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Calvete-Torre I, Sabater C, Villamiel M, Margolles A, Méndez-Albiñana P, Ruiz L, Hernandez-Hernandez O. Exploring the modulatory effect of trehalose-derived galactooligosaccharides on key gut microbiota groups. Int J Biol Macromol 2024; 273:133053. [PMID: 38857723 DOI: 10.1016/j.ijbiomac.2024.133053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 05/31/2024] [Accepted: 06/07/2024] [Indexed: 06/12/2024]
Abstract
Trehalose (α-d-glucopyranosyl-(1-1)-α-D-glucopyranoside) has found applications in diverse food products as a sweetener, stabilizer, and humectant. Recent attention has focused on trehalose due to its contradictory effects on the virulence of Clostridium difficile. In this study, we investigate the impact of novel trehalose-derived galactooligosaccharides (Treh-GOS) on the human gut microbiota using in vitro fecal fermentation models. Distinct Treh-GOS structures elicit varying taxonomic responses. For instance, β-Gal-(1-4)-trehalose [DP3(1-4)] leads to an increase of Bifidobacterium, comparable to results observed with commercial GOS. Conversely, β-Gal-(1-6)-trehalose [DP3(1-6)] prompts an increase in Lactobacillus. Notably, both of these trisaccharides yield the highest concentrations of butyric acid across all samples. On the other hand, Treh-GOS tetrasaccharide mixture (DP4), featuring a novel trehalose galactosylation in both glucose units, fosters the growth of Parabacteroides. Our findings underscore the capacity of novel Treh-GOS to modulate the human gut microbiota. Consequently, these innovative galactooligosaccharides emerge as promising candidates for novel prebiotic applications.
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Affiliation(s)
- Ines Calvete-Torre
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias-Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Asturias, Spain; Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Asturias, Spain
| | - Carlos Sabater
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias-Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Asturias, Spain; Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Asturias, Spain.
| | - Mar Villamiel
- Instituto de Investigación en Ciencias de la Alimentación (CIAL) (CSIC-UAM) CEI (CSIC+UAM), Madrid, Spain
| | - Abelardo Margolles
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias-Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Asturias, Spain; Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Asturias, Spain
| | - Pablo Méndez-Albiñana
- Instituto de Investigación en Ciencias de la Alimentación (CIAL) (CSIC-UAM) CEI (CSIC+UAM), Madrid, Spain
| | - Lorena Ruiz
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias-Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Asturias, Spain; Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Asturias, Spain
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Calvete‐Torre I, Sabater C, Muñoz‐Almagro N, Campelo AB, Moreno FJ, Margolles A, Ruiz L. A methyl esterase from Bifidobacterium longum subsp. longum reshapes the prebiotic properties of apple pectin by triggering differential modulatory capacity in faecal cultures. Microb Biotechnol 2024; 17:e14443. [PMID: 38722820 PMCID: PMC11081426 DOI: 10.1111/1751-7915.14443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 02/23/2024] [Accepted: 02/28/2024] [Indexed: 05/13/2024] Open
Abstract
Pectin structures have received increasing attention as emergent prebiotics due to their capacity to promote beneficial intestinal bacteria. Yet the collective activity of gut bacterial communities to cooperatively metabolize structural variants of this substrate remains largely unknown. Herein, the characterization of a pectin methylesterase, BpeM, from Bifidobacterium longum subsp. longum, is reported. The purified enzyme was able to remove methyl groups from highly methoxylated apple pectin, and the mathematical modelling of its activity enabled to tightly control the reaction conditions to achieve predefined final degrees of methyl-esterification in the resultant pectin. Demethylated pectin, generated by BpeM, exhibited differential fermentation patterns by gut microbial communities in in vitro mixed faecal cultures, promoting a stronger increase of bacterial genera associated with beneficial effects including Lactobacillus, Bifidobacterium and Collinsella. Our findings demonstrate that controlled pectin demethylation by the action of a B. longum esterase selectively modifies its prebiotic fermentation pattern, producing substrates that promote targeted bacterial groups more efficiently. This opens new possibilities to exploit biotechnological applications of enzymes from gut commensals to programme prebiotic properties.
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Affiliation(s)
- Inés Calvete‐Torre
- Group of Functionality and Ecology of Beneficial Microorganisms (MicroHealth)Dairy Research Institute of Asturias (IPLA‐CSIC)VillaviciosaAsturiasSpain
- Health Research Institute of Asturias (ISPA)OviedoAsturiasSpain
| | - Carlos Sabater
- Group of Functionality and Ecology of Beneficial Microorganisms (MicroHealth)Dairy Research Institute of Asturias (IPLA‐CSIC)VillaviciosaAsturiasSpain
- Health Research Institute of Asturias (ISPA)OviedoAsturiasSpain
| | - Nerea Muñoz‐Almagro
- Group of Chemistry and Functionality of Carbohydrates and DerivativesInstitute of Food Science Research, CIAL (CSIC‐UAM), Universidad Autónoma de MadridMadridSpain
| | - Ana Belén Campelo
- Dairy Research Institute of Asturias (IPLA‐CSIC)VillaviciosaAsturiasSpain
| | - F. Javier Moreno
- Group of Chemistry and Functionality of Carbohydrates and DerivativesInstitute of Food Science Research, CIAL (CSIC‐UAM), Universidad Autónoma de MadridMadridSpain
| | - Abelardo Margolles
- Group of Functionality and Ecology of Beneficial Microorganisms (MicroHealth)Dairy Research Institute of Asturias (IPLA‐CSIC)VillaviciosaAsturiasSpain
- Health Research Institute of Asturias (ISPA)OviedoAsturiasSpain
| | - Lorena Ruiz
- Group of Functionality and Ecology of Beneficial Microorganisms (MicroHealth)Dairy Research Institute of Asturias (IPLA‐CSIC)VillaviciosaAsturiasSpain
- Health Research Institute of Asturias (ISPA)OviedoAsturiasSpain
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Vázquez X, Lumbreras-Iglesias P, Rodicio MR, Fernández J, Bernal T, Moreno AF, de Ugarriza PL, Fernández-Verdugo A, Margolles A, Sabater C. Study of the intestinal microbiota composition and the effect of treatment with intensive chemotherapy in patients recovered from acute leukemia. Sci Rep 2024; 14:5585. [PMID: 38454103 PMCID: PMC10920697 DOI: 10.1038/s41598-024-56054-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 03/01/2024] [Indexed: 03/09/2024] Open
Abstract
A dataset comprising metagenomes of outpatients (n = 28) with acute leukemia (AL) and healthy controls (n = 14) was analysed to investigate the associations between gut microbiota composition and metabolic activity and AL. According to the results obtained, no significant differences in the microbial diversity between AL outpatients and healthy controls were found. However, significant differences in the abundance of specific microbial clades of healthy controls and AL outpatients were found. We found some differences at taxa level. The relative abundance of Enterobacteriaceae, Prevotellaceae and Rikenellaceae was increased in AL outpatients, while Bacteirodaceae, Bifidobacteriaceae and Lachnospiraceae was decreased. Interestingly, the abundances of several taxa including Bacteroides and Faecalibacterium species showed variations based on recovery time from the last cycle of chemotherapy. Functional annotation of metagenome-assembled genomes (MAGs) revealed the presence of functional domains corresponding to therapeutic enzymes including L-asparaginase in a wide range of genera including Prevotella, Ruminococcus, Faecalibacterium, Alistipes, Akkermansia. Metabolic network modelling revealed potential symbiotic relationships between Veillonella parvula and Levyella massiliensis and several species found in the microbiota of AL outpatients. These results may contribute to develop strategies for the recovery of microbiota composition profiles in the treatment of patients with AL.
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Grants
- FIS PI21/01590 Fondo de Investigación Sanitaria, Instituto de Salud Carlos III, Ministerio de Economía y Competitividad, Spain
- FIS PI21/01590 Fondo de Investigación Sanitaria, Instituto de Salud Carlos III, Ministerio de Economía y Competitividad, Spain
- FIS PI21/01590 Fondo de Investigación Sanitaria, Instituto de Salud Carlos III, Ministerio de Economía y Competitividad, Spain
- FIS PI21/01590 Fondo de Investigación Sanitaria, Instituto de Salud Carlos III, Ministerio de Economía y Competitividad, Spain
- FIS PI21/01590 Fondo de Investigación Sanitaria, Instituto de Salud Carlos III, Ministerio de Economía y Competitividad, Spain
- FIS PI21/01590 Fondo de Investigación Sanitaria, Instituto de Salud Carlos III, Ministerio de Economía y Competitividad, Spain
- FIS PI21/01590 Fondo de Investigación Sanitaria, Instituto de Salud Carlos III, Ministerio de Economía y Competitividad, Spain
- FIS PI21/01590 Fondo de Investigación Sanitaria, Instituto de Salud Carlos III, Ministerio de Economía y Competitividad, Spain
- FIS PI21/01590 Fondo de Investigación Sanitaria, Instituto de Salud Carlos III, Ministerio de Economía y Competitividad, Spain
- FIS PI21/01590 Fondo de Investigación Sanitaria, Instituto de Salud Carlos III, Ministerio de Economía y Competitividad, Spain
- GRUPIN IDI/2022/000033 Regional Ministry of Science of Asturias
- GRUPIN IDI/2022/000033 Regional Ministry of Science of Asturias
- GRUPIN IDI/2022/000033 Regional Ministry of Science of Asturias
- GRUPIN IDI/2022/000033 Regional Ministry of Science of Asturias
- GRUPIN IDI/2022/000033 Regional Ministry of Science of Asturias
- GRUPIN IDI/2022/000033 Regional Ministry of Science of Asturias
- GRUPIN IDI/2022/000033 Regional Ministry of Science of Asturias
- GRUPIN IDI/2022/000033 Regional Ministry of Science of Asturias
- GRUPIN IDI/2022/000033 Regional Ministry of Science of Asturias
- GRUPIN IDI/2022/000033 Regional Ministry of Science of Asturias
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Affiliation(s)
- Xenia Vázquez
- Dairy Research Institute of Asturias (IPLA), Spanish National Research Council, (CSIC), Villaviciosa, Asturias, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), MicroHealth Group, Oviedo, Spain
| | - Pilar Lumbreras-Iglesias
- Traslational Microbiology Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
- Department of Clinical Microbiology, Hospital Universitario Central de Asturias (HUCA), Oviedo, Spain
- Department of Hematology Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Instituto de Oncología del Principado de Asturias (IUOPA), Hospital Universitario Central de Asturias (HUCA), 33011, Oviedo, Spain
| | - M Rosario Rodicio
- Traslational Microbiology Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
- Department of Functional Biology, Microbiology Area, University of Oviedo, Oviedo, Spain
| | - Javier Fernández
- Traslational Microbiology Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
- Department of Clinical Microbiology, Hospital Universitario Central de Asturias (HUCA), Oviedo, Spain
- Research & Innovation, Artificial Intelligence and Statistical Department, Pragmatech AI Solutions, Oviedo, Spain
- Centro de Investigación Biomédica en Red-Enfermedades Respiratorias, Madrid, Spain
| | - Teresa Bernal
- Department of Hematology Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Instituto de Oncología del Principado de Asturias (IUOPA), Hospital Universitario Central de Asturias (HUCA), 33011, Oviedo, Spain
| | - Ainhoa Fernández Moreno
- Department of Hematology Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Instituto de Oncología del Principado de Asturias (IUOPA), Hospital Universitario Central de Asturias (HUCA), 33011, Oviedo, Spain
| | - Paula López de Ugarriza
- Department of Hematology Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Instituto de Oncología del Principado de Asturias (IUOPA), Hospital Universitario Central de Asturias (HUCA), 33011, Oviedo, Spain
| | - Ana Fernández-Verdugo
- Traslational Microbiology Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
- Department of Clinical Microbiology, Hospital Universitario Central de Asturias (HUCA), Oviedo, Spain
| | - Abelardo Margolles
- Dairy Research Institute of Asturias (IPLA), Spanish National Research Council, (CSIC), Villaviciosa, Asturias, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), MicroHealth Group, Oviedo, Spain
| | - Carlos Sabater
- Dairy Research Institute of Asturias (IPLA), Spanish National Research Council, (CSIC), Villaviciosa, Asturias, Spain.
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), MicroHealth Group, Oviedo, Spain.
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Calvete-Torre I, Sabater C, Cantabrana B, Margolles A, Sánchez M, Ruiz L. Gut microbiota modulation and effects of a diet enriched in apple pomace on inflammation in a DSS-induced colitis mouse model. Food Funct 2024; 15:2314-2326. [PMID: 38323473 DOI: 10.1039/d3fo04277d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
Certain types of soluble dietary fibre, such as pectin and pectic oligosaccharides from different sources, have demonstrated protective effects against inflammation in DSS-induced colitis mouse models. In this work, we have evaluated the impact of a diet enriched in apple pomace (AP-diet), an agricultural by-product with a significant content of pectin and that previously demonstrated prebiotic properties in human fecal batch fermentation models, on the gut microbiota composition, intestinal damage and inflammation markers in a DSS-induced colitis model. We found that the apple pomace enriched diet (AP-diet), providing a significant amount of pectin with demonstrated prebiotic properties, was associated with a slower increase in the disease activity index, translating into better clinical symptomatology of the animals. Histological damage scoring confirmed less severe damage in those animals receiving an AP-diet before and during the DSS administration period. Some serum inflammatory markers, such as TNFα, also demonstrated lower levels in the group receiving the AP-diet, compared to the control diet. AP-diet administration is also associated with the modulation of key taxa in the colonic microbiota of animals, such as some Lachnospiraceae genera and Ruminococcus species, including commensal short chain fatty acid producers that could play a role in attenuating inflammation at the intestinal level.
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Affiliation(s)
- Inés Calvete-Torre
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias-Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Río Linares s/n, 33300, Villaviciosa, Asturias, Spain.
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Asturias, Spain
| | - Carlos Sabater
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias-Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Río Linares s/n, 33300, Villaviciosa, Asturias, Spain.
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Asturias, Spain
| | - Begoña Cantabrana
- Farmacología, Departamento de Medicina, Universidad de Oviedo, Oviedo, Spain
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Oviedo, Spain
- Pharmacology of Therapeutic Targets Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Asturias, Spain
| | - Abelardo Margolles
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias-Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Río Linares s/n, 33300, Villaviciosa, Asturias, Spain.
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Asturias, Spain
| | - Manuel Sánchez
- Farmacología, Departamento de Medicina, Universidad de Oviedo, Oviedo, Spain
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Oviedo, Spain
- Pharmacology of Therapeutic Targets Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Asturias, Spain
| | - Lorena Ruiz
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias-Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Río Linares s/n, 33300, Villaviciosa, Asturias, Spain.
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Asturias, Spain
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Xu R, Feng N, Li Q, Wang H, Li L, Feng X, Su Y, Zhu W. Pectin supplementation accelerates post-antibiotic gut microbiome reconstitution orchestrated with reduced gut redox potential. THE ISME JOURNAL 2024; 18:wrae101. [PMID: 38857378 PMCID: PMC11203915 DOI: 10.1093/ismejo/wrae101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Revised: 05/31/2024] [Accepted: 06/09/2024] [Indexed: 06/12/2024]
Abstract
Antibiotic-induced gut dysbiosis (AID) presents a big challenge to host health, and the recovery from this dysbiosis is often slow and incomplete. AID is typically characterized by elevation in redox potential, Enterobacteriaceae load, and aerobic metabolism. In our previous study, a pectin-enriched diet was demonstrated to decrease fecal redox potential and modulate the gut microbiome. Therefore, we propose that pectin supplementation may modulate gut redox potential and favor post-antibiotic gut microbiome reconstitution from dysbiosis. In the present study, rats with AIDwere used to investigate the effects of pectin supplementation on post-antibiotic gut microbiome reconstitution from dysbiosis. The results showed that pectin supplementation accelerated post-antibiotic reconstitution of gut microbiome composition and function and led to enhancement of anabolic reductive metabolism and weakening of catabolic oxidative pathways. These results were corroborated by the measurement of redox potential, findings suggesting that pectin favors post-antibiotic recovery from dysbiosis. Pectin-modulated fecal microbiota transplantation accelerated the decrease in antibiotics-elevated redox potential and Enterobacteriaceae load similarly to pectin supplementation. Moreover, both pectin supplementation and Pectin-modulated fecal microbiota transplantation enriched anaerobic members, primarily from Lachnospiraceae orchestration with enhancement of microbial reductive metabolism in post-antibiotic rats. These findings suggested that pectin supplementation accelerated post-antibiotic gut microbiome reconstitution orchestrated with reduced gut redox potential and that the effect of pectin on redox potential was mediated by remodeling of the intestinal microbiota.
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Affiliation(s)
- Rongying Xu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
| | - Ni Feng
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
| | - Qiuke Li
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
| | - Hongyu Wang
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
| | - Lian Li
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaobo Feng
- Research Institute of General Surgery, Jinling Hospital, Nanjing University School of Medicine, Nanjing 210095, China
| | - Yong Su
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
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Calvete-Torre I, Sabater C, Delgado S, Ruas-Madiedo P, Rupérez-García A, Montilla A, Javier Moreno F, Margolles A, Ruiz L. Arabinoxylan-based substrate preferences and predicted metabolic properties of Bifidobacterium longum subspecies as a basis to design differential media. Food Res Int 2023; 167:112711. [PMID: 37087214 DOI: 10.1016/j.foodres.2023.112711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 03/09/2023] [Accepted: 03/14/2023] [Indexed: 03/30/2023]
Abstract
Arabinoxylan (AX) and arabinoxylo-oligosaccharides (AXOS) derived therefrom are emergent prebiotics with promising health promoting properties, likely linked to its capacity to foster beneficial species in the human gut. Bifidobacteria appear to be one taxa that is frequently promoted following AX or AXOS consumption, and that is known to establish metabolic cross-feeding networks with other beneficial commensal species. Therefore, probiotic bifidobacteria with the capability to metabolize AX-derived prebiotics represent interesting candidates to develop novel probiotic and synbiotic combinations with AX-based prebiotics. In this work we have deepen into the metabolic capabilities of bifidobacteria related to AX and AXOS metabolization through a combination of in silico an in vitro tools. Both approaches revealed that Bifidobacterium longum and, particularly, B. longum subsp. longum, appears as the better equipped to metabolize complex AX substrates, although other related subspecies such as B. longum subsp. infantis, also hold some machinery related to AXOS metabolization. This correlates to the growth profiles exhibited by representative strains of both subspecies in AX or AXOS enriched media. Based on these results, we formulated a differential carbohydrate free medium (CFM) supplemented with a combination of AX and AXOS that enabled to recover a wide diversity of Bifidobacterium species from complex fecal samples, while allowing easy discrimination of AX metabolising strains by the appearance of a precipitation halo. This new media represent an appealing alternative to isolate novel probiotic bifidobacteria, rapidly discriminating their capacity to metabolize structurally complex AX-derived prebiotics. This can be convenient to assist formulation of novel functional foods and supplements, including bifidobacterial species with capacity to metabolize AX-derived prebiotic ingredients.
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Affiliation(s)
- Ines Calvete-Torre
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias-Consejo Superior de Investigaciones Científicas IPLA, CSIC, Paseo Río Linares s/n, 33300, Villaviciosa, Asturias, Spain; Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Asturias, Spain
| | - Carlos Sabater
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias-Consejo Superior de Investigaciones Científicas IPLA, CSIC, Paseo Río Linares s/n, 33300, Villaviciosa, Asturias, Spain; Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Asturias, Spain
| | - Susana Delgado
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias-Consejo Superior de Investigaciones Científicas IPLA, CSIC, Paseo Río Linares s/n, 33300, Villaviciosa, Asturias, Spain; Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Asturias, Spain
| | - Patricia Ruas-Madiedo
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias-Consejo Superior de Investigaciones Científicas IPLA, CSIC, Paseo Río Linares s/n, 33300, Villaviciosa, Asturias, Spain; Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Asturias, Spain
| | - Alicia Rupérez-García
- Instituto de Investigación en Ciencias de la Alimentación CIAL, (CSIC-UAM) CEI (CSIC+UAM), Madrid, Spain
| | - Antonia Montilla
- Instituto de Investigación en Ciencias de la Alimentación CIAL, (CSIC-UAM) CEI (CSIC+UAM), Madrid, Spain
| | - F Javier Moreno
- Instituto de Investigación en Ciencias de la Alimentación CIAL, (CSIC-UAM) CEI (CSIC+UAM), Madrid, Spain
| | - Abelardo Margolles
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias-Consejo Superior de Investigaciones Científicas IPLA, CSIC, Paseo Río Linares s/n, 33300, Villaviciosa, Asturias, Spain; Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Asturias, Spain.
| | - Lorena Ruiz
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias-Consejo Superior de Investigaciones Científicas IPLA, CSIC, Paseo Río Linares s/n, 33300, Villaviciosa, Asturias, Spain; Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Asturias, Spain.
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Sabater C, Iglesias-Gutiérrez E, Ruiz L, Margolles A. Next-generation sequencing of the athletic gut microbiota: a systematic review. MICROBIOME RESEARCH REPORTS 2023; 2:5. [PMID: 38045609 PMCID: PMC10688803 DOI: 10.20517/mrr.2022.16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 01/30/2023] [Accepted: 02/16/2023] [Indexed: 12/05/2023]
Abstract
Aim: There is growing evidence that physical activity modulates gut microbiota composition through complex interactions between diet and microbial species. On the other hand, next-generation sequencing techniques include shotgun metagenomics and 16S amplicon sequencing. These methodologies allow a comprehensive characterisation of microbial communities of athletes from different disciplines as well as non-professional players and sedentary adults exposed to training. This systematic review summarises recent applications of next-generation sequencing to characterise the athletic gut microbiome. Methods: A systematic review of microbiome research was performed to determine the association of microbiota composition profiles with sports performance. Results: Bibliographic analysis revealed the importance of a novel research trend aiming at deciphering the associations between individual microbial species and sports performance. In addition, literature review highlighted the role of butyrate-producing bacteria such as Anaerostipes hadrus, Clostridium bolteae, Faecalibacterium prausnitzii, Roseburia hominis and unidentified species belonging to Clostridiales, Lachnospiraceae and Subdoligranulum species in gut health and sports performance across several disciplines. Interestingly, metabolic activities of Prevotella copri and Veillonella atypica involved in branched amino acid and lactate metabolism may contribute to reducing muscular fatigue. Other microbial metabolic pathways of interest involved in carbohydrate metabolism showed increased proportions in athletes´ metagenomes. Conclusion: Future research will aim at developing personalised nutrition interventions to modulate key species associated with certain components of exercise.
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Affiliation(s)
- Carlos Sabater
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias-Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Río Linares s/n, Villaviciosa 33300, Spain
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo 33011, Spain
| | - Eduardo Iglesias-Gutiérrez
- Department of Functional Biology, Area of Physiology, Universidad de Oviedo, Avda. Julián Clavería 6, Oviedo 33006, Spain
- Traslational Interventions for Health (ITS) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo 33011, Spain
| | - Lorena Ruiz
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias-Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Río Linares s/n, Villaviciosa 33300, Spain
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo 33011, Spain
| | - Abelardo Margolles
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias-Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Río Linares s/n, Villaviciosa 33300, Spain
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo 33011, Spain
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Prebiotic potential of apple pomace and pectins from different apple varieties: Modulatory effects on key target commensal microbial populations. Food Hydrocoll 2022. [DOI: 10.1016/j.foodhyd.2022.107958] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Srinivas M, O’Sullivan O, Cotter PD, van Sinderen D, Kenny JG. The Application of Metagenomics to Study Microbial Communities and Develop Desirable Traits in Fermented Foods. Foods 2022; 11:3297. [PMCID: PMC9601669 DOI: 10.3390/foods11203297] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The microbial communities present within fermented foods are diverse and dynamic, producing a variety of metabolites responsible for the fermentation processes, imparting characteristic organoleptic qualities and health-promoting traits, and maintaining microbiological safety of fermented foods. In this context, it is crucial to study these microbial communities to characterise fermented foods and the production processes involved. High Throughput Sequencing (HTS)-based methods such as metagenomics enable microbial community studies through amplicon and shotgun sequencing approaches. As the field constantly develops, sequencing technologies are becoming more accessible, affordable and accurate with a further shift from short read to long read sequencing being observed. Metagenomics is enjoying wide-spread application in fermented food studies and in recent years is also being employed in concert with synthetic biology techniques to help tackle problems with the large amounts of waste generated in the food sector. This review presents an introduction to current sequencing technologies and the benefits of their application in fermented foods.
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Affiliation(s)
- Meghana Srinivas
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, P61 C996 Cork, Ireland
- APC Microbiome Ireland, University College Cork, T12 CY82 Cork, Ireland
- School of Microbiology, University College Cork, T12 CY82 Cork, Ireland
| | - Orla O’Sullivan
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, P61 C996 Cork, Ireland
- APC Microbiome Ireland, University College Cork, T12 CY82 Cork, Ireland
- VistaMilk SFI Research Centre, Fermoy, P61 C996 Cork, Ireland
| | - Paul D. Cotter
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, P61 C996 Cork, Ireland
- APC Microbiome Ireland, University College Cork, T12 CY82 Cork, Ireland
- VistaMilk SFI Research Centre, Fermoy, P61 C996 Cork, Ireland
| | - Douwe van Sinderen
- APC Microbiome Ireland, University College Cork, T12 CY82 Cork, Ireland
- School of Microbiology, University College Cork, T12 CY82 Cork, Ireland
| | - John G. Kenny
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, P61 C996 Cork, Ireland
- APC Microbiome Ireland, University College Cork, T12 CY82 Cork, Ireland
- VistaMilk SFI Research Centre, Fermoy, P61 C996 Cork, Ireland
- Correspondence:
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Apple Pomace Modulates the Microbiota and Increases the Propionate Ratio in an In Vitro Piglet Gastrointestinal Model. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8080408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Apple pomace (AP) contains biomolecules that induce changes in intestinal fermentation of monogastrics with positive expected health effects. The weaning of piglets can induce economic losses due to intestinal disturbances; new weaning strategies are, thus, welcome. The purpose of this study was to test the effect of AP on fermentation products by using baby-SPIME, an in vitro multi-compartment model dedicated to piglet weaning. A comparison was done on short chain fatty acid (SCFA) ratio and the microbiota induced in bioreactors between a control culture medium vs. an AP culture medium. The results of 2 preliminary runs showed that AP medium increased the molar ratio of propionate (p = 0.021) and decreased the molar ratio of butyrate (p = 0.009). Moreover, this medium increased the cumulative relative abundance of Prevotella sp. and Akkermansia sp. in bioreactors. AP could promote an ecosystem enriched with bacteria known as next-generation probiotics (NGP)—likely influencing the energy metabolism of piglets by their fermentation metabolites. AP could be used as a dietary strategy to influence bacterial changes in the intestine by stimulating the growth of bacteria identified as NGP.
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11
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Puhlmann ML, de Vos WM. Intrinsic dietary fibers and the gut microbiome: Rediscovering the benefits of the plant cell matrix for human health. Front Immunol 2022; 13:954845. [PMID: 36059540 PMCID: PMC9434118 DOI: 10.3389/fimmu.2022.954845] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 08/01/2022] [Indexed: 11/13/2022] Open
Abstract
Dietary fibers contribute to structure and storage reserves of plant foods and fundamentally impact human health, partly by involving the intestinal microbiota, notably in the colon. Considerable attention has been given to unraveling the interaction between fiber type and gut microbiota utilization, focusing mainly on single, purified fibers. Studying these fibers in isolation might give us insights into specific fiber effects, but neglects how dietary fibers are consumed daily and impact our digestive tract: as intrinsic structures that include the cell matrix and content of plant tissues. Like our ancestors we consume fibers that are entangled in a complex network of plants cell walls that further encapsulate and shield intra-cellular fibers, such as fructans and other components from immediate breakdown. Hence, the physiological behavior and consequent microbial breakdown of these intrinsic fibers differs from that of single, purified fibers, potentially entailing unexplored health effects. In this mini-review we explain the difference between intrinsic and isolated fibers and discuss their differential impact on digestion. Subsequently, we elaborate on how food processing influences intrinsic fiber structure and summarize available human intervention studies that used intrinsic fibers to assess gut microbiota modulation and related health outcomes. Finally, we explore current research gaps and consequences of the intrinsic plant tissue structure for future research. We postulate that instead of further processing our already (extensively) processed foods to create new products, we should minimize this processing and exploit the intrinsic health benefits that are associated with the original cell matrix of plant tissues.
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Affiliation(s)
- Marie-Luise Puhlmann
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
- Division of Human Nutrition and Health, Wageningen University & Research, Wageningen, Netherlands
- *Correspondence: Marie-Luise Puhlmann,
| | - Willem M. de Vos
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
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Lopes de Oliveira F, Yanka Portes Arruda T, Caldeira Morzelle M, Paula Aparecida Pereira A, Neves Casarotti S. Fruit by-products as potential prebiotics and promising functional ingredients to produce fermented milk. Food Res Int 2022; 161:111841. [DOI: 10.1016/j.foodres.2022.111841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 08/18/2022] [Accepted: 08/21/2022] [Indexed: 11/04/2022]
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Arabinoxylan and Pectin Metabolism in Crohn’s Disease Microbiota: An In Silico Study. Int J Mol Sci 2022; 23:ijms23137093. [PMID: 35806099 PMCID: PMC9266297 DOI: 10.3390/ijms23137093] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 12/03/2022] Open
Abstract
Inflammatory bowel disease is a chronic disorder including ulcerative colitis and Crohn’s disease (CD). Gut dysbiosis is often associated with CD, and metagenomics allows a better understanding of the microbial communities involved. The objective of this study was to reconstruct in silico carbohydrate metabolic capabilities from metagenome-assembled genomes (MAGs) obtained from healthy and CD individuals. This computational method was developed as a mean to aid rationally designed prebiotic interventions to rebalance CD dysbiosis, with a focus on metabolism of emergent prebiotics derived from arabinoxylan and pectin. Up to 1196 and 1577 MAGs were recovered from CD and healthy people, respectively. MAGs of Akkermansia muciniphila, Barnesiella viscericola DSM 18177 and Paraprevotella xylaniphila YIT 11841 showed a wide range of unique and specific enzymes acting on arabinoxylan and pectin. These glycosidases were also found in MAGs recovered from CD patients. Interestingly, these arabinoxylan and pectin degraders are predicted to exhibit metabolic interactions with other gut microbes reduced in CD. Thus, administration of arabinoxylan and pectin may ameliorate dysbiosis in CD by promoting species with key metabolic functions, capable of cross-feeding other beneficial species. These computational methods may be of special interest for the rational design of prebiotic ingredients targeting at CD.
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