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Kim YT, Mills DA. Exploring the gut microbiome: probiotics, prebiotics, synbiotics, and postbiotics as key players in human health and disease improvement. Food Sci Biotechnol 2024; 33:2065-2080. [PMID: 39130661 PMCID: PMC11315840 DOI: 10.1007/s10068-024-01620-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/15/2024] [Accepted: 05/23/2024] [Indexed: 08/13/2024] Open
Abstract
The human gut microbiome accompanies us from birth, and it is developed and matured by diet, lifestyle, and environmental factors. During aging, the bacterial composition evolves in reciprocal communication with the host's physiological properties. Many diseases are closely related to the gut microbiome, which means the modulation of the gut microbiome can promote the disease targeting remote organs. This review explores the intricate interaction between the gut microbiome and other organs, and their improvement from disease by prebiotics, probiotics, synbiotics, and postbiotics. Each section of the review is supported by clinical trials that substantiate the benefits of modulation the gut microbiome through dietary intervention for improving primary health outcomes across various axes with the gut. In conclusion, the review underscores the significant potential of targeting the gut microbiome for therapeutic and preventative interventions in a wide range of diseases, calling for further research to fully unlock the microbiome's capabilities in enhancing human health.
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Affiliation(s)
- You-Tae Kim
- Department of Food Science and Technology, University of California-Davis, Davis, CA USA
| | - David A. Mills
- Department of Food Science and Technology, University of California-Davis, Davis, CA USA
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2
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Fujita K, Tsunomachi H, Lixia P, Maruyama S, Miyake M, Dakeshita A, Kitahara K, Tanaka K, Ito Y, Ishiwata A, Fushinobu S. Bifidobacterial GH146 β-L-arabinofuranosidase for the removal of β1,3-L-arabinofuranosides on plant glycans. Appl Microbiol Biotechnol 2024; 108:199. [PMID: 38324037 PMCID: PMC10850190 DOI: 10.1007/s00253-024-13014-8] [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: 11/16/2023] [Revised: 12/29/2023] [Accepted: 01/14/2024] [Indexed: 02/08/2024]
Abstract
L-Arabinofuranosides with β-linkages are present in several plant molecules, such as arabinogalactan proteins (AGPs), extensin, arabinan, and rhamnogalacturonan-II. We previously characterized a β-L-arabinofuranosidase from Bifidobacterium longum subsp. longum JCM 1217, Bll1HypBA1, which was found to belong to the glycoside hydrolase (GH) family 127. This strain encodes two GH127 genes and two GH146 genes. In the present study, we characterized a GH146 β-L-arabinofuranosidase, Bll3HypBA1 (BLLJ_1848), which was found to constitute a gene cluster with AGP-degrading enzymes. This recombinant enzyme degraded AGPs and arabinan, which contain Araf-β1,3-Araf structures. In addition, the recombinant enzyme hydrolyzed oligosaccharides containing Araf-β1,3-Araf structures but not those containing Araf-β1,2-Araf and Araf-β1,5-Araf structures. The crystal structures of Bll3HypBA1 were determined at resolutions up to 1.7 Å. The monomeric structure of Bll3HypBA1 comprised a catalytic (α/α)6 barrel and two β-sandwich domains. A hairpin structure with two β-strands was observed in Bll3HypBA1, to extend from a β-sandwich domain and partially cover the active site. The active site contains a Zn2+ ion coordinated by Cys3-Glu and exhibits structural conservation of the GH127 cysteine glycosidase Bll1HypBA1. This is the first study to report on a β1,3-specific β-L-arabinofuranosidase. KEY POINTS: • β1,3-l-Arabinofuranose residues are present in arabinogalactan proteins and arabinans as a terminal sugar. • β-l-Arabinofuranosidases are widely present in intestinal bacteria. • Bll3HypBA1 is the first enzyme characterized as a β1,3-linkage-specific β-l-arabinofuranosidase.
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Affiliation(s)
- Kiyotaka Fujita
- Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima, Kagoshima, 890-0065, Japan.
- The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima, Kagoshima, 890-0065, Japan.
| | - Hanako Tsunomachi
- Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima, Kagoshima, 890-0065, Japan
| | - Pan Lixia
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo, 113-8657, Japan
- National Key Laboratory of Non-food Biomass Energy Technology, Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Academy of Sciences, Nanning, 530007, China
| | - Shun Maruyama
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo, 113-8657, Japan
| | - Masayuki Miyake
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo, 113-8657, Japan
| | - Aimi Dakeshita
- Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima, Kagoshima, 890-0065, Japan
| | - Kanefumi Kitahara
- Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima, Kagoshima, 890-0065, Japan
- The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima, Kagoshima, 890-0065, Japan
| | - Katsunori Tanaka
- RIKEN, Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Department of Chemical Science and Engineering, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-Ku, Tokyo, 152-8552, Japan
| | - Yukishige Ito
- RIKEN, Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Graduate School of Science, Osaka University, 1-1 Machikaneyama-Cho, Toyonaka, Osaka, 560-0043, Japan
| | - Akihiro Ishiwata
- RIKEN, Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Shinya Fushinobu
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo, 113-8657, Japan.
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo, 113-8657, Japan.
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Yin P, Zhang C, Du T, Yi S, Yu L, Tian F, Chen W, Zhai Q. Meta-analysis reveals different functional characteristics of human gut Bifidobacteria associated with habitual diet. Food Res Int 2023; 170:112981. [PMID: 37316017 DOI: 10.1016/j.foodres.2023.112981] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 05/03/2023] [Accepted: 05/13/2023] [Indexed: 06/16/2023]
Abstract
Dietary habits contribute to the composition and function of the gut microbiota. Different dietary structures, including vegan, vegetarian, and omnivorous diets, affect intestinal Bifidobacteria; however, the relationship between Bifidobacterial function and host metabolism in subjects with different dietary patterns is unclear. Here, we analyzed five metagenomics studies and six 16S sequencing studies, including 206 vegetarians (VG), 249 omnivores (O), and 270 vegans (V), through an unbiased theme-level meta-analysis framework and discovered that diet significantly affects the composition and functionality of intestinal Bifidobacteria. The relative abundance of Bifidobacterium pseudocatenulatum was significantly higher in V than in O and Bifidobacterium longum, Bifidobacterium adolescentis, and B. pseudocatenulatum differed significantly in carbohydrate transport and metabolism in subjects with different diet types. Diets high in fiber were associated with B. longum with increased capacity for carbohydrate catabolism and genes encoding GH29 and GH43_27 were significantly enriched in V. Bifidobacterium adolescentis and B. pseudocatenulatum, associated with O, had a higher prevalence of the genes related to carbohydrate transport and metabolism, which showed the enrichment of GH26 and GH27 families. The same Bifidobacterium species has different functions in subjects with different diet types, resulting in different physiological significance. The diversification and functionalities of Bifidobacterial species in the gut microbiome can be influenced by the host diet and this aspect should be considered when studying host-microbe associations.
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Affiliation(s)
- Pingping Yin
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Chengcheng Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Ting Du
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Shanrong Yi
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Leilei Yu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Fengwei Tian
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wei Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China.
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Peterson CT, Pérez-Santiago J, Iablokov SN, Rodionov DA, Peterson SN. Alteration of Community Metabolism by Prebiotics and Medicinal Herbs. Microorganisms 2023; 11:868. [PMID: 37110291 PMCID: PMC10141170 DOI: 10.3390/microorganisms11040868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/15/2023] [Accepted: 03/22/2023] [Indexed: 03/31/2023] Open
Abstract
Several studies have examined the impact of prebiotics on gut microbiota and associated changes in host physiology. Here, we used the in vitro cultivation of human fecal samples stimulated with a series of chemically related prebiotics and medicinal herbs commonly used in Ayurvedic medicine, followed by 16S rRNA sequencing. We applied a genome-wide metabolic reconstruction of enumerated communities to compare and contrast the structural and functional impact of prebiotics and medicinal herbs. In doings so, we examined the relationships between discrete variations in sugar composition and sugar linkages associated with each prebiotic to drive changes in microbiota composition. The restructuring of microbial communities with glycan substrates alters community metabolism and its potential impact on host physiology. We analyzed sugar fermentation pathways and products predicted to be formed and prebiotic-induced changes in vitamin and amino acid biosynthesis and degradation. These results highlight the utility of combining a genome-wide metabolic reconstruction methodology with 16S rRNA sequence-based community profiles to provide insights pertaining to community metabolism. This process also provides a rational means for prioritizing in vivo analysis of prebiotics and medicinal herbs in vivo to test hypotheses related to therapeutic potential in specific diseases of interest.
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Affiliation(s)
- Christine Tara Peterson
- Center of Excellence for Research and Training in Integrative Health, Department of Family Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Josué Pérez-Santiago
- Division of Cancer Biology, University of Puerto Rico Comprehensive Cancer Center, San Juan, PR 00927, USA
- School of Dental Medicine, Office of Research, University of Puerto Rico Medical Sciences Campus, San Juan, PR 00921, USA
| | | | - Dmitry A. Rodionov
- Bioinformatics and Structural Biology Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Scott N. Peterson
- Tumor Microenvironment and Cancer Immunology Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
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Bautil A, Bedford MR, Buyse J, Courtin CM. Reduced-particle size wheat bran and endoxylanase supplementation in broiler feed affect arabinoxylan hydrolysis and fermentation with broiler age differently. ANIMAL NUTRITION (ZHONGGUO XU MU SHOU YI XUE HUI) 2022; 12:308-320. [PMID: 36733780 PMCID: PMC9874015 DOI: 10.1016/j.aninu.2022.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 09/12/2022] [Accepted: 11/11/2022] [Indexed: 11/27/2022]
Abstract
Since the caecal microbiota of young broilers are not yet able to ferment the dietary fibre (DF) fraction of the feed to a large extent, increasing the accessibility of DF substrates along the gastrointestinal tract is crucial to benefit from the health stimulating metabolic end-products (e.g. butyric acid) generated upon microbial DF fermentation. Therefore, the present study aimed to evaluate the potential of reduced-particle size wheat bran (RPS-WB) and endoxylanases as feed additives to stimulate arabinoxylan (AX) hydrolysis and fermentation along the hindgut of young broilers. To this end, RPS-WB and endoxylanase supplementation were evaluated in a 2 × 2 factorial design using a total of 256 male 1-d-old chicks (Ross 308). Broilers were assigned to 4 dietary treatments: a basal wheat-based diet with (1) no feed additives (control, CTRL), (2) an endoxylanase (XYL; Econase XT 25 at 0.10 g/kg diet), (3) 1% wheat bran with an average reduced particle size of 297 μm (RPS-WB) and (4) an endoxylanase and 1% RPS-WB (RPS-WB + XYL). Each dietary treatment was replicated 8 times and on d 10 and 28, respectively, 24 and 16 broilers per treatment group were euthanised to analyse AX degradation, short-chain fatty acid production and digesta viscosity in the ileum and caecum. Broilers receiving XYL in their diet showed increased AX solubilisation and fermentation at both d 10 and 28 compared to the CTRL group (P < 0.05). Adding RPS-WB to the diet stimulated wheat AX utilisation by the primary AX degraders in the caecum at 10 d of age compared to the CTRL group, as observed by the high AX digestibility coefficient for the RPS-WB supplemented group at this young age (P < 0.05). At 28 d, RPS-WB supplementation lowered body-weight gains but increased butyric acid concentrations compared to the XYL and CTRL group (P < 0.05). Although no synergistic effect for RPS-WB + XYL broilers was observed for AX hydrolysis and fermentation, these findings suggest that both additives can raise a dual benefit to the broiler as a butyrogenic effect and improved AX fermentation along the ileum and caecum were observed throughout the broiler's life.
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Affiliation(s)
- An Bautil
- Laboratory of Food Chemistry and Biochemistry, Department of Microbial and Molecular Systems (MS), KU Leuven, Leuven, 3001, Belgium,Corresponding author.
| | | | - Johan Buyse
- Laboratory of Livestock Physiology, Department of Biosystems, KU Leuven, Leuven, 3001, Belgium
| | - Christophe M. Courtin
- Laboratory of Food Chemistry and Biochemistry, Department of Microbial and Molecular Systems (MS), KU Leuven, Leuven, 3001, Belgium
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Wang H, Huang X, Tan H, Chen X, Chen C, Nie S. Interaction between dietary fiber and bifidobacteria in promoting intestinal health. Food Chem 2022; 393:133407. [PMID: 35696956 DOI: 10.1016/j.foodchem.2022.133407] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 06/01/2022] [Accepted: 06/03/2022] [Indexed: 01/10/2023]
Abstract
Bifidobacteria are considered as probiotics due to their role in promoting intestinal health, including regulating intestinal flora, controlling glycolipid metabolism, anti-colitis effects. Dietary fiber is considered as prebiotic favoring gut health. It also can be used as carbon source to support the growth and colonization of probiotics like bifidobacteria. However, because of genetic diversity, different bifidobacterial species differ in their ability to utilize dietary fiber. Meanwhile, dietary fiber with different structural properties has different effects on the bifidobacteria proliferation. The interaction between dietary fiber and bifidobacteria will consequently lead to a synergistic or antagonistic function in promoting intestinal health, therefore affecting the application of combined use of dietary fiber and bifidobacteria. In this case, we summarize the biological function of bifidobacteria, and their interaction with different dietary fiber in promoting gut health, and finally provide several strategies about their combined use.
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Affiliation(s)
- Hui Wang
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang 330047, China
| | - Xiaojun Huang
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang 330047, China.
| | - Huizi Tan
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang 330047, China
| | - Xiaomin Chen
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang 330047, China
| | - Chunhua Chen
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang 330047, China
| | - Shaoping Nie
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang 330047, China
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7
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Mary PR, Monica P, Kapoor M. Insights into β-manno-oligosaccharide uptake and metabolism in Bifidobacterium adolescentis DSMZ 20083 from whole-genome microarray analysis. Microbiol Res 2022; 266:127215. [DOI: 10.1016/j.micres.2022.127215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 09/14/2022] [Accepted: 09/26/2022] [Indexed: 10/14/2022]
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Qiu Z, Qiao Y, Zhang B, Sun-Waterhouse D, Zheng Z. Bioactive polysaccharides and oligosaccharides from garlic (Allium sativum L.): Production, physicochemical and biological properties, and structure-function relationships. Compr Rev Food Sci Food Saf 2022; 21:3033-3095. [PMID: 35765769 DOI: 10.1111/1541-4337.12972] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 02/08/2022] [Accepted: 04/11/2022] [Indexed: 02/06/2023]
Abstract
Garlic is a common food, and many of its biological functions are attributed to its components including functional carbohydrates. Garlic polysaccharides and oligosaccharides as main components are understudied but have future value due to the growing demand for bioactive polysaccharides/oligosaccharides from natural sources. Garlic polysaccharides have molecular weights of 1 × 103 to 2 × 106 Da, containing small amounts of pectins and fructooligosaccharides and large amounts of inulin-type fructans ((2→1)-linked β-d-Fruf backbones alone or with attached (2→6)-linked β-d-Fruf branched chains). This article provides a detailed review of research progress and identifies knowledge gaps in extraction, production, composition, molecular characteristics, structural features, physicochemical properties, bioactivities, and structure-function relationships of garlic polysaccharides/oligosaccharides. Whether the extraction processes, synthesis approaches, and modification methods established for other non-garlic polysaccharides are also effective for garlic polysaccharides/oligosaccharides (to preserve their desired molecular structures and bioactivities) requires verification. The metabolic processes of ingested garlic polysaccharides/oligosaccharides (as food ingredients/dietary supplements), their modes of action in healthy humans or populations with chronic conditions, and molecular/chain organization-bioactivity relationships remain unclear. Future research directions related to garlic polysaccharides/oligosaccharides are discussed.
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Affiliation(s)
- Zhichang Qiu
- Key Laboratory of Food Processing Technology and Quality Control of Shandong Higher Education Institutes, College of Food Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Yiteng Qiao
- Key Laboratory of Food Processing Technology and Quality Control of Shandong Higher Education Institutes, College of Food Science and Engineering, Shandong Agricultural University, Tai'an, China.,School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Bin Zhang
- Key Laboratory of Food Processing Technology and Quality Control of Shandong Higher Education Institutes, College of Food Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Dongxiao Sun-Waterhouse
- Key Laboratory of Food Processing Technology and Quality Control of Shandong Higher Education Institutes, College of Food Science and Engineering, Shandong Agricultural University, Tai'an, China.,School of Chemical Sciences, The University of Auckland, Auckland, New Zealand
| | - Zhenjia Zheng
- Key Laboratory of Food Processing Technology and Quality Control of Shandong Higher Education Institutes, College of Food Science and Engineering, Shandong Agricultural University, Tai'an, China
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Akkerman R, Logtenberg MJ, Beukema M, de Haan BJ, Faas MM, Zoetendal EG, Schols HA, de Vos P. Combining galacto-oligosaccharides and 2'-fucosyllactose alters their fermentation kinetics by infant fecal microbiota and influences AhR-receptor dependent cytokine responses in immature dendritic cells. Food Funct 2022; 13:6510-6521. [PMID: 35642586 PMCID: PMC9208271 DOI: 10.1039/d2fo00550f] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Galacto-oligosaccharides (GOS) and 2′-fucosyllactose (2′-FL) are non-digestible carbohydrates (NDCs) that are often added to infant formula to replace the functionalities of human milk oligosaccharides (HMOs). It is not known if combining GOS and 2′-FL will affect their fermentation kinetics and subsequent immune-modulatory effects such as AhR-receptor stimulation. Here, we used an in vitro set-up for the fermentation of 2′-FL and GOS, either individually or combined, by fecal microbiota of 8-week-old infants. We found that GOS was fermented two times faster by the infant fecal microbiota when combined with 2′-FL, while the combination of GOS and 2′-FL did not result in a complete degradation of 2′-FL. Fermentation of both GOS and 2′-FL increased the relative abundance of Bifidobacterium, which coincided with the production of acetate and lactate. Digesta of the fermentations influenced dendritic cell cytokine secretion differently under normal conditions and in the presence of the AhR-receptor blocker CH223191. We show that, combining GOS and 2′-FL accelerates GOS fermentation by the infant fecal microbiota of 8-week-old infants. In addition, we show that the fermentation digesta of GOS and 2′-FL, either fermented individually or combined, can attenuate DC cytokine responses in a similar and in an AhR-receptor dependent way. Galacto-oligosaccharides (GOS) and 2′-fucosyllactose (2′-FL) are non-digestible carbohydrates (NDCs) that are often added to infant formula to replace the functionalities of human milk oligosaccharides (HMOs).![]()
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Affiliation(s)
- Renate Akkerman
- Immunoendocrinology, Division of Medical Biology, Department of Pathology and Medical Biology, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands.
| | - Madelon J Logtenberg
- Laboratory of Food Chemistry, Wageningen University & Research, Wageningen, The Netherlands
| | - Martin Beukema
- Immunoendocrinology, Division of Medical Biology, Department of Pathology and Medical Biology, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands.
| | - Bart J de Haan
- Immunoendocrinology, Division of Medical Biology, Department of Pathology and Medical Biology, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands.
| | - Marijke M Faas
- Immunoendocrinology, Division of Medical Biology, Department of Pathology and Medical Biology, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands.
| | - Erwin G Zoetendal
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Henk A Schols
- Laboratory of Food Chemistry, Wageningen University & Research, Wageningen, The Netherlands
| | - Paul de Vos
- Immunoendocrinology, Division of Medical Biology, Department of Pathology and Medical Biology, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands.
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The Comparative Analysis of Genomic Diversity and Genes Involved in Carbohydrate Metabolism of Eighty-Eight Bifidobacterium pseudocatenulatum Isolates from Different Niches of China. Nutrients 2022; 14:nu14112347. [PMID: 35684146 PMCID: PMC9183100 DOI: 10.3390/nu14112347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/03/2022] [Accepted: 06/01/2022] [Indexed: 02/06/2023] Open
Abstract
Eighty-eight Bifidobacterium pseudocatenulatum strains, which were isolated from human, chicken and cow fecal samples from different niches of China, were compared genomically in this study to evaluate their diversity. It was found that B. pseudocatenulatum displayed a closed pan-genome, including abundant glycoside hydrolase families of the carbohydrate active enzyme (CAZy). A total of 30 kinds of glycoside hydrolases (GHs), 14 kinds of glycosyl transferases (GTs), 13 kinds of carbohydrate-binding modules (CBMs), 6 kinds of carbohydrate-esterases (CEs), and 2 kinds of auxiliary activities (AAs) gene families were identified across the genomes of the 88 B. pseudocatenulatum strains. Specifically, this showed that significant differences were also present in the number of 10 carbohydrate-active enzyme gene families (GT51, GH13_32, GH26, GH42, GH121, GH3, AA3, CBM46, CE2, and CE6) among the strains derived from the hosts of different age groups, particularly between strains from infants and those from other human age groups. Twelve different individuals of B. pseudocatenulatum from four main clusters were selected for further study to reveal the genetic diversity of carbohydrate metabolism-related genes within the same phylogenetics. The animal experiment showed that 3 weeks of oral administration and 1 week after cessation of administration of these strains did not markedly alter the serum routine inflammatory indicators in mice. Furthermore, the administration of these strains did not significantly cause adverse changes in the gut microbiota, as indicated by the α- and β-diversity indexes, relative to the control group (normal diet). Beyond that, FAHBZ9L5 significantly increased the abundance of B. pseudocatenulatum after 3 weeks and significantly increased the abundance of acetic acid and butyric acid in the host’s intestinal tract 3 and 4 weeks after the first administration, respectively, compared with the control group. Corresponding to this, comparative genomic analyses of 12 B. pseudocatenulatum suggest that FAHBZ9L5-specific genes were rich in ABC transporters and carbohydrate esterase. Combining the results of comparative genomics analyses and animal experiment, it is suggested that the strains containing certain gene clusters contribute to another competitive growth advantage of B. pseudocatenulatum, which facilitates its intestinal carbohydrate metabolism in a host.
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11
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Zhang B, Zhong Y, Dong D, Zheng Z, Hu J. Gut microbial utilization of xylan and its implication in gut homeostasis and metabolic response. Carbohydr Polym 2022; 286:119271. [DOI: 10.1016/j.carbpol.2022.119271] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/16/2022] [Accepted: 02/16/2022] [Indexed: 12/16/2022]
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12
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Effect of Different Polymerized Xylooligosaccharides on the Metabolic Pathway in Bifidobacterium adolescentis. J FOOD QUALITY 2022. [DOI: 10.1155/2022/4412324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Metabolic pathway analysis of Bifidobacterium adolescent (B. adolescentis) grown on either xylobiose and xylotriose (X2/X3) or xylopentaose (X5) and identifying key regulatory-related genes and metabolites from RNA-seq and UHPLC system was performed. Compared with X5, X2/X3 highly promoted the growth of B. adolescentis. Also, the transcriptome analysis showed that a total of 268 differentially expressed genes (DEGs) of B. adolescentis cultured with X2/X3 and X5 were screened, including 163 upregulated and 105 downregulated genes (X2/X3 vs. X5), which mainly were ABC transporters. Furthermore, the qRT-PCR results of 16 DGEs validated the accuracy of the RNA-seq data. Meanwhile, metabolomics analysis showed that 192 differential metabolites noted on MS2 included 127 upregulated and 65 downregulated metabolites; mainly, metabolites were amino acids and organic acids. The abundance difference of specific genes and metabolites highlighted regulatory mechanisms involved in utilizing different polymerized xylooligosaccharides by B. adolescentis.
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Shehata AA, Yalçın S, Latorre JD, Basiouni S, Attia YA, Abd El-Wahab A, Visscher C, El-Seedi HR, Huber C, Hafez HM, Eisenreich W, Tellez-Isaias G. Probiotics, Prebiotics, and Phytogenic Substances for Optimizing Gut Health in Poultry. Microorganisms 2022; 10:microorganisms10020395. [PMID: 35208851 PMCID: PMC8877156 DOI: 10.3390/microorganisms10020395] [Citation(s) in RCA: 68] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 02/01/2022] [Accepted: 02/05/2022] [Indexed: 02/06/2023] Open
Abstract
The gut microbiota has been designated as a hidden metabolic ‘organ’ because of its enormous impact on host metabolism, physiology, nutrition, and immune function. The connection between the intestinal microbiota and their respective host animals is dynamic and, in general, mutually beneficial. This complicated interaction is seen as a determinant of health and disease; thus, intestinal dysbiosis is linked with several metabolic diseases. Therefore, tractable strategies targeting the regulation of intestinal microbiota can control several diseases that are closely related to inflammatory and metabolic disorders. As a result, animal health and performance are improved. One of these strategies is related to dietary supplementation with prebiotics, probiotics, and phytogenic substances. These supplements exert their effects indirectly through manipulation of gut microbiota quality and improvement in intestinal epithelial barrier. Several phytogenic substances, such as berberine, resveratrol, curcumin, carvacrol, thymol, isoflavones and hydrolyzed fibers, have been identified as potential supplements that may also act as welcome means to reduce the usage of antibiotics in feedstock, including poultry farming, through manipulation of the gut microbiome. In addition, these compounds may improve the integrity of tight junctions by controlling tight junction-related proteins and inflammatory signaling pathways in the host animals. In this review, we discuss the role of probiotics, prebiotics, and phytogenic substances in optimizing gut function in poultry.
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Affiliation(s)
- Awad A. Shehata
- Research and Development Section, PerNaturam GmbH, 56290 Gödenroth, Germany
- Avian and Rabbit Diseases Department, Faculty of Veterinary Medicine, University of Sadat City, Sadat City 32897, Egypt
- Correspondence: (A.A.S.); (G.T.-I.)
| | - Sakine Yalçın
- Department of Animal Nutrition and Nutritional Diseases, Faculty of Veterinary Medicine, Ankara University (AU), 06110 Ankara, Turkey;
| | - Juan D. Latorre
- Department of Poultry Science, University of Arkansas, Fayetteville, AR 72701, USA;
| | - Shereen Basiouni
- Clinical Pathology Department, Faculty of Veterinary Medicine, Benha University, Benha 13518, Egypt;
| | - Youssef A. Attia
- Department of Agriculture, Faculty of Environmental Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
| | - Amr Abd El-Wahab
- Institute for Animal Nutrition, University of Veterinary Medicine Hannover, 30173 Hannover, Germany; (A.A.E.-W.); (C.V.)
- Department of Nutrition and Nutritional Deficiency Diseases, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt
| | - Christian Visscher
- Institute for Animal Nutrition, University of Veterinary Medicine Hannover, 30173 Hannover, Germany; (A.A.E.-W.); (C.V.)
| | - Hesham R. El-Seedi
- Pharmacognosy Group, Biomedical Centre, Department of Pharmaceutical Biosciences, Uppsala University, SE 75124 Uppsala, Sweden;
- International Research Center for Food Nutrition and Safety, Jiangsu University, Zhenjiang 212013, China
- International Joint Research Laboratory of Intelligent Agriculture and Agri-Products Processing, Jiangsu Education Department, Jiangsu University, Zhenjiang 212013, China
| | - Claudia Huber
- Bavarian NMR Center, Structural Membrane Biochemistry, Department of Chemistry, Technische Universität München, Lichtenbegstr. 4, 85748 Garching, Germany; (C.H.); (W.E.)
| | - Hafez M. Hafez
- Institute of Poultry Diseases, Faculty of Veterinary Medicine, Free University of Berlin, 14163 Berlin, Germany;
| | - Wolfgang Eisenreich
- Bavarian NMR Center, Structural Membrane Biochemistry, Department of Chemistry, Technische Universität München, Lichtenbegstr. 4, 85748 Garching, Germany; (C.H.); (W.E.)
| | - Guillermo Tellez-Isaias
- Department of Poultry Science, University of Arkansas, Fayetteville, AR 72701, USA;
- Correspondence: (A.A.S.); (G.T.-I.)
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Hamed NF, Alamri SA, Hamdi NH. Overview of the Updates in Nutrient Profiles, Types, Indications and Side Effects of Infant Formula. ARCHIVES OF PHARMACY PRACTICE 2022. [DOI: 10.51847/confqadrfw] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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15
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Logtenberg MJ, Akkerman R, Hobé RG, Donners KMH, Van Leeuwen SS, Hermes GDA, de Haan BJ, Faas MM, Buwalda PL, Zoetendal EG, de Vos P, Schols HA. Structure-Specific Fermentation of Galacto-Oligosaccharides, Isomalto-Oligosaccharides and Isomalto/Malto-Polysaccharides by Infant Fecal Microbiota and Impact on Dendritic Cell Cytokine Responses. Mol Nutr Food Res 2021; 65:e2001077. [PMID: 34060703 PMCID: PMC8459273 DOI: 10.1002/mnfr.202001077] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 04/18/2021] [Indexed: 12/23/2022]
Abstract
SCOPE Next to galacto-oligosaccharides (GOS), starch-derived isomalto-oligosaccharide preparation (IMO) and isomalto/malto-polysaccharides (IMMP) could potentially be used as prebiotics in infant formulas. However, it remains largely unknown how the specific molecular structures of these non-digestible carbohydrates (NDCs) impact fermentability and immune responses in infants. METHODS AND RESULTS In vitro fermentation of GOS, IMO and IMMP using infant fecal inoculum of 2- and 8-week-old infants shows that only GOS and IMO are fermented by infant fecal microbiota. The degradation of GOS and IMO coincides with an increase in Bifidobacterium and production of acetate and lactate, which is more pronounced with GOS. Individual isomers with an (1↔1)-linkage or di-substituted reducing terminal glucose residue are more resistant to fermentation. GOS, IMO, and IMMP fermentation digesta attenuates cytokine profiles in immature dendritic cells (DCs), but the extent is dependent on the infants age and NDC structure. CONCLUSION The IMO preparation, containing reducing and non-reducing isomers, shows similar fermentation patterns as GOS in fecal microbiota of 2-week-old infants. Knowledge obtained on the substrate specificities of infant fecal microbiota and the subsequent regulatory effects of GOS, IMO and IMMP on DC responses might contribute to the design of tailored NDC mixtures for infants of different age groups.
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Affiliation(s)
- Madelon J. Logtenberg
- Laboratory of Food ChemistryWageningen University & ResearchBornse Weilanden 9Wageningen6708 WGThe Netherlands
| | - Renate Akkerman
- ImmunoendocrinologyDivision of Medical BiologyDepartment of Pathology and Medical BiologyUniversity of Groningen and University Medical Centre GroningenGroningenThe Netherlands
| | - Rosan G. Hobé
- Laboratory of Food ChemistryWageningen University & ResearchBornse Weilanden 9Wageningen6708 WGThe Netherlands
| | - Kristel M. H. Donners
- Laboratory of Food ChemistryWageningen University & ResearchBornse Weilanden 9Wageningen6708 WGThe Netherlands
| | - Sander S. Van Leeuwen
- Cluster Human Nutrition & HealthDepartment of Laboratory MedicineUniversity Medical Center GroningenGroningenThe Netherlands
| | - Gerben D. A. Hermes
- Laboratory of MicrobiologyWageningen University & ResearchWageningenThe Netherlands
| | - Bart J. de Haan
- ImmunoendocrinologyDivision of Medical BiologyDepartment of Pathology and Medical BiologyUniversity of Groningen and University Medical Centre GroningenGroningenThe Netherlands
| | - Marijke M. Faas
- ImmunoendocrinologyDivision of Medical BiologyDepartment of Pathology and Medical BiologyUniversity of Groningen and University Medical Centre GroningenGroningenThe Netherlands
| | - Piet L. Buwalda
- Biobased Chemistry and TechnologyWageningen University & ResearchWageningenThe Netherlands
- Avebe Innovation CenterGroningenThe Netherlands
| | - Erwin G. Zoetendal
- Laboratory of MicrobiologyWageningen University & ResearchWageningenThe Netherlands
| | - Paul de Vos
- ImmunoendocrinologyDivision of Medical BiologyDepartment of Pathology and Medical BiologyUniversity of Groningen and University Medical Centre GroningenGroningenThe Netherlands
| | - Henk A. Schols
- Laboratory of Food ChemistryWageningen University & ResearchBornse Weilanden 9Wageningen6708 WGThe Netherlands
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Bujna E, Styevko G, Laskawy P, Rezessy-Szabo J, Nguyen VD, Tran AMT, Ta Phuong L, Farkas C, Gupta VK, Nguyen QD. Synthesis of oligosaccharides with prebiotic potential by crude enzyme preparation from Bifidobacterium. Food Chem 2021; 367:130696. [PMID: 34364145 DOI: 10.1016/j.foodchem.2021.130696] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 07/21/2021] [Accepted: 07/22/2021] [Indexed: 01/13/2023]
Abstract
Oligosaccharides especially prebiotics take high attention in the development of foods because of their physiological properties in human health. They are generally synthetized enzymatically via transferases or hydrolases from mold or bacteria. The fact is that such oligosaccharides synthetized by probiotic bacteria, should be utilized by these microorganisms. This study focused on the production of oligosaccharides with prebiotic potential by crude enzyme preparation from bifidobacteria. Both monosubstrates and bisubstrates systems together with TLC and HPLC techniques, were applied. The crude enzyme preparation has different hydrolase activities such as α-glucosidase (2U/mL), β-glucosidase (0.3 U/mL), α-galactosidase (1.2 U/mL), β-galactosidase (0.4 U/mL), β-fructosidase (11.5 U/mL). Additionally, it also has transglycosylation activities on lactose, lactulose, maltose and sucrose substrates. Two or three types of oligosaccharides were detected. The glycosyltransferase activity peaked at 45 °C, pH 6.6 and 30 g/100 mL substrate concentration. Significant high amount of oligosaccharides were formed in the case of lactose:sucrose combination than others. Both glucooligosaccharides and galactooligosaccharides are detected in the reaction mixtures of bisubstrate. When the lactose is present, the galactosyltransferation is predominated. One-one new types of oligosaccharides were detected in the reaction mixture of bioconversion. Among newly synthetized oligosaccharides, the fraction namely OS4 was utilized by probiotic bifidobacteria only. In conclusion, new types of galacto- and glucooligosaccharides with high prebiotic potentials were synthetized by the crude enzyme from probiotic Bifidobacterium strains.
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Affiliation(s)
- Erika Bujna
- Hungarian University of Agriculture and Life Sciences, Institute of Food Science and Technology, Department of Bioengineering and Alcoholic Drink Technology H-1118 Budapest, Ménesi út 45. Hungary
| | - Gabriella Styevko
- Hungarian University of Agriculture and Life Sciences, Institute of Food Science and Technology, Department of Bioengineering and Alcoholic Drink Technology H-1118 Budapest, Ménesi út 45. Hungary
| | - Peter Laskawy
- Hungarian University of Agriculture and Life Sciences, Institute of Food Science and Technology, Department of Bioengineering and Alcoholic Drink Technology H-1118 Budapest, Ménesi út 45. Hungary
| | - Judit Rezessy-Szabo
- Hungarian University of Agriculture and Life Sciences, Institute of Food Science and Technology, Department of Bioengineering and Alcoholic Drink Technology H-1118 Budapest, Ménesi út 45. Hungary
| | - Vuong D Nguyen
- Hungarian University of Agriculture and Life Sciences, Institute of Food Science and Technology, Department of Bioengineering and Alcoholic Drink Technology H-1118 Budapest, Ménesi út 45. Hungary; Institute of Biotechnology and Food Technology, Industrial University of Ho Chi Minh City, No. 12 Nguyen Van Bao, Ward 4, Go Vap District, Ho Chi Minh City, Viet Nam
| | - Anh M T Tran
- Hungarian University of Agriculture and Life Sciences, Institute of Food Science and Technology, Department of Bioengineering and Alcoholic Drink Technology H-1118 Budapest, Ménesi út 45. Hungary; Institute of Biotechnology and Food Technology, Industrial University of Ho Chi Minh City, No. 12 Nguyen Van Bao, Ward 4, Go Vap District, Ho Chi Minh City, Viet Nam
| | - Linh Ta Phuong
- Hungarian University of Agriculture and Life Sciences, Institute of Food Science and Technology, Department of Bioengineering and Alcoholic Drink Technology H-1118 Budapest, Ménesi út 45. Hungary
| | - Csilla Farkas
- Hungarian University of Agriculture and Life Sciences, Institute of Food Science and Technology, Department of Bioengineering and Alcoholic Drink Technology H-1118 Budapest, Ménesi út 45. Hungary
| | - Vijai Kumar Gupta
- Hungarian University of Agriculture and Life Sciences, Institute of Food Science and Technology, Department of Bioengineering and Alcoholic Drink Technology H-1118 Budapest, Ménesi út 45. Hungary; Center for Safe and Improved Food, Scotland's Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh EH9 3JG, UK; Biorefining and Advanced Materials Research Center, Scotland's Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh EH9 3JG, UK.
| | - Quang D Nguyen
- Hungarian University of Agriculture and Life Sciences, Institute of Food Science and Technology, Department of Bioengineering and Alcoholic Drink Technology H-1118 Budapest, Ménesi út 45. Hungary.
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Bivolarski V, Iliev I, Ivanova I, Nikolova M, Salim A, Mihaylova G, Vasileva T. Characterization of structure/prebiotic potential correlation of glucans and oligosaccharides synthetized by glucansucrases from fructophilic lactic acid bacteria from honey bee Apis mellifera. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1911683] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Affiliation(s)
- Veselin Bivolarski
- Department of Biochemistry and Microbiology, Faculty of Biology, Plovdiv University “Paisii Hilendarski”, Plovdiv, Bulgaria
| | - Ilia Iliev
- Department of Biochemistry and Microbiology, Faculty of Biology, Plovdiv University “Paisii Hilendarski”, Plovdiv, Bulgaria
| | - Iskra Ivanova
- Department of General and Industrial Microbiology, Faculty of Biology, Sofia University “St. Kliment Ohridski”, Sofia, Bulgaria
| | - Mariana Nikolova
- Department of Biochemistry and Microbiology, Faculty of Biology, Plovdiv University “Paisii Hilendarski”, Plovdiv, Bulgaria
| | - Ayshe Salim
- Department of Biochemistry, Molecular Medicine and Nutrigenomics, Faculty of Pharmacy, Medical University of Varna, Varna, Bulgaria
| | - Galya Mihaylova
- Department of Biochemistry, Molecular Medicine and Nutrigenomics, Faculty of Pharmacy, Medical University of Varna, Varna, Bulgaria
| | - Tonka Vasileva
- Department of Biochemistry and Microbiology, Faculty of Biology, Plovdiv University “Paisii Hilendarski”, Plovdiv, Bulgaria
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Bioactive Compounds in Infant Formula and Their Effects on Infant Nutrition and Health: A Systematic Literature Review. INTERNATIONAL JOURNAL OF FOOD SCIENCE 2021; 2021:8850080. [PMID: 34095293 PMCID: PMC8140835 DOI: 10.1155/2021/8850080] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 04/22/2021] [Indexed: 12/12/2022]
Abstract
Infant formulas are an alternative to replace or supplement human milk when breastfeeding is not possible. The knowledge of human milk's bioactive compounds and their beneficial effects has attracted the interest of researchers in the field of infant nutrition, as well as researchers of technology and food sciences that seek to improve the nutritional characteristics of infant formulas. Several scientific studies evaluate the optimization of infant formula composition. The bioactive compound inclusion has been used to upgrade the quality and nutrition of infant formulas. In this context, the purpose of this systematic literature review is to assess the scientific evidence of bioactive compounds present in infant formulas (α-lactalbumin, lactoferrin, taurine, milk fat globule membrane, folates, polyamines, long-chain polyunsaturated fatty acids, prebiotics, and probiotics) and their effects on infant nutrition and health. Through previously determined criteria, studies published in the last fifteen years from five different databases were included to identify the advances in the optimization of infant formula composition. Over the last few years, there has been optimization of the infant formula composition, not only to increase the similarities in their content of macro and micronutrients but also to include novel bioactive ingredients with potential health benefits for infants. Although the infant food industry has advanced in the last years, there is no consensus on whether novel bioactive ingredients added to infant formulas have the same functional effects as the compounds found in human milk. Thus, further studies about the impact of bioactive compounds in infant nutrition are fundamental to infant health.
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Kelly SM, Munoz-Munoz J, van Sinderen D. Plant Glycan Metabolism by Bifidobacteria. Front Microbiol 2021; 12:609418. [PMID: 33613480 PMCID: PMC7889515 DOI: 10.3389/fmicb.2021.609418] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 01/04/2021] [Indexed: 12/18/2022] Open
Abstract
Members of the genus Bifidobacterium, of which the majority have been isolated as gut commensals, are Gram-positive, non-motile, saccharolytic, non-sporulating, anaerobic bacteria. Many bifidobacterial strains are considered probiotic and therefore are thought to bestow health benefits upon their host. Bifidobacteria are highly abundant among the gut microbiota of healthy, full term, breast-fed infants, yet the relative average abundance of bifidobacteria tends to decrease as the human host ages. Because of the inverse correlation between bifidobacterial abundance/prevalence and health, there has been an increasing interest in maintaining, increasing or restoring bifidobacterial populations in the infant, adult and elderly gut. In order to colonize and persist in the gastrointestinal environment, bifidobacteria must be able to metabolise complex dietary and/or host-derived carbohydrates, and be resistant to various environmental challenges of the gut. This is not only important for the autochthonous bifidobacterial species colonising the gut, but also for allochthonous bifidobacteria provided as probiotic supplements in functional foods. For example, Bifidobacterium longum subsp. longum is a taxon associated with the metabolism of plant-derived poly/oligosaccharides in the adult diet, being capable of metabolising hemicellulose and various pectin-associated glycans. Many of these plant glycans are believed to stimulate the metabolism and growth of specific bifidobacterial species and are for this reason classified as prebiotics. In this review, bifidobacterial carbohydrate metabolism, with a focus on plant poly-/oligosaccharide degradation and uptake, as well as its associated regulation, will be discussed.
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Affiliation(s)
- Sandra M Kelly
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Jose Munoz-Munoz
- Microbial Enzymology Group, Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Douwe van Sinderen
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
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Song AX, Li LQ, Yin JY, Chiou JC, Wu JY. Mechanistic insights into the structure-dependant and strain-specific utilization of wheat arabinoxylan by Bifidobacterium longum. Carbohydr Polym 2020; 249:116886. [PMID: 32933699 DOI: 10.1016/j.carbpol.2020.116886] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 08/01/2020] [Accepted: 08/01/2020] [Indexed: 12/11/2022]
Abstract
Arabinoxylan (AX), an important dietary fiber from cereal grains, is mainly metabolised in the large intestine by gut bacteria, especially bifidobacteria. This study investigated the uptake and metabolism of wheat AX by a Bifidobacterium longum strain that could grow well with AX as the sole carbon source. The bacterial growth rate showed a significant correlation to the molecular weight (MW) of AX and its acid hydrolysates. Assessment of the key AX degrading enzymes suggested that the uptake and consumption of AX involved extracellular cleavage of xylan backbone and intracellular degradation of both the backbone and the arabinose substitution. The preference for native or partially hydrolysed AX with single substitutions and a sufficiently high MW suggested the structure-dependant uptake by the bacterial cells. Genetic analysis of B. longum showed the lack of β-xylosidase, suggesting the existence of unknown enzymes or dual/multiple-specific enzymes for hydrolysis of the non-reducing end of xylan backbone.
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Affiliation(s)
- Ang-Xin Song
- Food Safety and Technology Research Center, Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Long-Qing Li
- Food Safety and Technology Research Center, Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Jun-Yi Yin
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi, 330047, China
| | - Jia-Chi Chiou
- Food Safety and Technology Research Center, Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong.
| | - Jian-Yong Wu
- Food Safety and Technology Research Center, Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong.
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Bai X, Shen L, Gao X, Yu Z, Sakandar HA, Kwok LY, Sun Z. Differential structures and enterotype-like clusters of Bifidobacterium responses to probiotic fermented milk consumption across subjects using a Bifidobacterium-target procedure. Food Res Int 2020; 140:109839. [PMID: 33648165 DOI: 10.1016/j.foodres.2020.109839] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/13/2020] [Accepted: 10/18/2020] [Indexed: 02/07/2023]
Abstract
The health-promoting attributes of bifidobacteria have piqued interest of researchers worldwide. However, scant published studies are available pertinent to bifidobacteria in microbiota/metagenomics datasets due to its intrinsic low abundance and limitations of detection methods. In this work, we designed a procedure to optimize the detection of the bifidobacterial population in complex biological samples with single-molecule real-time sequencing (SMRT) technology, including one primer pair designated as Bif-6 and a Bifidobacterium-specific database. The optimized procedure detected 14 bifidobacterial species/subspecies in ten human stool samples (2024 sequences per sample) and eight breast milk samples (3473 sequences per sample), respectively. Furthermore, by using the optimized procedure of SMRT, we investigated the effect of a 4-week-intervention of probiotic fermented milk (PFM; 200 g/day) on the gut bifidobacteria population of adults. The results showed that consuming PFM changed the structure and enterotype-like clusters of Bifidobacterium. After the consumption of PFM, the level of gut Bifidobacterium animalis increased significantly, replacing several originally dominating taxa in some subjects, including B. catenulatum, B. breve, and B. bifidum. On the other hand, B. adolescentis was, unaffectedly, the representative species in subjects having an original enterotype-like cluster of B. adolescentis. In conclusion, our work designed a procedure for detecting the bifidobacterial population in complex samples. By applying the currently designed procedure, we found that the PFM intervention changed the bifidobacterial enterotype-like cluster of some subjects, and such change was dependent on the basal bifidobacterial population.
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Affiliation(s)
- Xiaoye Bai
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Lingling Shen
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Xu Gao
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Zhongjie Yu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Hafiz Arbab Sakandar
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Lai-Yu Kwok
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Zhihong Sun
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Huhhot 010018, China.
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Jung DH, Seo DH, Kim YJ, Chung WH, Nam YD, Park CS. The presence of resistant starch-degrading amylases in Bifidobacterium adolescentis of the human gut. Int J Biol Macromol 2020; 161:389-397. [DOI: 10.1016/j.ijbiomac.2020.05.235] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/25/2020] [Accepted: 05/26/2020] [Indexed: 01/11/2023]
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Kobayashi M, Kumagai Y, Yamamoto Y, Yasui H, Kishimura H. Identification of a Key Enzyme for the Hydrolysis of β-(1→3)-Xylosyl Linkage in Red Alga Dulse Xylooligosaccharide from Bifidobacterium Adolescentis. Mar Drugs 2020; 18:E174. [PMID: 32245121 PMCID: PMC7142710 DOI: 10.3390/md18030174] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/10/2020] [Accepted: 03/18/2020] [Indexed: 01/15/2023] Open
Abstract
Red alga dulse possesses a unique xylan, which is composed of a linear β-(1→3)/β-(1→4)-xylosyl linkage. We previously prepared characteristic xylooligosaccharide (DX3, (β-(1→3)-xylosyl-xylobiose)) from dulse. In this study, we evaluated the prebiotic effect of DX3 on enteric bacterium. Although DX3 was utilized by Bacteroides sp. and Bifidobacterium adolescentis, Bacteroides Ksp. grew slowly as compared with β-(1→4)-xylotriose (X3) but B. adolescentis grew similar to X3. Therefore, we aimed to find the key DX3 hydrolysis enzymes in B. adolescentis. From bioinformatics analysis, two enzymes from the glycoside hydrolase family 43 (BAD0423: subfamily 12 and BAD0428: subfamily 11) were selected and expressed in Escherichia coli. BAD0423 hydrolyzed β-(1→3)-xylosyl linkage in DX3 with the specific activity of 2988 mU/mg producing xylose (X1) and xylobiose (X2), and showed low activity on X2 and X3. BAD0428 showed high activity on X2 and X3 producing X1, and the activity of BAD0428 on DX3 was 1298 mU/mg producing X1. Cooperative hydrolysis of DX3 was found in the combination of BAD0423 and BAD0428 producing X1 as the main product. From enzymatic character, hydrolysis of X3 was completed by one enzyme BAD0428, whereas hydrolysis of DX3 needed more than two enzymes.
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Affiliation(s)
- Manami Kobayashi
- Chair of Marine Chemical Resource Development, Graduate School of Fisheries Sciences, Hokkaido University, Hakodate 041-8611, Hokkaido, Japan (Y.Y.)
| | - Yuya Kumagai
- Laboratory of Marine Chemical Resource Development, Faculty of Fisheries Sciences, Hokkaido University, Hakodate 041-8611, Hokkaido, Japan;
| | - Yohei Yamamoto
- Chair of Marine Chemical Resource Development, Graduate School of Fisheries Sciences, Hokkaido University, Hakodate 041-8611, Hokkaido, Japan (Y.Y.)
| | - Hajime Yasui
- Laboratory of Humans and the Ocean, Faculty of Fisheries Sciences, Hokkaido University, Hakodate 041-8611, Hokkaido, Japan;
| | - Hideki Kishimura
- Laboratory of Marine Chemical Resource Development, Faculty of Fisheries Sciences, Hokkaido University, Hakodate 041-8611, Hokkaido, Japan;
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24
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Rational use of prebiotics for gut microbiota alterations: Specific bacterial phylotypes and related mechanisms. J Funct Foods 2020. [DOI: 10.1016/j.jff.2020.103838] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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25
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In vitro digestion and fermentation of released exopolysaccharides (r-EPS) from Lactobacillus delbrueckii ssp. bulgaricus SRFM-1. Carbohydr Polym 2020; 230:115593. [DOI: 10.1016/j.carbpol.2019.115593] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 11/08/2019] [Accepted: 11/08/2019] [Indexed: 12/18/2022]
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26
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Deloule V, Boisset C, Hannani D, Suau A, Le Gouellec A, Chroboczek J, Botté C, Yamaryo-Botté Y, Chirat C, Toussaint B. Prebiotic role of softwood hemicellulose in healthy mice model. J Funct Foods 2020. [DOI: 10.1016/j.jff.2019.103688] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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27
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Lanigan N, Kelly E, Arzamasov AA, Stanton C, Rodionov DA, van Sinderen D. Transcriptional control of central carbon metabolic flux in Bifidobacteria by two functionally similar, yet distinct LacI-type regulators. Sci Rep 2019; 9:17851. [PMID: 31780796 PMCID: PMC6882875 DOI: 10.1038/s41598-019-54229-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 11/06/2019] [Indexed: 12/21/2022] Open
Abstract
Bifidobacteria resident in the gastrointestinal tract (GIT) are subject to constantly changing environmental conditions, which require rapid adjustments in gene expression. Here, we show that two predicted LacI-type transcription factors (TFs), designated AraQ and MalR1, are involved in regulating the central, carbohydrate-associated metabolic pathway (the so-called phosphoketolase pathway or bifid shunt) of the gut commensal Bifidobacterium breve UCC2003. These TFs appear to not only control transcription of genes involved in the bifid shunt and each other, but also seem to commonly and directly affect transcription of other TF-encoding genes, as well as genes related to uptake and metabolism of various carbohydrates. This complex and interactive network of AraQ/MalR1-mediated gene regulation provides previously unknown insights into the governance of carbon metabolism in bifidobacteria.
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Affiliation(s)
- Noreen Lanigan
- School of Microbiology & APC Microbiome Ireland, University College Cork, Ireland University College Cork, Cork, Ireland
| | - Emer Kelly
- School of Microbiology & APC Microbiome Ireland, University College Cork, Ireland University College Cork, Cork, Ireland
| | - Aleksandr A Arzamasov
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, United States.,A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | | | - Dmitry A Rodionov
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, United States.,A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Douwe van Sinderen
- School of Microbiology & APC Microbiome Ireland, University College Cork, Ireland University College Cork, Cork, Ireland.
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28
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Oh NS, Kim K, Oh S, Kim Y. Enhanced Production of Galactooligosaccharides Enriched Skim Milk and Applied to Potentially Synbiotic Fermented Milk with Lactobacillus rhamnosus 4B15. Food Sci Anim Resour 2019; 39:725-741. [PMID: 31728443 PMCID: PMC6837896 DOI: 10.5851/kosfa.2019.e55] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 07/15/2019] [Accepted: 07/18/2019] [Indexed: 12/14/2022] Open
Abstract
In the current study, we first investigated a method for directly transforming
lactose into galacto-oligosaccharides (GOS) for manufacturing low-lactose and
GOS-enriched skim milk (GSM) and then evaluated its prebiotic potential by
inoculating five strains of Bifidobacterium spp. In addition,
fermented GSM (FGSM) was prepared using a potentially probiotic
Lactobacillus strain and its fermentation characteristics
and antioxidant capacities were determined. We found that GOS in GSM were
metabolized by all five Bifidobacterium strains after
incubation and promoted their growth. The levels of antioxidant activities
including radical scavenging activities and 3-hydroxy-3-methylglutaryl-CoA
reductase inhibition rate in GSM were significantly increased by fermentation
with the probiotic Lactobacillus strain. Moreover, thirty-nine
featured peptides in FGSM was detected. In particular, six peptides derived from
β-casein, two peptides originated from αs1-casein and
κ-casein were newly identified, respectively. Our findings indicate that
GSM can potentially be used as a prebiotic substrate and FGSM can potentially
prevent oxidative stress during the production of synbiotic fermented milk in
the food industry.
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Affiliation(s)
- Nam Su Oh
- Department of Food and Biotechnology, Korea University, Sejong 30019, Korea
| | - Kyeongmu Kim
- R&D Center, Seoul Dairy Cooperative, Ansan, Kyunggi 15407, Korea.,Department of Food Bioscience and Technology, Korea University, Seoul 02841, Korea
| | - Sangnam Oh
- Department of Functional Food and Biotechnology, Jeonju University, Jeonju 55069, Korea
| | - Younghoon Kim
- Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Science, Seoul National University, Seoul 08826, Korea
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29
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Genes Involved in Galactooligosaccharide Metabolism in Lactobacillus reuteri and Their Ecological Role in the Gastrointestinal Tract. Appl Environ Microbiol 2019; 85:AEM.01788-19. [PMID: 31519661 DOI: 10.1128/aem.01788-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 09/03/2019] [Indexed: 01/09/2023] Open
Abstract
Strains of Lactobacillus reuteri are commonly used as probiotics due to their demonstrated therapeutic properties. Many strains of L. reuteri also utilize the prebiotic galactooligosaccharide (GOS), providing a basis for formulating synergistic synbiotics that could enhance growth or persistence of this organism in vivo In this study, in-frame deletion mutants were constructed to characterize the molecular basis of GOS utilization in L. reuteri ATCC PTA-6475. Results suggested that GOS transport relies on a permease encoded by lacS, while a second unidentified protein may function as a galactoside transporter. Two β-galactosidases, encoded by lacA and lacLM, sequentially degrade GOS oligosaccharides and GOS disaccharides, respectively. Inactivation of lacL and lacM resulted in impaired growth in the presence of GOS and lactose. In vitro competition experiments between the wild-type and ΔlacS ΔlacM strains revealed that the GOS-utilizing genes conferred a selective advantage in media with GOS but not glucose. GOS also provided an advantage to the wild-type strain in experiments in gnotobiotic mice but only on a purified, no sucrose diet. Differences in cell numbers between GOS-fed mice and mice that did not receive GOS were small, suggesting that carbohydrates other than GOS were sufficient to support growth. On a complex diet, the ΔlacS ΔlacM strain was outcompeted by the wild-type strain in gnotobiotic mice, suggesting that lacL and lacM are involved in the utilization of alternative dietary carbohydrates. Indeed, the growth of the mutants was impaired in raffinose and stachyose, which are common in plants, demonstrating that α-galactosides may constitute alternate substrates of the GOS pathway.IMPORTANCE This study shows that lac genes in Lactobacillus reuteri encode hydrolases and transporters that are necessary for the metabolism of GOS, as well as α-galactoside substrates. Coculture experiments with the wild-type strain and a gos mutant clearly demonstrated that GOS utilization confers a growth advantage in medium containing GOS as the sole carbohydrate source. However, the wild-type strain also outcompeted the mutant in germfree mice, suggesting that GOS genes in L. reuteri also provide a basis for utilization of other carbohydrates, including α-galactosides, ordinarily present in the diets of humans and other animals. Collectively, our work provides information on the metabolism of L. reuteri in its natural niche in the gut and may provide a basis for the development of synbiotic strategies.
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30
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Extraction and Characterization of Inulin-Type Fructans from Artichoke Wastes and Their Effect on the Growth of Intestinal Bacteria Associated with Health. BIOMED RESEARCH INTERNATIONAL 2019; 2019:1083952. [PMID: 31662964 PMCID: PMC6778948 DOI: 10.1155/2019/1083952] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 07/19/2019] [Accepted: 08/06/2019] [Indexed: 02/08/2023]
Abstract
Globe artichoke is an intriguing source of indigestible sugar polymers such as inulin-type fructans. In this study, the effect of ultrasound in combination with ethanol precipitation to enhance the extraction of long chain fructans from artichoke wastes has been evaluated. The inulin-type fructans content both from bracts and stems was measured using an enzymatic fructanase-based assay, while its average degree of polymerization (DP) was determined by HPLC-RID analysis. Results show that this method provides artichoke extracts with an inulin-type fructans content of 70% with an average DP between 32 and 42 both in bracts and in stems. The prebiotic effect of long chain inulins from artichoke extract wastes was demonstrated by its ability to support the growth of five Lactobacillus and four Bifidobacterium species, previously characterized as probiotics. Besides, we considered the possibility to industrialize the process developing a simpler method for the production of inulin-type fructans from the artichoke wastes so that the artichoke inulin preparation could be suitable for its use in synbiotic formulations in combination with different probiotics for further studies including in vivo trials.
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31
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Kok CR, Gomez Quintero DF, Niyirora C, Rose D, Li A, Hutkins R. An In Vitro Enrichment Strategy for Formulating Synergistic Synbiotics. Appl Environ Microbiol 2019; 85:e01073-19. [PMID: 31201276 PMCID: PMC6677857 DOI: 10.1128/aem.01073-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 06/06/2019] [Indexed: 12/23/2022] Open
Abstract
Research on the role of diet on gut and systemic health has led to considerable interest toward identifying novel therapeutic modulators of the gut microbiome, including the use of prebiotics and probiotics. However, various host responses have often been reported among many clinical trials. This is in part due to competitive exclusion as a result of the absence of ecological niches as well as host-mediated constraints via colonization resistance. In this research, we developed a novel in vitro enrichment (IVE) method for isolating autochthonous strains that can function as synergistic synbiotics and overcome these constraints. The method relied on stepwise in vitro fecal fermentations to enrich for and isolate Bifidobacterium strains that ferment the prebiotic xylooligosaccharide (XOS). We subsequently isolated Bifidobacterium longum subsp. longum CR15 and then tested its establishment in 20 unique fecal samples with or without XOS. The strain was established in up to 18 samples but only in the presence of XOS. Our findings revealed that the IVE method is suitable for isolating potential synergistic probiotic strains that possess the genetic and biochemical ability to ferment specific prebiotic substrates. The IVE method can be used as an initial high-throughput screen for probiotic selection and isolation prior to further characterization and in vivo tests.IMPORTANCE This study describes an in vitro enrichment method to formulate synergistic synbiotics that have potential for establishing autochthonous strains across multiple individuals. The rationale for this approach-that the chance of survival of a bacterial strain is improved by providing it with its required resources-is based on classic ecological theory. From these experiments, a human-derived strain, Bifidobacterium longum subsp. longum CR15, was identified as a xylooligosaccharide (XOS) fermenter in fecal environments and displayed synergistic effects in vitro The high rate of strain establishment observed in this study provides a basis for using synergistic synbiotics to overcome the responder/nonresponder phenomenon that occurs frequently in clinical trials with probiotic and prebiotic interventions. In addition, this approach can be applied in other protocols that require enrichment of specific bacterial populations prior to strain isolation.
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Affiliation(s)
- Car Reen Kok
- Department of Food Science and Technology, Nebraska Food for Health Center, Lincoln, Nebraska, USA
| | | | - Clement Niyirora
- Department of Food Science and Technology, Nebraska Food for Health Center, Lincoln, Nebraska, USA
| | - Devin Rose
- Department of Food Science and Technology, Nebraska Food for Health Center, Lincoln, Nebraska, USA
| | - Amanda Li
- Department of Food Science and Technology, Nebraska Food for Health Center, Lincoln, Nebraska, USA
| | - Robert Hutkins
- Department of Food Science and Technology, Nebraska Food for Health Center, Lincoln, Nebraska, USA
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32
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Zhuang H, Cheng L, Wang Y, Zhang YK, Zhao MF, Liang GD, Zhang MC, Li YG, Zhao JB, Gao YN, Zhou YJ, Liu SL. Dysbiosis of the Gut Microbiome in Lung Cancer. Front Cell Infect Microbiol 2019; 9:112. [PMID: 31065547 PMCID: PMC6489541 DOI: 10.3389/fcimb.2019.00112] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 04/01/2019] [Indexed: 12/21/2022] Open
Abstract
Lung cancer (LC) is one of the most serious malignant tumors, which has the fastest growing morbidity and mortality worldwide. A role of the lung microbiota in LC pathogenesis has been analyzed, but a comparable role of the gut microbiota has not yet been investigated. In this study, the gut microbiota of 30 LC patients and 30 healthy controls were examined via next-generation sequencing of 16S rRNA and analyzed for diversity and biomarkers. We found that there was no decrease in significant microbial diversity (alpha diversity) in LC patients compared to controls (P observed = 0.1422), while the composition (beta diversity) differed significantly between patients and controls (phylum [stress = 0.153], class [stress = 0.16], order [stress = 0.146], family [stress = 0.153]). Controls had a higher abundance of the bacterial phylum Actinobacteria and genus Bifidobacterium, while patients with LC showed elevated levels of Enterococcus. These bacteria were found as possible biomarkers for LC. A decline of normal function of the gut microbiome in LC patients was also observed. These results provide the basic guidance for a systematic, multilayered assessment of the role of the gut microbiome in LC, which has a promising potential for early prevention and targeted intervention.
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Affiliation(s)
- He Zhuang
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China.,HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Liang Cheng
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China.,College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yao Wang
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China.,HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Yu-Kun Zhang
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China.,HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China.,Department of Colorectal Cancer, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Man-Fei Zhao
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China.,HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China.,Department of Epidemiology, Public Health School, Harbin Medical University, Harbin, China
| | - Gong-Da Liang
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China.,HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China.,Department of Epidemiology, Public Health School, Harbin Medical University, Harbin, China
| | - Meng-Chun Zhang
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China.,HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Yong-Guo Li
- Department of Infectious Diseases, The First Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Jing-Bo Zhao
- Department of Epidemiology, Public Health School, Harbin Medical University, Harbin, China
| | - Yi-Na Gao
- Department of Respiration, The Third Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yu-Jie Zhou
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China.,HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Shu-Lin Liu
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China.,HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China.,Department of Epidemiology, Public Health School, Harbin Medical University, Harbin, China.,Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
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33
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De Paepe K, Verspreet J, Rezaei MN, Hidalgo Martinez S, Meysman F, Van de Walle D, Dewettinck K, Raes J, Courtin C, Van de Wiele T. Isolation of wheat bran-colonizing and metabolizing species from the human fecal microbiota. PeerJ 2019; 7:e6293. [PMID: 30701133 PMCID: PMC6348960 DOI: 10.7717/peerj.6293] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 12/17/2018] [Indexed: 01/03/2023] Open
Abstract
Undigestible, insoluble food particles, such as wheat bran, are important dietary constituents that serve as a fermentation substrate for the human gut microbiota. The first step in wheat bran fermentation involves the poorly studied solubilization of fibers from the complex insoluble wheat bran structure. Attachment of bacteria has been suggested to promote the efficient hydrolysis of insoluble substrates, but the mechanisms and drivers of this microbial attachment and colonization, as well as subsequent fermentation remain to be elucidated. We have previously shown that an individually dependent subset of gut bacteria is able to colonize the wheat bran residue. Here, we isolated these bran-attached microorganisms, which can then be used to gain mechanistic insights in future pure culture experiments. Four healthy fecal donors were screened to account for inter-individual differences in gut microbiota composition. A combination of a direct plating and enrichment method resulted in the isolation of a phylogenetically diverse set of species, belonging to the Bacteroidetes, Firmicutes, Proteobacteria and Actinobacteria phyla. A comparison with 16S rRNA gene sequences that were found enriched on wheat bran particles in previous studies, however, showed that the isolates do not yet cover the entire diversity of wheat-bran colonizing species, comprising among others a broad range of Prevotella, Bacteroides and Clostridium cluster XIVa species. We, therefore, suggest several modifications to the experiment set-up to further expand the array of isolated species.
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Affiliation(s)
- Kim De Paepe
- Faculty of Bioscience Engineering, Department of Biotechnology, Center for Microbial Ecology and Technology (CMET), Universiteit Gent, Gent, Belgium
| | - Joran Verspreet
- Faculty of Bioscience Engineering, Leuven Food Science and Nutrition Research Centre (LFoRCe), Laboratory of Food Chemistry and Biochemistry, KU Leuven, Heverlee, Belgium
- Current affiliation: Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Mohammad Naser Rezaei
- Faculty of Bioscience Engineering, Leuven Food Science and Nutrition Research Centre (LFoRCe), Laboratory of Food Chemistry and Biochemistry, KU Leuven, Heverlee, Belgium
| | - Silvia Hidalgo Martinez
- Faculty of Sciences, Department of Biology, Ecosystem Management Research Group (ECOBE), Universiteit Antwerpen, Antwerpen, Belgium
| | - Filip Meysman
- Faculty of Sciences, Department of Biology, Ecosystem Management Research Group (ECOBE), Universiteit Antwerpen, Antwerpen, Belgium
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Davy Van de Walle
- Faculty of Bioscience Engineering, Department of Food Technology, Safety and Health, Laboratory of Food Technology and Engineering (FTE), Universiteit Gent, Gent, Belgium
| | - Koen Dewettinck
- Faculty of Bioscience Engineering, Department of Food Technology, Safety and Health, Laboratory of Food Technology and Engineering (FTE), Universiteit Gent, Gent, Belgium
| | - Jeroen Raes
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Christophe Courtin
- Faculty of Bioscience Engineering, Leuven Food Science and Nutrition Research Centre (LFoRCe), Laboratory of Food Chemistry and Biochemistry, KU Leuven, Heverlee, Belgium
| | - Tom Van de Wiele
- Faculty of Bioscience Engineering, Department of Biotechnology, Center for Microbial Ecology and Technology (CMET), Universiteit Gent, Gent, Belgium
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34
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Characterization of GH2 and GH42 β-galactosidases derived from bifidobacterial infant isolates. AMB Express 2019; 9:9. [PMID: 30661116 PMCID: PMC6339635 DOI: 10.1186/s13568-019-0735-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Accepted: 01/11/2019] [Indexed: 12/22/2022] Open
Abstract
Bifidobacteria are among the first and most abundant bacterial colonizers of the gastrointestinal tract of (breast-fed) healthy infants. Their success of colonising the infant gut is believed to be, at least partly, due to their ability to metabolize available carbon sources by means of secreted or intracellular glycosyl hydrolases (GHs). Among these, β-galactosidases are particularly relevant as they allow bifidobacteria to grow on β-galactosyl-linked saccharidic substrates, which are present in copious amounts in the milk-based diet of their infant host (e.g. lactose and human milk oligosaccharides). In the present study we employed an in silico analysis to identify GH family 2 and 42 β-galactosidases encoded by typical infant-associated bifidobacteria. Comparative genome analysis followed by characterisation of selected β-galactosidases revealed how these GH2 and GH42 members are distributed among these infant-associated bifidobacteria, while their hydrolytic activity towards growth substrates commonly available in the infant gut were also assessed.
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35
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Degradative enzymes for type II arabinogalactan side chains in Bifidobacterium longum subsp. longum. Appl Microbiol Biotechnol 2018; 103:1299-1310. [PMID: 30564851 DOI: 10.1007/s00253-018-9566-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 12/03/2018] [Accepted: 12/05/2018] [Indexed: 10/27/2022]
Abstract
Type II arabinogalactan (AG) is a soluble prebiotic fiber stimulating the proliferation of bifidobacteria in the human gut. Larch AG, which is comprised of type II AG, is known to be utilized as an energy source for Bifidobacterium longum subsp. longum (B. longum). We have previously characterized GH43_24 exo-β-1,3-galactanase (Bl1,3Gal) for the degradation of type II AG main chains in B. longum JCM1217. In this study, we characterized GH30_5 exo-β-1,6-galactobiohydrolase (Bl1,6Gal) and GH43_22 α-L-arabinofuranosidase (BlArafA), which are degradative enzymes for type II AG side chains in cooperation with exo-β-1,3-galactanase. The recombinant exo-β-1,6-galactobiohydrolase specifically released β-1,6-galactobiose (β-1,6-Gal2) from the nonreducing terminal of β-1,6-galactooligosaccharides, and the recombinant α-L-arabinofuranosidase released arabinofuranose (Araf) from α-1,3-Araf-substituted β-1,6-galactooligosaccharides. β-1,6-Gal2 was additively released from larch AG by the combined use of type II AG degradative enzymes, including Bl1,3Gal, Bl1,6Gal, and BlArafA. The gene cluster encoding the type II AG degradative enzymes is conserved in all B. longum strains, but not in other bifidobacterial species. The degradative enzymes for type II AG side chains are thought to be important for the acquisition of type II AG in B. longum.
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36
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Kaprasob R, Kerdchoechuen O, Laohakunjit N, Somboonpanyakul P. B vitamins and prebiotic fructooligosaccharides of cashew apple fermented with probiotic strains Lactobacillus spp., Leuconostoc mesenteroides and Bifidobacterium longum. Process Biochem 2018. [DOI: 10.1016/j.procbio.2018.04.009] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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37
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Adamberg K, Adamberg S, Ernits K, Larionova A, Voor T, Jaagura M, Visnapuu T, Alamäe T. Composition and metabolism of fecal microbiota from normal and overweight children are differentially affected by melibiose, raffinose and raffinose-derived fructans. Anaerobe 2018; 52:100-110. [PMID: 29935270 DOI: 10.1016/j.anaerobe.2018.06.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Revised: 06/12/2018] [Accepted: 06/18/2018] [Indexed: 12/28/2022]
Abstract
The aim of the study was to investigate the metabolism of non-digestible oligo- and polysaccharides by fecal microbiota, using isothermal microcalorimetry. The five tested substrates were raffinose, melibiose, a mixture of oligo- and polysaccharides produced from raffinose by levansucrase, levan synthesized from raffinose, and levan from timothy grass. Two inocula were comprised of pooled fecal samples from overweight or normal-weight children, from healthy adult volunteers and a pure culture of Bacteroides thetaiotaomicron as a reference bacterium for colon microbiota. The growth was analyzed based on the heat evolution curves, and the production of organic acids and gases. Taxonomic profiles of the microbiota were assessed by 16S rDNA sequencing. Raffinose and melibiose promoted the growth of bifidobacteria in all fecal pools. Several pool-specific substrate-related responses to raffinose and melibiose were revealed. Lactate-producing bacteria (Streptococcus and Enterococcus) became enriched in the pool of overweight children resulting in lactic acid as the major fermentation product on short saccharides. Acetic and butyric acids were prevalent at fermentation in the normal-weight pool coinciding with the enrichment of Catenibacterium. In the adult pool, the specific promotion of Bacteroides and Lachnospiraceae by levans was disclosed. In the fecal pool of normal-weight children, levans stimulated the growth of Senegalimassilia and Lachnoclostridium and this particular pool also showed the highest maximum heat production rate at levan fermentation. Levans and raffinose-derived oligosaccharides, but not raffinose and melibiose were completely fermented by a pure culture of Bacteroides thetaiotaomicron. The main conclusion from the study is that fecal microbiota of normal and overweight children have different compositions and they respond in specific manners to non-digestible oligo- and polysaccharides: raffinose, melibiose, raffinose-derived oligosaccharides and levans. The potential of the tested saccharides to support a healthy balance of colon microbiota requires further studies.
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Affiliation(s)
- Kaarel Adamberg
- Department of Chemistry and Biotechnology, Tallinn University of Technology, 19086, Tallinn, Estonia; Center of Food and Fermentation Technologies, 12618, Tallinn, Estonia.
| | - Signe Adamberg
- Department of Chemistry and Biotechnology, Tallinn University of Technology, 19086, Tallinn, Estonia.
| | - Karin Ernits
- Department of Genetics, Institute of Molecular and Cell Biology, University of Tartu, 51010, Tartu, Estonia.
| | - Anneli Larionova
- Department of Pediatrics, Institute of Clinical Medicine, University of Tartu, 51014, Tartu, Estonia.
| | - Tiia Voor
- Department of Pediatrics, Institute of Clinical Medicine, University of Tartu, 51014, Tartu, Estonia.
| | - Madis Jaagura
- Center of Food and Fermentation Technologies, 12618, Tallinn, Estonia.
| | - Triinu Visnapuu
- Department of Genetics, Institute of Molecular and Cell Biology, University of Tartu, 51010, Tartu, Estonia.
| | - Tiina Alamäe
- Department of Genetics, Institute of Molecular and Cell Biology, University of Tartu, 51010, Tartu, Estonia.
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Liu Y, Espinosa CD, Abelilla JJ, Casas GA, Lagos LV, Lee SA, Kwon WB, Mathai JK, Navarro DM, Jaworski NW, Stein HH. Non-antibiotic feed additives in diets for pigs: A review. ANIMAL NUTRITION (ZHONGGUO XU MU SHOU YI XUE HUI) 2018; 4:113-125. [PMID: 30140751 PMCID: PMC6103469 DOI: 10.1016/j.aninu.2018.01.007] [Citation(s) in RCA: 165] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 12/14/2017] [Accepted: 01/17/2018] [Indexed: 01/08/2023]
Abstract
A number of feed additives are marketed to assist in boosting the pigs' immune system, regulate gut microbiota, and reduce negative impacts of weaning and other environmental challenges. The most commonly used feed additives include acidifiers, zinc and copper, prebiotics, direct-fed microbials, yeast products, nucleotides, and plant extracts. Inclusion of pharmacological levels of zinc and copper, certain acidifiers, and several plant extracts have been reported to result in improved pig performance or improved immune function of pigs. It is also possible that use of prebiotics, direct-fed microbials, yeast, and nucleotides may have positive impacts on pig performance, but results have been less consistent and there is a need for more research in this area.
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Affiliation(s)
- Yanhong Liu
- Department of Animal Science, University of California, Davis, CA 95817, USA
| | | | | | - Gloria A. Casas
- Department of Animal Sciences, University of Illinois, Urbana, IL 61801, USA
- Department of Animal Production, College of Animal and Veterinary Sciences, University of Colombia, Bogota 111321, Colombia
| | - L. Vanessa Lagos
- Department of Animal Sciences, University of Illinois, Urbana, IL 61801, USA
| | - Su A. Lee
- Department of Animal Sciences, University of Illinois, Urbana, IL 61801, USA
| | - Woong B. Kwon
- Department of Animal Sciences, University of Illinois, Urbana, IL 61801, USA
| | - John K. Mathai
- Department of Animal Sciences, University of Illinois, Urbana, IL 61801, USA
| | | | | | - Hans H. Stein
- Department of Animal Sciences, University of Illinois, Urbana, IL 61801, USA
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Arzamasov AA, van Sinderen D, Rodionov DA. Comparative Genomics Reveals the Regulatory Complexity of Bifidobacterial Arabinose and Arabino-Oligosaccharide Utilization. Front Microbiol 2018; 9:776. [PMID: 29740413 PMCID: PMC5928203 DOI: 10.3389/fmicb.2018.00776] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 04/05/2018] [Indexed: 11/13/2022] Open
Abstract
Members of the genus Bifidobacterium are common inhabitants of the human gastrointestinal tract. Previously it was shown that arabino-oligosaccharides (AOS) might act as prebiotics and stimulate the bifidobacterial growth in the gut. However, despite the rapid accumulation of genomic data, the precise mechanisms by which these sugars are utilized and associated transcription control still remain unclear. In the current study, we used a comparative genomic approach to reconstruct arabinose and AOS utilization pathways in over 40 bacterial species belonging to the Bifidobacteriaceae family. The results indicate that the gene repertoire involved in the catabolism of these sugars is highly diverse, and even phylogenetically close species may differ in their utilization capabilities. Using bioinformatics analysis we identified potential DNA-binding motifs and reconstructed putative regulons for the arabinose and AOS utilization genes in the Bifidobacteriaceae genomes. Six LacI-family transcriptional factors (named AbfR, AauR, AauU1, AauU2, BauR1 and BauR2) and a TetR-family regulator (XsaR) presumably act as local repressors for AOS utilization genes encoding various α- or β-L-arabinofuranosidases and predicted AOS transporters. The ROK-family regulator AraU and the LacI-family regulator AraQ control adjacent operons encoding putative arabinose transporters and catabolic enzymes, respectively. However, the AraQ regulator is universally present in all Bifidobacterium species including those lacking the arabinose catabolic genes araBDA, suggesting its control of other genes. Comparative genomic analyses of prospective AraQ-binding sites allowed the reconstruction of AraQ regulons and a proposed binary repression/activation mechanism. The conserved core of reconstructed AraQ regulons in bifidobacteria includes araBDA, as well as genes from the central glycolytic and fermentation pathways (pyk, eno, gap, tkt, tal, galM, ldh). The current study expands the range of genes involved in bifidobacterial arabinose/AOS utilization and demonstrates considerable variations in associated metabolic pathways and regulons. Detailed comparative and phylogenetic analyses allowed us to hypothesize how the identified reconstructed regulons evolved in bifidobacteria. Our findings may help to improve carbohydrate catabolic phenotype prediction and metabolic modeling, while it may also facilitate rational development of novel prebiotics.
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Affiliation(s)
- Aleksandr A Arzamasov
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, University College Cork, Cork, Ireland
| | - Dmitry A Rodionov
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia.,Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
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Lynch KM, Zannini E, Coffey A, Arendt EK. Lactic Acid Bacteria Exopolysaccharides in Foods and Beverages: Isolation, Properties, Characterization, and Health Benefits. Annu Rev Food Sci Technol 2018; 9:155-176. [DOI: 10.1146/annurev-food-030117-012537] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Kieran M. Lynch
- School of Food and Nutritional Sciences, University College Cork, Cork, Ireland
| | - Emanuele Zannini
- School of Food and Nutritional Sciences, University College Cork, Cork, Ireland
| | - Aidan Coffey
- Department of Biological Sciences, Cork Institute of Technology, Bishopstown, Cork, Ireland
| | - Elke K. Arendt
- School of Food and Nutritional Sciences, University College Cork, Cork, Ireland
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In vitro and in silico characterisation of Lactobacillus paraplantarum D2-1, a starter culture for soymilk fermentation. Int J Food Sci Nutr 2018; 69:857-869. [PMID: 29318897 DOI: 10.1080/09637486.2017.1422701] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Soymilk contains several functional nutrients and is thus a promising ingredient for production of functional foods. The present research aimed to study starter properties, functional characteristics and safety of Lactobacillus paraplantarum D2-1, a promising starter culture for soymilk fermentation. Strain D2-1 actively fermented soymilk within 24 h but had weak activity of additional acid production after 7 d. Succinate and acetoin, which could be linked to flavour and taste, were accumulated in fermented soymilk. In vitro study revealed that the organism has several beneficial properties, including high survival ability in artificial gastric juice, high abilities of mucus adhesion and biofilm formation and production of γ-aminobutyric acid and conjugated linoleic acid, without any significant risks for consumption. Genome sequencing supported the desirable metabolic properties of the strain. These results indicate that L. paraplantarum D2-1 is a suitable starter for soymilk fermentation and is a promising probiotic candidate that can be used safely.
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Guadamuro L, Flórez AB, Alegría Á, Vázquez L, Mayo B. Characterization of four β-glucosidases acting on isoflavone-glycosides from Bifidobacterium pseudocatenulatum IPLA 36007. Food Res Int 2017; 100:522-528. [DOI: 10.1016/j.foodres.2017.07.024] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 07/11/2017] [Accepted: 07/13/2017] [Indexed: 12/17/2022]
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Charnchai P, Jantama SS, Jantama K. Genome analysis of food-processing stressful-resistant probiotic Bifidobacterium animalis subsp. lactis BF052, and its potential application in fermented soymilk. FEMS Microbiol Lett 2017; 364:4084568. [PMID: 28911187 DOI: 10.1093/femsle/fnx180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 08/16/2017] [Indexed: 01/13/2023] Open
Abstract
In this study, Bifidobacterium animalis subsp. lactis BF052 was demonstrated the growth capability in soymilk and could be thus supplemented as a probiotic starter that employed soymilk as one of its food vehicles. The complete genome sequence of BF052 was therefore determined to understand the genetic basis of BF052 as a technological and functional probiotic starter. The whole genome sequence of BF052 consists of a circular genome of 1938 624 bp with a G+C content of 60.50%. This research highlights relevant genes involving in its adaptive responses to industrial and/or environmental stresses and utilization of α-galacto-oligosaccharides in BF052 strain compared with other representative bifidobacterial genomes.
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Affiliation(s)
- Pattra Charnchai
- Metabolic Engineering Research Unit, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, 111 University Avenue, Suranaree, Muang, Nakhon Ratchasima 30000, Thailand
| | - Sirima Suvarnakuta Jantama
- Division of Biopharmacy, Faculty of Pharmaceutical Sciences, Ubon Ratchathani University, Sathonlamark Road, Warin chamrap, Ubon Ratchathani 34190, Thailand
| | - Kaemwich Jantama
- Metabolic Engineering Research Unit, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, 111 University Avenue, Suranaree, Muang, Nakhon Ratchasima 30000, Thailand
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A Human Gut Commensal Ferments Cranberry Carbohydrates To Produce Formate. Appl Environ Microbiol 2017; 83:AEM.01097-17. [PMID: 28667113 DOI: 10.1128/aem.01097-17] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 06/22/2017] [Indexed: 02/07/2023] Open
Abstract
Commensal bifidobacteria colonize the human gastrointestinal tract and catabolize glycans that are impervious to host digestion. Accordingly, Bifidobacterium longum typically secretes acetate and lactate as fermentative end products. This study tested the hypothesis that B. longum utilizes cranberry-derived xyloglucans in a strain-dependent manner. Interestingly, the B. longum strain that efficiently utilizes cranberry xyloglucans secretes 2.0 to 2.5 mol of acetate-lactate. The 1.5 acetate:lactate ratio theoretical yield obtained in hexose fermentations shifts during xyloglucan metabolism. Accordingly, this metabolic shift is characterized by increased acetate and formate production at the expense of lactate. α-l-Arabinofuranosidase, an arabinan endo-1,5-α-l-arabinosidase, and a β-xylosidase with a carbohydrate substrate-binding protein and carbohydrate ABC transporter membrane proteins are upregulated (>2-fold change), which suggests carbon flux through this catabolic pathway. Finally, syntrophic interactions occurred with strains that utilize carbohydrate products derived from initial degradation from heterologous bacteria.IMPORTANCE This was a study of bacterial metabolism of complex cranberry carbohydrates termed xyloglucans that are likely not digested prior to reaching the colon. This is significant, as bifidobacteria interact with this dietary compound to potentially impact human host health through energy and metabolite production by utilizing these substrates. Specific bacterial strains utilize cranberry xyloglucans as a nutritive source, indicating unknown mechanisms that are not universal in bifidobacteria. In addition, xyloglucan metabolism proceeds by using an alternative pathway that could lead to further research to investigate mechanisms underlying this interaction. Finally, we observed cross-feeding between bacteria in which one strain degrades the cranberry xyloglucan to make it available to a second strain. Similar nutritive strategies are known to occur within the gut. In aggregate, this study may lead to novel foods or supplements used to impact human health through rational manipulation of the human microbiome.
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De Paepe K, Kerckhof F, Verspreet J, Courtin CM, Van de Wiele T. Inter‐individual differences determine the outcome of wheat bran colonization by the human gut microbiome. Environ Microbiol 2017; 19:3251-3267. [DOI: 10.1111/1462-2920.13819] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 06/03/2017] [Accepted: 06/07/2017] [Indexed: 01/11/2023]
Affiliation(s)
- Kim De Paepe
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience EngineeringGhent UniversityGhent Belgium
| | - Frederiek‐Maarten Kerckhof
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience EngineeringGhent UniversityGhent Belgium
| | - Joran Verspreet
- Faculty of Bioscience Engineering, KU LeuvenLaboratory of Food Chemistry and Biochemistry, Leuven Food Science and Nutrition Research Centre (LFoRCe)Heverlee Belgium
| | - Christophe M. Courtin
- Faculty of Bioscience Engineering, KU LeuvenLaboratory of Food Chemistry and Biochemistry, Leuven Food Science and Nutrition Research Centre (LFoRCe)Heverlee Belgium
| | - Tom Van de Wiele
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience EngineeringGhent UniversityGhent Belgium
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Fernando WMADB, Flint SH, Ranaweera KKDS, Bamunuarachchi A, Johnson SK, Brennan CS. The potential synergistic behaviour of inter- and intra-genus probiotic combinations in the pattern and rate of short chain fatty acids formation during fibre fermentation. Int J Food Sci Nutr 2017; 69:144-154. [DOI: 10.1080/09637486.2017.1340932] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | - Steve H. Flint
- School of Food and Nutrition, Massey University, Palmerston North, New Zealand
| | - K. K. D. S. Ranaweera
- Department of Food Science and Technology, Sri Jayewardenepura University, Nugegoda, Colombo, Sri Lanka
| | - Arthur Bamunuarachchi
- Department of Food Science and Technology, Sri Jayewardenepura University, Nugegoda, Colombo, Sri Lanka
| | - Stuart K. Johnson
- School of Public Health, Curtin Health Innovation Research Institute, Curtin University, Bentley, Australia
| | - Charles S. Brennan
- Department of Wine, Food and Molecular Biosciences, Centre for Food Research and Innovation Lincoln University, Lincoln, New Zealand
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Vazquez-Gutierrez P, Stevens MJA, Gehrig P, Barkow-Oesterreicher S, Lacroix C, Chassard C. The extracellular proteome of two Bifidobacterium species reveals different adaptation strategies to low iron conditions. BMC Genomics 2017; 18:41. [PMID: 28061804 PMCID: PMC5219805 DOI: 10.1186/s12864-016-3472-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 12/26/2016] [Indexed: 12/30/2022] Open
Abstract
Background Bifidobacteria are among the first anaerobic bacteria colonizing the gut. Bifidobacteria require iron for growth and their iron-sequestration mechanisms are important for their fitness and possibly inhibit enteropathogens. Here we used combined genomic and proteomic analyses to characterize adaptations to low iron conditions of B. kashiwanohense PV20-2 and B. pseudolongum PV8-2, 2 strains isolated from the feces of iron-deficient African infants and selected for their high iron-sequestering ability. Results Analyses of the genome contents revealed evolutionary adaptation to low iron conditions. A ferric and a ferrous iron operon encoding binding proteins and transporters were found in both strains. Remarkably, the ferric iron operon of B. pseudolongum PV8-2 is not found in other B. pseudolongum strains and likely acquired via horizontal gene transfer. The genome B. kashiwanohense PV20-2 harbors a unique region encoding genes putatively involved in siderophore production. Additionally, the secretomes of the two strains grown under low-iron conditions were analyzed using a combined genomic-proteomic approach. A ferric iron transporter was found in the secretome of B. pseudolongum PV8-2, while ferrous binding proteins were detected in the secretome of B. kashiwanohense PV20-2, suggesting different strategies to take up iron in the strains. In addition, proteins such as elongation factors, a glyceraldehyde-3-phosphate dehydrogenase, and the stress proteins GroEL and DnaK were identified in both secretomes. These proteins have been previously associated with adhesion of lactobacilli to epithelial cells. Conclusion Analyses of the genome and secretome of B. kashiwanohense PV20-2 and B. pseudolongum PV8-2 revealed different adaptations to low iron conditions and identified extracellular proteins for iron transport. The identified extracellular proteins might be involved in competition for iron in the gastrointestinal tract. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3472-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pamela Vazquez-Gutierrez
- Laboratory of Food Biotechnology, ETH Zurich, Institute of Food, Nutrition and Health, Schmelzbergstrasse 7, 8092, Zurich, Switzerland
| | - Marc J A Stevens
- Laboratory of Food Biotechnology, ETH Zurich, Institute of Food, Nutrition and Health, Schmelzbergstrasse 7, 8092, Zurich, Switzerland
| | - Peter Gehrig
- Functional Genomics Center Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | | | - Christophe Lacroix
- Laboratory of Food Biotechnology, ETH Zurich, Institute of Food, Nutrition and Health, Schmelzbergstrasse 7, 8092, Zurich, Switzerland.
| | - Christophe Chassard
- Laboratory of Food Biotechnology, ETH Zurich, Institute of Food, Nutrition and Health, Schmelzbergstrasse 7, 8092, Zurich, Switzerland.,Present Address: Institut National de la Recherche Agronomique, UR 545 URF, 15000, Aurillac, France
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Rivière A, Selak M, Lantin D, Leroy F, De Vuyst L. Bifidobacteria and Butyrate-Producing Colon Bacteria: Importance and Strategies for Their Stimulation in the Human Gut. Front Microbiol 2016; 7:979. [PMID: 27446020 PMCID: PMC4923077 DOI: 10.3389/fmicb.2016.00979] [Citation(s) in RCA: 930] [Impact Index Per Article: 116.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 06/07/2016] [Indexed: 12/11/2022] Open
Abstract
With the increasing amount of evidence linking certain disorders of the human body to a disturbed gut microbiota, there is a growing interest for compounds that positively influence its composition and activity through diet. Besides the consumption of probiotics to stimulate favorable bacterial communities in the human gastrointestinal tract, prebiotics such as inulin-type fructans (ITF) and arabinoxylan-oligosaccharides (AXOS) can be consumed to increase the number of bifidobacteria in the colon. Several functions have been attributed to bifidobacteria, encompassing degradation of non-digestible carbohydrates, protection against pathogens, production of vitamin B, antioxidants, and conjugated linoleic acids, and stimulation of the immune system. During life, the numbers of bifidobacteria decrease from up to 90% of the total colon microbiota in vaginally delivered breast-fed infants to <5% in the colon of adults and they decrease even more in that of elderly as well as in patients with certain disorders such as antibiotic-associated diarrhea, inflammatory bowel disease, irritable bowel syndrome, obesity, allergies, and regressive autism. It has been suggested that the bifidogenic effects of ITF and AXOS are the result of strain-specific yet complementary carbohydrate degradation mechanisms within cooperating bifidobacterial consortia. Except for a bifidogenic effect, ITF and AXOS also have shown to cause a butyrogenic effect in the human colon, i.e., an enhancement of colon butyrate production. Butyrate is an essential metabolite in the human colon, as it is the preferred energy source for the colon epithelial cells, contributes to the maintenance of the gut barrier functions, and has immunomodulatory and anti-inflammatory properties. It has been shown that the butyrogenic effects of ITF and AXOS are the result of cross-feeding interactions between bifidobacteria and butyrate-producing colon bacteria, such as Faecalibacterium prausnitzii (clostridial cluster IV) and Anaerostipes, Eubacterium, and Roseburia species (clostridial cluster XIVa). These kinds of interactions possibly favor the co-existence of bifidobacterial strains with other bifidobacteria and with butyrate-producing colon bacteria in the human colon.
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Affiliation(s)
| | | | | | | | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit BrusselBrussels, Belgium
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O'Callaghan A, van Sinderen D. Bifidobacteria and Their Role as Members of the Human Gut Microbiota. Front Microbiol 2016; 7:925. [PMID: 27379055 PMCID: PMC4908950 DOI: 10.3389/fmicb.2016.00925] [Citation(s) in RCA: 506] [Impact Index Per Article: 63.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 05/31/2016] [Indexed: 12/11/2022] Open
Abstract
Members of the genus Bifidobacterium are among the first microbes to colonize the human gastrointestinal tract and are believed to exert positive health benefits on their host. Due to their purported health-promoting properties, bifidobacteria have been incorporated into many functional foods as active ingredients. Bifidobacteria naturally occur in a range of ecological niches that are either directly or indirectly connected to the animal gastrointestinal tract, such as the human oral cavity, the insect gut and sewage. To be able to survive in these particular ecological niches, bifidobacteria must possess specific adaptations to be competitive. Determination of genome sequences has revealed genetic attributes that may explain bifidobacterial ecological fitness, such as metabolic abilities, evasion of the host adaptive immune system and colonization of the host through specific appendages. However, genetic modification is crucial toward fully elucidating the mechanisms by which bifidobacteria exert their adaptive abilities and beneficial properties. In this review we provide an up to date summary of the general features of bifidobacteria, whilst paying particular attention to the metabolic abilities of this species. We also describe methods that have allowed successful genetic manipulation of bifidobacteria.
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Affiliation(s)
- Amy O'Callaghan
- Alimentary Pharmabiotic Centre and School of Microbiology, University College Cork Cork, Ireland
| | - Douwe van Sinderen
- Alimentary Pharmabiotic Centre and School of Microbiology, University College Cork Cork, Ireland
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50
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Effect of Overgrowth or Decrease in Gut Microbiota on Health and Disease. ARCHIVES OF PEDIATRIC INFECTIOUS DISEASES 2016. [DOI: 10.5812/pedinfect.34558] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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