1
|
Bommasamudram J, Muthu A, Devappa S. Effect of prebiotics on thermally acclimatized lactobacilli cultures and their application as synbiotics in RTD fruit drinks. 3 Biotech 2023; 13:311. [PMID: 37621320 PMCID: PMC10444933 DOI: 10.1007/s13205-023-03737-2] [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: 02/28/2023] [Accepted: 08/08/2023] [Indexed: 08/26/2023] Open
Abstract
In this study, the effect of prebiotics such as fructooligosaccharides (FOS), galactooligosaccharides (GOS), isomaltooligosaccharides (IMO), and inulin on the probiotic biomass and its probiotic properties were studied for thermally acclimatized Lactobacillus helveticus (H-45) and Lacticaseibacillus casei N (N-45) strains at 45 ℃ using adaptive laboratory evolution method. Among the prebiotics studied, GOS was found to be more suitable for synbiotic preparation. The tolerance of lactobacilli cultures H-45 and N-45 in the presence of acid and bile were 4.79 and 8.60% and 2.84 and 4.65% higher than their wild-type strains (H-37 and N-37). Similarly, H-45 and N-45 showed an increase in survivability of 5.29 and 8.63% under simulated gastric conditions and 9.21 and 7.70% under simulated intestinal conditions than H-37 and N-37. Propionic acid yield increased by 0.65-fold in N-45 compared to N-37 in the presence of GOS as a prebiotic, whereas H-37 showed 0.26-fold higher propionic acid production than H-45. Thermally acclimatized strain N-45 showed better survivability under stress conditions than H-45. The synbiotic combination of N45 + GOS was spray-dried using corn starch (CS) as carrier material to obtain spray-dried synbiotic powder (N45 + CS + GOS). This synbiotic powder was added to the ready-to-drink (RTD) fruit drinks prepared from five fruit-flavoured squashes (pineapple, orange, grape, mango, and lemon ginger). The varied amounts of added synbiotic powder did not significantly alter the physicochemical properties of the fruit drinks. Hence, synbiotic formulation N45 + GOS + CS may find application in developing various functional foods.
Collapse
Affiliation(s)
- Jyothna Bommasamudram
- Microbiology and Fermentation Technology Department, CSIR-Central Food Technological Research Institute, Mysore, Karnataka 570020 India
| | - Arjun Muthu
- Microbiology and Fermentation Technology Department, CSIR-Central Food Technological Research Institute, Mysore, Karnataka 570020 India
| | - Somashekar Devappa
- Microbiology and Fermentation Technology Department, CSIR-Central Food Technological Research Institute, Mysore, Karnataka 570020 India
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Garcia CA, Gardner JG. Bacterial α-diglucoside metabolism: perspectives and potential for biotechnology and biomedicine. Appl Microbiol Biotechnol 2021; 105:4033-4052. [PMID: 33961116 PMCID: PMC8237927 DOI: 10.1007/s00253-021-11322-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/20/2021] [Accepted: 04/26/2021] [Indexed: 12/16/2022]
Abstract
In a competitive microbial environment, nutrient acquisition is a major contributor to the survival of any individual bacterial species, and the ability to access uncommon energy sources can provide a fitness advantage. One set of soluble carbohydrates that have attracted increased attention for use in biotechnology and biomedicine is the α-diglucosides. Maltose is the most well-studied member of this class; however, the remaining four less common α-diglucosides (trehalose, kojibiose, nigerose, and isomaltose) are increasingly used in processed food and fermented beverages. The consumption of trehalose has recently been shown to be a contributing factor in gut microbiome disease as certain pathogens are using α-diglucosides to outcompete native gut flora. Kojibiose and nigerose have also been examined as potential prebiotics and alternative sweeteners for a variety of foods. Compared to the study of maltose metabolism, our understanding of the synthesis and degradation of uncommon α-diglucosides is lacking, and several fundamental questions remain unanswered, particularly with regard to the regulation of bacterial metabolism for α-diglucosides. Therefore, this minireview attempts to provide a focused analysis of uncommon α-diglucoside metabolism in bacteria and suggests some future directions for this research area that could potentially accelerate biotechnology and biomedicine developments. KEY POINTS: • α-diglucosides are increasingly important but understudied bacterial metabolites. • Kinetically superior α-diglucoside enzymes require few amino acid substitutions. • In vivo studies are required to realize the biotechnology potential of α-diglucosides.
Collapse
Affiliation(s)
- Cecelia A Garcia
- Department of Biological Sciences, University of Maryland-Baltimore County, Baltimore, MD, USA
| | - Jeffrey G Gardner
- Department of Biological Sciences, University of Maryland-Baltimore County, Baltimore, MD, USA.
| |
Collapse
|
4
|
Gene-Phenotype Associations Involving Human-Residential Bifidobacteria (HRB) Reveal Significant Species- and Strain-Specificity in Carbohydrate Catabolism. Microorganisms 2021; 9:microorganisms9050883. [PMID: 33919102 PMCID: PMC8143103 DOI: 10.3390/microorganisms9050883] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/16/2021] [Accepted: 04/18/2021] [Indexed: 12/17/2022] Open
Abstract
Bifidobacteria are among the first colonizers of the human gastrointestinal tract. Different bacterial species use different mechanisms for utilization of various carbon sources in order to establish themselves in the complex microbial ecosystem of the gut. However, these mechanisms still need to be explored. Here, a large gene–phenotype correlation analysis was carried out to explore the metabolic and genetic diversity of bifidobacterial carbohydrate utilization abilities. In this study, we used 21 different carbohydrates to determine the growth phenotypes, the distribution of glycoside hydrolases (GHs), and gene clusters related to the utilization of multiple carbon sources in six human-residential Bifidobacterium species. Five carbohydrates significantly stimulated growth of almost all strains, while the remaining sugars exhibited species- and strain-specificity. Correspondingly, different Bifidobacterium species also had specific GHs involved in fermentation of plant or host glycans. Moreover, we analyzed several carbohydrate utilization gene clusters, such as 2-fucosyllactose (2′FL), sialic acid (SA), and fructooligosaccharide (FOS). In summary, by using 217 bifidobacterial strains and a wide range of growth substrates, our research revealed inter- and intra-species differences in bifidobacterial in terms of carbohydrate utilization. The findings of this study are useful for the process of developing prebiotics for optimum growth of probiotics, especially Bifidobacterium species.
Collapse
|
5
|
Yang Y, Ma Y, Hu X, Cui SW, Zhang T, Miao M. Reuteransucrase-catalytic kinetic modeling and functional characteristics for novel prebiotic gluco-oligomers. Food Funct 2020; 11:7037-7047. [PMID: 32812985 DOI: 10.1039/d0fo00225a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
This work describes the reuteransucrase-catalyzed reaction and structural characterization as well as in vitro fermentation for the acceptor products of gluco-oligomers from sucrose and maltose. At a low concentration of sucrose, the production of gluco-oligomers was favored, resulting in a relatively large number of acceptor products (DP3-5). A mathematical model was also proposed to simulate gluco-oligomer production depending on the reaction conditions. The fine structures of major linear gluco-oligomer fractions for a sucrose : maltose ratio of 1 : 1 were assigned as follows: α-d-Glcp-(1→6)-α-d-Glcp-(1→4)-d-Glcp, α-d-Glcp-(1→4)-α-d-Glcp-(1→4)-α-d-Glcp-(1→4)-d-Glcp, α-d-Glcp-(1→4)-α-d-Glcp-(1→6)-α-d-Glcp-(1→4)-d-Glcp, and α-d-Glcp-(1→6)-α-d-Glcp-(1→4)-α-d-Glcp-(1→6)-α-d-Glcp-(1→4)-d-Glcp, respectively. Compared with dextran and GOS57, the results of fermentation selectivity indicated that gluco-oligomers promoted the proliferation of gut bacteria and total SCFA production with a higher concentration of propionate. These data suggested that the gluco-oligomers synthesized via the reuteransucrase acceptor reaction had a prebiotic effect on gastrointestinal health.
Collapse
Affiliation(s)
- Yuqi Yang
- State Key Laboratory of Food Science & Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, P. R. China.
| | - Yajun Ma
- State Key Laboratory of Food Science & Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, P. R. China.
| | - Xiuting Hu
- State Key Laboratory of Food Science & Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, P. R. China.
| | - Steve W Cui
- State Key Laboratory of Food Science & Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, P. R. China. and Guelph Food Research Centre, Agriculture and Agri-Food Canada, 93 Stone Road West, Guelph, Ont., Canada N1G 5C9
| | - Tao Zhang
- State Key Laboratory of Food Science & Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, P. R. China.
| | - Ming Miao
- State Key Laboratory of Food Science & Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, P. R. China.
| |
Collapse
|
6
|
Wong CB, Odamaki T, Xiao JZ. Insights into the reason of Human-Residential Bifidobacteria (HRB) being the natural inhabitants of the human gut and their potential health-promoting benefits. FEMS Microbiol Rev 2020; 44:369-385. [PMID: 32319522 PMCID: PMC7326374 DOI: 10.1093/femsre/fuaa010] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 04/20/2020] [Indexed: 12/11/2022] Open
Abstract
Members of Bifidobacterium are among the first microbes to colonise the human gut, and certain species are recognised as the natural resident of human gut microbiota. Their presence in the human gut has been associated with health-promoting benefits and reduced abundance of this genus is linked with several diseases. Bifidobacterial species are assumed to have coevolved with their hosts and include members that are naturally present in the human gut, thus recognised as Human-Residential Bifidobacteria (HRB). The physiological functions of these bacteria and the reasons why they occur in and how they adapt to the human gut are of immense significance. In this review, we provide an overview of the biology of bifidobacteria as members of the human gut microbiota and address factors that contribute to the preponderance of HRB in the human gut. We highlight some of the important genetic attributes and core physiological traits of these bacteria that may explain their adaptive advantages, ecological fitness, and competitiveness in the human gut. This review will help to widen our understanding of one of the most important human commensal bacteria and shed light on the practical consideration for selecting bifidobacterial strains as human probiotics.
Collapse
Affiliation(s)
- Chyn Boon Wong
- Next Generation Science Institute, Morinaga Milk Industry Co., Ltd., 5-1-83, Higashihara, Zama, Kanagawa, 252–8583 Japan
| | - Toshitaka Odamaki
- Next Generation Science Institute, Morinaga Milk Industry Co., Ltd., 5-1-83, Higashihara, Zama, Kanagawa, 252–8583 Japan
| | - Jin-zhong Xiao
- Next Generation Science Institute, Morinaga Milk Industry Co., Ltd., 5-1-83, Higashihara, Zama, Kanagawa, 252–8583 Japan
| |
Collapse
|
7
|
Fan G, Fu Z, Teng C, Liu P, Wu Q, Rahman MKR, Li X. Effects of aging on the quality of roasted sesame-like flavor Daqu. BMC Microbiol 2020; 20:67. [PMID: 32216749 PMCID: PMC7098102 DOI: 10.1186/s12866-020-01745-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 03/05/2020] [Indexed: 02/06/2023] Open
Abstract
Background Daqu, the saccharification, fermentation, and aroma-producing agents for Baijiu brewing, is prepared using a complex process. Aging is important for improving the quality of Daqu, but its impact has rarely been studied. This study investigated changes in the physicochemical properties, flavor compounds, and microbial communities during aging of Daqu with a roasted sesame-like flavor. Results The physicochemical properties changed continuously during aging to provide a high esterifying activity. Aging removed unpleasant flavor compounds and helped to stabilize the flavor compounds in mature Daqu. A high-throughput sequencing approach was used to analyze the changing composition of the microbial communities during aging. Aging helped to modify the microbial population to produce better Baijiu by eliminating low-abundance microbial communities and optimizing the proportion of predominant microbial communities. Nine genera of prokaryotic microbes formed the core microbiota in Daqu after aging. Regarding eukaryotic microbes, Zygomycota, the predominant community, increased in the first 2 months, then decreased in the third month of aging, while Ascomycota, the subdominant community, showed the opposite behavior. Absidia, Trichocomaceae_norank and Rhizopus were the predominant genera in the mature Daqu. Conclusions Significant correlations between microbiota and physicochemical properties or flavor compounds were observed, indicating that optimizing microbial communities is essential for aging Daqu. This study provides detailed information on aging during Daqu preparation.
Collapse
Affiliation(s)
- Guangsen Fan
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing, 100048, China.,School of Food and health, Beijing Technology and Business University (BTBU), Beijing, 100048, China.,Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University (BTBU), No 11 Fucheng Street, Haidian District, Beijing, 100048, China
| | - Zhilei Fu
- School of Food and health, Beijing Technology and Business University (BTBU), Beijing, 100048, China
| | - Chao Teng
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing, 100048, China.,School of Food and health, Beijing Technology and Business University (BTBU), Beijing, 100048, China.,Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University (BTBU), No 11 Fucheng Street, Haidian District, Beijing, 100048, China
| | - Pengxiao Liu
- School of Food and health, Beijing Technology and Business University (BTBU), Beijing, 100048, China
| | - Qiuhua Wu
- School of Food and health, Beijing Technology and Business University (BTBU), Beijing, 100048, China
| | - Md Khondakar Raziur Rahman
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing, 100048, China.,School of Food and health, Beijing Technology and Business University (BTBU), Beijing, 100048, China
| | - Xiuting Li
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing, 100048, China. .,School of Food and health, Beijing Technology and Business University (BTBU), Beijing, 100048, China. .,Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University (BTBU), No 11 Fucheng Street, Haidian District, Beijing, 100048, China.
| |
Collapse
|
8
|
Hu X, Song L, Yang Y, Jin Z, Miao M. Synthesis of potential prebiotic α-glucooligosaccharides using microbial glucansucrase and their in vitro fecal fermentation. Food Funct 2020; 11:1672-1683. [PMID: 32031198 DOI: 10.1039/c9fo02054c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Novel α-glucooligosaccharides were synthesized by the acceptor reaction of Leuconostoc citreum SK24.002 glucansucrase with maltose and sucrose. The impact of synthesis conditions, including the ratio of sucrose to maltose and the substrate concentration, on the formation of α-glucooligosaccharides was evaluated. Under the optimized experimental conditions, the yield of a mixture of α-glucooligosaccharides with DP 3-5 reached approximately 56.4% with a concentration of 170.7 mg mL-1. Each of these α-glucooligosaccharides was purified, and the structures were assigned as follows: α-D-Glcp-(1,6)-α-D-Glcp-(1,4)-D-Glcp (DP3), α-D-Glcp-(1,3)-α-D-Glcp-(1,6)-α-D-Glcp-(1,4)-D-Glcp (DP4), and α-D-Glcp-(1,6)-α-D-Glcp-(1,3)-α-D-Glcp-(1,6)-α-D-Glcp-(1,4)-D-Glcp (DP5), respectively. For these three structurally different oligosaccharides, the fermentation selectivity by fecal bacteria was determined in anaerobic batch culture. Fructooligosaccharide (FOS) was used as a positive prebiotic control. Similar to FOS, all three α-glucooligosaccharides selectively stimulated the proliferation of Bifidobacteria and Lactobacilli compared with the control. DP3 exhibited the strongest prebiotic ability to increase the Bifidobacterium and Lactobacillus population, whereas DP5 produced the most short-chain fatty acids. In addition, DP4 produced the highest butyrate concentration and resulted in the lowest acetate : propionate ratio. These results suggested that the enzymatically synthesized α-glucooligosaccharides were potential prebiotics, underlining correlations between the structural features of oligosaccharides and their impact on the metabolism of fecal microbiota.
Collapse
Affiliation(s)
- Xiuting Hu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P.R. China.
| | | | | | | | | |
Collapse
|
9
|
Dong Z, Tang C, Lu Y, Yao L, Kan Y. Microbial Oligo‐α‐1,6‐Glucosidase: Current Developments and Future Perspectives. STARCH-STARKE 2019. [DOI: 10.1002/star.201900172] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Zixing Dong
- Henan Provincial Engineering Laboratory of Insect Bio‐reactor and Henan Key Laboratory of Ecological Security for Water Region of Mid‐line of South‐to‐NorthNanyang Normal University Nanyang 473061 P. R. China
| | - Cunduo Tang
- Henan Provincial Engineering Laboratory of Insect Bio‐reactor and Henan Key Laboratory of Ecological Security for Water Region of Mid‐line of South‐to‐NorthNanyang Normal University Nanyang 473061 P. R. China
| | - Yunfeng Lu
- School of Life Science and TechnologyNanyang Normal University Nanyang 473061 P. R. China
| | - Lunguang Yao
- Henan Provincial Engineering Laboratory of Insect Bio‐reactor and Henan Key Laboratory of Ecological Security for Water Region of Mid‐line of South‐to‐NorthNanyang Normal University Nanyang 473061 P. R. China
| | - Yunchao Kan
- Henan Provincial Engineering Laboratory of Insect Bio‐reactor and Henan Key Laboratory of Ecological Security for Water Region of Mid‐line of South‐to‐NorthNanyang Normal University Nanyang 473061 P. R. China
| |
Collapse
|
10
|
Pham HTT, Boger MCL, Dijkhuizen L, van Leeuwen SS. Stimulatory effects of novel glucosylated lactose derivatives GL34 on growth of selected gut bacteria. Appl Microbiol Biotechnol 2018; 103:707-718. [PMID: 30406451 PMCID: PMC6373440 DOI: 10.1007/s00253-018-9473-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 10/18/2018] [Accepted: 10/19/2018] [Indexed: 12/11/2022]
Abstract
Previously we structurally characterized five glucosylated lactose derivatives (F1-F5) with a degree of polymerization (DP) of 3-4 (GL34), products of Lactobacillus reuteri glucansucrases, with lactose and sucrose as substrates. Here, we show that these GL34 compounds are largely resistant to the hydrolytic activities of common carbohydrate-degrading enzymes. Also, the ability of single strains of gut bacteria, bifidobacteria, lactobacilli, and commensal bacteria, to ferment the GL34 compounds was studied. Bifidobacteria clearly grew better on the GL34 mixture than lactobacilli and commensal bacteria. Lactobacilli and the commensal bacteria Escherichia coli Nissle and Bacteroides thetaiotaomicron only degraded the F2 compound α-D-Glcp-(1 → 2)-[β-D-Galp-(1 → 4)-]D-Glcp, constituting around 30% w/w of GL34. Bifidobacteria digested more than one compound from the GL34 mixture, varying with the specific strain tested. Bifidobacterium adolescentis was most effective, completely degrading four of the five GL34 compounds, leaving only one minor constituent. GL34 thus represents a novel oligosaccharide mixture with (potential) synbiotic properties towards B. adolescentis, synthesized from cheap and abundantly available lactose and sucrose.
Collapse
Affiliation(s)
- Hien T T Pham
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Markus C L Boger
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Lubbert Dijkhuizen
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands. .,CarbExplore Research B.V, Zernikepark 12, 9747 AN, Groningen, The Netherlands.
| | - Sander S van Leeuwen
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.,Department of Laboratory Medicine, University Medical Center Groningen, University of Groningen, 9713 GZ, Groningen, The Netherlands
| |
Collapse
|
11
|
A Transposon Mutagenesis System for Bifidobacterium longum subsp. longum Based on an IS 3 Family Insertion Sequence, IS Blo11. Appl Environ Microbiol 2018; 84:AEM.00824-18. [PMID: 29934330 DOI: 10.1128/aem.00824-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Accepted: 06/16/2018] [Indexed: 12/29/2022] Open
Abstract
Bifidobacteria are a major component of the intestinal microbiota in humans, particularly breast-fed infants. Therefore, elucidation of the mechanisms by which these bacteria colonize the intestine is desired. One approach is transposon mutagenesis, a technique currently attracting much attention because, in combination with next-generation sequencing, it enables exhaustive identification of genes that contribute to microbial fitness. We now describe a transposon mutagenesis system for Bifidobacterium longum subsp. longum 105-A (JCM 31944) based on ISBlo11, a native IS3 family insertion sequence. To build this system, xylose-inducible or constitutive bifidobacterial promoters were tested to drive the expression of full-length or a truncated form at the N terminus of the ISBlo11 transposase. An artificial transposon plasmid, pBFS12, in which ISBlo11 terminal inverted repeats are separated by a 3-bp spacer, was also constructed to mimic the transposition intermediate of IS3 elements. The introduction of this plasmid into a strain expressing transposase resulted in the insertion of the plasmid with an efficiency of >103 CFU/μg DNA. The plasmid targets random 3- to 4-bp sequences, but with a preference for noncoding regions. This mutagenesis system also worked at least in B. longum NCC2705. Characterization of a transposon insertion mutant revealed that a putative α-glucosidase mediates palatinose and trehalose assimilation, demonstrating the suitability of transposon mutagenesis for loss-of-function analysis. We anticipate that this approach will accelerate functional genomic studies of B. longum subsp. longumIMPORTANCE Several hundred species of bacteria colonize the mammalian intestine. However, the genes that enable such bacteria to colonize and thrive in the intestine remain largely unexplored. Transposon mutagenesis, combined with next-generation sequencing, is a promising tool to comprehensively identify these genes but has so far been applied only to a small number of intestinal bacterial species. In this study, a transposon mutagenesis system was established for Bifidobacterium longum subsp. longum, a representative health-promoting Bifidobacterium species. The system enables the identification of genes that promote colonization and survival in the intestine and should help illuminate the physiology of this species.
Collapse
|
12
|
Comparative genomics and genotype-phenotype associations in Bifidobacterium breve. Sci Rep 2018; 8:10633. [PMID: 30006593 PMCID: PMC6045613 DOI: 10.1038/s41598-018-28919-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 07/01/2018] [Indexed: 12/26/2022] Open
Abstract
Bifidobacteria are common members of the gastro-intestinal microbiota of a broad range of animal hosts. Their successful adaptation to this particular niche is linked to their saccharolytic metabolism, which is supported by a wide range of glycosyl hydrolases. In the current study a large-scale gene-trait matching (GTM) effort was performed to explore glycan degradation capabilities in B. breve. By correlating the presence/absence of genes and associated genomic clusters with growth/no-growth patterns across a dataset of 20 Bifidobacterium breve strains and nearly 80 different potential growth substrates, we not only validated the approach for a number of previously characterized carbohydrate utilization clusters, but we were also able to discover novel genetic clusters linked to the metabolism of salicin and sucrose. Using GTM, genetic associations were also established for antibiotic resistance and exopolysaccharide production, thereby identifying (novel) bifidobacterial antibiotic resistance markers and showing that the GTM approach is applicable to a variety of phenotypes. Overall, the GTM findings clearly expand our knowledge on members of the B. breve species, in particular how their variable genetic features can be linked to specific phenotypes.
Collapse
|
13
|
Carbohydrate Syntrophy enhances the establishment of Bifidobacterium breve UCC2003 in the neonatal gut. Sci Rep 2018; 8:10627. [PMID: 30006512 PMCID: PMC6045583 DOI: 10.1038/s41598-018-29034-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 06/19/2018] [Indexed: 12/21/2022] Open
Abstract
The non-digestible oligosaccharide fraction of maternal milk represents an important of carbohydrate and energy source for saccharolytic bifidobacteria in the gastrointestinal tract during early life. However, not all neonatal bifidobacteria isolates can directly metabolise the complex sialylated, fucosylated, sulphated and/or N-acetylglucosamine-containing oligosaccharide structures present in mothers milk. For some bifidobacterial strains, efficient carbohydrate syntrophy or crossfeeding is key to their establishment in the gut. In this study, we have adopted advanced functional genomic approaches to create single and double in-frame deletions of the N-acetyl glucosamine 6-phosphate deacetylase encoding genes, nagA1 and nagA2, of B. breve UCC2003. In vitro phenotypic analysis followed by in vivo studies on co-colonisation, mother to infant transmission, and evaluation of the relative co-establishment of B. bifidum and B. breve UCC2003 or UCC2003ΔnagA1ΔnagA2 in dam-reared neonatal mice demonstrates the importance of crossfeeding on sialic acid, fucose and N-acetylglucosamine-containing oligosaccharides for the establishment of B. breve UCC2003 in the neonatal gut. Furthermore, transcriptomic analysis of in vivo gene expression shows upregulation of genes associated with the utilisation of lactose, sialic acid, GlcNAc-6-S and fucose in B. breve UCC2003, while for UCC2003ΔnagA1ΔnagA2 only genes for lactose metabolism were upregulated.
Collapse
|
14
|
Glycan Utilization and Cross-Feeding Activities by Bifidobacteria. Trends Microbiol 2018; 26:339-350. [DOI: 10.1016/j.tim.2017.10.001] [Citation(s) in RCA: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 10/02/2017] [Accepted: 10/12/2017] [Indexed: 01/16/2023]
|
15
|
Turroni F, Milani C, Duranti S, Ferrario C, Lugli GA, Mancabelli L, van Sinderen D, Ventura M. Bifidobacteria and the infant gut: an example of co-evolution and natural selection. Cell Mol Life Sci 2018; 75:103-118. [PMID: 28983638 PMCID: PMC11105234 DOI: 10.1007/s00018-017-2672-0] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 09/29/2017] [Indexed: 12/16/2022]
Abstract
Throughout the human life, the gut microbiota interacts with us in a number of different ways, thereby influencing our health status. The acquisition of such an interactive gut microbiota commences at birth. Medical and environmental factors including diet, antibiotic exposure and mode of delivery are major factors that shape the composition of the microbial communities in the infant gut. Among the most abundant members of the infant microbiota are species belonging to the Bifidobacterium genus, which are believed to confer beneficial effects upon their host. Bifidobacteria may be acquired directly from the mother by vertical transmission and their persistence in the infant gut is associated with their saccharolytic activity toward glycans that are abundant in the infant gut. Here, we discuss the establishment of the infant gut microbiota and the contribution of bifidobacteria to this early life microbial consortium.
Collapse
Affiliation(s)
- Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Chiara Ferrario
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.
- Microbiome Research Hub, University of Parma, Parma, Italy.
| |
Collapse
|
16
|
Milani C, Duranti S, Bottacini F, Casey E, Turroni F, Mahony J, Belzer C, Delgado Palacio S, Arboleya Montes S, Mancabelli L, Lugli GA, Rodriguez JM, Bode L, de Vos W, Gueimonde M, Margolles A, van Sinderen D, Ventura M. The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota. Microbiol Mol Biol Rev 2017; 81:e00036-17. [PMID: 29118049 PMCID: PMC5706746 DOI: 10.1128/mmbr.00036-17] [Citation(s) in RCA: 970] [Impact Index Per Article: 138.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The human gut microbiota is engaged in multiple interactions affecting host health during the host's entire life span. Microbes colonize the neonatal gut immediately following birth. The establishment and interactive development of this early gut microbiota are believed to be (at least partially) driven and modulated by specific compounds present in human milk. It has been shown that certain genomes of infant gut commensals, in particular those of bifidobacterial species, are genetically adapted to utilize specific glycans of this human secretory fluid, thus representing a very intriguing example of host-microbe coevolution, where both partners are believed to benefit. In recent years, various metagenomic studies have tried to dissect the composition and functionality of the infant gut microbiome and to explore the distribution across the different ecological niches of the infant gut biogeography of the corresponding microbial consortia, including those corresponding to bacteria and viruses, in healthy and ill subjects. Such analyses have linked certain features of the microbiota/microbiome, such as reduced diversity or aberrant composition, to intestinal illnesses in infants or disease states that are manifested at later stages of life, including asthma, inflammatory bowel disease, and metabolic disorders. Thus, a growing number of studies have reported on how the early human gut microbiota composition/development may affect risk factors related to adult health conditions. This concept has fueled the development of strategies to shape the infant microbiota composition based on various functional food products. In this review, we describe the infant microbiota, the mechanisms that drive its establishment and composition, and how microbial consortia may be molded by natural or artificial interventions. Finally, we discuss the relevance of key microbial players of the infant gut microbiota, in particular bifidobacteria, with respect to their role in health and disease.
Collapse
Affiliation(s)
- Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Francesca Bottacini
- APC Microbiome Institute and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Eoghan Casey
- APC Microbiome Institute and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
| | - Jennifer Mahony
- APC Microbiome Institute and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Susana Delgado Palacio
- Departamento de Microbiologia y Bioquimica de Productos Lacteos, IPLA-CSIC, Villaviciosa, Asturias, Spain
| | - Silvia Arboleya Montes
- Departamento de Microbiologia y Bioquimica de Productos Lacteos, IPLA-CSIC, Villaviciosa, Asturias, Spain
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Juan Miguel Rodriguez
- Department of Nutrition, Food Science and Food Technology, Complutense University of Madrid, Madrid, Spain
| | - Lars Bode
- Department of Pediatrics and Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence, University of California-San Diego, La Jolla, California, USA
| | - Willem de Vos
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
- Department of Bacteriology & Immunology, RPU Immunobiology, University of Helsinki, Helsinki, Finland
| | - Miguel Gueimonde
- Departamento de Microbiologia y Bioquimica de Productos Lacteos, IPLA-CSIC, Villaviciosa, Asturias, Spain
| | - Abelardo Margolles
- Departamento de Microbiologia y Bioquimica de Productos Lacteos, IPLA-CSIC, Villaviciosa, Asturias, Spain
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
| |
Collapse
|
17
|
Strahsburger E, de Lacey AML, Marotti I, DiGioia D, Biavati B, Dinelli G. In vivo assay to identify bacteria with β-glucosidase activity. ELECTRON J BIOTECHN 2017. [DOI: 10.1016/j.ejbt.2017.08.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
|
18
|
Characterization of novel thermophilic alpha-glucosidase from Bifidobacterium longum. Int J Biol Macromol 2017; 99:594-599. [DOI: 10.1016/j.ijbiomac.2017.03.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 03/01/2017] [Accepted: 03/02/2017] [Indexed: 12/17/2022]
|
19
|
Genetic and biochemical characterization of an oligo-α-1,6-glucosidase from Lactobacillus plantarum. Int J Food Microbiol 2017; 246:32-39. [DOI: 10.1016/j.ijfoodmicro.2017.01.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 11/03/2016] [Accepted: 01/30/2017] [Indexed: 01/01/2023]
|
20
|
Pokusaeva K, Johnson C, Luk B, Uribe G, Fu Y, Oezguen N, Matsunami RK, Lugo M, Major A, Mori‐Akiyama Y, Hollister EB, Dann SM, Shi XZ, Engler DA, Savidge T, Versalovic J. GABA-producing Bifidobacterium dentium modulates visceral sensitivity in the intestine. Neurogastroenterol Motil 2017; 29:e12904. [PMID: 27458085 PMCID: PMC5195897 DOI: 10.1111/nmo.12904] [Citation(s) in RCA: 179] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 06/21/2016] [Indexed: 12/11/2022]
Abstract
BACKGROUND Recurrent abdominal pain is a common and costly health-care problem attributed, in part, to visceral hypersensitivity. Increasing evidence suggests that gut bacteria contribute to abdominal pain perception by modulating the microbiome-gut-brain axis. However, specific microbial signals remain poorly defined. γ-aminobutyric acid (GABA) is a principal inhibitory neurotransmitter and a key regulator of abdominal and central pain perception from peripheral afferent neurons. Although gut bacteria are reported to produce GABA, it is not known whether the microbial-derived neurotransmitter modulates abdominal pain. METHODS To investigate the potential analgesic effects of microbial GABA, we performed daily oral administration of a specific Bifidobacterium strain (B. dentiumATCC 27678) in a rat fecal retention model of visceral hypersensitivity, and subsequently evaluated pain responses. KEY RESULTS We demonstrate that commensal Bifidobacterium dentium produces GABA via enzymatic decarboxylation of glutamate by GadB. Daily oral administration of this specific Bifidobacterium (but not a gadB deficient) strain modulated sensory neuron activity in a rat fecal retention model of visceral hypersensitivity. CONCLUSIONS & INFERENCES The functional significance of microbial-derived GABA was demonstrated by gadB-dependent desensitization of colonic afferents in a murine model of visceral hypersensitivity. Visceral pain modulation represents another potential health benefit attributed to bifidobacteria and other GABA-producing species of the intestinal microbiome. Targeting GABAergic signals along this microbiome-gut-brain axis represents a new approach for the treatment of abdominal pain.
Collapse
Affiliation(s)
- K. Pokusaeva
- Department of Pathology & ImmunologyBaylor College of MedicineHoustonTXUSA,Department of PathologyTexas Children's HospitalHoustonTXUSA
| | - C. Johnson
- Department of Pathology & ImmunologyBaylor College of MedicineHoustonTXUSA,Department of PathologyTexas Children's HospitalHoustonTXUSA
| | - B. Luk
- Department of Pathology & ImmunologyBaylor College of MedicineHoustonTXUSA,Department of PathologyTexas Children's HospitalHoustonTXUSA
| | - G. Uribe
- Department of Pathology & ImmunologyBaylor College of MedicineHoustonTXUSA,Molecular Virology & MicrobiologyBaylor College of MedicineHoustonTXUSA
| | - Y. Fu
- Department of Internal MedicineUniversity of Texas Medical BranchGalvestonTXUSA
| | - N. Oezguen
- Department of Pathology & ImmunologyBaylor College of MedicineHoustonTXUSA,Department of PathologyTexas Children's HospitalHoustonTXUSA
| | - R. K. Matsunami
- Proteomics Programmatic Core LaboratoryHouston Methodist Hospital Research InstituteHoustonTXUSA
| | - M. Lugo
- Department of Pathology & ImmunologyBaylor College of MedicineHoustonTXUSA
| | - A. Major
- Department of PathologyTexas Children's HospitalHoustonTXUSA
| | - Y. Mori‐Akiyama
- Department of Pathology & ImmunologyBaylor College of MedicineHoustonTXUSA,Department of PathologyTexas Children's HospitalHoustonTXUSA
| | - E. B. Hollister
- Department of Pathology & ImmunologyBaylor College of MedicineHoustonTXUSA,Department of PathologyTexas Children's HospitalHoustonTXUSA
| | - S. M. Dann
- Department of Internal MedicineUniversity of Texas Medical BranchGalvestonTXUSA
| | - X. Z. Shi
- Department of Internal MedicineUniversity of Texas Medical BranchGalvestonTXUSA
| | - D. A. Engler
- Proteomics Programmatic Core LaboratoryHouston Methodist Hospital Research InstituteHoustonTXUSA
| | - T. Savidge
- Department of Pathology & ImmunologyBaylor College of MedicineHoustonTXUSA,Department of PathologyTexas Children's HospitalHoustonTXUSA
| | - J. Versalovic
- Department of Pathology & ImmunologyBaylor College of MedicineHoustonTXUSA,Department of PathologyTexas Children's HospitalHoustonTXUSA,Molecular Virology & MicrobiologyBaylor College of MedicineHoustonTXUSA
| |
Collapse
|
21
|
Glycosulfatase-Encoding Gene Cluster in Bifidobacterium breve UCC2003. Appl Environ Microbiol 2016; 82:6611-6623. [PMID: 27590817 DOI: 10.1128/aem.02022-16] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 08/26/2016] [Indexed: 12/11/2022] Open
Abstract
Bifidobacteria constitute a specific group of commensal bacteria typically found in the gastrointestinal tract (GIT) of humans and other mammals. Bifidobacterium breve strains are numerically prevalent among the gut microbiota of many healthy breastfed infants. In the present study, we investigated glycosulfatase activity in a bacterial isolate from a nursling stool sample, B. breve UCC2003. Two putative sulfatases were identified on the genome of B. breve UCC2003. The sulfated monosaccharide N-acetylglucosamine-6-sulfate (GlcNAc-6-S) was shown to support the growth of B. breve UCC2003, while N-acetylglucosamine-3-sulfate, N-acetylgalactosamine-3-sulfate, and N-acetylgalactosamine-6-sulfate did not support appreciable growth. By using a combination of transcriptomic and functional genomic approaches, a gene cluster designated ats2 was shown to be specifically required for GlcNAc-6-S metabolism. Transcription of the ats2 cluster is regulated by a repressor open reading frame kinase (ROK) family transcriptional repressor. This study represents the first description of glycosulfatase activity within the Bifidobacterium genus. IMPORTANCE Bifidobacteria are saccharolytic organisms naturally found in the digestive tract of mammals and insects. Bifidobacterium breve strains utilize a variety of plant- and host-derived carbohydrates that allow them to be present as prominent members of the infant gut microbiota as well as being present in the gastrointestinal tract of adults. In this study, we introduce a previously unexplored area of carbohydrate metabolism in bifidobacteria, namely, the metabolism of sulfated carbohydrates. B. breve UCC2003 was shown to metabolize N-acetylglucosamine-6-sulfate (GlcNAc-6-S) through one of two sulfatase-encoding gene clusters identified on its genome. GlcNAc-6-S can be found in terminal or branched positions of mucin oligosaccharides, the glycoprotein component of the mucous layer that covers the digestive tract. The results of this study provide further evidence of the ability of this species to utilize mucin-derived sugars, a trait which may provide a competitive advantage in both the infant gut and adult gut.
Collapse
|
22
|
Ruiz L, Delgado S, Ruas-Madiedo P, Margolles A, Sánchez B. Proteinaceous Molecules Mediating Bifidobacterium-Host Interactions. Front Microbiol 2016; 7:1193. [PMID: 27536282 PMCID: PMC4971063 DOI: 10.3389/fmicb.2016.01193] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 07/19/2016] [Indexed: 12/28/2022] Open
Abstract
Bifidobacteria are commensal microoganisms found in the gastrointestinal tract. Several strains have been attributed beneficial traits at local and systemic levels, through pathogen exclusion or immune modulation, among other benefits. This has promoted a growing industrial and scientific interest in bifidobacteria as probiotic supplements. However, the molecular mechanisms mediating this cross-talk with the human host remain unknown. High-throughput technologies, from functional genomics to transcriptomics, proteomics, and interactomics coupled to the development of both in vitro and in vivo models to study the dynamics of the intestinal microbiota and their effects on host cells, have eased the identification of key molecules in these interactions. Numerous secreted or surface-associated proteins or peptides have been identified as potential mediators of bifidobacteria-host interactions and molecular cross-talk, directly participating in sensing environmental factors, promoting intestinal colonization, or mediating a dialogue with mucosa-associated immune cells. On the other hand, bifidobacteria induce the production of proteins in the intestine, by epithelial or immune cells, and other gut bacteria, which are key elements in orchestrating interactions among bifidobacteria, gut microbiota, and host cells. This review aims to give a comprehensive overview on proteinaceous molecules described and characterized to date, as mediators of the dynamic interplay between bifidobacteria and the human host, providing a framework to identify knowledge gaps and future research needs.
Collapse
Affiliation(s)
- Lorena Ruiz
- Department of Nutrition, Food Science and Food Technology, Universidad Complutense de Madrid Spain
| | - Susana Delgado
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias-Consejo Superior de Investigaciones Científicas Villaviciosa, Spain
| | - Patricia Ruas-Madiedo
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias-Consejo Superior de Investigaciones Científicas Villaviciosa, Spain
| | - Abelardo Margolles
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias-Consejo Superior de Investigaciones Científicas Villaviciosa, Spain
| | - Borja Sánchez
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias-Consejo Superior de Investigaciones Científicas Villaviciosa, Spain
| |
Collapse
|
23
|
Biochemical properties of Glu-SH3 as a family 13 glycoside hydrolase with remarkable substrate specificity for trehalose: Implications to sequence-based classification of CAZymes. Arch Biochem Biophys 2016; 603:1-9. [PMID: 27177969 DOI: 10.1016/j.abb.2016.05.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 04/13/2016] [Accepted: 05/09/2016] [Indexed: 11/24/2022]
Abstract
A novel glycoside hydrolase from Exiguobacterium sp. SH3 was characterized. The enzyme, designated as Glu-SH3, was predicted by in silico analysis to have structural similarity with members of oligo-1,6-glucosidase and trehalose-6-phosphate hydrolase subfamilies in the GH-13 family of glycoside hydrolases. The gene was expressed in Escherichia coli and the recombinant enzyme was purified as a His-tagged protein of about 60 kDa. The enzyme was shown to have remarkable substrate specificity for trehalose. The characteristic ability of Glu-SH3 to hydrolyze trehalose was ascertained by zymography, thin layer chromatography, and NMR spectroscopy. The maximum activity of Glu-SH3 was obtained at 35 °C and pH 7, but it was able to exhibit more than 90% of the activity within the pH range of 5-8. The Vmax and Km values were estimated to be 170 U and 4.5 mg ml(-1), respectively. By comparison with trehalases, Glu-SH3 with Kcat and Kcat/Km values of 1552 s(-1) and 119.4 mM(-1) s(-1) can be recognized as a very efficient trehalose-hydrolyzing glycosidase. Given the phylogeny and the substrate specificity of Glu-SH3, it may be assumed that the enzyme shares a common ancestor with oligo-1,6-glucosidases but have evolved distinctly to serve a physiological function in trehalose metabolism.
Collapse
|
24
|
Kelly ED, Bottacini F, O'Callaghan J, Motherway MO, O'Connell KJ, Stanton C, van Sinderen D. Glycoside hydrolase family 13 α-glucosidases encoded by Bifidobacterium breve UCC2003; A comparative analysis of function, structure and phylogeny. Int J Food Microbiol 2016; 224:55-65. [DOI: 10.1016/j.ijfoodmicro.2016.02.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 02/15/2016] [Accepted: 02/21/2016] [Indexed: 01/16/2023]
|
25
|
Gao G, Wang A, Gong BL, Li QQ, Liu YH, He ZM, Li G. A novel metagenome-derived gene cluster from termite hindgut: Encoding phosphotransferase system components and high glucose tolerant glucosidase. Enzyme Microb Technol 2016; 84:24-31. [DOI: 10.1016/j.enzmictec.2015.12.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 12/07/2015] [Accepted: 12/12/2015] [Indexed: 11/29/2022]
|
26
|
Genomics of the Genus Bifidobacterium Reveals Species-Specific Adaptation to the Glycan-Rich Gut Environment. Appl Environ Microbiol 2015; 82:980-991. [PMID: 26590291 DOI: 10.1128/aem.03500-15] [Citation(s) in RCA: 145] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Bifidobacteria represent one of the dominant microbial groups that occur in the gut of various animals, being particularly prevalent during the suckling period of humans and other mammals. Their ability to compete with other gut bacteria is largely attributed to their saccharolytic features. Comparative and functional genomic as well as transcriptomic analyses have revealed the genetic background that underpins the overall saccharolytic phenotype for each of the 47 bifidobacterial (sub)species representing the genus Bifidobacterium, while also generating insightful information regarding carbohydrate resource sharing and cross-feeding among bifidobacteria. The abundance of bifidobacterial saccharolytic features in human microbiomes supports the notion that metabolic accessibility to dietary and/or host-derived glycans is a potent evolutionary force that has shaped the bifidobacterial genome.
Collapse
|
27
|
Bottacini F, Ventura M, van Sinderen D, O'Connell Motherway M. Diversity, ecology and intestinal function of bifidobacteria. Microb Cell Fact 2014; 13 Suppl 1:S4. [PMID: 25186128 PMCID: PMC4155821 DOI: 10.1186/1475-2859-13-s1-s4] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The human gastrointestinal tract represents an environment which is a densely populated home for a microbiota that has evolved to positively contribute to host health. At birth the essentially sterile gastrointestinal tract (GIT) is rapidly colonized by microorganisms that originate from the mother and the surrounding environment. Within a short timeframe a microbiota establishes within the (breastfed) infant's GIT where bifidobacteria are among the dominant members, although their numerical dominance disappears following weaning. The numerous health benefits associated with bifidobacteria, and the consequent commercial relevance resulting from their incorporation into functional foods, has led to intensified research aimed at the molecular understanding of claimed probiotic attributes of this genus. In this review we provide the current status on the diversity and ecology of bifidobacteria. In addition, we will discuss the molecular mechanisms that allow this intriguing group of bacteria to colonize and persist in the GIT, so as to facilitate interaction with its host.
Collapse
|
28
|
Bottacini F, O'Connell Motherway M, Kuczynski J, O'Connell KJ, Serafini F, Duranti S, Milani C, Turroni F, Lugli GA, Zomer A, Zhurina D, Riedel C, Ventura M, van Sinderen D. Comparative genomics of the Bifidobacterium breve taxon. BMC Genomics 2014; 15:170. [PMID: 24581150 PMCID: PMC4007704 DOI: 10.1186/1471-2164-15-170] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 02/19/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bifidobacteria are commonly found as part of the microbiota of the gastrointestinal tract (GIT) of a broad range of hosts, where their presence is positively correlated with the host's health status. In this study, we assessed the genomes of thirteen representatives of Bifidobacterium breve, which is not only a frequently encountered component of the (adult and infant) human gut microbiota, but can also be isolated from human milk and vagina. RESULTS In silico analysis of genome sequences from thirteen B. breve strains isolated from different environments (infant and adult faeces, human milk, human vagina) shows that the genetic variability of this species principally consists of hypothetical genes and mobile elements, but, interestingly, also genes correlated with the adaptation to host environment and gut colonization. These latter genes specify the biosynthetic machinery for sortase-dependent pili and exopolysaccharide production, as well as genes that provide protection against invasion of foreign DNA (i.e. CRISPR loci and restriction/modification systems), and genes that encode enzymes responsible for carbohydrate fermentation. Gene-trait matching analysis showed clear correlations between known metabolic capabilities and characterized genes, and it also allowed the identification of a gene cluster involved in the utilization of the alcohol-sugar sorbitol. CONCLUSIONS Genome analysis of thirteen representatives of the B. breve species revealed that the deduced pan-genome exhibits an essentially close trend. For this reason our analyses suggest that this number of B. breve representatives is sufficient to fully describe the pan-genome of this species. Comparative genomics also facilitated the genetic explanation for differential carbon source utilization phenotypes previously observed in different strains of B. breve.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Marco Ventura
- Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland, Western Road, Cork, Ireland.
| | | |
Collapse
|
29
|
Similarities and differences in the biochemical and enzymological properties of the four isomaltases from Saccharomyces cerevisiae. FEBS Open Bio 2014; 4:200-12. [PMID: 24649402 PMCID: PMC3953731 DOI: 10.1016/j.fob.2014.02.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 01/29/2014] [Accepted: 02/10/2014] [Indexed: 11/21/2022] Open
Abstract
Isomaltases (Imap) preferably cleave α-(1,6) bonds, yet show clear substrate ambiguity. With only 3 different aa, Ima3p activities and thermostability diverge from Ima2p. The most distant protein, Ima5p, is extremely sensitive to temperature. Ima5p nevertheless displays most of the same catalytic properties as Ima1p and Ima2p. Ima5p challenges previous conclusions about specific aa needs for the active site.
The yeast Saccharomyces cerevisiae IMA multigene family encodes four isomaltases sharing high sequence identity from 65% to 99%. Here, we explore their functional diversity, with exhaustive in-vitro characterization of their enzymological and biochemical properties. The four isoenzymes exhibited a preference for the α-(1,6) disaccharides isomaltose and palatinose, with Michaëlis–Menten kinetics and inhibition at high substrates concentration. They were also able to hydrolyze trisaccharides bearing an α-(1,6) linkage, but also α-(1,2), α-(1,3) and α-(1,5) disaccharides including sucrose, highlighting their substrate ambiguity. While Ima1p and Ima2p presented almost identical characteristics, our results nevertheless showed many singularities within this protein family. In particular, Ima3p presented lower activities and thermostability than Ima2p despite only three different amino acids between the sequences of these two isoforms. The Ima3p_R279Q variant recovered activity levels of Ima2p, while the Leu-to-Pro substitution at position 240 significantly increased the stability of Ima3p and supported the role of prolines in thermostability. The most distant protein, Ima5p, presented the lowest optimal temperature and was also extremely sensitive to temperature. Isomaltose hydrolysis by Ima5p challenged previous conclusions about the requirement of specific amino acids for determining the specificity for α-(1,6) substrates. We finally found a mixed inhibition by maltose for Ima5p while, contrary to a previous work, Ima1p inhibition by maltose was competitive at very low isomaltose concentrations and uncompetitive as the substrate concentration increased. Altogether, this work illustrates that a gene family encoding proteins with strong sequence similarities can lead to enzyme with notable differences in biochemical and enzymological properties.
Collapse
|
30
|
O'Connell KJ, O'Connell Motherway M, O'Callaghan J, Fitzgerald GF, Ross RP, Ventura M, Stanton C, van Sinderen D. Metabolism of four α-glycosidic linkage-containing oligosaccharides by Bifidobacterium breve UCC2003. Appl Environ Microbiol 2013; 79:6280-92. [PMID: 23913435 PMCID: PMC3811189 DOI: 10.1128/aem.01775-13] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 08/01/2013] [Indexed: 11/20/2022] Open
Abstract
Members of the genus Bifidobacterium are common inhabitants of the gastrointestinal tracts of humans and other mammals, where they ferment many diet-derived carbohydrates that cannot be digested by their hosts. To extend our understanding of bifidobacterial carbohydrate utilization, we investigated the molecular mechanisms by which 11 strains of Bifidobacterium breve metabolize four distinct α-glucose- and/or α-galactose-containing oligosaccharides, namely, raffinose, stachyose, melibiose, and melezitose. Here we demonstrate that all B. breve strains examined possess the ability to utilize raffinose, stachyose, and melibiose. However, the ability to metabolize melezitose was not common to all B. breve strains tested. Transcriptomic and functional genomic approaches identified a gene cluster dedicated to the metabolism of α-galactose-containing carbohydrates, while an adjacent gene cluster, dedicated to the metabolism of α-glucose-containing melezitose, was identified in strains that are able to use this carbohydrate.
Collapse
Affiliation(s)
- Kerry Joan O'Connell
- Department of Microbiology
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Mary O'Connell Motherway
- Department of Microbiology
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - John O'Callaghan
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
- Teagasc Research Centre Moorepark, Fermoy, Cork, Ireland
| | - Gerald F. Fitzgerald
- Department of Microbiology
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - R. Paul Ross
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
- Teagasc Research Centre Moorepark, Fermoy, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Genetics, Biology of Microorganisms, Anthropology and Evolution, University of Parma, Parma, Italy
| | - Catherine Stanton
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
- Teagasc Research Centre Moorepark, Fermoy, Cork, Ireland
| | - Douwe van Sinderen
- Department of Microbiology
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| |
Collapse
|
31
|
Abou Hachem M, Andersen JM, Barrangou R, Møller MS, Fredslund F, Majumder A, Ejby M, Lahtinen SJ, Jacobsen S, Lo Leggio L, Goh YJ, Klaenhammer TR, Svensson B. Recent insight into oligosaccharide uptake and metabolism in probiotic bacteria. BIOCATAL BIOTRANSFOR 2013. [DOI: 10.3109/10242422.2013.828048] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
32
|
Andersen JM, Barrangou R, Abou Hachem M, Lahtinen SJ, Goh YJ, Svensson B, Klaenhammer TR. Transcriptional analysis of oligosaccharide utilization by Bifidobacterium lactis Bl-04. BMC Genomics 2013; 14:312. [PMID: 23663691 PMCID: PMC3684542 DOI: 10.1186/1471-2164-14-312] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 04/18/2013] [Indexed: 02/02/2023] Open
Abstract
Background Probiotic bifidobacteria in combination with prebiotic carbohydrates have documented positive effects on human health regarding gastrointestinal disorders and improved immunity, however the selective routes of uptake remain unknown for most candidate prebiotics. The differential transcriptomes of Bifidobacterium animalis subsp. lactis Bl-04, induced by 11 potential prebiotic oligosaccharides were analyzed to identify the genetic loci involved in the uptake and catabolism of α- and β-linked hexoses, and β-xylosides. Results The overall transcriptome was modulated dependent on the type of glycoside (galactosides, glucosides or xylosides) utilized. Carbohydrate transporters of the major facilitator superfamily (induced by gentiobiose and β-galacto-oligosaccharides (GOS)) and ATP-binding cassette (ABC) transporters (upregulated by cellobiose, GOS, isomaltose, maltotriose, melibiose, panose, raffinose, stachyose, xylobiose and β-xylo-oligosaccharides) were differentially upregulated, together with glycoside hydrolases from families 1, 2, 13, 36, 42, 43 and 77. Sequence analysis of the identified solute-binding proteins that determine the specificity of ABC transporters revealed similarities in the breadth and selectivity of prebiotic utilization by bifidobacteria. Conclusion This study identified the differential gene expression for utilization of potential prebiotics highlighting the extensive capabilities of Bifidobacterium lactis Bl-04 to utilize oligosaccharides. Results provide insights into the ability of this probiotic microbe to utilize indigestible carbohydrates in the human gastrointestinal tract.
Collapse
Affiliation(s)
- Joakim M Andersen
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Søltofts Plads Building 224, Kgs. Lyngby DK-2800, Denmark
| | | | | | | | | | | | | |
Collapse
|
33
|
O'Connell Motherway M, Kinsella M, Fitzgerald GF, van Sinderen D. Transcriptional and functional characterization of genetic elements involved in galacto-oligosaccharide utilization by Bifidobacterium breve UCC2003. Microb Biotechnol 2012. [PMID: 23199239 PMCID: PMC3815386 DOI: 10.1111/1751-7915.12011] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Several prebiotics, such as inulin, fructo-oligosaccharides and galacto-oligosaccharides, are widely used commercially in foods and there is convincing evidence, in particular for galacto-oligosaccharides, that prebiotics can modulate the microbiota and promote bifidobacterial growth in the intestinal tract of infants and adults. In this study we describe the identification and functional characterization of the genetic loci responsible for the transport and metabolism of purified galacto-oligosaccharides (PGOS) by Bifidobacterium breve UCC2003. We further demonstrate that an extracellular endogalactanase specified by several B. breve strains, including B. breve UCC2003, is essential for partial degradation of PGOS components with a high degree of polymerization. These partially hydrolysed PGOS components are presumed to be transported into the bifidobacterial cell via various ABC transport systems and sugar permeases where they are further degraded to galactose and glucose monomers that feed into the bifid shunt. This work significantly advances our molecular understanding of bifidobacterial PGOS metabolism and its associated genetic machinery to utilize this prebiotic.
Collapse
Affiliation(s)
- Mary O'Connell Motherway
- Alimentary Pharmabiotic Centre, National University of Ireland, Western Road, Cork, Ireland; Departments of Microbiology, National University of Ireland, Western Road, Cork, Ireland
| | | | | | | |
Collapse
|
34
|
In vitro fermentation of commercial α-gluco-oligosaccharide by faecal microbiota from lean and obese human subjects. Br J Nutr 2012; 109:1980-9. [PMID: 23116939 DOI: 10.1017/s0007114512004205] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The fermentation selectivity of a commercial source of a-gluco-oligosaccharides (BioEcolians; Solabia) was investigated in vitro. Fermentation by faecal bacteria from four lean and four obese healthy adults was determined in anaerobic, pH-controlled faecal batch cultures. Inulin was used as a positive prebiotic control. Samples were obtained at 0, 10, 24 and 36 h for bacterial enumeration by fluorescent in situ hybridisation and SCFA analyses. Gas production during fermentation was investigated in non-pH-controlled batch cultures. a-Gluco-oligosaccharides significantly increased the Bifidobacterium sp. population compared with the control. Other bacterial groups enumerated were unaffected with the exception of an increase in the Bacteroides–Prevotella group and a decrease in Faecalibacterium prausnitzii on both a-gluco-oligosaccharides and inulin compared with baseline. An increase in acetate and propionate was seen on both substrates. The fermentation of a-gluco-oligosaccharides produced less total gas at a more gradual rate of production than inulin. Generally, substrates fermented with the obese microbiota produced similar results to the lean fermentation regarding bacteriology and metabolic activity. No significant difference at baseline (0 h) was detected between the lean and obese individuals in any of the faecal bacterial groups studied.
Collapse
|
35
|
Kim JY, Wang Y, Park SJ, Ji GE, Park MS. Cloning and expression of β-glucosidases from Bifidobacterium lactis AD011. Food Sci Biotechnol 2012. [DOI: 10.1007/s10068-012-0095-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
|
36
|
Enzymology and structure of the GH13_31 glucan 1,6-α-glucosidase that confers isomaltooligosaccharide utilization in the probiotic Lactobacillus acidophilus NCFM. J Bacteriol 2012; 194:4249-59. [PMID: 22685275 DOI: 10.1128/jb.00622-12] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Isomaltooligosaccharides (IMO) have been suggested as promising prebiotics that stimulate the growth of probiotic bacteria. Genomes of probiotic lactobacilli from the acidophilus group, as represented by Lactobacillus acidophilus NCFM, encode α-1,6 glucosidases of the family GH13_31 (glycoside hydrolase family 13 subfamily 31) that confer degradation of IMO. These genes reside frequently within maltooligosaccharide utilization operons, which include an ATP-binding cassette transporter and α-glucan active enzymes, e.g., maltogenic amylases and maltose phosphorylases, and they also occur separated from any carbohydrate transport or catabolism genes on the genomes of some acidophilus complex members, as in L. acidophilus NCFM. Besides the isolated locus encoding a GH13_31 enzyme, the ABC transporter and another GH13 in the maltooligosaccharide operon were induced in response to IMO or maltotetraose, as determined by reverse transcription-PCR (RT-PCR) transcriptional analysis, suggesting coregulation of α-1,6- and α-1,4-glucooligosaccharide utilization loci in L. acidophilus NCFM. The L. acidophilus NCFM GH13_31 (LaGH13_31) was produced recombinantly and shown to be a glucan 1,6-α-glucosidase active on IMO and dextran and product-inhibited by glucose. The catalytic efficiency of LaGH13_31 on dextran and the dextran/panose (trisaccharide) efficiency ratio were the highest reported for this class of enzymes, suggesting higher affinity at distal substrate binding sites. The crystal structure of LaGH13_31 was determined to a resolution of 2.05 Å and revealed additional substrate contacts at the +2 subsite in LaGH13_31 compared to the GH13_31 from Streptococcus mutans (SmGH13_31), providing a possible structural rationale to the relatively high affinity for dextran. A comprehensive phylogenetic and activity motif analysis mapped IMO utilization enzymes from gut microbiota to rationalize preferential utilization of IMO by gut residents.
Collapse
|
37
|
Cronin M, Zomer A, Fitzgerald GF, van Sinderen D. Identification of iron-regulated genes of Bifidobacterium breve UCC2003 as a basis for controlled gene expression. Bioeng Bugs 2012; 3:157-67. [PMID: 22179149 DOI: 10.4161/bbug.18985] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Iron is an essential growth factor for virtually all organisms. However, iron is not readily available in most environments and microorganisms have evolved specialized mechanisms, such as the use of siderophores and high-affinity transport systems, to acquire iron when confronted with iron-limiting conditions. In general these systems are tightly regulated to prevent iron-induced toxicity and because they are quite costly to the microbe. Because of this tight regulation we chose to explore the response of Bifidobacterium breve UCC2003 to iron limitation. Through microarray and complementation analyses we identified and characterized a presumed ferrous iron uptake system, encoded by bfeUOB, from B. breve UCC2003 and exploited its regulated transcription to develop an inducible expression system for use in bifidobacteria.
Collapse
Affiliation(s)
- Michelle Cronin
- Alimentary Pharmabiotic Centre and Department of Microbiology, University College Cork, Cork, Ireland
| | | | | | | |
Collapse
|
38
|
Sarbini SR, Kolida S, Naeye T, Einerhand A, Brison Y, Remaud-Simeon M, Monsan P, Gibson GR, Rastall RA. In vitro fermentation of linear and alpha-1,2-branched dextrans by the human fecal microbiota. Appl Environ Microbiol 2011; 77:5307-15. [PMID: 21666027 PMCID: PMC3147461 DOI: 10.1128/aem.02568-10] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Accepted: 05/16/2011] [Indexed: 01/10/2023] Open
Abstract
The role of structure and molecular weight in fermentation selectivity in linear α-1,6 dextrans and dextrans with α-1,2 branching was investigated. Fermentation by gut bacteria was determined in anaerobic, pH-controlled fecal batch cultures after 36 h. Inulin (1%, wt/vol), which is a known prebiotic, was used as a control. Samples were obtained at 0, 10, 24, and 36 h of fermentation for bacterial enumeration by fluorescent in situ hybridization and short-chain fatty acid analyses. The gas production of the substrate fermentation was investigated in non-pH-controlled, fecal batch culture tubes after 36 h. Linear and branched 1-kDa dextrans produced significant increases in Bifidobacterium populations. The degree of α-1,2 branching did not influence the Bifidobacterium populations; however, α-1,2 branching increased the dietary fiber content, implying a decrease in digestibility. Other measured bacteria were unaffected by the test substrates except for the Bacteroides-Prevotella group, the growth levels of which were increased on inulin and 6- and 70-kDa dextrans, and the Faecalibacterium prausnitzii group, the growth levels of which were decreased on inulin and 1-kDa dextrans. A considerable increase in short-chain fatty acid concentration was measured following the fermentation of all dextrans and inulin. Gas production rates were similar among all dextrans tested but were significantly slower than that for inulin. The linear 1-kDa dextran produced lower total gas and shorter time to attain maximal gas production compared to those of the 70-kDa dextran (branched) and inulin. These findings indicate that dextrans induce a selective effect on the gut flora, short-chain fatty acids, and gas production depending on their length.
Collapse
Affiliation(s)
- Shahrul R. Sarbini
- Department of Food and Nutritional Sciences, University of Reading, Whiteknights, P.O. Box 226, Reading RG6 6AP, United Kingdom
| | - Sofia Kolida
- Department of Food and Nutritional Sciences, University of Reading, Whiteknights, P.O. Box 226, Reading RG6 6AP, United Kingdom
| | - Thierry Naeye
- Tate and Lyle Innovation Centre 22, Avenue de'Horizon, Parc Scientifique de la Haute Borne, Villeneuve d'Asq, 59650 France
| | - Alexandra Einerhand
- Tate and Lyle Innovation Centre 22, Avenue de'Horizon, Parc Scientifique de la Haute Borne, Villeneuve d'Asq, 59650 France
| | - Yoann Brison
- Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés UMR CNRS/INSA 5504, UMR INRA/INSA 792, INSA, 135 Avenue de Rangueil, 31077 Toulouse Cedex 4, France
| | - Magali Remaud-Simeon
- Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés UMR CNRS/INSA 5504, UMR INRA/INSA 792, INSA, 135 Avenue de Rangueil, 31077 Toulouse Cedex 4, France
| | - Pierre Monsan
- Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés UMR CNRS/INSA 5504, UMR INRA/INSA 792, INSA, 135 Avenue de Rangueil, 31077 Toulouse Cedex 4, France
| | - Glenn R. Gibson
- Department of Food and Nutritional Sciences, University of Reading, Whiteknights, P.O. Box 226, Reading RG6 6AP, United Kingdom
| | - Robert A. Rastall
- Department of Food and Nutritional Sciences, University of Reading, Whiteknights, P.O. Box 226, Reading RG6 6AP, United Kingdom
| |
Collapse
|
39
|
O'Connell Motherway M, Zomer A, Leahy SC, Reunanen J, Bottacini F, Claesson MJ, O'Brien F, Flynn K, Casey PG, Moreno Munoz JA, Kearney B, Houston AM, O'Mahony C, Higgins DG, Shanahan F, Palva A, de Vos WM, Fitzgerald GF, Ventura M, O'Toole PW, van Sinderen D. Functional genome analysis of Bifidobacterium breve UCC2003 reveals type IVb tight adherence (Tad) pili as an essential and conserved host-colonization factor. Proc Natl Acad Sci U S A 2011; 108:11217-22. [PMID: 21690406 PMCID: PMC3131351 DOI: 10.1073/pnas.1105380108] [Citation(s) in RCA: 281] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Development of the human gut microbiota commences at birth, with bifidobacteria being among the first colonizers of the sterile newborn gastrointestinal tract. To date, the genetic basis of Bifidobacterium colonization and persistence remains poorly understood. Transcriptome analysis of the Bifidobacterium breve UCC2003 2.42-Mb genome in a murine colonization model revealed differential expression of a type IVb tight adherence (Tad) pilus-encoding gene cluster designated "tad(2003)." Mutational analysis demonstrated that the tad(2003) gene cluster is essential for efficient in vivo murine gut colonization, and immunogold transmission electron microscopy confirmed the presence of Tad pili at the poles of B. breve UCC2003 cells. Conservation of the Tad pilus-encoding locus among other B. breve strains and among sequenced Bifidobacterium genomes supports the notion of a ubiquitous pili-mediated host colonization and persistence mechanism for bifidobacteria.
Collapse
MESH Headings
- Amino Acid Sequence
- Animals
- Bacterial Proteins/genetics
- Bacterial Proteins/physiology
- Base Sequence
- Bifidobacterium/genetics
- Bifidobacterium/growth & development
- Bifidobacterium/physiology
- Bifidobacterium/ultrastructure
- Comparative Genomic Hybridization
- DNA, Bacterial/genetics
- Female
- Fimbriae, Bacterial/genetics
- Fimbriae, Bacterial/physiology
- Fimbriae, Bacterial/ultrastructure
- Gastrointestinal Tract/microbiology
- Gene Expression Regulation, Bacterial
- Genome, Bacterial
- Germ-Free Life
- Humans
- Male
- Metagenome
- Mice
- Mice, Inbred BALB C
- Microscopy, Electron, Transmission
- Microscopy, Immunoelectron
- Molecular Sequence Data
- Multigene Family
- Mutation
- Sequence Homology, Amino Acid
Collapse
Affiliation(s)
| | - Aldert Zomer
- Alimentary Pharmabiotic Centre and Departments of
| | - Sinead C. Leahy
- Alimentary Pharmabiotic Centre and Departments of
- Microbiology
| | - Justus Reunanen
- Division of Microbiology and Epidemiology, Department of Basic Veterinary Medicine, University of Helsinki, FIN-00014, Helsinki, Finland
| | - Francesca Bottacini
- Alimentary Pharmabiotic Centre and Departments of
- Microbiology
- Laboratory of Probiogenomics, Department of Genetics, Biology of Microorganisms, Anthropology, and Evolution, University of Parma, 43100 Parma, Italy
| | | | | | - Kiera Flynn
- Alimentary Pharmabiotic Centre and Departments of
| | | | | | | | | | | | - Des G. Higgins
- Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland; and
| | - Fergus Shanahan
- Alimentary Pharmabiotic Centre and Departments of
- Medicine, and
| | - Airi Palva
- Division of Microbiology and Epidemiology, Department of Basic Veterinary Medicine, University of Helsinki, FIN-00014, Helsinki, Finland
| | - Willem M. de Vos
- Division of Microbiology and Epidemiology, Department of Basic Veterinary Medicine, University of Helsinki, FIN-00014, Helsinki, Finland
- Laboratory of Microbiology, Wageningen University, 6703 HB, Wageningen, The Netherlands
| | - Gerald F. Fitzgerald
- Alimentary Pharmabiotic Centre and Departments of
- Microbiology
- Food and Nutritional Sciences, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Genetics, Biology of Microorganisms, Anthropology, and Evolution, University of Parma, 43100 Parma, Italy
| | - Paul W. O'Toole
- Alimentary Pharmabiotic Centre and Departments of
- Microbiology
| | | |
Collapse
|
40
|
Pokusaeva K, Fitzgerald GF, van Sinderen D. Carbohydrate metabolism in Bifidobacteria. GENES AND NUTRITION 2011; 6:285-306. [PMID: 21484167 DOI: 10.1007/s12263-010-0206-6] [Citation(s) in RCA: 485] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 10/18/2010] [Accepted: 12/15/2010] [Indexed: 12/17/2022]
Abstract
Members of the genus Bifidobacterium can be found as components of the gastrointestinal microbiota, and are believed to play an important role in maintaining and promoting human health by eliciting a number of beneficial properties. Bifidobacteria can utilize a diverse range of dietary carbohydrates that escape degradation in the upper parts of the intestine, many of which are plant-derived oligo- and polysaccharides. The gene content of a bifidobacterial genome reflects this apparent metabolic adaptation to a complex carbohydrate-rich gastrointestinal tract environment as it encodes a large number of predicted carbohydrate-modifying enzymes. Different bifidobacterial strains may possess different carbohydrate utilizing abilities, as established by a number of studies reviewed here. Carbohydrate-degrading activities described for bifidobacteria and their relevance to the deliberate enhancement of number and/or activity of bifidobacteria in the gut are also discussed in this review.
Collapse
Affiliation(s)
- Karina Pokusaeva
- Alimentary Pharmabiotic Centre, Department of Microbiology, University College Cork, Western Road, Cork, Ireland
| | | | | |
Collapse
|
41
|
Cronin M, Ventura M, Fitzgerald GF, van Sinderen D. Progress in genomics, metabolism and biotechnology of bifidobacteria. Int J Food Microbiol 2011; 149:4-18. [PMID: 21320731 DOI: 10.1016/j.ijfoodmicro.2011.01.019] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Revised: 01/06/2011] [Accepted: 01/10/2011] [Indexed: 12/16/2022]
Abstract
Members of the genus Bifidobacterium were first described over a century ago and were quickly associated with a healthy intestinal tract due to their numerical dominance in breast-fed babies as compared to bottle-fed infants. Health benefits elicited by bifidobacteria to its host, as supported by clinical trials, have led to their wide application as probiotic components of health-promoting foods, especially in fermented dairy products. However, the relative paucity of genetic tools available for bifidobacteria has impeded development of a comprehensive molecular understanding of this genus. In this review we present a summary of current knowledge on bifidobacterial metabolism, classification, physiology and genetics and outline the currently available methods for genetically accessing and manipulating the genus.
Collapse
Affiliation(s)
- Michelle Cronin
- Cork Cancer Research Centre, Mercy University Hospital and Leslie C. Quick Jnr. Laboratory, University College Cork, Cork, Ireland
| | | | | | | |
Collapse
|
42
|
Cellodextrin utilization by bifidobacterium breve UCC2003. Appl Environ Microbiol 2011; 77:1681-90. [PMID: 21216899 DOI: 10.1128/aem.01786-10] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Cellodextrins, the incomplete hydrolysis products from insoluble cellulose, are accessible as a carbon source to certain members of the human gut microbiota, such as Bifidobacterium breve UCC2003. Transcription of the cldEFGC gene cluster of B. breve UCC2003 was shown to be induced upon growth on cellodextrins, implicating this cluster in the metabolism of these sugars. Phenotypic analysis of a B. breve UCC2003::cldE insertion mutant confirmed that the cld gene cluster is exclusively required for cellodextrin utilization by this commensal. Moreover, our results suggest that transcription of the cld cluster is controlled by a LacI-type regulator encoded by cldR, located immediately upstream of cldE. Gel mobility shift assays using purified CldR(His) (produced by the incorporation of a His(12)-encoding sequence into the 3' end of the cldC gene) indicate that the cldEFGC promoter is subject to negative control by CldR(His), which binds to two inverted repeats. Analysis by high-performance anion-exchange chromatography with pulsed amperometric detection (HPAEC-PAD) of medium samples obtained during growth of B. breve UCC2003 on a mixture of cellodextrins revealed its ability to utilize cellobiose, cellotriose, cellotetraose, and cellopentaose, with cellotriose apparently representing the preferred substrate. The cldC gene of the cld operon of B. breve UCC2003 is, to the best of our knowledge, the first described bifidobacterial β-glucosidase exhibiting hydrolytic activity toward various cellodextrins.
Collapse
|
43
|
Turroni F, van Sinderen D, Ventura M. Genomics and ecological overview of the genus Bifidobacterium. Int J Food Microbiol 2010; 149:37-44. [PMID: 21276626 DOI: 10.1016/j.ijfoodmicro.2010.12.010] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Revised: 12/09/2010] [Accepted: 12/10/2010] [Indexed: 01/01/2023]
Abstract
Members of the genus Bifidobacterium are high G+C Gram positive bacteria belonging to the phylum Actinobacteria, and represent common inhabitants of the gastro-intestinal tract (GIT) of mammals, birds and certain cold-blooded animals. The overall microbial population that resides in the GIT, referred to as the "gut microbiota", is an extremely complex community of microorganisms whose functions are believed to have a significant impact on human physiology. Different ecological relationships between bifidobacteria and their host can be developed, ranging from opportunistic pathogenic interactions (e.g. in the case of Bifidobacterium dentium) to a commensal or even health-promoting relationship (e.g. in the case of Bifidobacterium bifidum and Bifidobacterium breve species). Among the known health-promoting or probiotic microorganisms, bifidobacteria represent one of the most dominant group and some bifidobacterial species are frequently used as the probiotic ingredient in many functional foods. However, despite the generally accepted importance of bifidobacteria as constituents of the human microbiota, there is only limited information available on their phylogeny, physiology and genetics. Moreover, host-microbiota interactions and cross-talk between different members of the gut microbiota are far from completely understood although they represent a crucial factor in the development and maintenance of human physiology and immune system. The aim of this review is to highlight the genetic and functional features of bifidobacteria residing in the human GIT using genomic and ecology-based information.
Collapse
Affiliation(s)
- Francesca Turroni
- Laboratory of Probiogenomics, Department of Genetics, Biology of Microorganisms, Anthropology and Evolution University of Parma, Italy
| | | | | |
Collapse
|
44
|
O'Connell Motherway M, Fitzgerald GF, van Sinderen D. Metabolism of a plant derived galactose-containing polysaccharide by Bifidobacterium breve UCC2003. Microb Biotechnol 2010; 4:403-16. [PMID: 21375716 PMCID: PMC3818998 DOI: 10.1111/j.1751-7915.2010.00218.x] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
In this study, we describe the functional characterization of the Bifidobacterium breve UCC2003 gal locus, which is dedicated to the utilization of galactan, a plant‐derived polysaccharide. Using a combination of molecular approaches we conclude that the galA gene of B. breve UCC2003 encodes a β‐1,4‐endogalactanase producing galacto‐oligosaccharides, which are specifically internalized by an ABC transport system, encoded by galBCDE, and which are then hydrolysed to galactose moieties by a dedicated intracellular β‐galactosidase, specified by galG. The generated galactose molecules are presumed to be fed into the fructose‐6‐phosphate phosphoketolase pathway via the Leloir pathway, thereby allowing B. breve UCC2003 to use galactan as its sole carbon and energy source. In addition to these findings we demonstrate that GalR is a LacI‐type DNA‐binding protein, which not only appears to control transcription of the galCDEGR operon, but also that of the galA gene.
Collapse
Affiliation(s)
- Mary O'Connell Motherway
- Alimentary Pharmabiotic Centre, National University of Ireland, Cork, Western Road, Cork, Ireland
| | | | | |
Collapse
|
45
|
Pokusaeva K, Neves AR, Zomer A, O'Connell-Motherway M, MacSharry J, Curley P, Fitzgerald GF, van Sinderen D. Ribose utilization by the human commensal Bifidobacterium breve UCC2003. Microb Biotechnol 2009; 3:311-23. [PMID: 21255330 PMCID: PMC3815373 DOI: 10.1111/j.1751-7915.2009.00152.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Growth of Bifidobacterium breve UCC2003 on ribose leads to the transcriptional induction of the rbsACBDK gene cluster. Generation and phenotypic analysis of an rbsA insertion mutant established that the rbs gene cluster is essential for ribose utilization, and that its transcription is likely regulated by a LacI‐type regulator encoded by rbsR, located immediately upstream of rbsA. Gel mobility shift assays using purified RbsRHis indicate that the promoter upstream of rbsABCDK is negatively controlled by RbsRHis binding to an 18 bp inverted repeat and that RbsRHis binding activity is modulated by d‐ribose. The rbsK gene of the rbs operon of B. breve UCC2003 was shown to specify a ribokinase (EC 2.7.1.15), which specifically directs its phosphorylating activity towards d‐ribose, converting this pentose sugar to ribose‐5‐phosphate.
Collapse
Affiliation(s)
- Karina Pokusaeva
- Alimentary Pharmabiotic Centre, Department of Microbiology, University College Cork, Western Road, Cork, Ireland
| | | | | | | | | | | | | | | |
Collapse
|