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7. Targeted remodeling of the human gut microbiome using Juemingzi (Senna seed extracts).

Author

Narrowe, Adrienne B., Lemons, Johanna M. S., Mahalak, Karley K., Firrman, Jenni, Van den Abbeele, Pieter, Baudot, Aurélien, Deyaert, Stef, Yanfang Li, Liangli (Lucy) Yu, and LinShu Liu

Subjects
GUT microbiome, HUMAN microbiota, SHORT-chain fatty acids, SHOTGUN sequencing, MICROBIAL diversity, SEED yield
Abstract

The genus Senna contains globally distributed plant species of which the leaves, roots, and seeds have multiple traditional medicinal and nutritional uses. Notable chemical compounds derived from Senna spp. include sennosides and emodin which have been tested for antimicrobial effects in addition to their known laxative functions. However, studies of the effects of the combined chemical components on intact human gut microbiome communities are lacking. This study evaluated the effects of Juemingzi (Senna sp.) extract on the human gut microbiome using SIFR® (Systemic Intestinal Fermentation Research) technology. After a 48-hour human fecal incubation, we measured total bacterial cell density and fermentation products including pH, gas production and concentrations of short chain fatty acids (SCFAs). The initial and postincubation microbial community structure and functional potential were characterized using shotgun metagenomic sequencing. Juemingzi (Senna seed) extracts displayed strong, taxon-specific anti-microbial effects as indicated by significant reductions in cell density (40%) and intra-sample community diversity. Members of the Bacteroidota were nearly eliminated over the 48-hour incubation. While generally part of a healthy gut microbiome, specific species of Bacteroides can be pathogenic. The active persistence of the members of the Enterobacteriaceae and selected Actinomycetota despite the reduction in overall cell numbers was demonstrated by increased fermentative outputs including high concentrations of gas and acetate with correspondingly reduced pH. These large-scale shifts in microbial community structure indicate the need for further evaluation of dosages and potential administration with prebiotic or synbiotic supplements. Overall, the very specific effects of these extracts may offer the potential for targeted antimicrobial uses or as a tool in the targeted remodeling of the gut microbiome. [ABSTRACT FROM AUTHOR]

Published
2024
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14. The Simulator of the Human Intestinal Microbial Ecosystem (SHIME®)

Author

Van de Wiele, Tom, Van den Abbeele, Pieter, Ossieur, Wendy, Possemiers, Sam, Marzorati, Massimo, Verhoeckx, Kitty, editor, Cotter, Paul, editor, López-Expósito, Iván, editor, Kleiveland, Charlotte, editor, Lea, Tor, editor, Mackie, Alan, editor, Requena, Teresa, editor, Swiatecka, Dominika, editor, and Wichers, Harry, editor

Published
2015
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20. Capacity of a Microbial Synbiotic To Rescue the In Vitro Metabolic Activity of the Gut Microbiome following Perturbation with Alcohol or Antibiotics

Author

Tierney, Braden T., primary, Van den Abbeele, Pieter, additional, Al-Ghalith, Gabriel A., additional, Verstrepen, Lynn, additional, Ghyselinck, Jonas, additional, Calatayud, Marta, additional, Marzorati, Massimo, additional, Gadir, Azza A., additional, Daisley, Brendan, additional, Reid, Gregor, additional, Bron, Peter A., additional, Gevers, Dirk, additional, Dhir, Raja, additional, and Simmons, Sheri L., additional

Published
2023
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23. Comparative Genomics and Physiology of Akkermansia muciniphila Isolates from Human Intestine Reveal Specialized Mucosal Adaptation

Author

Ouwerkerk, Janneke P., primary, Tytgat, Hanne L. P., additional, Elzinga, Janneke, additional, Koehorst, Jasper, additional, Van den Abbeele, Pieter, additional, Henrissat, Bernard, additional, Gueimonde, Miguel, additional, Cani, Patrice D., additional, Van de Wiele, Tom, additional, Belzer, Clara, additional, and de Vos, Willem M., additional

Published
2022
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28. The Effect of Amino Acids on Production of SCFA and bCFA by Members of the Porcine Colonic Microbiota

Author

Van den Abbeele, Pieter, Ghyselinck, Jonas, Marzorati, Massimo, Koch, Anna-Maria, Lambert, William, Michiels, Joris, and Chalvon-Demersay, Tristan

Subjects
ARGININE SUPPLEMENTATION, Microbiology (medical), amino acids, FERMENTATION, gut microbiota, colon, Biology and Life Sciences, SCFA, Microbiology, PROPIONATE, COMMUNITY, GLUTAMATE, CHAIN FATTY-ACIDS, BUTYRATE, Virology, INULIN, BACTERIA, bCFA, piglet, ALTERS
Abstract

Functional amino acids supplementation to farm animals is considered to not only be beneficial by regulating intestinal barrier, oxidative stress, and immunity, but potentially also by impacting the gut microbiota. The impact of amino acids on a piglet-derived colonic microbiota was evaluated using a 48-h in vitro batch incubation strategy. The combination of 16S rRNA gene profiling with flow cytometry demonstrated that specific microbial taxa were involved in the fermentation of each of the amino acids resulting in the production of specific metabolites. Branched chain amino acids (leucine, isoleucine, valine) strongly increased branched-chain fatty acids (+23.0 mM) and valerate levels (+3.0 mM), coincided with a marked increase of Peptostreptococcaceae. Further, glutamine and glutamate specifically stimulated acetate (similar to 20 mM) and butyrate (similar to 10 mM) production, relating to a stimulation of a range of families containing known butyrate-producing species (Ruminococcaceae, Oscillospiraceae, and Christensenellaceae). Finally, while tryptophan was only fermented to a minor extent, arginine and lysine specifically increased propionate levels (similar to 2 mM), likely produced by Muribaculaceae members. Overall, amino acids were thus shown to be selectively utilized by microbes originating from the porcine colonic microbiota, resulting in the production of health-related shortchain fatty acids, thus confirming the prebiotic potential of specific functional amino acids.

Published
2022

29. Development of a reproducible small intestinal microbiota model and its integration into the SHIME®-system, a dynamic in vitro gut model

Author

Deyaert, Stef, Moens, Frédéric, Pirovano, Walter, van den Bogert, Bartholomeus, Klaassens, Eline Suzanne, Marzorati, Massimo, Van de Wiele, Tom, Kleerebezem, Michiel, and Van den Abbeele, Pieter

Subjects
Microbiology (medical), Microbiology, simulator of the human intestinal microbial ecosystem, in vitro model, WIAS, microbiota, ileum, Host-Microbe Interactomics, short-chain fatty acid, small intestine, Departement dierwetenschappen, Department of Animal Sciences, VLAG
Abstract

The human gastrointestinal tract consists of different regions, each characterized by a distinct physiology, anatomy, and microbial community. While the colonic microbiota has received a lot of attention in recent research projects, little is known about the small intestinal microbiota and its interactions with ingested compounds, primarily due to the inaccessibility of this region in vivo. This study therefore aimed to develop and validate a dynamic, long-term simulation of the ileal microbiota using the SHIME®-technology. Essential parameters were identified and optimized from a screening experiment testing different inoculation strategies, nutritional media, and environmental parameters over an 18-day period. Subjecting a synthetic bacterial consortium to the selected conditions resulted in a stable microbiota that was representative in terms of abundance [8.81 ± 0.12 log (cells/ml)], composition and function. Indeed, the observed community mainly consisted of the genera Streptococcus, Veillonella, Enterococcus, Lactobacillus, and Clostridium (qPCR and 16S rRNA gene targeted Illumina sequencing), while nutrient administration boosted lactate production followed by cross-feeding interactions towards acetate and propionate. Furthermore, similarly as in vivo, bile salts were only partially deconjugated and only marginally converted into secondary bile salts. After confirming reproducibility of the small intestinal microbiota model, it was integrated into the established M-SHIME® where it further increased the compositional relevance of the colonic community. This long-term in vitro model provides a representative simulation of the ileal bacterial community, facilitating research of the ileum microbiota dynamics and activity when, for example, supplemented with microbial or diet components. Furthermore, integration of this present in vitro simulation increases the biological relevance of the current M-SHIME® technology.

Published
2022

30. Serum-Derived Bovine Immunoglobulin Stimulates SCFA Production by Specific Microbes in the Ex Vivo SIFR ® Technology.

Author

Van den Abbeele, Pieter, Detzel, Christopher, Rose, Alexis, Deyaert, Stef, Baudot, Aurélien, and Warner, Christopher

Subjects
BOS, BLOOD proteins, GUT microbiome, RUMEN fermentation, HUMAN microbiota, INTESTINAL absorption, DIGESTION
Abstract

Serum-derived bovine immunoglobulins (SBI) exert health benefits mediated by their ability to bind microbial components, thereby preventing translocation and subsequent inflammation. While in vivo studies have shown that a fraction of SBI also reaches the colon, little is known about the impact of SBI on the dense colonic microbiota that has great potential to impact human health. This study, therefore, investigated the impact of three bovine plasma protein fractions (SBI, bovine plasma (BP) and albumin-enriched bovine plasma (ABP)) on the gut microbiota of six human adults using the novel ex vivo SIFR® technology, recently demonstrated to generate predictive findings for clinical studies. When dosed at an equivalent of 5 g/day, all protein fractions significantly increased health-related metabolites—acetate, propionate, and butyrate. Upon simulating small intestinal absorption, SBI still markedly increased acetate and propionate, demonstrating that SBI is more resistant to small intestinal digestion and absorption compared to the other protein sources. Despite noticeable interindividual differences in microbiota composition among human adults, SBI consistently stimulated a narrow spectrum of gut microbes, which largely differed from the ones that are typically involved in carbohydrate fermentation. The SBI-fermenting consortium included B. vulgatus and L. edouardi (correlating with acetate and propionate) along with Dorea longicatena, Coprococcus comes and the butyrate-producing bacterium SS3/4 (correlating with butyrate). Overall, this study revealed that protein bovine fractions can contribute to health benefits by specifically modulating the human gut microbiota. While health benefits could follow from the production of SCFA, a broader range of protein-derived metabolites could also be produced. This study also confirms that the concept of prebiotics (substrates selectively utilized by host microorganisms conferring a health benefit) could go beyond the use of ingestible carbohydrates and extend to partially indigestible proteins. [ABSTRACT FROM AUTHOR]

Published
2023
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32. FunHoMic: A Marie Skłodowska-Curie Innovative Training Network for the study of the Fungus-Host-Microbiota interplay

Author

Cole, Nathaniel, primary, Marsaux, Benoît, additional, Rosati, Diletta, additional, Delavy, Margot, additional, Kosmala, Daria, additional, Xie, Zixuan, additional, Kaune, Ann-Kristin, additional, Valentine, Marisa, additional, Chakraborty, Sayoni, additional, Kaur, Manjyot, additional, Alaban, Leovigildo Rey, additional, Morelli, Moran, additional, Fróis-Martins, Ricardo, additional, Walker, Alan, additional, Van den Abbeele, Pieter, additional, Netea, Mihai, additional, Bougnoux, Marie-Elisabeth, additional, Manichanh, Chaysavanh, additional, Munro, Carol, additional, Hube, Bernhard, additional, Jacobsen, Ilse, additional, Roget, Karine, additional, Thomas, Vincent, additional, Queiroz, Karla, additional, Leibundgut-Landmann, Salomé, additional, Brown, Alistair, additional, and d'Enfert, Christophe, additional

Published
2021
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34. Long-Term Lactulose Administration Improves Dysbiosis Induced by Antibiotic and C. difficile in the PathoGut TM SHIME Model.

Author

Calatayud, Marta, Duysburgh, Cindy, Van den Abbeele, Pieter, Franckenstein, Dennis, Kuchina-Koch, Angelika, and Marzorati, Massimo

Subjects
CLOSTRIDIOIDES difficile, LACTULOSE, BACTERIAL colonies, ANTIBIOTICS, DYSBIOSIS
Abstract

Clostridioides difficile infection (CDI) is the leading cause of antibiotic-associated diarrhea and an important nosocomial infection with different severity degrees. Disruption of the gut microbiota by broad-spectrum antibiotics creates a proper environment for C. difficile colonization, proliferation, and clinical disease onset. Restoration of the gut microbial ecosystem through prebiotic interventions can constitute an effective complementary treatment of CDI. Using an adapted simulator of the human gut microbial ecosystem, the PathoGutTM SHIME, the effect of different long-term and repeated dose lactulose treatments was tested on C. difficile germination and growth in antibiotic-induced dysbiotic gut microbiota environments. The results showed that lactulose reduced the growth of viable C. difficile cells following clindamycin treatment, shifted the antibiotic-induced dysbiotic microbial community, and stimulated the production of health-promoting metabolites (especially butyrate). Recovery of the gut microenvironment by long-term lactulose administration following CDI was also linked to lactate production, decrease in pH and modulation of bile salt metabolism. At a structural level, lactulose showed a significant bifidogenic potential and restored key commensal members of the gut ecosystem such as Lactobacillaceae, Veillonellaceae and Lachnospiraceae. These results support further human intervention studies aiming to validate the in vitro beneficial effects of lactulose on gut microbiome recovery during antibiotic exposure and CDI. [ABSTRACT FROM AUTHOR]

Published
2022
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42. impact of environmental pH on the gut microbiota community structure and short chain fatty acid production.

Author

Firrman, Jenni, Liu, LinShu, Mahalak, Karley, Tanes, Ceylan, Bittinger, Kyle, Tu, Vincent, Bobokalonov, Jamshed, Mattei, Lisa, Zhang, Huanjia, and Van den Abbeele, Pieter

Subjects
SHORT-chain fatty acids, GUT microbiome, BUTYRIC acid, ACETIC acid, VALERIC acid, PROPIONIC acid
Abstract

Environmental pH is a critical parameter for maintenance of the gut microbiota. Here, the impact of pH on the gut microbiota luminal and mucosal community structure and short chain fatty acid (SCFA) production was evaluated i n vitro , and data compiled to reveal a donor-independent response to an increase or decrease in environmental pH. The results found that raising environmental pH significantly increased luminal community richness and decreased mucosal community evenness. This corresponded with an increased abundance of Ruminococcaceae Ruminococcus and Erysipelotrichaceae Erysipelatoclostridium , and a decreased abundance of Coriobacteriaceae Collinsella and Enterobacteriaceae Shigella for both the luminal and mucosal communities. Total SCFA levels were significantly higher, primarily due to an increase in acetic and 2-methylbutanoic acids. Lowering pH decreased luminal community evenness and decreased mucosal community evenness and richness. This corresponded with an increased abundance of Lachnospiraceae Enterocloster, Veillonellaceae Megasphaera, Veillonellaceae Sporomusa, Erysipelotrichaceae Eubacterium , and Alcaligenaceae Sutterella , and decreased abundance of Odoribacteraceae Butyricimonas, Fusobacteriaceae Fusobacterium, Veillonellaceae Phascolarctobacterium , and multiple Enterobacteriaceae species for both the luminal and mucosal communities. Total SCFA levels were significantly lower, with an observed drop in acetic and propionic acids, and increased butyric and valeric acids. Taken together, these results indicate that alterations to environmental pH can modulate the gut microbiota community structure and function, and some changes may occur in a donor-independent manner. [ABSTRACT FROM AUTHOR]

Published
2022
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44. Development of an Affordable, Sustainable and Efficacious Plant-Based Immunomodulatory Food Ingredient Based on Bell Pepper or Carrot RG-I Pectic Polysaccharides

Author

McKay, Sue, primary, Oranje, Paul, additional, Helin, Jari, additional, Koek, Jean H., additional, Kreijveld, Ellen, additional, van den Abbeele, Pieter, additional, Pohl, Ute, additional, Bothe, Gordana, additional, Tzoumaki, Maria, additional, Aparicio-Vergara, Marcela, additional, Mercenier, Annick, additional, Schols, Henk, additional, and Albers, Ruud, additional

Published
2021
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46. In vitro–in vivo Validation of Stimulatory Effect of Oat Ingredients on Lactobacilli

Author

Duysburgh, Cindy, primary, Van den Abbeele, Pieter, additional, Kamil, Alison, additional, Fleige, Lisa, additional, De Chavez, Peter John, additional, Chu, YiFang, additional, Barton, Wiley, additional, O’Sullivan, Orla, additional, Cotter, Paul D., additional, Quilter, Karina, additional, Joyce, Susan A., additional, Murphy, Mike, additional, DunnGalvin, Gillian, additional, Dinan, Timothy G, additional, and Marzorati, Massimo, additional

Published
2021
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48. Development and validation of the simulator of the Canine Intestinal Microbial Ecosystem (SCIME)

Author

Duysburgh, Cindy, Ossieur, Wendy, De Paepe, Kim, Van den Abbeele, Pieter, Vichez-Vargas, Ramiro, Vital, Marius, Pieper, Dietmar H., Van de Wiele, Tom, Hesta, Myriam, Possemiers, Sam, and Marzorati, Massimo

Subjects
ADULT DOGS, validation, FERMENTATION, FOS, PROTEIN CATABOLITES, EFFECTS MODELS, in vitro, METABOLISM, GUT MICROBIOME, TRACT NUTRIENT DIGESTIBILITIES, INULIN, dog, FECAL MICROBIOTA, SCIME, POPULATIONS, Veterinary Sciences
Abstract

Whereas a wide variety of in vitro models have been developed and validated to assess the effect of specific food ingredients on the human gut microbiome, such models have only been developed and applied to a limited extent for companion animals. Since the use of pre- and probiotics to improve gut health is an emerging research topic in the field of companion animals and as dogs are often used as laboratory animals in developing and testing of pharmaceuticals, the current study aimed to establish an adequate canine in vitro model. This consisted of a four-stage reactor composed of a stomach and small intestinal compartment followed by a proximal and distal colon. This semi-continuous gastrointestinal tract model allowed a long-term, region-dependent, and pH-controlled simulation of the colon-associated microbial community of dogs. Upon reaching a functional steady state, the simulated canine microbial community composition proved to be representative of the in vivo situation. Indeed, the predominant bacterial phyla present in the in vitro proximal and distal colon corresponded with the main bacterial phyla detected in the fecal material of the dogs, resulting in an average community composition along the simulated canine gastrointestinal tract of 50.5% Firmicutes, 34.5% Bacteroidetes, 7.4% Fusobacteria, 4.9% Actinobacteria, and 2.7% Proteobacteria. A parallel in vivo-in vitro comparison assessing the effects of fructooligosaccharides (FOS) on the canine microbial community composition showed a consistent stimulation of Lactobacillus concentrations in the in vivo fecal samples as well as in the in vitro canine gut model. Furthermore, the in vitro platform provided additional insights about the prebiotic effect of FOS supplementation of dogs, such as a reduced abundance of Megamonas spp. which are only present in very low abundance in in vivo fecal samples, indicating an interesting application potential of the developed canine in vitro model in research related to gastrointestinal health of dogs.

Published
2020

50. The impact of the Fungus-Host-Microbiota interplay uponCandida albicansinfections: current knowledge and new perspectives

Author

d'Enfert, Christophe, primary, Kaune, Ann-Kristin, additional, Alaban, Leovigildo-Rey, additional, Chakraborty, Sayoni, additional, Cole, Nathaniel, additional, Delavy, Margot, additional, Kosmala, Daria, additional, Marsaux, Benoît, additional, Fróis-Martins, Ricardo, additional, Morelli, Moran, additional, Rosati, Diletta, additional, Valentine, Marisa, additional, Xie, Zixuan, additional, Emritloll, Yoan, additional, Warn, Peter A, additional, Bequet, Frédéric, additional, Bougnoux, Marie-Elisabeth, additional, Bornes, Stephanie, additional, Gresnigt, Mark S, additional, Hube, Bernhard, additional, Jacobsen, Ilse D, additional, Legrand, Mélanie, additional, Leibundgut-Landmann, Salomé, additional, Manichanh, Chaysavanh, additional, Munro, Carol A, additional, Netea, Mihai G, additional, Queiroz, Karla, additional, Roget, Karine, additional, Thomas, Vincent, additional, Thoral, Claudia, additional, Van den Abbeele, Pieter, additional, Walker, Alan W, additional, and Brown, Alistair J P, additional

Published
2020
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