich, Switzerland
| | - Alexandra Sontheimer-Phelps
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
- Department of Biology, University of Freiburg, 79085, Freiburg, Germany
| | - Annelies Geirnaert
- Department of Health Sciences and Technology, ETH Zurich, 8092, Zurich, Switzerland
| | - Rachelle Prantil-Baun
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
| | - Diogo M Camacho
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
| | - David B Chou
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02115, USA
| | - Sasan Jalili-Firoozinezhad
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
- Department of Bioengineering and iBB, Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, 1649-004, Lisbon, Portugal
| | - Tomás de Wouters
- Department of Health Sciences and Technology, ETH Zurich, 8092, Zurich, Switzerland
| | - Magdalena Kasendra
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
- Present Address: Emulate Inc., 27 Drydock Avenue, Boston, MA, 02210, USA
| | - Michael Super
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
| | - Mark J Cartwright
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
| | - Camilla A Richmond
- Division of Gastroenterology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
- Harvard Stem Cell Institute, Harvard University, Boston, MA, 02139, USA
| | - David T Breault
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
- Harvard Stem Cell Institute, Harvard University, Boston, MA, 02139, USA
- Division of Endocrinology, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Christophe Lacroix
- Department of Health Sciences and Technology, ETH Zurich, 8092, Zurich, Switzerland
| | - Donald E Ingber
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.
- Vascular Biology Program and Department of Surgery, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
- Harvard John A. Paulson School of Engineering and Applied Sciences, Cambridge, MA, 02139, USA.
| |
Collapse
|
24
|
Bircher L, Geirnaert A, Hammes F, Lacroix C, Schwab C. Effect of cryopreservation and lyophilization on viability and growth of strict anaerobic human gut microbes. Microb Biotechnol 2018; 11:721-733. [PMID: 29663668 PMCID: PMC6011992 DOI: 10.1111/1751-7915.13265] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [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: 12/11/2017] [Revised: 02/22/2018] [Accepted: 03/08/2018] [Indexed: 01/22/2023] Open
Abstract
Strict anaerobic gut microbes have been suggested as ‘next‐generation probiotics’ for treating several intestinal disorders. The development of preservation techniques is of major importance for therapeutic application. This study investigated cryopreservation (−80°C) and lyophilization survival and storage stability (4°C for 3 months) of the strict anaerobic gut microbes Bacteroides thetaiotaomicron, Faecalibacterium prausnitzii, Roseburia intestinalis, Anaerostipes caccae, Eubacterium hallii and Blautia obeum. To improve preservation survival, protectants sucrose and inulin (both 5% w/v) were added for lyophilization and were also combined with glycerol (15% v/v) for cryopreservation. Bacterial fitness, evaluated by maximum growth rate and lag phase, viability and membrane integrity were determined using a standardized growth assay and by flow cytometry as markers for preservation resistance. Lyophilization was more detrimental to viability and fitness than cryopreservation, but led to better storage stability. Adding sucrose and inulin enhanced viability and the proportion of intact cells during lyophilization of all strains. Viability of protectant‐free B. thetaiotaomicron, A. caccae and F. prausnitzii was above 50% after cryopreservation and storage and increased to above 80% if protectants were present. The addition of glycerol, sucrose and inulin strongly enhanced the viability of B. obeum, E. hallii and R. intestinalis from 0.03–2% in protectant‐free cultures to 11–37%. This is the first study that quantitatively compared the effect of cryopreservation and lyophilization and the addition of selected protectants on viability and fitness of six strict anaerobic gut microbes. Our results suggest that efficiency of protectants is process‐ and species‐specific.
Collapse
Affiliation(s)
- Lea Bircher
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, Schmelzbergstrasse 7, 8092, Zürich, Switzerland
| | - Annelies Geirnaert
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, Schmelzbergstrasse 7, 8092, Zürich, Switzerland
| | | | - Christophe Lacroix
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, Schmelzbergstrasse 7, 8092, Zürich, Switzerland
| | - Clarissa Schwab
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, Schmelzbergstrasse 7, 8092, Zürich, Switzerland
| |
Collapse
|
25
|
Bircher L, Schwab C, Geirnaert A, Lacroix C. Cryopreservation of artificial gut microbiota produced with in vitro fermentation technology. Microb Biotechnol 2017; 11:163-175. [PMID: 28980453 PMCID: PMC5743790 DOI: 10.1111/1751-7915.12844] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [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: 01/24/2017] [Revised: 06/29/2017] [Accepted: 07/28/2017] [Indexed: 12/13/2022] Open
Abstract
Interest in faecal microbiota transplantation (FMT) has increased as therapy for intestinal diseases, but safety issues limit its widespread use. Intestinal fermentation technology (IFT) can produce controlled, diverse and metabolically active ‘artificial’ colonic microbiota as potential alternative to common FMT. However, suitable processing technology to store this artificial microbiota is lacking. In this study, we evaluated the impact of the two cryoprotectives, glycerol (15% v/v) and inulin (5% w/v) alone and in combination, in preserving short‐chain fatty acid formation and recovery of major butyrate‐producing bacteria in three artificial microbiota during cryopreservation for 3 months at −80°C. After 24 h anaerobic fermentation of the preserved microbiota, butyrate and propionate production were maintained when glycerol was used as cryoprotectant, while acetate and butyrate were formed more rapidly with glycerol in combination with inulin. Glycerol supported cryopreservation of the Roseburia spp./Eubacterium rectale group, while inulin improved the recovery of Faecalibacterium prausnitzii. Eubacterium hallii growth was affected minimally by cryopreservation. Our data indicate that butyrate producers, which are key organisms for gut health, can be well preserved with glycerol and inulin during frozen storage. This is of high importance if artificially produced colonic microbiota is considered for therapeutic purposes.
Collapse
Affiliation(s)
- Lea Bircher
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, Schmelzbergstrasse 7, 8092, Zürich, Switzerland
| | - Clarissa Schwab
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, Schmelzbergstrasse 7, 8092, Zürich, Switzerland
| | - Annelies Geirnaert
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, Schmelzbergstrasse 7, 8092, Zürich, Switzerland
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, Schmelzbergstrasse 7, 8092, Zürich, Switzerland
| |
Collapse
|
26
|
Devriese S, Eeckhaut V, Geirnaert A, Van den Bossche L, Hindryckx P, Van de Wiele T, Van Immerseel F, Ducatelle R, De Vos M, Laukens D. Reduced Mucosa-associated Butyricicoccus Activity in Patients with Ulcerative Colitis Correlates with Aberrant Claudin-1 Expression. J Crohns Colitis 2017; 11:229-236. [PMID: 27484096 DOI: 10.1093/ecco-jcc/jjw142] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [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: 05/08/2015] [Revised: 07/15/2016] [Accepted: 07/27/2016] [Indexed: 12/16/2022]
Abstract
BACKGROUND AND AIMS Butyricicoccus is a butyrate-producing clostridial cluster IV genus whose numbers are reduced in the stool of ulcerative colitis [UC] patients. Conditioned medium of Butyricicoccus [B.] pullicaecorum prevents tumour necrosis factor alpha [TNFα]-induced increase in epithelial permeability in vitro. Since butyrate influences intestinal barrier integrity, we further investigated the relationship between the abundance of mucosa-associated Butyricicoccus and the expression of butyrate-regulated tight junction [TJ] genes. METHODS Tight junction protein 1 [TJP1], occludin [OCLN], claudin-1 [CLDN1], and Butyricicoccus 16S rRNA expression was analysed in a collection of colonic biopsies of healthy controls and UC patients with active disease. The effect of butyrate and B. pullicaecorum conditioned medium on TJ gene expression was investigated in TNFα-stimulated Caco-2 monolayers and inflamed mucosal biopsies of UC patients. RESULTS TJP1 expression was significantly decreased in inflamed UC mucosa, whereas CLDN1 mRNA levels were increased. OCLN did not differ significantly between the groups. Mucosa-associated Butyricicoccus 16S rRNA transcripts were reduced in active UC patients compared with healthy controls. Interestingly, Butyricicoccus activity negatively correlated with CLDN1 expression. Butyrate reversed the inflammation-induced increase of CLDN1 protein levels, and stimulation of inflamed UC biopsies with B. pullicaecorum conditioned medium normalized CLDN1 mRNA levels. CONCLUSIONS Butyricicoccus is a mucosa-associated bacterial genus under-represented in colonic mucosa of patients with active UC, whose activity inversely correlates with CLDN1 expression. Butyrate and B. pullicaecorum conditioned medium reduce CLDN1 expression, supporting its use as a pharmabiotic preserving epithelial TJ integrity.
Collapse
Affiliation(s)
- Sarah Devriese
- Department of Gastroenterology, Ghent University, Ghent, Belgium
| | - Venessa Eeckhaut
- Department of Pathology, Bacteriology and Avian Diseases, Ghent University, Merelbeke, Belgium
| | - Annelies Geirnaert
- Laboratory of Microbial Ecology and Technology [LabMET], Ghent University, Ghent, Belgium
| | | | - Pieter Hindryckx
- Department of Gastroenterology, Ghent University, Ghent, Belgium
| | - Tom Van de Wiele
- Laboratory of Microbial Ecology and Technology [LabMET], Ghent University, Ghent, Belgium
| | - Filip Van Immerseel
- Department of Pathology, Bacteriology and Avian Diseases, Ghent University, Merelbeke, Belgium
| | - Richard Ducatelle
- Department of Pathology, Bacteriology and Avian Diseases, Ghent University, Merelbeke, Belgium
| | - Martine De Vos
- Department of Gastroenterology, Ghent University, Ghent, Belgium
| | - Debby Laukens
- Department of Gastroenterology, Ghent University, Ghent, Belgium
| |
Collapse
|
27
|
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
| |
Collapse
|
28
|
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.
Collapse
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
| |
Collapse
|
29
|
Selak M, Rivière A, Moens F, Van den Abbeele P, Geirnaert A, Rogelj I, Leroy F, De Vuyst L. Inulin-type fructan fermentation by bifidobacteria depends on the strain rather than the species and region in the human intestine. Appl Microbiol Biotechnol 2016; 100:4097-107. [PMID: 26861055 DOI: 10.1007/s00253-016-7351-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 01/08/2016] [Accepted: 01/23/2016] [Indexed: 01/01/2023]
Abstract
Inulin-type fructans (ITF) are known to cause a health-promoting bifidogenic effect, although the ITF degradation capacity of bifidobacteria in different intestinal regions remains unclear. The present study aims at offering new insights into this link, making use of a collection of 190 bifidobacterial strains, encompassing strains from gut biopsies (terminal ileum and proximal colon; mucosa-associated strains) and the simulator of the human intestinal microbial ecosystem (SHIME®; proximal and distal colon vessels; lumen-associated strains). A multivariate data analysis of all fermentation data revealed four clusters corresponding with different types of ITF degradation fingerprints, which were not correlated with the region in the intestine, suggesting that the degradation of ITF is uniform along the human intestine. Strains from cluster 1 consumed fructose, while strains from cluster 2 consumed more oligofructose than fructose. Higher fructose and oligofructose consumption was characteristic for clusters 3 and 4 strains, which degraded inulin too. In general, the mucosa-associated strains from biopsy origin seemed to be more specialized in the consumption of fructose and oligofructose, while the lumen-associated strains from SHIME origin displayed a higher degradation degree of inulin. Further, intra-species variability in ITF degradation was found, indicating strain-specific variations. The coexistence of different bifidobacterial strains with different ITF degradation fingerprints within the same intestinal region suggests cooperation for the degradation of ITF, with opportunities for cross-feeding on strain and/or species level.
Collapse
Affiliation(s)
- Marija Selak
- Research Group of Industrial Microbiology and Food Biotechnology, Department of Bioengineering Sciences, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050, Brussels, Belgium
| | - Audrey Rivière
- Research Group of Industrial Microbiology and Food Biotechnology, Department of Bioengineering Sciences, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050, Brussels, Belgium
| | - Frédéric Moens
- Research Group of Industrial Microbiology and Food Biotechnology, Department of Bioengineering Sciences, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050, Brussels, Belgium
| | - Pieter Van den Abbeele
- Laboratory of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, B-9000, Ghent, Belgium
| | - Annelies Geirnaert
- Laboratory of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, B-9000, Ghent, Belgium
| | - Irena Rogelj
- Institute of Dairy Science and Probiotics, Biotechnical Faculty, University of Ljubljana, Groblje 3, 1230, Domžale, Slovenia
| | - Frédéric Leroy
- Research Group of Industrial Microbiology and Food Biotechnology, Department of Bioengineering Sciences, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050, Brussels, Belgium
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology, Department of Bioengineering Sciences, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050, Brussels, Belgium.
| |
Collapse
|
30
|
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]
|
31
|
Prévoteau A, Geirnaert A, Arends JBA, Lannebère S, Van de Wiele T, Rabaey K. Hydrodynamic chronoamperometry for probing kinetics of anaerobic microbial metabolism--case study of Faecalibacterium prausnitzii. Sci Rep 2015; 5:11484. [PMID: 26127013 PMCID: PMC4486957 DOI: 10.1038/srep11484] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [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: 04/21/2015] [Accepted: 05/12/2015] [Indexed: 01/26/2023] Open
Abstract
Monitoring in vitro the metabolic activity of microorganisms aids bioprocesses and enables better understanding of microbial metabolism. Redox mediators can be used for this purpose via different electrochemical techniques that are either complex or only provide non-continuous data. Hydrodynamic chronoamperometry using a rotating disc electrode (RDE) can alleviate these issues but was seldom used and is poorly characterized. The kinetics of Faecalibacterium prausnitzii A2-165, a beneficial gut microbe, were determined using a RDE with riboflavin as redox probe. This butyrate producer anaerobically ferments glucose and reduces riboflavin whose continuous monitoring on a RDE provided highly accurate kinetic measurements of its metabolism, even at low cell densities. The metabolic reaction rate increased linearly over a broad range of cell concentrations (9 × 10(4) to 5 × 10(7) cells.mL(-1)). Apparent Michaelis-Menten kinetics was observed with respect to riboflavin (KM = 6 μM; kcat = 5.3 × 10(5) s(-1), at 37 °C) and glucose (KM = 6 μM; kcat = 2.4 × 10(5) s(-1)). The short temporal resolution allows continuous monitoring of fast cellular events such as kinetics inhibition with butyrate. Furthermore, we detected for the first time riboflavin reduction by another potential probiotic, Butyricicoccus pullicaecorum. The ability of the RDE for fast, accurate, simple and continuous measurements makes it an ad hoc tool for assessing bioprocesses at high resolution.
Collapse
Affiliation(s)
- Antonin Prévoteau
- Laboratory of Microbial Ecology and Technology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Annelies Geirnaert
- Laboratory of Microbial Ecology and Technology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Jan B A Arends
- Laboratory of Microbial Ecology and Technology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Sylvain Lannebère
- University of Coimbra, Department of Electrical Engineering - Instituto de Telecomunicações, Coimbra 3030-290, Portugal
| | - Tom Van de Wiele
- Laboratory of Microbial Ecology and Technology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Korneel Rabaey
- Laboratory of Microbial Ecology and Technology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| |
Collapse
|
32
|
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
|
33
|
Geirnaert A, Steyaert A, Eeckhaut V, Debruyne B, Arends JBA, Van Immerseel F, Boon N, Van de Wiele T. Butyricicoccus pullicaecorum, a butyrate producer with probiotic potential, is intrinsically tolerant to stomach and small intestine conditions. Anaerobe 2014; 30:70-4. [PMID: 25179909 DOI: 10.1016/j.anaerobe.2014.08.010] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 07/24/2014] [Accepted: 08/19/2014] [Indexed: 02/05/2023]
Abstract
Butyrate has several beneficial properties that are essential to maintain gastrointestinal health. Therefore butyrate-producing bacteria are seen as the next generation of probiotics. The butyrate-producing bacterium Butyricicoccus pullicaecorum (a clostridial cluster IV strain) is such a promising probiotic candidate for people suffering from inflammatory bowel disease. To exert its beneficial properties, it is crucial that B. pullicaecorum survives the harsh conditions of the upper gastrointestinal tract to arrive in the colon in a viable and metabolically active state. Before developing a stable formulation of B. pullicaecorum for oral administration, it is important to know its intrinsic acid and bile tolerance. We monitored the survival during and short chain fatty acid production after incubation in conditions simulating the stomach and small intestine using in vitro batch experiments. In case of acid conditions (pH 2 and pH 3), B. pullicaecorum was viable and active but not cultivable. Cultivability was restored during subsequent small intestine conditions. Importantly, bile and pancreatic juice had no lethal effect. Milk, as a suspension medium, only had a protective effect on the cultivability during the first hour at pH 2. B. pullicaecorum was still metabolically active after upper gastrointestinal conditions and produced short chain fatty acids, but a shift from butyrate to acetate production was observed. Although the butyrate-producing anaerobe B. pullicaecorum showed good intrinsic acid and bile tolerance in terms of viability and metabolic activity, colonization efficiency and butyrate production under colon conditions is needed to further evaluate its probiotic potential.
Collapse
Affiliation(s)
- Annelies Geirnaert
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Alix Steyaert
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Venessa Eeckhaut
- Department of Pathology, Bacteriology and Avian Diseases, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Bo Debruyne
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Jan B A Arends
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Filip Van Immerseel
- Department of Pathology, Bacteriology and Avian Diseases, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Nico Boon
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Tom Van de Wiele
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium.
| |
Collapse
|
34
|
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.
Collapse
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:
| |
Collapse
|
35
|
Van den Abbeele P, Verstraete W, El Aidy S, Geirnaert A, Van de Wiele T. Prebiotics, faecal transplants and microbial network units to stimulate biodiversity of the human gut microbiome. Microb Biotechnol 2013; 6:335-40. [PMID: 23594389 PMCID: PMC3917468 DOI: 10.1111/1751-7915.12049] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [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: 01/29/2013] [Revised: 02/14/2013] [Accepted: 02/14/2013] [Indexed: 12/21/2022] Open
Abstract
Accumulating evidence demonstrates the intimate association between human hosts and the gut microbiome. Starting at birth, the sterile gut of the newborn acquires a diverse spectrum of microbes, needed for immunological priming. However, current practices (caesarean sections, use of formula milk) deprive newborns from being exposed to this broad spectrum of microbes. Unnecessary use of antibiotics and excessive hygienic precautions (e.g. natural versus chlorinated drinking water) together with the Western diet further contribute to a decreased microbial diversity in the adult gut. This has been correlated with recurrent Clostridium difficile infection, inflammatory bowel diseases and obesity, among others. A healthy gut microbiome is thus characterized by a diverse network of metabolically interacting microbial members. In this context, we review several existing and novel approaches to manage the gut microbiome. First, prebiotic compounds should be re-defined in the sense that they should enhance the ecological biodiversity rather than stimulating single species. Recent studies highlight that structurally different polysaccharides require specific primary degraders but also enhance a similar network of secondary degraders that benefit from cross-feeding. A faecal transplantation is a second approach to restore biodiversity when the microbiota is severely dysbiosed, with promising results regarding C. difficile-associated disease and obesity-related metabolic syndromes. A final strategy is the introduction of key microbial network units, i.e. pre-organized microbial associations, which strengthen the overall microbial network of the gut microbiome that supports human health.
Collapse
Affiliation(s)
- Pieter Van den Abbeele
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | | | | | | | | |
Collapse
|
36
|
Geirnaert A, Steyaert A, Van den Abbeele P, Eeckhaut V, Van Immerseel F, Boon N, Van de Wiele T. In vitro characterization of gastrointestinal behavior of Butyricicoccus pullicaecorum, a novel butyrate producing isolate with probiotic potential to counterbalance dysbiosis in inflammatory bowel disease. Commun Agric Appl Biol Sci 2013; 78:157-163. [PMID: 23875313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Affiliation(s)
- A Geirnaert
- Laboratory of Microbial Ecology and Technology (LabMET), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Gent, Belgium
| | | | | | | | | | | | | |
Collapse
|
37
|
Geirnaert A, Debruyne B, Eeckhaut V, Van Immerseel F, Booni N, Van de Wiele T. In vitro evaluation of the upper gastrointestinal passage of a novel butyrate producing isolate to counterbalance dysbiosis in inflammatory bowel disease. Commun Agric Appl Biol Sci 2012; 77:45-49. [PMID: 22558754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Affiliation(s)
- A Geirnaert
- Laboratory of Microbial Ecology and Technology (LabMET), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, BE-9000 Gent, Belgium
| | | | | | | | | | | |
Collapse
|
38
|
Geirnaert A, Debruyne B, Eeckhaut V, Van Immerseel F, Boon N, Van de Wiele T. In vitro evaluation of the upper gastrointestinal passage of a novel butyrate producing isolate to counterbalance dysbiosis in inflammatory bowel disease. Commun Agric Appl Biol Sci 2012; 77:195-199. [PMID: 22558780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Affiliation(s)
- A Geirnaert
- Laboratory of Microbial Ecology and Technology (LabMET), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, BE-9000 Gent, Belgium
| | | | | | | | | | | |
Collapse
|