1
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Zhang P, Xue Y, Cao Z, Guo Y, Pang X, Chen C, Zhang W. Raffinose Ameliorates DSS-Induced Colitis in Mice by Modulating Gut Microbiota and Targeting the Inflammatory TLR4-MyD88-NF-κB Signaling Pathway. Foods 2024; 13:1849. [PMID: 38928791 PMCID: PMC11203344 DOI: 10.3390/foods13121849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 06/02/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024] Open
Abstract
This study aimed to explore the protective effects of raffinose (Raf) against inflammatory bowel disease in mice with colitis. Mice were administered 100, 200, or 400 mg/kg Raf for 21 d, followed by drinking-water containing 3% dextran sulfate sodium salt (DSS) for 3 d. Thereafter, the phenotype, pathological lesions in the colon, cytokines levels, and gut microbiota were evaluated. Treatment with Raf reduced the severity of the pathological changes in the colon, mitigating the reduction in colon length. Following Raf intervention, serum levels of inflammatory cytokines (IL-2, IL-6, IL-1β, and TNF-α) tended to return to normal. These results suggest that the anti-inflammatory effects of Raf are associated with a reduction in TLR4-MyD88-NF-κB pathway expression in mouse colonic tissues. Analysis of gut microbiota abundance and its correlation with colitis parameters revealed that DSS-induced dysbiosis was partially mitigated by Raf. In conclusion, Raf exerts a protective effect in colitis by modulating the gut microbiota and TLR4-MyD88-NF-κB pathway.
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2
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Yu L, Xiao M, Tian F, Chen W, Zhai Q. Glycan utilization properties govern the cross-feeding network in gut microbiota: A focus on Bifidobacteria. Sci Bull (Beijing) 2024; 69:299-302. [PMID: 38129235 DOI: 10.1016/j.scib.2023.11.060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Affiliation(s)
- Leilei Yu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Meifang Xiao
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Fengwei Tian
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Wei Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
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3
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Zhang C, Yu L, Ma C, Jiang S, Zhang Y, Wang S, Tian F, Xue Y, Zhao J, Zhang H, Liu L, Chen W, Huang S, Zhang J, Zhai Q. A key genetic factor governing arabinan utilization in the gut microbiome alleviates constipation. Cell Host Microbe 2023; 31:1989-2006.e8. [PMID: 37992712 DOI: 10.1016/j.chom.2023.10.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 09/01/2023] [Accepted: 10/11/2023] [Indexed: 11/24/2023]
Abstract
Impaired gastrointestinal motility is associated with gut dysbiosis. Probiotics, such as Bifidobacteria, can improve this bowel disorder; however, efficacy is strain-dependent. We determine that a genetic factor, the abfA cluster governing arabinan utilization, in Bifidobacterium longum impacts treatment efficacy against functional constipation (FC). In mice with FC, B. longum, but not an abfA mutant, improved gastrointestinal transit time, an affect that was dependent upon dietary arabinan. abfA genes were identified in other commensal bacteria, whose effects in ameliorating murine FC were similarly abfA-dependent. In a double-blind, randomized, placebo-controlled clinical trial, supplementation with abfA-cluster-carrying B. longum, but not an abfA-deficient strain, enriched arabinan-utilization residents, increased beneficial metabolites, and improved FC symptoms. Across human cohorts, abfA-cluster abundance can predict FC, and transplantation of abfA cluster-enriched human microbiota to FC-induced germ-free mice improved gut motility. Collectively, these findings demonstrate a role for microbial abfA cluster in ameliorating FC, establishing principles for genomics-directed probiotic therapies.
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Affiliation(s)
- Chengcheng Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Leilei Yu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Chenchen Ma
- College of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou 570228, China
| | - Shuaiming Jiang
- College of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou 570228, China
| | - Yufeng Zhang
- Faculty of Dentistry, University of Hong Kong, Hong Kong SAR, China
| | - Shunhe Wang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Fengwei Tian
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Yuzheng Xue
- Department of Gastroenterology, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Liming Liu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China
| | - Wei Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Shi Huang
- Faculty of Dentistry, University of Hong Kong, Hong Kong SAR, China.
| | - Jiachao Zhang
- College of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou 570228, China.
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
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4
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SHIMADA M, KAWASE Y, SONOYAMA K, OGURA Y, HAYASHI T, YOKOTA A, FUKIYA S. Development of an improved colonization system for human-derived Bifidobacterium longum subsp. longum in conventional mice through the feeding of raffinose or 1-kestose. BIOSCIENCE OF MICROBIOTA, FOOD AND HEALTH 2023; 43:110-119. [PMID: 38562544 PMCID: PMC10981944 DOI: 10.12938/bmfh.2023-055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 11/05/2023] [Indexed: 04/04/2024]
Abstract
How bifidobacteria colonize and survive in the intestine is not fully understood. The administration of bifidobacteria to conventional mice can be used to evaluate their ability to colonize the intestine in the presence of endogenous gut microbiota. However, human-derived bifidobacteria do not readily colonize the intestines of conventional mice, and although colonization by Bifidobacterium breve UCC2003 has been achieved, the viability of such populations requires improvement. Therefore, we aimed to establish a colonization system with human-derived bifidobacteria of high viability in conventional mice using Bifidobacterium longum subsp. longum 105-A. Lactose, raffinose, and 1-kestose were identified as the preferred carbohydrate sources for the growth of this strain in culture. The administration of B. longum 105-A to conventional BALB/c mice fed these carbohydrates showed that diets containing 6% (w/w) raffinose or 1-kestose facilitated colonization with >108 colony-forming units/g feces for 2 weeks. The population of this strain was more stable in the raffinose-fed group than in the 1-kestose-fed group. The ingestion of these prebiotics had a greater impact on the composition of the microbiota than the administration of B. longum 105-A. The ingestion of these prebiotics also increased the fecal concentrations of organic acids, which was indicative of greater intestinal fermentation. Collectively, we established a colonization system for B. longum 105-A with high viability in conventional mice by feeding the mice raffinose or 1-kestose. This system should be useful for elucidation of the mechanisms of colonization and survival of bifidobacteria in the intestines in the presence of the endogenous gut microbiota.
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Affiliation(s)
- Mina SHIMADA
- Laboratory of Microbial Physiology, Research Faculty of
Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo, Hokkaido 060-8589,
Japan
| | - Youhei KAWASE
- Laboratory of Microbial Physiology, Research Faculty of
Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo, Hokkaido 060-8589,
Japan
| | - Kei SONOYAMA
- Laboratory of Food Biochemistry, Research Faculty of
Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo, Hokkaido 060-8589,
Japan
| | - Yoshitoshi OGURA
- Department of Bacteriology, Faculty of Medical Sciences,
Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan
- Department of Infectious Medicine, Kurume University School
of Medicine, 67 Asahi-machi, Kurume-shi, Fukuoka 830-0011, Japan
| | - Tetsuya HAYASHI
- Department of Bacteriology, Faculty of Medical Sciences,
Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan
| | - Atsushi YOKOTA
- Laboratory of Microbial Physiology, Research Faculty of
Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo, Hokkaido 060-8589,
Japan
| | - Satoru FUKIYA
- Laboratory of Microbial Physiology, Research Faculty of
Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo, Hokkaido 060-8589,
Japan
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5
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Hu Y, Hong H, Zhou J, Cui Y, Zhang B, Zhao J. Recent advances in enzymatic properties, preparation methods, and functions of glycoside hydrolase from Bifidobacterium: a review. World J Microbiol Biotechnol 2023; 39:344. [PMID: 37843698 DOI: 10.1007/s11274-023-03770-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 09/15/2023] [Indexed: 10/17/2023]
Abstract
Bifidobacterium is a major probiotic of intestinal gut flora and exerts many physiological activities, and it is widely applied in the fields of food and medicine. As an important part of Bifidobacterium, glycoside hydrolase plays a role in its physiological activity. With the continuous development and improvement of genetic engineering technology, research on this type of enzyme will play a crucial role in promoting the further development of Bifidobacterium in the field of probiotics. In this review, the preparation methods, enzymatic properties, and functions of glycoside hydrolase extracted from Bifidobacterium are described and summarized. The common method for preparing glycoside hydrolase derived from Bifidobacterium is heterologous expression in Escherichia coli BL21. The optimal pH range for these glycoside hydrolase enzymes is between 4.5 and 7.5; the optimal temperature is between 30 and 50 °C, which is close to the optimal growth condition of Bifidobacterium. Based on substrate specificity, these glycoside hydrolase could hydrolyze synthetic substrates and natural oligosaccharides, including a series of pNP artificial substrates, disaccharide, and trisaccharides, while they have little ability to hydrolyze polysaccharide substrates. This review will be expected to provide a basis for the development of Bifidobacterium as a probiotic element.
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Affiliation(s)
- Yanbo Hu
- School of Food Sciences and Engineering, Chang Chun University, Changchun, 130024, People's Republic of China
| | - Huili Hong
- School of Food Sciences and Engineering, Chang Chun University, Changchun, 130024, People's Republic of China
| | - Jianing Zhou
- School of Food Sciences and Engineering, Chang Chun University, Changchun, 130024, People's Republic of China
| | - Yangyang Cui
- School of Food Sciences and Engineering, Chang Chun University, Changchun, 130024, People's Republic of China
| | - Baochun Zhang
- School of Food Sciences and Engineering, Chang Chun University, Changchun, 130024, People's Republic of China
| | - Jun Zhao
- School of Food Sciences and Engineering, Chang Chun University, Changchun, 130024, People's Republic of China.
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6
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Singh RP, Niharika J, Thakur R, Wagstaff BA, Kumar G, Kurata R, Patel D, Levy CW, Miyazaki T, Field RA. Utilization of dietary mixed-linkage β-glucans by the Firmicute Blautia producta. J Biol Chem 2023:104806. [PMID: 37172725 DOI: 10.1016/j.jbc.2023.104806] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 05/03/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023] Open
Abstract
The β-glucans are structurally varied, naturally occurring components of the cell walls and storage materials of a variety of plant and microbial species. In the human diet, mixed-linkage glucans [MLG - β-(1,3/4)-glucans] influence the gut microbiome and the host immune system. Although consumed daily, the molecular mechanism by which human gut Gram-positive bacteria utilize MLG largely remains unknown. In this study, we used Blautia producta ATCC 27340 as a model organism to develop understanding of MLG utilization. B. producta encodes a gene locus comprising a multi-modular cell-anchored endo-glucanase (BpGH16MLG), an ABC transporter, and a glycoside phosphorylase (BpGH94MLG) for utilizing MLG, as evidenced by the up-regulation of expression of the enzyme- and solute binding protein (SBP)-encoding genes in this cluster when the organism is grown on MLG. We determined that recombinant BpGH16MLG cleaved various types of β-glucan, generating oligosaccharides suitable for cellular uptake by B. producta. Cytoplasmic digestion of these oligosaccharides is then performed by recombinant BpGH94MLG and β-glucosidases (BpGH3-AR8MLG and BpGH3-X62MLG). Using targeted deletion, we demonstrated BpSBPMLG is essential for B. producta growth on barley β-glucan. Furthermore, we revealed that beneficial bacteria, such as Roseburia faecis JCM 17581T, Bifidobacterium pseudocatenulatum JCM 1200T, Bifidobacterium adolescentis JCM 1275T, and Bifidobacterium bifidum JCM 1254, can also utilize oligosaccharides resulting from the action of BpGH16MLG. Disentangling the β-glucan utilizing capability of B. producta provides a rational basis on which to consider the probiotic potential of this class of organism.
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Affiliation(s)
- Ravindra Pal Singh
- Gujarat Biotechnology University, Gujarat International Finance Tec (GIFT)-City, Gandhinagar- 382355, Gujarat, India; Division of Food and Nutritional Biotechnology, National Agri-Food Biotechnology Institute, SAS Nagar, Punjab, 140306, India.
| | - Jayashree Niharika
- Gujarat Biotechnology University, Gujarat International Finance Tec (GIFT)-City, Gandhinagar- 382355, Gujarat, India; Division of Food and Nutritional Biotechnology, National Agri-Food Biotechnology Institute, SAS Nagar, Punjab, 140306, India
| | - Raksha Thakur
- Division of Food and Nutritional Biotechnology, National Agri-Food Biotechnology Institute, SAS Nagar, Punjab, 140306, India
| | - Ben A Wagstaff
- Department of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Gulshan Kumar
- Division of Food and Nutritional Biotechnology, National Agri-Food Biotechnology Institute, SAS Nagar, Punjab, 140306, India
| | - Rikuya Kurata
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka City, Shizuoka, 422-8529, Japan
| | - Dhaval Patel
- Gujarat Biotechnology University, Gujarat International Finance Tec (GIFT)-City, Gandhinagar- 382355, Gujarat, India
| | - Colin W Levy
- Department of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Takatsugu Miyazaki
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka City, Shizuoka, 422-8529, Japan; Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka City, Shizuoka, 422-8529, Japan
| | - Robert A Field
- Department of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
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7
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Arzamasov AA, Nakajima A, Sakanaka M, Ojima MN, Katayama T, Rodionov DA, Osterman AL. Human Milk Oligosaccharide Utilization in Intestinal Bifidobacteria Is Governed by Global Transcriptional Regulator NagR. mSystems 2022; 7:e0034322. [PMID: 36094076 PMCID: PMC9599254 DOI: 10.1128/msystems.00343-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 08/23/2022] [Indexed: 12/24/2022] Open
Abstract
Bifidobacterium longum subsp. infantis is a prevalent beneficial bacterium that colonizes the human neonatal gut and is uniquely adapted to efficiently use human milk oligosaccharides (HMOs) as a carbon and energy source. Multiple studies have focused on characterizing the elements of HMO utilization machinery in B. longum subsp. infantis; however, the regulatory mechanisms governing the expression of these catabolic pathways remain poorly understood. A bioinformatic regulon reconstruction approach used in this study implicated NagR, a transcription factor from the ROK family, as a negative global regulator of gene clusters encoding lacto-N-biose/galacto-N-biose (LNB/GNB), lacto-N-tetraose (LNT), and lacto-N-neotetraose (LNnT) utilization pathways in B. longum subsp. infantis. This conjecture was corroborated by transcriptome profiling upon nagR genetic inactivation and experimental assessment of binding of recombinant NagR to predicted DNA operators. The latter approach also implicated N-acetylglucosamine (GlcNAc), a universal intermediate of LNT and LNnT catabolism, and its phosphorylated derivatives as plausible NagR transcriptional effectors. Reconstruction of NagR regulons in various Bifidobacterium lineages revealed multiple potential regulon expansion events, suggesting evolution from a local regulator of GlcNAc catabolism in ancestral bifidobacteria to a global regulator controlling the utilization of mixtures of GlcNAc-containing host glycans in B. longum subsp. infantis and Bifidobacterium bifidum. IMPORTANCE The predominance of bifidobacteria in the gut of breastfed infants is attributed to the ability of these bacteria to metabolize human milk oligosaccharides (HMOs). Thus, individual HMOs such as lacto-N-tetraose (LNT) and lacto-N-neotetraose (LNnT) are considered promising prebiotics that would stimulate the growth of bifidobacteria and confer multiple health benefits to preterm and malnourished children suffering from impaired (stunted) gut microbiota development. However, the rational selection of HMO-based prebiotics is hampered by the incomplete knowledge of regulatory mechanisms governing HMO utilization in target bifidobacteria. This study describes NagR-mediated transcriptional regulation of LNT and LNnT utilization in Bifidobacterium longum subsp. infantis. The elucidated regulatory network appears optimally adapted to simultaneous utilization of multiple HMOs, providing a rationale to add HMO mixtures (rather than individual components) to infant formulas. The study also provides insights into the evolutionary trajectories of complex regulatory networks controlling carbohydrate metabolism in bifidobacteria.
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Affiliation(s)
- Aleksandr A. Arzamasov
- Infectious and Inflammatory Diseases Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Aruto Nakajima
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | | | - Miriam N. Ojima
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Takane Katayama
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Dmitry A. Rodionov
- Infectious and Inflammatory Diseases Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Andrei L. Osterman
- Infectious and Inflammatory Diseases Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
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8
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Huang Y, Lin X, Yu S, Chen R, Chen W. Intestinal Engineered Probiotics as Living Therapeutics: Chassis Selection, Colonization Enhancement, Gene Circuit Design, and Biocontainment. ACS Synth Biol 2022; 11:3134-3153. [PMID: 36094344 DOI: 10.1021/acssynbio.2c00314] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Intestinal probiotics are often used for the in situ treatment of diseases, such as metabolic disorders, tumors, and chronic inflammatory infections. Recently, there has been an increased emphasis on intelligent, customized treatments with a focus on long-term efficacy; however, traditional probiotic therapy has not kept up with this trend. The use of synthetic biology to construct gut-engineered probiotics as live therapeutics is a promising avenue in the treatment of specific diseases, such as phenylketonuria and inflammatory bowel disease. These studies generally involve a series of fundamental design issues: choosing an engineered chassis, improving the colonization ability of engineered probiotics, designing functional gene circuits, and ensuring the safety of engineered probiotics. In this review, we summarize the relevant past research, the progress of current research, and discuss the key issues that restrict the widespread application of intestinal engineered probiotic living therapeutics.
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Affiliation(s)
- Yan Huang
- Team SZU-China at iGEM 2021, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Xiaojun Lin
- Team SZU-China at iGEM 2021, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Siyang Yu
- Team SZU-China at iGEM 2021, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Ruiyue Chen
- Team SZU-China at iGEM 2021, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Weizhao Chen
- Team SZU-China at iGEM 2021, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China.,Shenzhen Key Laboratory for Microbial Gene Engineering, Shenzhen University, Shenzhen 518060, China
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9
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Singh RP, Shadan A, Ma Y. Biotechnological Applications of Probiotics: A Multifarious Weapon to Disease and Metabolic Abnormality. Probiotics Antimicrob Proteins 2022; 14:1184-1210. [PMID: 36121610 PMCID: PMC9483357 DOI: 10.1007/s12602-022-09992-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/30/2022] [Indexed: 12/25/2022]
Abstract
Consumption of live microorganisms "Probiotics" for health benefits and well-being is increasing worldwide. Their use as a therapeutic approach to confer health benefits has fascinated humans for centuries; however, its conceptuality gradually evolved with methodological advancement, thereby improving our understanding of probiotics-host interaction. However, the emerging concern regarding safety aspects of live microbial is enhancing the interest in non-viable or microbial cell extracts, as they could reduce the risks of microbial translocation and infection. Due to technical limitations in the production and formulation of traditionally used probiotics, the scientific community has been focusing on discovering new microbes to be used as probiotics. In many scientific studies, probiotics have been shown as potential tools to treat metabolic disorders such as obesity, type-2 diabetes, non-alcoholic fatty liver disease, digestive disorders (e.g., acute and antibiotic-associated diarrhea), and allergic disorders (e.g., eczema) in infants. However, the mechanistic insight of strain-specific probiotic action is still unknown. In the present review, we analyzed the scientific state-of-the-art regarding the mechanisms of probiotic action, its physiological and immuno-modulation on the host, and new direction regarding the development of next-generation probiotics. We discuss the use of recently discovered genetic tools and their applications for engineering the probiotic bacteria for various applications including food, biomedical applications, and other health benefits. Finally, the review addresses the future development of biological techniques in combination with clinical and preclinical studies to explain the molecular mechanism of action, and discover an ideal multifunctional probiotic bacterium.
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Affiliation(s)
- Rajnish Prakash Singh
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand India
| | - Afreen Shadan
- Dr. Shyama Prasad Mukherjee University, Ranchi, Jharkhand India
| | - Ying Ma
- College of Resource and Environment, Southwest University, Chongqing, China
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10
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Laursen MF, Sakanaka M, von Burg N, Mörbe U, Andersen D, Moll JM, Pekmez CT, Rivollier A, Michaelsen KF, Mølgaard C, Lind MV, Dragsted LO, Katayama T, Frandsen HL, Vinggaard AM, Bahl MI, Brix S, Agace W, Licht TR, Roager HM. Bifidobacterium species associated with breastfeeding produce aromatic lactic acids in the infant gut. Nat Microbiol 2021; 6:1367-1382. [PMID: 34675385 PMCID: PMC8556157 DOI: 10.1038/s41564-021-00970-4] [Citation(s) in RCA: 184] [Impact Index Per Article: 61.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 08/26/2021] [Indexed: 12/12/2022]
Abstract
Breastfeeding profoundly shapes the infant gut microbiota, which is critical for early life immune development, and the gut microbiota can impact host physiology in various ways, such as through the production of metabolites. However, few breastmilk-dependent microbial metabolites mediating host-microbiota interactions are currently known. Here, we demonstrate that breastmilk-promoted Bifidobacterium species convert aromatic amino acids (tryptophan, phenylalanine and tyrosine) into their respective aromatic lactic acids (indolelactic acid, phenyllactic acid and 4-hydroxyphenyllactic acid) via a previously unrecognized aromatic lactate dehydrogenase (ALDH). The ability of Bifidobacterium species to convert aromatic amino acids to their lactic acid derivatives was confirmed using monocolonized mice. Longitudinal profiling of the faecal microbiota composition and metabolome of Danish infants (n = 25), from birth until 6 months of age, showed that faecal concentrations of aromatic lactic acids are correlated positively with the abundance of human milk oligosaccharide-degrading Bifidobacterium species containing the ALDH, including Bifidobacterium longum, B. breve and B. bifidum. We further demonstrate that faecal concentrations of Bifidobacterium-derived indolelactic acid are associated with the capacity of these samples to activate in vitro the aryl hydrocarbon receptor (AhR), a receptor important for controlling intestinal homoeostasis and immune responses. Finally, we show that indolelactic acid modulates ex vivo immune responses of human CD4+ T cells and monocytes in a dose-dependent manner by acting as an agonist of both the AhR and hydroxycarboxylic acid receptor 3 (HCA3). Our findings reveal that breastmilk-promoted Bifidobacterium species produce aromatic lactic acids in the gut of infants and suggest that these microbial metabolites may impact immune function in early life.
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Affiliation(s)
- Martin F Laursen
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Mikiyasu Sakanaka
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
- Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, Ishikawa, Japan
| | - Nicole von Burg
- Mucosal Immunology Group, Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Urs Mörbe
- Mucosal Immunology Group, Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Daniel Andersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Janne Marie Moll
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Ceyda T Pekmez
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg C, Denmark
| | - Aymeric Rivollier
- Mucosal Immunology Group, Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Kim F Michaelsen
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg C, Denmark
| | - Christian Mølgaard
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg C, Denmark
| | - Mads Vendelbo Lind
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg C, Denmark
| | - Lars O Dragsted
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg C, Denmark
| | - Takane Katayama
- Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, Ishikawa, Japan
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Henrik L Frandsen
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | | | - Martin I Bahl
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Susanne Brix
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - William Agace
- Mucosal Immunology Group, Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, Denmark
- Immunology Section, BMC D14, Department of Experimental Medicine, Lund University, Lund, Sweden
| | - Tine R Licht
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark.
| | - Henrik M Roager
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark.
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg C, Denmark.
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11
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Song I, Gotoh Y, Ogura Y, Hayashi T, Fukiya S, Yokota A. Comparative Genomic and Physiological Analysis against Clostridium scindens Reveals Eubacterium sp. c-25 as an Atypical Deoxycholic Acid Producer of the Human Gut Microbiota. Microorganisms 2021; 9:microorganisms9112254. [PMID: 34835380 PMCID: PMC8623032 DOI: 10.3390/microorganisms9112254] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/22/2021] [Accepted: 10/22/2021] [Indexed: 12/27/2022] Open
Abstract
The human gut houses bile acid 7α-dehydroxylating bacteria that produce secondary bile acids such as deoxycholic acid (DCA) from host-derived bile acids through enzymes encoded by the bai operon. While recent metagenomic studies suggest that these bacteria are highly diverse and abundant, very few DCA producers have been identified. Here, we investigated the physiology and determined the complete genome sequence of Eubacterium sp. c-25, a DCA producer that was isolated from human feces in the 1980s. Culture experiments showed a preference for neutral to slightly alkaline pH in both growth and DCA production. Genomic analyses revealed that c-25 is phylogenetically distinct from known DCA producers and possesses a multi-cluster arrangement of predicted bile-acid inducible (bai) genes that is considerably different from the typical bai operon structure. This arrangement is also found in other intestinal bacterial species, possibly indicative of unconfirmed 7α-dehydroxylation capabilities. Functionality of the predicted bai genes was supported by the induced expression of baiB, baiCD, and baiH in the presence of cholic acid substrate. Taken together, Eubacterium sp. c-25 is an atypical DCA producer with a novel bai gene cluster structure that may represent an unexplored genotype of DCA producers in the human gut.
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Affiliation(s)
- Isaiah Song
- Laboratory of Microbial Physiology, Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan; (I.S.); (A.Y.)
| | - Yasuhiro Gotoh
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan; (Y.G.); (T.H.)
| | - Yoshitoshi Ogura
- Department of Infectious Medicine, Kurume University School of Medicine, Kurume 830-0011, Japan;
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan; (Y.G.); (T.H.)
| | - Satoru Fukiya
- Laboratory of Microbial Physiology, Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan; (I.S.); (A.Y.)
- Correspondence: ; Tel.: +81-11-706-2501
| | - Atsushi Yokota
- Laboratory of Microbial Physiology, Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan; (I.S.); (A.Y.)
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12
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Bifidobacterium response to lactulose ingestion in the gut relies on a solute-binding protein-dependent ABC transporter. Commun Biol 2021; 4:541. [PMID: 33972677 PMCID: PMC8110962 DOI: 10.1038/s42003-021-02072-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 03/31/2021] [Indexed: 02/06/2023] Open
Abstract
This study aims to understand the mechanistic basis underlying the response of Bifidobacterium to lactulose ingestion in guts of healthy Japanese subjects, with specific focus on a lactulose transporter. An in vitro assay using mutant strains of Bifidobacterium longum subsp. longum 105-A shows that a solute-binding protein with locus tag number BL105A_0502 (termed LT-SBP) is primarily involved in lactulose uptake. By quantifying faecal abundance of LT-SBP orthologues, which is defined by phylogenetic analysis, we find that subjects with 107 to 109 copies of the genes per gram of faeces before lactulose ingestion show a marked increase in Bifidobacterium after ingestion, suggesting the presence of thresholds between responders and non-responders to lactulose. These results help predict the prebiotics-responder and non-responder status and provide an insight into clinical interventions that test the efficacy of prebiotics.
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13
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Hoedt EC, Bottacini F, Cash N, Bongers RS, van Limpt K, Ben Amor K, Knol J, MacSharry J, van Sinderen D. Broad Purpose Vector for Site-Directed Insertional Mutagenesis in Bifidobacterium breve. Front Microbiol 2021; 12:636822. [PMID: 33833740 PMCID: PMC8021953 DOI: 10.3389/fmicb.2021.636822] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 03/02/2021] [Indexed: 11/28/2022] Open
Abstract
Members of the genus Bifidobacterium are notoriously recalcitrant to genetic manipulation due to their extensive and variable repertoire of Restriction-Modification (R-M) systems. Non-replicating plasmids are currently employed to achieve insertional mutagenesis in Bifidobacterium. One of the limitations of using such insertion vectors is the presence within their sequence of various restriction sites, making them sensitive to the activity of endogenous restriction endonucleases encoded by the target strain. For this reason, vectors have been developed with the aim of methylating and protecting the vector using a methylase-positive Escherichia coli strain, in some cases containing a cloned bifidobacterial methylase. Here, we present a mutagenesis approach based on a modified and synthetically produced version of the suicide vector pORI28 (named pFREM28), where all known restriction sites targeted by Bifidobacterium breve R-M systems were removed by base substitution (thus preserving the codon usage). After validating the integrity of the erythromycin marker, the vector was successfully employed to target an α-galactosidase gene responsible for raffinose metabolism, an alcohol dehydrogenase gene responsible for mannitol utilization and a gene encoding a priming glycosyltransferase responsible for exopolysaccharides (EPS) production in B. breve. The advantage of using this modified approach is the reduction of the amount of time, effort and resources required to generate site-directed mutants in B. breve and a similar approach may be employed to target other (bifido)bacterial species.
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Affiliation(s)
- Emily C Hoedt
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,NHMRC Centre of Research Excellence in Digestive Health, School of Medicine and Public Health, The University of Newcastle, Callaghan, NSW, Australia
| | - Francesca Bottacini
- NHMRC Centre of Research Excellence in Digestive Health, School of Medicine and Public Health, The University of Newcastle, Callaghan, NSW, Australia.,Department of Biological Sciences, Munster Technological University, Cork, Ireland
| | - Nora Cash
- NHMRC Centre of Research Excellence in Digestive Health, School of Medicine and Public Health, The University of Newcastle, Callaghan, NSW, Australia
| | | | | | | | - Jan Knol
- Danone Nutricia Research, Utrecht, Netherlands.,Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands
| | - John MacSharry
- NHMRC Centre of Research Excellence in Digestive Health, School of Medicine and Public Health, The University of Newcastle, Callaghan, NSW, Australia.,School of Microbiology, University College Cork, Cork, Ireland.,School of Medicine, University College Cork, Cork, Ireland
| | - Douwe van Sinderen
- NHMRC Centre of Research Excellence in Digestive Health, School of Medicine and Public Health, The University of Newcastle, Callaghan, NSW, Australia.,School of Microbiology, University College Cork, Cork, Ireland
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14
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A Resource for Cloning and Expression Vectors Designed for Bifidobacteria: Overview of Available Tools and Biotechnological Applications. Methods Mol Biol 2021. [PMID: 33649956 DOI: 10.1007/978-1-0716-1274-3_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2023]
Abstract
Bifidobacteria represent an important group of (mostly) commensal microorganisms, which have enjoyed increasing scientific and industrial attention due to their purported health-promoting attributes. For the latter reason, several species have been granted "generally recognized as safe" (GRAS) and "qualified presumption of safety" (QPS) status by the Food and Drugs Administration (FDA) and European Food Safety Authority (EFSA) organizations. Increasing scientific evidence supports their potential as oral delivery vectors to produce bioactive and therapeutic molecules at intestinal level. In order to achieve an efficient utilization of bifidobacterial strains as health-promoting (food) ingredients, it is necessary to provide evidence on the molecular mechanisms behind their purported beneficial and probiotic traits, and precise mechanisms of interaction with their human (or other mammalian) host. In this context, developing appropriate molecular tools to generate and investigate recombinant strains is necessary. While bifidobacteria have long remained recalcitrant to genetic manipulation, a wide array of Bifidobacterium-specific replicating vectors and genetic modification procedures have been described in literature. The current chapter intends to provide an updated overview on the vectors used to genetically modify and manipulate bifidobacteria, including their general characteristics, reviewing examples of their use to successfully generate recombinant bifidobacterial strains for specific purposes, and providing a general workflow and cautions to design and conduct heterologous expression in bifidobacteria. Knowledge gaps and fields of research that may help to widen the molecular toolbox to improve the functional and technological potential of bifidobacteria are also discussed.
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15
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Wada M, Fukiya S, Suzuki A, Matsumoto N, Matsuo M, Yokota A. Methionine utilization by bifidobacteria: possible existence of a reverse transsulfuration pathway. BIOSCIENCE OF MICROBIOTA FOOD AND HEALTH 2021; 40:80-83. [PMID: 33520573 PMCID: PMC7817509 DOI: 10.12938/bmfh.2020-031] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 08/07/2020] [Indexed: 01/04/2023]
Abstract
Although bifidobacteria are already widely used as beneficial microbes with
health-promoting effects, their amino acid utilization and metabolism are not yet fully
understood. Knowledge about the metabolism of sulfur-containing amino acids in
bifidobacteria is especially limited. In this study, we tested the methionine utilization
ability of several bifidobacterial strains when it was the sole available sulfur source.
Although bifidobacteria have long been predominantly considered to be cysteine auxotrophs,
we showed that this is not necessarily the case.
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Affiliation(s)
- Masaru Wada
- Laboratory of Microbial Physiology, Research Faculty of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo, Hokkaido 060-8589, Japan.,Present address: Faculty of Agriculture, Setsunan University, 45-1 Nagaotouge-cho, Hirakata-shi, Osaka 573-0101, Japan
| | - Satoru Fukiya
- Laboratory of Microbial Physiology, Research Faculty of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo, Hokkaido 060-8589, Japan
| | - Azusa Suzuki
- Laboratory of Microbial Physiology, Research Faculty of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo, Hokkaido 060-8589, Japan
| | - Nanae Matsumoto
- Laboratory of Microbial Physiology, Research Faculty of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo, Hokkaido 060-8589, Japan
| | - Miki Matsuo
- Laboratory of Microbial Physiology, Research Faculty of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo, Hokkaido 060-8589, Japan
| | - Atsushi Yokota
- Laboratory of Microbial Physiology, Research Faculty of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo, Hokkaido 060-8589, Japan
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16
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Zuo F, Marcotte H. Advancing mechanistic understanding and bioengineering of probiotic lactobacilli and bifidobacteria by genome editing. Curr Opin Biotechnol 2021; 70:75-82. [PMID: 33445135 DOI: 10.1016/j.copbio.2020.12.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/02/2020] [Accepted: 12/17/2020] [Indexed: 12/01/2022]
Abstract
Typical traditional probiotics lactobacilli and bifidobacteria are gaining great interest to be developed as living diagnostics and therapeutics for improving human health. However, the mechanistic basis underlying their inherent health beneficial property remain incompletely understood which can slow down the translational pipeline in the functional food and pharmaceutical field. Efficient genome editing will advance the understanding of the molecular mechanism of the probiotics' physiological properties and their interaction with the host and the host microbiota, thereby further promote the development of next-generation designer probiotics with improved robustness and tailored functionalities. With the expansion of genome editing strategies such as CRISPR-Cas-based tools and IPSD assisted genome engineering as well as other synthetic biology technologies, the research and application of these health-promoting bacteria for the food and pharmaceutical industry will be further enhanced.
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Affiliation(s)
- Fanglei Zuo
- Department of Laboratory Medicine, Division of Clinical Immunology and Transfusion Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm SE-141 86, Sweden; Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm SE-106 91, Sweden.
| | - Harold Marcotte
- Department of Laboratory Medicine, Division of Clinical Immunology and Transfusion Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm SE-141 86, Sweden
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17
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Hirano R, Sakanaka M, Yoshimi K, Sugimoto N, Eguchi S, Yamauchi Y, Nara M, Maeda S, Ami Y, Gotoh A, Katayama T, Iida N, Kato T, Ohno H, Fukiya S, Yokota A, Nishimoto M, Kitaoka M, Nakai H, Kurihara S. Next-generation prebiotic promotes selective growth of bifidobacteria, suppressing Clostridioides difficile. Gut Microbes 2021; 13:1973835. [PMID: 34553672 PMCID: PMC8475593 DOI: 10.1080/19490976.2021.1973835] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 08/12/2021] [Accepted: 08/19/2021] [Indexed: 02/04/2023] Open
Abstract
Certain existing prebiotics meant to facilitate the growth of beneficial bacteria in the intestine also promote the growth of other prominent bacteria. Therefore, the growth-promoting effects of β-galactosides on intestinal bacteria were analyzed. Galactosyl-β1,4-l-rhamnose (Gal-β1,4-Rha) selectively promoted the growth of Bifidobacterium. Bifidobacterium longum subsp. longum 105-A (JCM 31944) has multiple solute-binding proteins belonging to ATP-binding cassette transporters for sugars. Each strain in the library of 11 B. longum subsp. longum mutants, in which each gene of the solute-binding protein was disrupted, was cultured in a medium containing Gal-β1,4-Rha as the sole carbon source, and only the BL105A_0502 gene-disruption mutant showed delayed and reduced growth compared to the wild-type strain. BL105A_0502 homolog is highly conserved in bifidobacteria. In a Gal-β1,4-Rha-containing medium, Bifidobacterium longum subsp. infantis JCM 1222T, which possesses BLIJ_2090, a homologous protein to BL105A_0502, suppressed the growth of enteric pathogen Clostridioides difficile, whereas the BLIJ_2090 gene-disrupted mutant did not. In vivo, administration of B. infantis and Gal-β1,4-Rha alleviated C. difficile infection-related weight loss in mice. We have successfully screened Gal-β1,4-Rha as a next-generation prebiotic candidate that specifically promotes the growth of beneficial bacteria without promoting the growth of prominent bacteria and pathogens.
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Affiliation(s)
- Rika Hirano
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Ishikawa, Japan
- Faculty of Biology-Oriented Science and Technology, Kindai University, Kinokawa, Wakayama, Japan
| | - Mikiyasu Sakanaka
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Ishikawa, Japan
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Kazuto Yoshimi
- Division of Animal Genetics, Laboratory Animal Research Center, Institute of Medical Science, the University of Tokyo, Minato-ku, Tokyo, Japan
- Institute of Experimental Animal Sciences, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | | | - Syogo Eguchi
- Faculty of Agriculture, Niigata University, Niigata, Japan
| | - Yuko Yamauchi
- Division of Animal Genetics, Laboratory Animal Research Center, Institute of Medical Science, the University of Tokyo, Minato-ku, Tokyo, Japan
- Institute of Experimental Animal Sciences, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Misaki Nara
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Ishikawa, Japan
| | - Shingo Maeda
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Ishikawa, Japan
| | - Yuta Ami
- Faculty of Biology-Oriented Science and Technology, Kindai University, Kinokawa, Wakayama, Japan
| | - Aina Gotoh
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Takane Katayama
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Ishikawa, Japan
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Noriho Iida
- Department of Gastroenterology, Kanazawa University Hospital, Kanazawa, Ishikawa, Japan
| | - Tamotsu Kato
- Laboratory for Intestinal Ecosystem, Riken Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Hiroshi Ohno
- Laboratory for Intestinal Ecosystem, Riken Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Satoru Fukiya
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Atsushi Yokota
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Mamoru Nishimoto
- Institute of Food Research, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Motomitsu Kitaoka
- Faculty of Agriculture, Niigata University, Niigata, Japan
- Institute of Food Research, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Hiroyuki Nakai
- Faculty of Agriculture, Niigata University, Niigata, Japan
| | - Shin Kurihara
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Ishikawa, Japan
- Faculty of Biology-Oriented Science and Technology, Kindai University, Kinokawa, Wakayama, Japan
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18
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Engineer probiotic bifidobacteria for food and biomedical applications - Current status and future prospective. Biotechnol Adv 2020; 45:107654. [DOI: 10.1016/j.biotechadv.2020.107654] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 09/14/2020] [Accepted: 11/01/2020] [Indexed: 12/15/2022]
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19
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Kurihara S. The importance of genetic research on the dominant species of human intestinal indigenous microbiota. BIOSCIENCE OF MICROBIOTA FOOD AND HEALTH 2020; 40:19-26. [PMID: 33520565 PMCID: PMC7817506 DOI: 10.12938/bmfh.2020-011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 08/24/2020] [Indexed: 11/13/2022]
Abstract
Comparisons of the changes in the gut microbiota and transcriptomes as a result of
changes in diet have demonstrated that the regulation of the gene functions of intestinal
bacteria is fundamental for the regulation of the intestinal environment. However, the
functions of only about half of the genes can be predicted using nucleotide sequences
obtained from the metagenomic data of the human gut microbiota. Therefore, the regulation
of gut bacterial gene functions is hindered. To resolve this issue, the functions of the
genes of intestinal bacteria must be identified. In our previous study, a high-throughput
cultivation system was established for the dominant species of indigenous human intestinal
microbiota. Using this system, we analyzed the synthesis and transport of polyamines by
intestinal bacteria. Comparison of the results with those obtained by in
silico analysis indicated the existence of novel polyamine synthetic enzymes
and transport proteins. Next, strains with gene deletions and complementation for the
polyamine synthetic system of the genus Bacteroides were analyzed.
Furthermore, we co-cultured genetically engineered Escherichia coli and
Enterococcus faecalis strains to demonstrate the presence of a
polyamine synthetic pathway spanning multiple bacterial species. Here, we outline the
trends of research using genetically engineered intestinal bacteria and the ripple effects
of studies in which intestinal bacteria have been analyzed genetically. Moreover, because
studies on intestinal bacteria at the gene level are indispensable for improving our
understanding of their regulation, the importance of this research will continue to
increase in the future.
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Affiliation(s)
- Shin Kurihara
- Faculty of Biology-Oriented Science and Technology, Kindai University, Kinokawa, Wakayama 649-6493, Japan
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20
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Identification of Bradyrhizobium elkanii USDA61 Type III Effectors Determining Symbiosis with Vigna mungo. Genes (Basel) 2020; 11:genes11050474. [PMID: 32349348 PMCID: PMC7291247 DOI: 10.3390/genes11050474] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/20/2020] [Accepted: 04/24/2020] [Indexed: 01/13/2023] Open
Abstract
Bradyrhizobium elkanii USDA61 possesses a functional type III secretion system (T3SS) that controls host-specific symbioses with legumes. Here, we demonstrated that B. elkanii T3SS is essential for the nodulation of several southern Asiatic Vigna mungo cultivars. Strikingly, inactivation of either Nod factor synthesis or T3SS in B. elkanii abolished nodulation of the V. mungo plants. Among the effectors, NopL was identified as a key determinant for T3SS-dependent symbiosis. Mutations of other effector genes, such as innB, nopP2, and bel2-5, also impacted symbiotic effectiveness, depending on host genotypes. The nopL deletion mutant formed no nodules on V. mungo, but infection thread formation was still maintained, thereby suggesting its pivotal role in nodule organogenesis. Phylogenetic analyses revealed that NopL was exclusively conserved among Bradyrhizobium and Sinorhizobium (Ensifer) species and showed a different phylogenetic lineage from T3SS. These findings suggest that V. mungo evolved a unique symbiotic signaling cascade that requires both NFs and T3Es (NopL).
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21
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Katoh T, Ojima MN, Sakanaka M, Ashida H, Gotoh A, Katayama T. Enzymatic Adaptation of Bifidobacterium bifidum to Host Glycans, Viewed from Glycoside Hydrolyases and Carbohydrate-Binding Modules. Microorganisms 2020; 8:microorganisms8040481. [PMID: 32231096 PMCID: PMC7232152 DOI: 10.3390/microorganisms8040481] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 03/16/2020] [Accepted: 03/26/2020] [Indexed: 12/14/2022] Open
Abstract
Certain species of the genus Bifidobacterium represent human symbionts. Many studies have shown that the establishment of symbiosis with such bifidobacterial species confers various beneficial effects on human health. Among the more than ten (sub)species of human gut-associated Bifidobacterium that have significantly varied genetic characteristics at the species level, Bifidobacterium bifidum is unique in that it is found in the intestines of a wide age group, ranging from infants to adults. This species is likely to have adapted to efficiently degrade host-derived carbohydrate chains, such as human milk oligosaccharides (HMOs) and mucin O-glycans, which enabled the longitudinal colonization of intestines. The ability of this species to assimilate various host glycans can be attributed to the possession of an adequate set of extracellular glycoside hydrolases (GHs). Importantly, the polypeptides of those glycosidases frequently contain carbohydrate-binding modules (CBMs) with deduced affinities to the target glycans, which is also a distinct characteristic of this species among members of human gut-associated bifidobacteria. This review firstly describes the prevalence and distribution of B. bifidum in the human gut and then explains the enzymatic machinery that B. bifidum has developed for host glycan degradation by referring to the functions of GHs and CBMs. Finally, we show the data of co-culture experiments using host-derived glycans as carbon sources, which underpin the interesting altruistic behavior of this species as a cross-feeder.
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Affiliation(s)
- Toshihiko Katoh
- Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan; (T.K.); (M.N.O.); (A.G.)
| | - Miriam N. Ojima
- Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan; (T.K.); (M.N.O.); (A.G.)
| | - Mikiyasu Sakanaka
- National Food Institute, Technical University of Denmark, Kemitorvet, DK-2800 Kgs. Lyngby, Denmark;
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Ishikawa 921-8836, Japan
| | - Hisashi Ashida
- Faculty of Biology-Oriented Science and Technology, Kindai University, Kinokawa, Wakayama 649-6493, Japan;
| | - Aina Gotoh
- Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan; (T.K.); (M.N.O.); (A.G.)
| | - Takane Katayama
- Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan; (T.K.); (M.N.O.); (A.G.)
- Correspondence: ; Tel.: +81-75-753-9233
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22
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Application of Recombinase-Based In Vivo Expression Technology to Bifidobacterium longum subsp. longum for Identification of Genes Induced in the Gastrointestinal Tract of Mice. Microorganisms 2020; 8:microorganisms8030410. [PMID: 32183191 PMCID: PMC7143038 DOI: 10.3390/microorganisms8030410] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 03/07/2020] [Accepted: 03/10/2020] [Indexed: 12/13/2022] Open
Abstract
Bifidobacteria are one of the major components in human gut microbiota and well-known as beneficial microbes. However, clarification of commensal mechanisms of bifidobacteria in the intestines is still ongoing, especially in the presence of the gut microbiota. Here, we applied recombinase-based in vivo expression technology (R-IVET) using the bacteriophage P1 Cre/loxP system to Bifidobacterium longum subsp. longum 105-A (B. longum 105-A) to identify genes that are specifically expressed in the gastrointestinal tract of conventionally raised mice. Oral administration of the genomic DNA library of B. longum 105-A to conventionally raised mice resulted in the identification of 73 in vivo-induced genes. Four out of seven tested genes were verified in vivo-specific induction at least in the cecum by quantitative reverse transcription PCR. Although there is still room for improvement of the system, our findings can contribute to expanding our understanding of the commensal behavior of B. longum in the gut ecosystem.
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Development of a rapid method for site-directed mutagenesis in Streptococcus zooepidemicus. J Biotechnol 2020; 324S:100025. [PMID: 34154731 DOI: 10.1016/j.btecx.2020.100025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 08/10/2020] [Accepted: 08/19/2020] [Indexed: 11/21/2022]
Abstract
This paper describes the development of a straightforward method for site-directed gene mutagenesis in Streptococcus zooepidemicus, inspired by the mechanism of natural competence regulated by ComX in other streptococci. An alternative sigma factor comX gene was overexpressed from a plasmid in S. zooepidemicus and electrocompetent cells were prepared. As proof of concept, a DNA cassette with two targeting regions flanking a kanamycin resistance gene was spliced in an overlap extension PCR and electroporated. The cassette was then integrated in the genomic DNA by homologous recombination. Next, the gene SeseC_00180 (fibrinogen- and Ig-binding protein precursor) was selected as target for markerless gene deletion and the impact of its loss on the resulting hyaluronan production was determined. The new method of site-directed mutagenesis is significant because it is not necessary to clone the DNA cassette in an auxiliary vector, electroporating it in S. zooepidemicus cells is enough, which allows to bypass the problems with hard to clone DNA sequences and speeds up the whole process of mutation generation in S. zooepidemicus.
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Sakanaka M, Sugiyama Y, Nara M, Kitakata A, Kurihara S. Functional analysis of arginine decarboxylase gene speA of Bacteroides dorei by markerless gene deletion. FEMS Microbiol Lett 2019; 365:4793251. [PMID: 29319802 DOI: 10.1093/femsle/fny003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 01/03/2018] [Indexed: 12/18/2022] Open
Abstract
Polyamine concentrations in the intestine are regulated by their biosynthesis by hundreds of gut microbial species and these polyamines are involved in host health and disease. However, polyamine biosynthesis has not been sufficiently analyzed in major members of the human gut microbiota, possibly owing to a lack of gene manipulation systems. In this study, we successfully performed markerless gene deletion in Bacteroides dorei, one of the major members of the human gut microbiota. The combination of a thymidine kinase gene (tdk) deletion mutant and a counter-selection marker tdk, which has been applied in other Bacteroides species, was used for the markerless gene deletion. Deletion of tdk in B. dorei caused 5-fluoro-2΄-deoxyuridine resistance, suggesting the utility of B. dorei Δtdk as the host for future markerless gene deletions. Compared to parental strains, an arginine decarboxylase gene (speA) deletion mutant generated in this system showed a severe growth defect and decreased concentration of spermidine in the cells and culture supernatant. Collectively, our results indicate the accessibility of gene deletion and the important role of speA in polyamine biosynthesis in B. dorei.
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Affiliation(s)
- Mikiyasu Sakanaka
- Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, Nonoichi, Ishikawa 921-8836, Japan
| | - Yuta Sugiyama
- Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, Nonoichi, Ishikawa 921-8836, Japan
| | - Misaki Nara
- Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, Nonoichi, Ishikawa 921-8836, Japan
| | - Aya Kitakata
- Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, Nonoichi, Ishikawa 921-8836, Japan
| | - Shin Kurihara
- Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, Nonoichi, Ishikawa 921-8836, Japan
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Sakanaka M, Hansen ME, Gotoh A, Katoh T, Yoshida K, Odamaki T, Yachi H, Sugiyama Y, Kurihara S, Hirose J, Urashima T, Xiao JZ, Kitaoka M, Fukiya S, Yokota A, Lo Leggio L, Abou Hachem M, Katayama T. Evolutionary adaptation in fucosyllactose uptake systems supports bifidobacteria-infant symbiosis. SCIENCE ADVANCES 2019; 5:eaaw7696. [PMID: 31489370 PMCID: PMC6713505 DOI: 10.1126/sciadv.aaw7696] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 07/18/2019] [Indexed: 05/10/2023]
Abstract
The human gut microbiota established during infancy has persistent effects on health. In vitro studies have suggested that human milk oligosaccharides (HMOs) in breast milk promote the formation of a bifidobacteria-rich microbiota in infant guts; however, the underlying molecular mechanism remains elusive. Here, we characterized two functionally distinct but overlapping fucosyllactose transporters (FL transporter-1 and -2) from Bifidobacterium longum subspecies infantis. Fecal DNA and HMO consumption analyses, combined with deposited metagenome data mining, revealed that FL transporter-2 is primarily associated with the bifidobacteria-rich microbiota formation in breast-fed infant guts. Structural analyses of the solute-binding protein (SBP) of FL transporter-2 complexed with 2'-fucosyllactose and 3-fucosyllactose, together with phylogenetic analysis of SBP homologs of both FL transporters, highlight a unique adaptation strategy of Bifidobacterium to HMOs, in which the gain-of-function mutations enable FL transporter-2 to efficiently capture major fucosylated HMOs. Our results provide a molecular insight into HMO-mediated symbiosis and coevolution between bifidobacteria and humans.
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Affiliation(s)
- Mikiyasu Sakanaka
- Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, Nonoichi, Ishikawa 921-8836, Japan
| | - Morten Ejby Hansen
- Department of Biotechnology and Bioengineering, Technical University of Denmark, Søltofts Plads, DK-2800 Kgs. Lyngby, Denmark
| | - Aina Gotoh
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Toshihiko Katoh
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Keisuke Yoshida
- Next Generation Science Institute, Morinaga Milk Industry Co. Ltd., Zama, Kanagawa 252-8583, Japan
| | - Toshitaka Odamaki
- Next Generation Science Institute, Morinaga Milk Industry Co. Ltd., Zama, Kanagawa 252-8583, Japan
| | - Hiroyuki Yachi
- Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, Nonoichi, Ishikawa 921-8836, Japan
| | - Yuta Sugiyama
- Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, Nonoichi, Ishikawa 921-8836, Japan
| | - Shin Kurihara
- Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, Nonoichi, Ishikawa 921-8836, Japan
| | - Junko Hirose
- School of Human Cultures, The University of Shiga Prefecture, Hikone, Shiga 522-8533, Japan
| | - Tadasu Urashima
- Department of Animal and Food Hygiene, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan
| | - Jin-zhong Xiao
- Next Generation Science Institute, Morinaga Milk Industry Co. Ltd., Zama, Kanagawa 252-8583, Japan
| | - Motomitsu Kitaoka
- Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8642, Japan
| | - Satoru Fukiya
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Atsushi Yokota
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, Copenhagen 2100, Denmark
| | - Maher Abou Hachem
- Department of Biotechnology and Bioengineering, Technical University of Denmark, Søltofts Plads, DK-2800 Kgs. Lyngby, Denmark
- Corresponding author. (T.K.); (M.A.H.)
| | - Takane Katayama
- Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, Nonoichi, Ishikawa 921-8836, Japan
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
- Corresponding author. (T.K.); (M.A.H.)
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Abstract
Random transposon mutagenesis allows for relatively rapid, genome-wide surveys to detect genes involved in functional traits, by performing screens of mutant libraries. This approach has been widely applied to identify genes responsible for activities of interest in multiple eukaryote and prokaryote organisms, although most studies on microorganisms have focused on pathogenic and clinically relevant bacteria. In this chapter we describe the implementation of an in vitro Tn5-based transposome strategy to generate a large collection of random mutants in the gut commensal Bifidobacterium breve UCC2003, and discuss considerations when applying this mutagenesis system to other Bifidobacterium species or strains of interest.
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Affiliation(s)
- Lorena Ruiz
- Department of Microbiology and Biochemistry of Dairy Products, IPLA-CSIC, Villaviciosa, Asturias, Spain
| | - Douwe van Sinderen
- APC Microbiome Ireland, University College Cork, Cork, Ireland.
- School of Microbiology, University College Cork, Cork, Ireland.
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O'Connell Motherway M, Houston A, O’Callaghan G, Reunanen J, O’Brien F, O’Driscoll T, Casey PG, de Vos WM, van Sinderen D, Shanahan F. A Bifidobacterial pilus-associated protein promotes colonic epithelial proliferation. Mol Microbiol 2018; 111:287-301. [DOI: 10.1111/mmi.14155] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/16/2018] [Indexed: 01/15/2023]
Affiliation(s)
- Mary O'Connell Motherway
- APC Microbiome Ireland, National University of Ireland; Western Road Cork Ireland
- School of Microbiology; National University of Ireland; Western Road Cork Ireland
| | - Aileen Houston
- APC Microbiome Ireland, National University of Ireland; Western Road Cork Ireland
- Department of Medicine; National University of Ireland, Cork University Hospital; Cork Ireland
| | - Grace O’Callaghan
- APC Microbiome Ireland, National University of Ireland; Western Road Cork Ireland
- Department of Medicine; National University of Ireland, Cork University Hospital; Cork Ireland
| | - Justus Reunanen
- Research Programme Unit Immunobiology, Department of Bacteriology and Immunology; Helsinki University; Helsinki Finland
- Cancer and Translational Medicine Research Unit and Biocenter Oulu; University of Oulu; Oulu Finland
| | - Frances O’Brien
- APC Microbiome Ireland, National University of Ireland; Western Road Cork Ireland
| | - Tara O’Driscoll
- APC Microbiome Ireland, National University of Ireland; Western Road Cork Ireland
| | - Patrick G. Casey
- APC Microbiome Ireland, National University of Ireland; Western Road Cork Ireland
| | - Willem M. de Vos
- Research Programme Unit Immunobiology, Department of Bacteriology and Immunology; Helsinki University; Helsinki Finland
- Laboratory of Microbiology; Wageningen University; The Netherlands
| | - Douwe van Sinderen
- APC Microbiome Ireland, National University of Ireland; Western Road Cork Ireland
- School of Microbiology; National University of Ireland; Western Road Cork Ireland
| | - Fergus Shanahan
- APC Microbiome Ireland, National University of Ireland; Western Road Cork Ireland
- Department of Medicine; National University of Ireland, Cork University Hospital; Cork Ireland
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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.
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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.
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Nezametdinova VZ, Mavletova DA, Alekseeva MG, Chekalina MS, Zakharevich NV, Danilenko VN. Species-specific serine-threonine protein kinase Pkb2 of Bifidobacterium longum subsp. longum: Genetic environment and substrate specificity. Anaerobe 2018. [PMID: 29534913 DOI: 10.1016/j.anaerobe.2018.03.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The objective of this study was to determine for phosphorylated substrates of the species-specific serine-threonine protein kinase (STPK) Pkb2 from Bifidobacterium longum subsp. longum GT15. Two approaches were employed: analyses of phosphorylated membrane vesicles protein spectra following kinase reactions and analyses of the genes surrounding pkb2. A bioinformatics analysis of the genes surrounding pkb2 found a species-specific gene cluster PFNA in the genomes of 34 different bifidobacterial species. The identified cluster consisted of 5-8 genes depending on the species. The first five genes are characteristic for all considered species. These are the following genes encoding serine-threonine protein kinase (pkb2), fibronectin type III domain-containing protein (fn3), AAA-ATPase (aaa-atp), hypothetical protein with DUF58 domain (duf58) and transglutaminase (tgm). The sixth (protein phosphatase, prpC), seventh (hypothetical protein, BLGT_RS02790), and eighth (FHA domain-containing protein, fha) genes are included in this cluster, but they are not found in all species. The operon organization of the PFNA gene cluster was confirmed with transcriptional analysis. AAA-ATPase, which is encoded by a gene of the PFNA gene cluster, was found to be a substrate of the STPK Pkb2. Fourteen AAA-ATPase sites (seven serine, six threonine, and one tyrosine) phosphorylated by STPK Pkb2 were revealed. Analysis of the spectra of phosphorylated membrane vesicles proteins allowed us to identify eleven proteins that were considered as possible Pkb2 substrates. They belong to several functional classes: proteins involved in transcription and translation; proteins of the F1-domain of the FoF1-ATPase; ABC-transporters; molecular chaperone GroEL; and glutamine synthase, GlnA1. All identified proteins were considered moonlighting proteins. Three out of 11 proteins (glutamine synthetase GlnA1 and FoF1-ATPase alpha and beta subunits) were selected for further in vitro phosphorylation assays and were shown to be phosphorylated by Pkb2. Four phosphorylated substrates of the species-specific STPK Pkb2 from B. longum subsp. longum GT15 were identified for the first time. They included the moonlighting protein glutamine synthase GlnA, FoF1-ATPase alpha and beta subunits, and the chaperone MoxR family of AAA-ATPase. The ability of bifidobacterial STPK to phosphorylate the substrate on serine, threonine, and tyrosine residues was shown for the first time.
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Affiliation(s)
- V Z Nezametdinova
- Laboratory of Genetics of Microorganisms, Vavilov Institute of General Genetics Russian Academy of Sciences, 3 Gubkin Street, 119991, GSP-1, Moscow, Russian Federation.
| | - D A Mavletova
- Laboratory of Genetics of Microorganisms, Vavilov Institute of General Genetics Russian Academy of Sciences, 3 Gubkin Street, 119991, GSP-1, Moscow, Russian Federation
| | - M G Alekseeva
- Laboratory of Genetics of Microorganisms, Vavilov Institute of General Genetics Russian Academy of Sciences, 3 Gubkin Street, 119991, GSP-1, Moscow, Russian Federation
| | - M S Chekalina
- Laboratory of Genetics of Microorganisms, Vavilov Institute of General Genetics Russian Academy of Sciences, 3 Gubkin Street, 119991, GSP-1, Moscow, Russian Federation
| | - N V Zakharevich
- Laboratory of Genetics of Microorganisms, Vavilov Institute of General Genetics Russian Academy of Sciences, 3 Gubkin Street, 119991, GSP-1, Moscow, Russian Federation
| | - V N Danilenko
- Laboratory of Genetics of Microorganisms, Vavilov Institute of General Genetics Russian Academy of Sciences, 3 Gubkin Street, 119991, GSP-1, Moscow, Russian Federation
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Castro-Bravo N, Hidalgo-Cantabrana C, Rodriguez-Carvajal MA, Ruas-Madiedo P, Margolles A. Gene Replacement and Fluorescent Labeling to Study the Functional Role of Exopolysaccharides in Bifidobacterium animalis subsp. lactis. Front Microbiol 2017; 8:1405. [PMID: 28790996 PMCID: PMC5524739 DOI: 10.3389/fmicb.2017.01405] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 07/11/2017] [Indexed: 01/01/2023] Open
Abstract
An extracellular layer of exopolysaccharides (EPS) covers the surface of some Bifidobacterium animalis subsp. lactis strains, which could be of relevance for its probiotic performance. In order to understand the functional characteristics of B. animalis subsp. lactis, two isogenic strains that differ in their EPS-producing phenotype, due to a single mutation in the gene Balat_1410, were studied. By means of a double crossover recombination strategy, successfully used for the first time in bifidobacteria, Balat_1410 in the type strain B. animalis subsp. lactis DSM10140 was replaced by a mutated gene containing a non-synonymous mutation previously associated with the appearance of a mucoid-ropy phenotype. Nuclear magnetic resonance and SEC-MALS analyses showed that the novel strain harboring the mutation acquired a ropy phenotype, due to the production of a high molecular weight (HMW)-EPS that is not produced in the wild-type strain. Fluorescence labeling of both strains with two fluorescent proteins, m-Cherry and Green Fluorescent Protein, was achieved by expressing the corresponding genes under the control of a native selected promoter (the elongation factor Tu promoter). Remarkably, qualitative and quantitative fluorescence analyses demonstrated that the ropy strain displays a lower capability to adhere to human intestinal epithelial cells. In addition, the presence of the HMW-EPS reduced the capability of the producing strain to form biofilms upon three different abiotic surfaces. This work also highlights the fact that different EPS confer variable functional characteristics to the bifidobacterial surface, which may be relevant for the performance of B. animalis subsp. lactis as a probiotic. The construction of molecular tools allowing the functional characterization of surface structures in next generation probiotics is still a challenging issue that deserves further attention, given the relevant role that such molecules must play in the interaction with the host.
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Affiliation(s)
- Nuria Castro-Bravo
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias – Consejo Superior de Investigaciones CientíficasVillaviciosa, Spain
| | - Claudio Hidalgo-Cantabrana
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias – Consejo Superior de Investigaciones CientíficasVillaviciosa, Spain
| | | | - Patricia Ruas-Madiedo
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias – Consejo Superior de Investigaciones CientíficasVillaviciosa, Spain
| | - Abelardo Margolles
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias – Consejo Superior de Investigaciones CientíficasVillaviciosa, Spain
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32
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Ruiz L, Bottacini F, Boinett CJ, Cain AK, O'Connell-Motherway M, Lawley TD, van Sinderen D. The essential genomic landscape of the commensal Bifidobacterium breve UCC2003. Sci Rep 2017; 7:5648. [PMID: 28717159 PMCID: PMC5514069 DOI: 10.1038/s41598-017-05795-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 06/02/2017] [Indexed: 01/15/2023] Open
Abstract
Bifidobacteria are common gut commensals with purported health-promoting effects. This has encouraged scientific research into bifidobacteria, though recalcitrance to genetic manipulation and scarcity of molecular tools has hampered our knowledge on the precise molecular determinants of their health-promoting attributes and gut adaptation. To overcome this problem and facilitate functional genomic analyses in bifidobacteria, we created a large Tn5 transposon mutant library of the commensal Bifidobacterium breve UCC2003 that was further characterized by means of a Transposon Directed Insertion Sequencing (TraDIS) approach. Statistical analysis of transposon insertion distribution revealed a set of 453 genes that are essential for or markedly contribute to growth of this strain under laboratory conditions. These essential genes encode functions involved in the so-called bifid-shunt, most enzymes related to nucleotide biosynthesis and a range of housekeeping functions. Comparison to the Bifidobacterium and B. breve core genomes highlights a high degree of conservation of essential genes at the species and genus level, while comparison to essential gene datasets from other gut bacteria identified essential genes that appear specific to bifidobacteria. This work establishes a useful molecular tool for scientific discovery of bifidobacteria and identifies targets for further studies aimed at characterizing essential functions not previously examined in bifidobacteria.
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Affiliation(s)
- Lorena Ruiz
- School of Microbiology and APC Microbiome Institute, National University of Ireland, Cork, Western Road, Ireland.,Department of Nutrition, Bromatology and Food Technology, Complutense University, Avda Puerta de Hierro s/n, 28040, Madrid, Spain
| | - Francesca Bottacini
- School of Microbiology and APC Microbiome Institute, National University of Ireland, Cork, Western Road, Ireland
| | | | - Amy K Cain
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Mary O'Connell-Motherway
- School of Microbiology and APC Microbiome Institute, National University of Ireland, Cork, Western Road, Ireland
| | | | - Douwe van Sinderen
- School of Microbiology and APC Microbiome Institute, National University of Ireland, Cork, Western Road, Ireland.
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Tahoun A, Masutani H, El-Sharkawy H, Gillespie T, Honda RP, Kuwata K, Inagaki M, Yabe T, Nomura I, Suzuki T. Capsular polysaccharide inhibits adhesion of Bifidobacterium longum 105-A to enterocyte-like Caco-2 cells and phagocytosis by macrophages. Gut Pathog 2017; 9:27. [PMID: 28469711 PMCID: PMC5412050 DOI: 10.1186/s13099-017-0177-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Accepted: 04/21/2017] [Indexed: 02/07/2023] Open
Abstract
Background Bifidobacterium longum 105-A produces markedly high amounts of capsular polysaccharides (CPS) and exopolysaccharides (EPS) that should play distinct roles in bacterial–host interactions. To identify the biological function of B. longum 105-A CPS/EPS, we carried out an informatics survey of the genome and identified the EPS-encoding genetic locus of B. longum 105-A that is responsible for the production of CPS/EPS. The role of CPS/EPS in the adaptation to gut tract environment and bacteria-gut cell interactions was investigated using the ΔcpsD mutant. Results A putative B. longum 105-A CPS/EPS gene cluster was shown to consist of 24 putative genes encoding a priming glycosyltransferase (cpsD), 7 glycosyltransferases, 4 CPS/EPS synthesis machinery proteins, and 3 dTDP-L-rhamnose synthesis enzymes. These enzymes should form a complex system that is involved in the biogenesis of CPS and/or EPS. To confirm this, we constructed a knockout mutant (ΔcpsD) by a double cross-over homologous recombination. Compared to wild-type, the ∆cpsD mutant showed a similar growth rate. However, it showed quicker sedimentation and formation of cell clusters in liquid culture. EPS was secreted by the ∆cpsD mutant, but had altered monosaccharide composition and molecular weight. Comparison of the morphology of B. longum 105-A wild-type and ∆cpsD by negative staining in light and electron microscopy revealed that the formation of fimbriae is drastically enhanced in the ∆cpsD mutant while the B. longum 105-A wild-type was coated by a thick capsule. The fimbriae expression in the ∆cpsD was closely associated with the disappearance of the CPS layer. The wild-type showed low pH tolerance, adaptation, and bile salt tolerance, but the ∆cpsD mutant had lost this survivability in gastric and duodenal environments. The ∆cpsD mutant was extensively able to bind to the human colon carcinoma Caco-2 cell line and was phagocytosed by murine macrophage RAW 264.7, whereas the wild-type did not bind to epithelial cells and totally resisted internalization by macrophages. Conclusions Our results suggest that CPS/EPS production and fimbriae formation are negatively correlated and play key roles in the survival, attachment, and colonization of B. longum 105-A in the gut. Electronic supplementary material The online version of this article (doi:10.1186/s13099-017-0177-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Amin Tahoun
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, 501-1193 Japan.,Faculty of Veterinary Medicine, Kafr El-Sheikh University, Kafr El-Sheikh, 33516 Egypt
| | - Hisayoshi Masutani
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, 501-1193 Japan
| | - Hanem El-Sharkawy
- Faculty of Veterinary Medicine, Kafr El-Sheikh University, Kafr El-Sheikh, 33516 Egypt.,Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu, 501-1193 Japan
| | - Trudi Gillespie
- CALM_live Imaging Facility, Centre for Inflammation Research, University of Edinburgh, Edinburgh, 47 EH16 4TJ UK
| | - Ryo P Honda
- Department of Molecular Pathobiochemistry, Graduate School of Medicine, Gifu University, 1-1 Yanagido, Gifu, 501-1193 Japan
| | - Kazuo Kuwata
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1 Yanagido, Gifu, 501-1193 Japan.,Department of Gene and Development, Graduate School of Medicine, Gifu University, 1-1 Yanagido, Gifu, 501-1193 Japan.,Center for Highly Advanced Integration of Nano and Life Sciences, Gifu University (G-CHAIN), Gifu University, 1-1 Yanagido, Gifu, 501-1193 Japan
| | - Mizuho Inagaki
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, 501-1193 Japan.,United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu, 501-1193 Japan
| | - Tomio Yabe
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, 501-1193 Japan.,Center for Highly Advanced Integration of Nano and Life Sciences, Gifu University (G-CHAIN), Gifu University, 1-1 Yanagido, Gifu, 501-1193 Japan.,United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu, 501-1193 Japan
| | - Izumi Nomura
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, 501-1193 Japan
| | - Tohru Suzuki
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, 501-1193 Japan.,United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu, 501-1193 Japan
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Molecular Insight into Evolution of Symbiosis between Breast-Fed Infants and a Member of the Human Gut Microbiome Bifidobacterium longum. Cell Chem Biol 2017; 24:515-524.e5. [PMID: 28392148 DOI: 10.1016/j.chembiol.2017.03.012] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 02/13/2017] [Accepted: 03/13/2017] [Indexed: 12/23/2022]
Abstract
Breast-fed infants generally have a bifidobacteria-rich microbiota with recent studies indicating that human milk oligosaccharides (HMOs) selectively promote bifidobacterial growth. Bifidobacterium bifidum possesses a glycoside hydrolase family 20 lacto-N-biosidase for liberating lacto-N-biose I from lacto-N-tetraose, an abundant HMO unique to human milk, while Bifidobacterium longum subsp. longum has a non-classified enzyme (LnbX). Here, we determined the crystal structure of the catalytic domain of LnbX and provide evidence for creation of a novel glycoside hydrolase family, GH136. The structure, in combination with inhibition and mutation studies, provides insight into the molecular mechanism and broader substrate specificity of this enzyme. Moreover, through genetic studies, we show that lnbX is indispensable for B. longum growth on lacto-N-tetraose and is a key genetic factor for persistence in the gut of breast-fed infants. Overall, this study reveals possible evolutionary routes for the emergence of symbiosis between humans and bifidobacterial species in the infant gut.
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Reddy SK, Bågenholm V, Pudlo NA, Bouraoui H, Koropatkin NM, Martens EC, Stålbrand H. A β-mannan utilization locus in Bacteroides ovatus involves a GH36 α-galactosidase active on galactomannans. FEBS Lett 2016; 590:2106-18. [PMID: 27288925 PMCID: PMC5094572 DOI: 10.1002/1873-3468.12250] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 06/07/2016] [Accepted: 06/09/2016] [Indexed: 11/25/2022]
Abstract
The Bacova_02091 gene in the β‐mannan utilization locus of Bacteroides ovatus encodes a family GH36 α‐galactosidase (BoGal36A), transcriptionally upregulated during growth on galactomannan. Characterization of recombinant BoGal36A reveals unique properties compared to other GH36 α‐galactosidases, which preferentially hydrolyse terminal α‐galactose in raffinose family oligosaccharides. BoGal36A prefers hydrolysing internal galactose substitutions from intact and depolymerized galactomannan. BoGal36A efficiently releases (> 90%) galactose from guar and locust bean galactomannans, resulting in precipitation of the polysaccharides. As compared to other GH36 structures, the BoGal36A 3D model displays a loop deletion, resulting in a wider active site cleft which likely can accommodate a galactose‐substituted polymannose backbone.
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Affiliation(s)
- Sumitha K Reddy
- Department of Biochemistry and Structural Biology, Lund University, Sweden
| | - Viktoria Bågenholm
- Department of Biochemistry and Structural Biology, Lund University, Sweden
| | - Nicholas A Pudlo
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Hanene Bouraoui
- Department of Biochemistry and Structural Biology, Lund University, Sweden
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Eric C Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Henrik Stålbrand
- Department of Biochemistry and Structural Biology, Lund University, Sweden
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O'Callaghan A, van Sinderen D. Bifidobacteria and Their Role as Members of the Human Gut Microbiota. Front Microbiol 2016; 7:925. [PMID: 27379055 PMCID: PMC4908950 DOI: 10.3389/fmicb.2016.00925] [Citation(s) in RCA: 506] [Impact Index Per Article: 63.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 05/31/2016] [Indexed: 12/11/2022] Open
Abstract
Members of the genus Bifidobacterium are among the first microbes to colonize the human gastrointestinal tract and are believed to exert positive health benefits on their host. Due to their purported health-promoting properties, bifidobacteria have been incorporated into many functional foods as active ingredients. Bifidobacteria naturally occur in a range of ecological niches that are either directly or indirectly connected to the animal gastrointestinal tract, such as the human oral cavity, the insect gut and sewage. To be able to survive in these particular ecological niches, bifidobacteria must possess specific adaptations to be competitive. Determination of genome sequences has revealed genetic attributes that may explain bifidobacterial ecological fitness, such as metabolic abilities, evasion of the host adaptive immune system and colonization of the host through specific appendages. However, genetic modification is crucial toward fully elucidating the mechanisms by which bifidobacteria exert their adaptive abilities and beneficial properties. In this review we provide an up to date summary of the general features of bifidobacteria, whilst paying particular attention to the metabolic abilities of this species. We also describe methods that have allowed successful genetic manipulation of bifidobacteria.
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Affiliation(s)
- Amy O'Callaghan
- Alimentary Pharmabiotic Centre and School of Microbiology, University College Cork Cork, Ireland
| | - Douwe van Sinderen
- Alimentary Pharmabiotic Centre and School of Microbiology, University College Cork Cork, Ireland
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O'Callaghan A, Bottacini F, O'Connell Motherway M, van Sinderen D. Pangenome analysis of Bifidobacterium longum and site-directed mutagenesis through by-pass of restriction-modification systems. BMC Genomics 2015; 16:832. [PMID: 26489930 PMCID: PMC4618763 DOI: 10.1186/s12864-015-1968-4] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 09/30/2015] [Indexed: 12/16/2022] Open
Abstract
Background Bifidobacterial genome analysis has provided insights as to how these gut commensals adapt to and persist in the human GIT, while also revealing genetic diversity among members of a given bifidobacterial (sub)species. Bifidobacteria are notoriously recalcitrant to genetic modification, which prevents exploration of their genomic functions, including those that convey (human) health benefits. Methods PacBio SMRT sequencing was used to determine the whole genome seqeunces of two B. longum subsp. longum strains. The B. longum pan-genome was computed using PGAP v1.2 and the core B. longum phylogenetic tree was constructed using a maximum-likelihood based approach in PhyML v3.0. M.blmNCII was cloned in E. coli and an internal fragment if arfBarfB was cloned into pORI19 for insertion mutagenesis. Results In this study we present the complete genome sequences of two Bifidobacterium longum subsp. longum strains. Comparative analysis with thirty one publicly available B. longum genomes allowed the definition of the B. longum core and dispensable genomes. This analysis also highlighted differences in particular metabolic abilities between members of the B. longum subspecies infantis, longum and suis. Furthermore, phylogenetic analysis of the B. longum core genome indicated the existence of a novel subspecies. Methylome data, coupled to the analysis of restriction-modification systems, allowed us to substantially increase the genetic accessibility of B. longum subsp. longum NCIMB 8809 to a level that was shown to permit site-directed mutagenesis. Conclusions Comparative genomic analysis of thirty three B. longum representatives revealed a closed pan-genome for this bifidobacterial species. Phylogenetic analysis of the B. longum core genome also provides evidence for a novel fifth B. longum subspecies. Finally, we improved genetic accessibility for the strain B. longum subsp. longum NCIMB 8809, which allowed the generation of a mutant of this strain. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1968-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- A O'Callaghan
- APC Microbiome Institute & School of Microbiology, University College Cork, Western Road, Cork, Ireland.
| | - F Bottacini
- APC Microbiome Institute & School of Microbiology, University College Cork, Western Road, Cork, Ireland.
| | - M O'Connell Motherway
- APC Microbiome Institute & School of Microbiology, University College Cork, Western Road, Cork, Ireland.
| | - D van Sinderen
- APC Microbiome Institute & School of Microbiology, University College Cork, Western Road, Cork, Ireland.
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Alekseeva MG, Mavletova DA, Kolchina NV, Nezametdinova VZ, Danilenko VN. Isolation and purification of recombinant serine/threonine protein kinases of the strain Bifidobacterium longum B379M and investigation of their activity. BIOCHEMISTRY (MOSCOW) 2015; 80:1303-11. [DOI: 10.1134/s0006297915100119] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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A single mutation in the gene responsible for the mucoid phenotype of Bifidobacterium animalis subsp. lactis confers surface and functional characteristics. Appl Environ Microbiol 2015; 81:7960-8. [PMID: 26362981 DOI: 10.1128/aem.02095-15] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 09/03/2015] [Indexed: 02/07/2023] Open
Abstract
Exopolysaccharides (EPS) are extracellular carbohydrate polymers synthesized by a large variety of bacteria. Their physiological functions have been extensively studied, but many of their roles have not yet been elucidated. We have sequenced the genomes of two isogenic strains of Bifidobacterium animalis subsp. lactis that differ in their EPS-producing phenotype. The original strain displays a nonmucoid appearance, and the mutant derived thereof has acquired a mucoid phenotype. The sequence analysis of their genomes revealed a nonsynonymous mutation in the gene Balat_1410, putatively involved in the elongation of the EPS chain. By comparing a strain from which this gene had been deleted with strains containing the wild-type and mutated genes, we were able to show that each strain displays different cell surface characteristics. The mucoid EPS synthesized by the strain harboring the mutation in Balat_1410 provided higher resistance to gastrointestinal conditions and increased the capability for adhesion to human enterocytes. In addition, the cytokine profiles of human peripheral blood mononuclear cells and ex vivo colon tissues suggest that the mucoid strain could have higher anti-inflammatory activity. Our findings provide relevant data on the function of Balat_1410 and reveal that the mucoid phenotype is able to alter some of the most relevant functional properties of the cells.
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Genome modifications and cloning using a conjugally transferable recombineering system. ACTA ACUST UNITED AC 2015; 8:24-35. [PMID: 28352570 PMCID: PMC4980705 DOI: 10.1016/j.btre.2015.08.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 08/24/2015] [Accepted: 08/24/2015] [Indexed: 11/21/2022]
Abstract
The genetic modification of primary bacterial disease isolates is challenging due to the lack of highly efficient genetic tools. Herein we describe the development of a modified PCR-based, λ Red-mediated recombineering system for efficient deletion of genes in Gram-negative bacteria. A series of conjugally transferrable plasmids were constructed by cloning an oriT sequence and different antibiotic resistance genes into recombinogenic plasmid pKD46. Using this system we deleted ten different genes from the genomes of Edwardsiella ictaluri and Aeromonas hydrophila. A temperature sensitive and conjugally transferable flp recombinase plasmid was developed to generate markerless gene deletion mutants. We also developed an efficient cloning system to capture larger bacterial genetic elements and clone them into a conjugally transferrable plasmid for facile transferring to Gram-negative bacteria. This system should be applicable in diverse Gram-negative bacteria to modify and complement genomic elements in bacteria that cannot be manipulated using available genetic tools.
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Sakanaka M, Fukiya S, Kobayashi R, Abe A, Hirayama Y, Kano Y, Yokota A. Isolation and transposition properties of ISBlo11, an active insertion sequence belonging to the IS3 family, from Bifidobacterium longum 105-A. FEMS Microbiol Lett 2015; 362:fnv032. [PMID: 25724534 DOI: 10.1093/femsle/fnv032] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Transposon mutagenesis systems are still under development in bifidobacteria, partly because intrinsic active insertion sequences are not well characterized in bifidobacteria. Here, we isolated an active insertion sequence, ISBlo11, from Bifidobacterium longum 105-A using a sacB-based counterselection system, which is generally used to screen for active insertion sequences from bacterial genomes. ISBlo11 is 1432 bp long and belongs to the IS3 family. It has a single ORF encoding a transposase and 25-bp inverted repeats at its termini. Full-length copies of ISBlo11 are specifically conserved among certain B. longum genomes and exist in different sites. Transposition analysis of an artificial ISBlo11 transposon using an Escherichia coli conjugation system revealed that ISBlo11 has adequate transposition activity, comparable to the reported activity of IS629, another IS3 family element initially isolated from Shigella sonnei. ISBlo11 also showed low transposition selectivity for non-conserved 3- or 4-bp target sequences. These characteristics of ISBlo11 seem suitable for the development of a new transposon mutagenesis system in bifidobacteria.
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Affiliation(s)
- Mikiyasu Sakanaka
- Laboratory of Microbial Physiology, Research Faculty of Agriculture, Hokkaido University, Kita 9 Nishi 9, Kita-ku, Sapporo, Hokkaido 060-8589, Japan
| | - Satoru Fukiya
- Laboratory of Microbial Physiology, Research Faculty of Agriculture, Hokkaido University, Kita 9 Nishi 9, Kita-ku, Sapporo, Hokkaido 060-8589, Japan
| | - Ryoko Kobayashi
- Laboratory of Microbial Physiology, Research Faculty of Agriculture, Hokkaido University, Kita 9 Nishi 9, Kita-ku, Sapporo, Hokkaido 060-8589, Japan
| | - Arisa Abe
- Laboratory of Microbial Physiology, Research Faculty of Agriculture, Hokkaido University, Kita 9 Nishi 9, Kita-ku, Sapporo, Hokkaido 060-8589, Japan
| | - Yosuke Hirayama
- Laboratory of Microbial Physiology, Research Faculty of Agriculture, Hokkaido University, Kita 9 Nishi 9, Kita-ku, Sapporo, Hokkaido 060-8589, Japan
| | - Yasunobu Kano
- Department of Molecular Genetics, Kyoto Pharmaceutical University, 5, Nakauchi-cho, Misasagi, Yamashina-ku, Kyoto 607-8414, Japan
| | - Atsushi Yokota
- Laboratory of Microbial Physiology, Research Faculty of Agriculture, Hokkaido University, Kita 9 Nishi 9, Kita-ku, Sapporo, Hokkaido 060-8589, Japan
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Complete Genome Sequence of Bifidobacterium longum 105-A, a Strain with High Transformation Efficiency. GENOME ANNOUNCEMENTS 2014; 2:2/6/e01311-14. [PMID: 25523770 PMCID: PMC4271160 DOI: 10.1128/genomea.01311-14] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Bifidobacterium longum 105-A shows high transformation efficiency and allows for the generation of gene knockout mutants through homologous recombination. Here, we report the complete genome sequence of strain 105-A. Genes encoding at least four putative restriction-modification systems were found in this genome, which might contribute to its transformation efficiency.
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Functional analysis of bifidobacterial promoters in Bifidobacterium longum and Escherichia coli using the α-galactosidase gene as a reporter. J Biosci Bioeng 2014; 118:489-95. [DOI: 10.1016/j.jbiosc.2014.05.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Revised: 04/27/2014] [Accepted: 05/01/2014] [Indexed: 01/15/2023]
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Ryu YS, Biswas RK, Shin K, Parisutham V, Kim SM, Lee SK. A simple and effective method for construction of Escherichia coli strains proficient for genome engineering. PLoS One 2014; 9:e94266. [PMID: 24747264 PMCID: PMC3991648 DOI: 10.1371/journal.pone.0094266] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 03/13/2014] [Indexed: 11/25/2022] Open
Abstract
Multiplex genome engineering is a standalone recombineering tool for large-scale programming and accelerated evolution of cells. However, this advanced genome engineering technique has been limited to use in selected bacterial strains. We developed a simple and effective strain-independent method for effective genome engineering in Escherichia coli. The method involves introducing a suicide plasmid carrying the λ Red recombination system into the mutS gene. The suicide plasmid can be excised from the chromosome via selection in the absence of antibiotics, thus allowing transient inactivation of the mismatch repair system during genome engineering. In addition, we developed another suicide plasmid that enables integration of large DNA fragments into the lacZ genomic locus. These features enable this system to be applied in the exploitation of the benefits of genome engineering in synthetic biology, as well as the metabolic engineering of different strains of E. coli.
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Affiliation(s)
- Young Shin Ryu
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Rajesh Kumar Biswas
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Kwangsu Shin
- School of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Vinuselvi Parisutham
- School of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Suk Min Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Sung Kuk Lee
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- School of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- * E-mail:
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O′Connell Motherway M, Watson D, Bottacini F, Clark TA, Roberts RJ, Korlach J, Garault P, Chervaux C, van Hylckama Vlieg JET, Smokvina T, van Sinderen D. Identification of restriction-modification systems of Bifidobacterium animalis subsp. lactis CNCM I-2494 by SMRT sequencing and associated methylome analysis. PLoS One 2014; 9:e94875. [PMID: 24743599 PMCID: PMC3990576 DOI: 10.1371/journal.pone.0094875] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Accepted: 03/20/2014] [Indexed: 01/25/2023] Open
Abstract
Bifidobacterium animalis subsp. lactis CNCM I-2494 is a component of a commercialized fermented dairy product for which beneficial effects on health has been studied by clinical and preclinical trials. To date little is known about the molecular mechanisms that could explain the beneficial effects that bifidobacteria impart to the host. Restriction-modification (R-M) systems have been identified as key obstacles in the genetic accessibility of bifidobacteria, and circumventing these is a prerequisite to attaining a fundamental understanding of bifidobacterial attributes, including the genes that are responsible for health-promoting properties of this clinically and industrially important group of bacteria. The complete genome sequence of B. animalis subsp. lactis CNCM I-2494 is predicted to harbour the genetic determinants for two type II R-M systems, designated BanLI and BanLII. In order to investigate the functionality and specificity of these two putative R-M systems in B. animalis subsp. lactis CNCM I-2494, we employed PacBio SMRT sequencing with associated methylome analysis. In addition, the contribution of the identified R-M systems to the genetic accessibility of this strain was assessed.
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Affiliation(s)
- Mary O′Connell Motherway
- Alimentary Pharmabiotic Centre and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Debbie Watson
- Alimentary Pharmabiotic Centre and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Francesca Bottacini
- Alimentary Pharmabiotic Centre and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Tyson A. Clark
- Pacific Biosciences, Menlo Park, California, United States of America
| | | | - Jonas Korlach
- Pacific Biosciences, Menlo Park, California, United States of America
| | | | | | | | | | - Douwe van Sinderen
- Alimentary Pharmabiotic Centre and School of Microbiology, National University of Ireland, Cork, Ireland
- * E-mail:
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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.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Marco Ventura
- Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland, Western Road, Cork, Ireland.
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Nezametdinova VZ, Zakharevich NV, Alekseeva MG, Averina OV, Mavletova DA, Danilenko VN. Identification and characterization of the serine/threonine protein kinases in Bifidobacterium. Arch Microbiol 2014; 196:125-36. [PMID: 24395073 DOI: 10.1007/s00203-013-0949-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 12/09/2013] [Accepted: 12/26/2013] [Indexed: 10/25/2022]
Abstract
Six genes encoding the bifidobacterial Hanks-type (eukaryote-like) serine/threonine protein kinases (STPK) were identified and classified. The genome of each bifidobacterial strain contains four conserved genes and one species-specific gene. Bifidobacterium longum and Bifidobacterium bifidum possess the unique gene found only in these species. The STPK genes of Russian industrial probiotic strain B. longum B379M were cloned and sequenced. The expression of these genes in Escherichia coli and bifidobacteria was observed. Autophosphorylation of the conserved STPK Pkb5 and species-specific STPK Pkb2 was demonstrated. This is the first report on Hanks-type STPK in bifidobacteria.
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Affiliation(s)
- Venera Z Nezametdinova
- Department of Genetics of Microorganisms, Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkin Street, 119991, Moscow, Russia,
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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.
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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
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Sakurama H, Kiyohara M, Wada J, Honda Y, Yamaguchi M, Fukiya S, Yokota A, Ashida H, Kumagai H, Kitaoka M, Yamamoto K, Katayama T. Lacto-N-biosidase encoded by a novel gene of Bifidobacterium longum subspecies longum shows unique substrate specificity and requires a designated chaperone for its active expression. J Biol Chem 2013; 288:25194-25206. [PMID: 23843461 DOI: 10.1074/jbc.m113.484733] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Infant gut-associated bifidobacteria possess species-specific enzymatic sets to assimilate human milk oligosaccharides, and lacto-N-biosidase (LNBase) is a key enzyme that degrades lacto-N-tetraose (Galβ1-3GlcNAcβ1-3Galβ1-4Glc), the main component of human milk oligosaccharides, to lacto-N-biose I (Galβ1-3GlcNAc) and lactose. We have previously identified LNBase activity in Bifidobacterium bifidum and some strains of Bifidobacterium longum subsp. longum (B. longum). Subsequently, we isolated a glycoside hydrolase family 20 (GH20) LNBase from B. bifidum; however, the genome of the LNBase(+) strain of B. longum contains no GH20 LNBase homolog. Here, we reveal that locus tags BLLJ_1505 and BLLJ_1506 constitute LNBase from B. longum JCM1217. The gene products, designated LnbX and LnbY, respectively, showed no sequence similarity to previously characterized proteins. The purified enzyme, which consisted of LnbX only, hydrolyzed via a retaining mechanism the GlcNAcβ1-3Gal linkage in lacto-N-tetraose, lacto-N-fucopentaose I (Fucα1-2Galβ1-3GlcNAcβ1-3Galβ1-4Glc), and sialyllacto-N-tetraose a (Neu5Acα2-3Galβ1-3GlcNAcβ1-3Galβ1-4Gal); the latter two are not hydrolyzed by GH20 LNBase. Among the chromogenic substrates examined, the enzyme acted on p-nitrophenyl (pNP)-β-lacto-N-bioside I (Galβ1-3GlcNAcβ-pNP) and GalNAcβ1-3GlcNAcβ-pNP. GalNAcβ1-3GlcNAcβ linkage has been found in O-mannosyl glycans of α-dystroglycan. Therefore, the enzyme may serve as a new tool for examining glycan structures. In vitro refolding experiments revealed that LnbY and metal ions (Ca(2+) and Mg(2+)) are required for proper folding of LnbX. The LnbX and LnbY homologs have been found only in B. bifidum, B. longum, and a few gut microbes, suggesting that the proteins have evolved in specialized niches.
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Affiliation(s)
- Haruko Sakurama
- From the Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Ishikawa 921-8836
| | - Masashi Kiyohara
- From the Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Ishikawa 921-8836
| | - Jun Wada
- From the Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Ishikawa 921-8836
| | - Yuji Honda
- From the Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Ishikawa 921-8836
| | - Masanori Yamaguchi
- the Department of Organic Chemistry, Wakayama University, Sakaedani, Wakayama, 640-8510
| | - Satoru Fukiya
- the Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589
| | - Atsushi Yokota
- the Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589
| | - Hisashi Ashida
- the Faculty of Biology-Oriented Science and Technology, Kinki University, Kinokawa, Wakayama 649-6493, and
| | - Hidehiko Kumagai
- From the Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Ishikawa 921-8836
| | - Motomitsu Kitaoka
- the National Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8642, Japan
| | - Kenji Yamamoto
- From the Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Ishikawa 921-8836
| | - Takane Katayama
- From the Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Ishikawa 921-8836,.
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50
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Development of a markerless gene deletion system for Streptococcus zooepidemicus: functional characterization of hyaluronan synthase gene. Appl Microbiol Biotechnol 2013; 97:8629-36. [DOI: 10.1007/s00253-013-5058-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Revised: 06/12/2013] [Accepted: 06/13/2013] [Indexed: 11/25/2022]
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