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Chettri D, Verma AK. Biological significance of carbohydrate active enzymes and searching their inhibitors for therapeutic applications. Carbohydr Res 2023; 529:108853. [PMID: 37235954 DOI: 10.1016/j.carres.2023.108853] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 05/01/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023]
Abstract
Glycans are the most abundant and diverse group of biomolecules with a crucial role in all the biological processes. Their structural and functional diversity is not genetically encoded, but depends on Carbohydrate Active Enzymes (CAZymes) which carry out all catalytic activities in terms of synthesis, modification, and degradation. CAZymes comprise large families of enzymes with specific functions and are widely used for various commercial applications ranging from biofuel production to textile and food industries with impact on biorefineries. To understand the structure and functional mechanism of these CAZymes for their modification for industrial use, together with knowledge of therapeutic aspects of their dysfunction associated with various diseases, CAZyme inhibitors can be used as a valuable tool. In search for new inhibitors, the screening of various secondary metabolites using high-throughput techniques and rational design techniques have been explored. The inhibitors can thus help tune CAZymes and are emerging as a potential research interest.
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Affiliation(s)
- Dixita Chettri
- Department of Microbiology, Sikkim University, Gangtok, 737102, Sikkim, India
| | - Anil Kumar Verma
- Department of Microbiology, Sikkim University, Gangtok, 737102, Sikkim, India.
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2
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D'Rose V, Bhat SG. Whole genome sequence analysis enabled affirmation of the probiotic potential of marine sporulater Bacillus amyloliquefaciens BTSS3 isolated from Centroscyllium fabricii. Gene 2023; 864:147305. [PMID: 36813058 DOI: 10.1016/j.gene.2023.147305] [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: 12/08/2022] [Revised: 02/05/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023]
Abstract
Probiotics are microorganisms when administered in adequate amounts, confer health benefits on the host. Many probiotics find application in various industries however, probiotic bacteria linked to marine environments are less explored.Although Bifidobacteria, Lactobacilli, and Streptococcus thermophilus are the most frequently used probiotics, Bacillus spp. have acquired much acceptance in human functional foods due to their increased tolerance and enduring competence in harsh environments like the gastrointestinal (GI) tract. In this study, the 4 Mbp genome sequence of Bacillus amyloliquefaciens strain BTSS3, a marine spore former isolated from deep-sea shark Centroscyllium fabricii, with antimicrobial and probiotic properties was sequenced, assembled, and annotated. Analysis revealed the presence of numerous genes presenting probiotic traits like production of vitamins, secondary metabolites, amino acids, secretory proteins, enzymes and other proteins that allow survival in GI tract as well as adhesion to intestinal mucosa. Adhesion by colonization in the gut was studied in vivo in zebrafish (Danio rerio) using FITC labelled B.amyloliquefaciens BTSS3. Preliminary study revealed the ability of the marine Bacillus to attach to the intestinal mucosa of the fish gut. The genomic data and the in vivo experiment affirms that this marine spore former is a promising probiotic candidate with potential biotechnological applications.
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Affiliation(s)
- Venetia D'Rose
- Department of Biotechnology, Cochin University of Science and Technology, Cochin 22, India.
| | - Sarita Ganapathy Bhat
- Department of Biotechnology, Cochin University of Science and Technology, Cochin 22, India; Inter University Centre for Nanomaterials and Devices, Cochin University of Science and Technology, Cochin 22, Kerala, India.
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3
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Shang J, Yang S, Tang Z, Chen Y, Duan B, Meng X. Bifidobacterium bifidum H3-R2 and Its Molecular Communication within the Context of Ulcerative Colitis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:11678-11688. [PMID: 36095239 DOI: 10.1021/acs.jafc.2c02909] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Bifidobacteria are important mediators of immune system development within the gastrointestinal system and immunological homeostasis. The present study explored the anti-colitic activity of Bifidobacterium bifidum H3-R2 in a murine dextran sulfate sodium (DSS)-induced model of ulcerative colitis (UC). Moreover, this study offers novel insight regarding the molecular basis for the probiotic properties of B. bifidum H3-R2 by analyzing the underlying mechanisms whereby B. bifidum H3-R2-derived proteins affect the intestinal barrier. B. bifidum H3-R2 administration was sufficient to alleviate clinical manifestations consistent with DSS-induced colitis, restoring aberrant inflammatory cytokine production, enhancing tight junction protein expression, and positively impacting overall intestinal microecological homeostasis in these animals. Moreover, the bifidobacteria-derived GroEL and transaldolase (TAL) proteins were found to regulate tight junction protein expression via the NF-κB, myosin light chain kinase (MLCK), RhoA/Rho-associated protein kinase (ROCK), and mitogen-activated protein kinase (MAPK) signaling pathways, preventing the lipopolysaccharide (LPS)-mediated disruption of the intestinal epithelial cell barrier.
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Affiliation(s)
- Jiacui Shang
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, China
- Food College, Northeast Agricultural University, Harbin 150030, China
| | - Shuo Yang
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, China
- Food College, Northeast Agricultural University, Harbin 150030, China
| | - Zongxin Tang
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, China
- Food College, Northeast Agricultural University, Harbin 150030, China
| | - Yuhan Chen
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, China
- Food College, Northeast Agricultural University, Harbin 150030, China
| | - Bofan Duan
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, China
- Food College, Northeast Agricultural University, Harbin 150030, China
| | - Xiangchen Meng
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, China
- Food College, Northeast Agricultural University, Harbin 150030, China
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4
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Moroz OV, Blagova E, Lebedev AA, Sánchez Rodríguez F, Rigden DJ, Tams JW, Wilting R, Vester JK, Longhin E, Hansen GH, Krogh KBRM, Pache RA, Davies GJ, Wilson KS. Multitasking in the gut: the X-ray structure of the multidomain BbgIII from Bifidobacterium bifidum offers possible explanations for its alternative functions. Acta Crystallogr D Struct Biol 2021; 77:1564-1578. [PMID: 34866612 DOI: 10.1107/s2059798321010949] [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: 06/03/2021] [Accepted: 10/20/2021] [Indexed: 11/10/2022] Open
Abstract
β-Galactosidases catalyse the hydrolysis of lactose into galactose and glucose; as an alternative reaction, some β-galactosidases also catalyse the formation of galactooligosaccharides by transglycosylation. Both reactions have industrial importance: lactose hydrolysis is used to produce lactose-free milk, while galactooligosaccharides have been shown to act as prebiotics. For some multi-domain β-galactosidases, the hydrolysis/transglycosylation ratio can be modified by the truncation of carbohydrate-binding modules. Here, an analysis of BbgIII, a multidomain β-galactosidase from Bifidobacterium bifidum, is presented. The X-ray structure has been determined of an intact protein corresponding to a gene construct of eight domains. The use of evolutionary covariance-based predictions made sequence docking in low-resolution areas of the model spectacularly easy, confirming the relevance of this rapidly developing deep-learning-based technique for model building. The structure revealed two alternative orientations of the CBM32 carbohydrate-binding module relative to the GH2 catalytic domain in the six crystallographically independent chains. In one orientation the CBM32 domain covers the entrance to the active site of the enzyme, while in the other orientation the active site is open, suggesting a possible mechanism for switching between the two activities of the enzyme, namely lactose hydrolysis and transgalactosylation. The location of the carbohydrate-binding site of the CBM32 domain on the opposite site of the module to where it comes into contact with the catalytic GH2 domain is consistent with its involvement in adherence to host cells. The role of the CBM32 domain in switching between hydrolysis and transglycosylation modes offers protein-engineering opportunities for selective β-galactosidase modification for industrial purposes in the future.
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Affiliation(s)
- Olga V Moroz
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Elena Blagova
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Andrey A Lebedev
- CCP4, STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0QX, United Kingdom
| | - Filomeno Sánchez Rodríguez
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Daniel J Rigden
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | | | | | | | - Elena Longhin
- Novozymes A/S, Biologiens Vej 2, 2800 Kgs. Lyngby, Denmark
| | | | | | - Roland A Pache
- Novozymes A/S, Biologiens Vej 2, 2800 Kgs. Lyngby, Denmark
| | - Gideon J Davies
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Keith S Wilson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
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Hassani S, Sotoodehnejadnematalahi F, Fateh A, Siadat SD. Evaluation of Association between Bifidobacterium bifidum Derived Extracellular Vesicles and Intestinal Epithelium Tight Junction Proteins through Notch-1 and AhR Activation in Caco-2 Cell Line. MOLECULAR GENETICS, MICROBIOLOGY AND VIROLOGY 2021; 36:S1-S6. [DOI: 10.3103/s0891416821050086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/30/2020] [Accepted: 07/30/2020] [Indexed: 10/13/2023]
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Nezametdinova VZ, Yunes RA, Dukhinova MS, Alekseeva MG, Danilenko VN. The Role of the PFNA Operon of Bifidobacteria in the Recognition of Host's Immune Signals: Prospects for the Use of the FN3 Protein in the Treatment of COVID-19. Int J Mol Sci 2021; 22:ijms22179219. [PMID: 34502130 PMCID: PMC8430577 DOI: 10.3390/ijms22179219] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/21/2021] [Accepted: 08/24/2021] [Indexed: 12/11/2022] Open
Abstract
Bifidobacteria are some of the major agents that shaped the immune system of many members of the animal kingdom during their evolution. Over recent years, the question of concrete mechanisms underlying the immunomodulatory properties of bifidobacteria has been addressed in both animal and human studies. A possible candidate for this role has been discovered recently. The PFNA cluster, consisting of five core genes, pkb2, fn3, aaa-atp, duf58, tgm, has been found in all gut-dwelling autochthonous bifidobacterial species of humans. The sensory region of the species-specific serine-threonine protein kinase (PKB2), the transmembrane region of the microbial transglutaminase (TGM), and the type-III fibronectin domain-containing protein (FN3) encoded by the I gene imply that the PFNA cluster might be implicated in the interaction between bacteria and the host immune system. Moreover, the FN3 protein encoded by one of the genes making up the PFNA cluster, contains domains and motifs of cytokine receptors capable of selectively binding TNF-α. The PFNA cluster could play an important role for sensing signals of the immune system. Among the practical implications of this finding is the creation of anti-inflammatory drugs aimed at alleviating cytokine storms, one of the dire consequences resulting from SARS-CoV-2 infection.
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Affiliation(s)
- Venera Z. Nezametdinova
- Laboratory of Bacterial Genetics, The Vavilov Institute of General Genetics, 117971 Moscow, Russia; (V.Z.N.); (R.A.Y.); (M.G.A.)
| | - Roman A. Yunes
- Laboratory of Bacterial Genetics, The Vavilov Institute of General Genetics, 117971 Moscow, Russia; (V.Z.N.); (R.A.Y.); (M.G.A.)
| | - Marina S. Dukhinova
- International Institute ‘Solution Chemistry of Advanced Materials and Technologies’, ITMO University, 197101 Saint-Petersburg, Russia;
| | - Maria G. Alekseeva
- Laboratory of Bacterial Genetics, The Vavilov Institute of General Genetics, 117971 Moscow, Russia; (V.Z.N.); (R.A.Y.); (M.G.A.)
| | - Valery N. Danilenko
- Laboratory of Bacterial Genetics, The Vavilov Institute of General Genetics, 117971 Moscow, Russia; (V.Z.N.); (R.A.Y.); (M.G.A.)
- Correspondence:
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Zhu MZ, Zhou F, Ouyang J, Wang QY, Li YL, Wu JL, Huang JA, Liu ZH. Combined use of epigallocatechin-3-gallate (EGCG) and caffeine in low doses exhibits marked anti-obesity synergy through regulation of gut microbiota and bile acid metabolism. Food Funct 2021; 12:4105-4116. [PMID: 33977918 DOI: 10.1039/d0fo01768j] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Epigallocatechin-3-gallate (EGCG) and caffeine constitute the most effective ingredients of weight loss in tea. However, whether combination of EGCG and caffeine exhibits anti-obesity synergy remains unclear. Here, we showed low-doses of EGCG and caffeine used in combination led to synergistic anti-obesity effects equivalent to those of high-dose EGCG. Furthermore, combination treatment exhibited a synergistic effect on altering gut microbiota, including decreased Firmicutes level and increased Bifidobacterium level. Other notable effects of combination treatment included synergistic effects on: increasing fecal acetic acid, propionic acid, and total SCFAs; decreasing expression of GPR43; and increasing microbial bile salt hydrolase gene copies in the gut, facilitating generation of unconjugated BAs and enhancing fecal BA loss. Additionally, combination treatment demonstrated synergistic effects toward increasing the expression of hepatic TGR5 and decreasing the expression of intestinal FXR-FGF15, resulting in increased expression of hepatic CYP7A1. Thus, the synergistic effect may be attributed to regulation of gut microbiota and BA metabolism.
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Affiliation(s)
- Ming-Zhi Zhu
- Key Laboratory of Tea Science of Ministry of Education, National Research Center of Engineering Technology for Utilization of Functional Ingredients from Botanicals, College of Horticulture, Hunan Agricultural University, Changsha, 410128, China. and Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, 410128, China
| | - Fang Zhou
- Key Laboratory of Tea Science of Ministry of Education, National Research Center of Engineering Technology for Utilization of Functional Ingredients from Botanicals, College of Horticulture, Hunan Agricultural University, Changsha, 410128, China. and Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, 410128, China
| | - Jian Ouyang
- Key Laboratory of Tea Science of Ministry of Education, National Research Center of Engineering Technology for Utilization of Functional Ingredients from Botanicals, College of Horticulture, Hunan Agricultural University, Changsha, 410128, China. and Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, 410128, China
| | - Qi-Ye Wang
- Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Laboratory of Animal Nutrition and Human Health, College of Life Sciences, Hunan Normal University, Changsha, 10081, China
| | - Yi-Long Li
- Key Laboratory of Tea Science of Ministry of Education, National Research Center of Engineering Technology for Utilization of Functional Ingredients from Botanicals, College of Horticulture, Hunan Agricultural University, Changsha, 410128, China. and Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, 410128, China
| | - Jian-Lin Wu
- State Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau 999078, China
| | - Jian-An Huang
- Key Laboratory of Tea Science of Ministry of Education, National Research Center of Engineering Technology for Utilization of Functional Ingredients from Botanicals, College of Horticulture, Hunan Agricultural University, Changsha, 410128, China. and Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, 410128, China
| | - Zhong-Hua Liu
- Key Laboratory of Tea Science of Ministry of Education, National Research Center of Engineering Technology for Utilization of Functional Ingredients from Botanicals, College of Horticulture, Hunan Agricultural University, Changsha, 410128, China. and Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, 410128, China
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Zeng H, Safratowich BD, Liu Z, Bukowski MR, Ishaq SL. Adequacy of calcium and vitamin D reduces inflammation, β-catenin signaling, and dysbiotic Parasutterela bacteria in the colon of C57BL/6 mice fed a western-style diet. J Nutr Biochem 2021; 92:108613. [PMID: 33705950 DOI: 10.1016/j.jnutbio.2021.108613] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 11/30/2020] [Accepted: 02/02/2021] [Indexed: 12/31/2022]
Abstract
Adoption of an obesogenic diet low in calcium and vitamin D (CaD) leads to increased obesity, colonic inflammation, and cancer. However, the underlying mechanisms remain to be elucidated. We tested the hypothesis that CaD supplementation (from inadequacy to adequacy) may reduce colonic inflammation, oncogenic signaling, and dysbiosis in the colon of C57BL/6 mice fed a Western diet. Male C57/BL6 mice (4-weeks old) were assigned to 3 dietary groups for 36 weeks: (1) AIN76A as a control diet (AIN); (2) a defined rodent "new Western diet" (NWD); or (3) NWD with CaD supplementation (NWD/CaD). Compared to the AIN, mice receiving the NWD or NWD/CaD exhibited more than 0.2-fold increase in the levels of plasma leptin, tumor necrosis factor α (TNF-α) and body weight. The levels of plasma interleukin 6 (IL-6), inflammatory cell infiltration, and β-catenin/Ki67 protein (oncogenic signaling) were increased more than 0.8-fold in the NWD (but not NWD/CaD) group compared to the AIN group. Consistent with the inflammatory phenotype, colonic secondary bile acid (inflammatory bacterial metabolite) levels increased more than 0.4-fold in the NWD group compared to the NWD/CaD and AIN groups. Furthermore, the abundance of colonic Proteobacteria (e.g., Parasutterela), considered signatures of dysbiosis, was increased more than four-fold; and the α diversity of colonic bacterial species, indicative of health, was decreased by 30% in the NWD group compared to the AIN and NWD/CaD groups. Collectively, CaD adequacy reduces colonic inflammation, β-catenin oncogenic signaling, secondary bile acids, and bacterial dysbiosis in mice fed with a Western diet.
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Affiliation(s)
- Huawei Zeng
- United States Department of Agriculture, Agricultural Research Service, Grand Forks Human Nutrition Research Center, Grand Forks, North Dakota.
| | - Bryan D Safratowich
- United States Department of Agriculture, Agricultural Research Service, Grand Forks Human Nutrition Research Center, Grand Forks, North Dakota
| | - Zhenhua Liu
- School of Public Health and Health Sciences, University of Massachusetts, Amherst, Massachusetts
| | - Michael R Bukowski
- United States Department of Agriculture, Agricultural Research Service, Grand Forks Human Nutrition Research Center, Grand Forks, North Dakota
| | - Suzanne L Ishaq
- School of Food and Agriculture, University of Maine, Orono, Maine
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Zhang S, Li T, Xie J, Zhang D, Pi C, Zhou L, Yang W. Gold standard for nutrition: a review of human milk oligosaccharide and its effects on infant gut microbiota. Microb Cell Fact 2021; 20:108. [PMID: 34049536 PMCID: PMC8162007 DOI: 10.1186/s12934-021-01599-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 05/21/2021] [Indexed: 02/08/2023] Open
Abstract
Human milk is the gold standard for nutrition of infant growth, whose nutritional value is mainly attributed to human milk oligosaccharides (HMOs). HMOs, the third most abundant component of human milk after lactose and lipids, are complex sugars with unique structural diversity which are indigestible by the infant. Acting as prebiotics, multiple beneficial functions of HMO are believed to be exerted through interactions with the gut microbiota either directly or indirectly, such as supporting beneficial bacteria growth, anti-pathogenic effects, and modulation of intestinal epithelial cell response. Recent studies have highlighted that HMOs can boost infants health and reduce disease risk, revealing potential of HMOs in food additive and therapeutics. The present paper discusses recent research in respect to the impact of HMO on the infant gut microbiome, with emphasis on the molecular basis of mechanism underlying beneficial effects of HMOs.
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Affiliation(s)
- Shunhao Zhang
- State Key Laboratory of Oral Disease, National Clinical Research Center for Oral Disease, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Tianle Li
- State Key Laboratory of Oral Disease, National Clinical Research Center for Oral Disease, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Jing Xie
- State Key Laboratory of Oral Disease, National Clinical Research Center for Oral Disease, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Demao Zhang
- State Key Laboratory of Oral Disease, National Clinical Research Center for Oral Disease, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Caixia Pi
- State Key Laboratory of Oral Disease, National Clinical Research Center for Oral Disease, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Lingyun Zhou
- Center of Infectious Diseases, West China Hospital of Sichuan University, No. 37 Guoxue Alley, Wuhou District, Chengdu, 610041, China.
| | - Wenbin Yang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Oral and Maxillofacial Surgery, Department of Medical Affairs, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3, South Renmin Road, Chengdu, 610041, Sichuan, China.
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Kononova S, Litvinova E, Vakhitov T, Skalinskaya M, Sitkin S. Acceptive Immunity: The Role of Fucosylated Glycans in Human Host-Microbiome Interactions. Int J Mol Sci 2021; 22:ijms22083854. [PMID: 33917768 PMCID: PMC8068183 DOI: 10.3390/ijms22083854] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/04/2021] [Accepted: 04/05/2021] [Indexed: 02/07/2023] Open
Abstract
The growth in the number of chronic non-communicable diseases in the second half of the past century and in the first two decades of the new century is largely due to the disruption of the relationship between the human body and its symbiotic microbiota, and not pathogens. The interaction of the human immune system with symbionts is not accompanied by inflammation, but is a physiological norm. This is achieved via microbiota control by the immune system through a complex balance of pro-inflammatory and suppressive responses, and only a disturbance of this balance can trigger pathophysiological mechanisms. This review discusses the establishment of homeostatic relationships during immune system development and intestinal bacterial colonization through the interaction of milk glycans, mucins, and secretory immunoglobulins. In particular, the role of fucose and fucosylated glycans in the mechanism of interactions between host epithelial and immune cells is discussed.
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Affiliation(s)
- Svetlana Kononova
- Department of Microbiology, State Research Institute of Highly Pure Biopreparations, 197110 St. Petersburg, Russia; (T.V.); (M.S.); (S.S.)
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia
- Correspondence:
| | - Ekaterina Litvinova
- Scientific-Research Institute of Neurosciences and Medicine, 630117 Novosibirsk, Russia;
- Siberian Federal Scientific Center of Agro-BioTechnologies, Russian Academy of Sciences, Krasnoobsk, 633501 Novosibirsk, Russia
| | - Timur Vakhitov
- Department of Microbiology, State Research Institute of Highly Pure Biopreparations, 197110 St. Petersburg, Russia; (T.V.); (M.S.); (S.S.)
| | - Maria Skalinskaya
- Department of Microbiology, State Research Institute of Highly Pure Biopreparations, 197110 St. Petersburg, Russia; (T.V.); (M.S.); (S.S.)
- Department of Internal Diseases, Gastroenterology and Dietetics, North-Western State Medical University Named after I.I. Mechnikov, 191015 St. Petersburg, Russia
| | - Stanislav Sitkin
- Department of Microbiology, State Research Institute of Highly Pure Biopreparations, 197110 St. Petersburg, Russia; (T.V.); (M.S.); (S.S.)
- Department of Internal Diseases, Gastroenterology and Dietetics, North-Western State Medical University Named after I.I. Mechnikov, 191015 St. Petersburg, Russia
- Institute of Perinatology and Pediatrics, Almazov National Medical Research Centre, 197341 St. Petersburg, Russia
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Kumar H, Collado MC, Wopereis H, Salminen S, Knol J, Roeselers G. The Bifidogenic Effect Revisited-Ecology and Health Perspectives of Bifidobacterial Colonization in Early Life. Microorganisms 2020; 8:E1855. [PMID: 33255636 PMCID: PMC7760687 DOI: 10.3390/microorganisms8121855] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/20/2020] [Accepted: 11/23/2020] [Indexed: 12/11/2022] Open
Abstract
Extensive microbial colonization of the infant gastrointestinal tract starts after parturition. There are several parallel mechanisms by which early life microbiome acquisition may proceed, including early exposure to maternal vaginal and fecal microbiota, transmission of skin associated microbes, and ingestion of microorganisms present in breast milk. The crucial role of vertical transmission from the maternal microbial reservoir during vaginal delivery is supported by the shared microbial strains observed among mothers and their babies and the distinctly different gut microbiome composition of caesarean-section born infants. The healthy infant colon is often dominated by members of the keystone genus Bifidobacterium that have evolved complex genetic pathways to metabolize different glycans present in human milk. In exchange for these host-derived nutrients, bifidobacteria's saccharolytic activity results in an anaerobic and acidic gut environment that is protective against enteropathogenic infection. Interference with early-life microbiota acquisition and development could result in adverse health outcomes. Compromised microbiota development, often characterized by decreased abundance of Bifidobacterium species has been reported in infants delivered prematurely, delivered by caesarean section, early life antibiotic exposure and in the case of early life allergies. Various microbiome modulation strategies such as probiotic, prebiotics, synbiotics and postbiotics have been developed that are able to generate a bifidogenic shift and help to restore the microbiota development. This review explores the evolutionary ecology of early-life type Bifidobacterium strains and their symbiotic relationship with humans and discusses examples of compromised microbiota development in which stimulating the abundance and activity of Bifidobacterium has demonstrated beneficial associations with health.
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Affiliation(s)
- Himanshu Kumar
- Danone Nutricia Research, 3584 CT Utrecht, The Netherlands; (H.K.); (H.W.); (J.K.)
| | - Maria Carmen Collado
- Department of Biotechnology, Institute of Agrochemistry and Food Technology-Spanish National Research Council (IATA-CSIC), Paterna, 46980 Valencia, Spain;
- Functional Foods Forum, Faculty of Medicine, University of Turku, 20500 Turku, Finland;
| | - Harm Wopereis
- Danone Nutricia Research, 3584 CT Utrecht, The Netherlands; (H.K.); (H.W.); (J.K.)
| | - Seppo Salminen
- Functional Foods Forum, Faculty of Medicine, University of Turku, 20500 Turku, Finland;
| | - Jan Knol
- Danone Nutricia Research, 3584 CT Utrecht, The Netherlands; (H.K.); (H.W.); (J.K.)
- Laboratory for Microbiology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Guus Roeselers
- Danone Nutricia Research, 3584 CT Utrecht, The Netherlands; (H.K.); (H.W.); (J.K.)
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12
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Dyakov IN, Mavletova DA, Chernyshova IN, Snegireva NA, Gavrilova MV, Bushkova KK, Dyachkova MS, Alekseeva MG, Danilenko VN. FN3 protein fragment containing two type III fibronectin domains from B. longum GT15 binds to human tumor necrosis factor alpha in vitro. Anaerobe 2020; 65:102247. [PMID: 32771620 PMCID: PMC7409735 DOI: 10.1016/j.anaerobe.2020.102247] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 07/09/2020] [Accepted: 07/21/2020] [Indexed: 12/19/2022]
Abstract
Most species of the genus Bifidobacterium contain the gene cluster PFNA, which is presumably involved in the species-specific communication between bacteria and their hosts. The gene cluster PFNA consists of five genes including fn3, which codes for a protein containing two fibronectin type III domains. Each fibronectin domain contains sites similar to cytokine-binding sites of human receptors. Based on this finding we assumed that this protein would bind specifically to human cytokines in vitro. We cloned a fragment of the fn3 gene (1503 bp; 501 aa) containing two fibronectin domains, from the strain B. longum subsp. longum GT15. After cloning the fragment into the expression vector pET16b and expressing it in E. coli, the protein product was purified to a homogenous state for further analysis. Using the immunoferment method, we tested the purified fragment's ability to bind the following human cytokines: IL-1β, IL-6, IL-10, TNFα. We developed a sandwich ELISA system to detect any specific interactions between the purified protein and any of the studied cytokines. We found that the purified protein fragment only binds to TNFα.
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Affiliation(s)
- Ilya N Dyakov
- I.I, Mechnikov Research Institute for Vaccines and Sera, Malyj Kazennyj Per., 5, Moscow, Russia, 105064
| | - Dilara A Mavletova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina St., 3, Moscow, Russia, 119991
| | - Irina N Chernyshova
- I.I, Mechnikov Research Institute for Vaccines and Sera, Malyj Kazennyj Per., 5, Moscow, Russia, 105064
| | - Nadezda A Snegireva
- I.I, Mechnikov Research Institute for Vaccines and Sera, Malyj Kazennyj Per., 5, Moscow, Russia, 105064
| | - Marina V Gavrilova
- I.I, Mechnikov Research Institute for Vaccines and Sera, Malyj Kazennyj Per., 5, Moscow, Russia, 105064
| | - Kristina K Bushkova
- I.I, Mechnikov Research Institute for Vaccines and Sera, Malyj Kazennyj Per., 5, Moscow, Russia, 105064
| | - Marina S Dyachkova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina St., 3, Moscow, Russia, 119991
| | - Maria G Alekseeva
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina St., 3, Moscow, Russia, 119991
| | - Valery N Danilenko
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina St., 3, Moscow, Russia, 119991; Peoples' Friendship University of Russia (RUDN University), Faculty of Ecology, International Institute for Strategic Development of Sectoral Economics, Miklukho-Maklaya St., 6, Moscow, Russia, 117198; Pharmabiotics Limited Liability Company, Bolshoy Boulevard, 42, Bldg. 1, 1238, Moscow, Russia, 121205.
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13
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Jackson MI, Waldy C, Cochrane C, Jewell DE. Consumption of identically formulated foods extruded under low and high shear force reveals that microbiome redox ratios accompany canine immunoglobulin A production. J Anim Physiol Anim Nutr (Berl) 2020; 104:1551-1567. [PMID: 32705743 PMCID: PMC7540571 DOI: 10.1111/jpn.13419] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 01/06/2020] [Accepted: 06/24/2020] [Indexed: 12/14/2022]
Abstract
Digestion-resistant starch (RS) can provide health benefits to the host via gut microbiome-mediated metabolism. This study tested the physiological effects on healthy dogs of identically formulated foods processed under high (n = 16) or low (n = 16) shear extrusion conditions resulting in respective lower and higher levels of RS. Faecal samples collected at weeks 3 and 6 were assayed for stool score, proximate analysis, short-chain fatty acids (SCFA), immunoglobulin A (IgA) and microbiome; faecal metabolome was characterized at week 6. Proximate and digestibility analyses of the foods and stool scores and stool proximate analysis showed few differences between the two shear methods except for increased apparent fibre digestibility in the low shear food. In contrast, levels of butyrate (p = .030) and total SCFA (p = .043) were significantly greater in faeces at week 6 from dogs who consumed the low versus high shear food. Faecal IgA levels were significantly higher at week 3 (p = .001) but not week 6 (p = .110) in the low shear food. Significant differences in 166 metabolites between consumption of the two foods were identified via faecal metabolomic analysis, with changes in sugars, bile acids, advanced glycation end products and few amino acids. Strikingly, consumption of the low shear food resulted in elevated levels of the reduced members of redox couples derived from metabolized sugars and branched-chain and phenyl amino acids. Alpha diversity of the microbiome showed significantly higher species richness in faeces from the low shear group at week 6, though other measures of diversity were similar for both foods. Twelve genus-level operational taxonomic units (OTU; half Firmicutes) significantly differed between the food types. Six OTU significantly correlated with RS-derived sugars and ratios of the redox couples. Taken together, these data show that RS impacts microbiome-mediated metabolism in the gut, resulting in changes in the reducing state.
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Affiliation(s)
| | | | | | - Dennis E. Jewell
- Department of Grain Science and IndustryKansas State UniversityManhattanKSUSA
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14
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Zhang Q, Hu J, Feng JW, Hu XT, Wang T, Gong WX, Huang K, Guo YX, Zou Z, Lin X, Zhou R, Yuan YQ, Zhang AD, Wei H, Cao G, Liu C, Chen LL, Jin ML. Influenza infection elicits an expansion of gut population of endogenous Bifidobacterium animalis which protects mice against infection. Genome Biol 2020; 21:99. [PMID: 32345342 PMCID: PMC7187530 DOI: 10.1186/s13059-020-02007-1] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 04/01/2020] [Indexed: 02/07/2023] Open
Abstract
Background Influenza is a severe respiratory illness that continually threatens global health. It has been widely known that gut microbiota modulates the host response to protect against influenza infection, but mechanistic details remain largely unknown. Here, we took advantage of the phenomenon of lethal dose 50 (LD50) and metagenomic sequencing analysis to identify specific anti-influenza gut microbes and analyze the underlying mechanism. Results Transferring fecal microbes from mice that survive virulent influenza H7N9 infection into antibiotic-treated mice confers resistance to infection. Some gut microbes exhibit differential features to lethal influenza infection depending on the infection outcome. Bifidobacterium pseudolongum and Bifidobacterium animalis levels are significantly elevated in surviving mice when compared to dead or mock-infected mice. Oral administration of B. animalis alone or the combination of both significantly reduces the severity of H7N9 infection in both antibiotic-treated and germ-free mice. Functional metagenomic analysis suggests that B. animalis mediates the anti-influenza effect via several specific metabolic molecules. In vivo tests confirm valine and coenzyme A produce an anti-influenza effect. Conclusions These findings show that the severity of influenza infection is closely related to the heterogeneous responses of the gut microbiota. We demonstrate the anti-influenza effect of B. animalis, and also find that the gut population of endogenous B. animalis can expand to enhance host influenza resistance when lethal influenza infection occurs, representing a novel interaction between host and gut microbiota. Further, our data suggest the potential utility of Bifidobacterium in the prevention and as a prognostic predictor of influenza.
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Affiliation(s)
- Qiang Zhang
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Jin Hu
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Jia-Wu Feng
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Xiao-Tong Hu
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Ting Wang
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Wen-Xiao Gong
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Kun Huang
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Yi-Xiong Guo
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Zhong Zou
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Xian Lin
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Run Zhou
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Yu-Qi Yuan
- Novogene Bioinformatics Institute, Beijing, 100000, People's Republic of China
| | - An-Ding Zhang
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.,Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Wuhan, 430070, People's Republic of China
| | - Hong Wei
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Gang Cao
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Chen Liu
- Novogene Bioinformatics Institute, Beijing, 100000, People's Republic of China.
| | - Ling-Ling Chen
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.
| | - Mei-Lin Jin
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China. .,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China. .,Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Wuhan, 430070, People's Republic of China.
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15
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Antibacterial Activity of Lactobacillus plantarum CRL 759 Against Methicillin-Resistant Staphylococcus aureus and Pseudomonas aeruginosa. ARABIAN JOURNAL FOR SCIENCE AND ENGINEERING 2020. [DOI: 10.1007/s13369-020-04491-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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16
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Delgado S, Sánchez B, Margolles A, Ruas-Madiedo P, Ruiz L. Molecules Produced by Probiotics and Intestinal Microorganisms with Immunomodulatory Activity. Nutrients 2020; 12:nu12020391. [PMID: 32024101 PMCID: PMC7071221 DOI: 10.3390/nu12020391] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 01/30/2020] [Accepted: 01/30/2020] [Indexed: 12/14/2022] Open
Abstract
Probiotics are live microorganisms that, when administered in adequate amounts, confer a health benefit on the host. The probiotic microorganisms most commonly used in the food and pharmacy industry belong to Lactobacillus and Bifidobacterium, and several strains of these genera have demonstrated beneficial attributes. In addition, some other intestinal bacteria inhabiting the human microbiota, such as Faecalibacterium prausnitzii and Akkermansia muciniphila, have recently been discovered and are able to display health-promoting effects in animal and human trials. The beneficial properties of probiotics have been known for a long time, although little is known about the molecular mechanisms and the molecules responsible for their effects. However, in recent years, advances in microbiome studies, and the use of novel analytical and molecular techniques have allowed a deeper insight into their effects at the molecular level. This review summarizes the current knowledge of some of the molecules of probiotics and other intestinal commensal bacteria responsible for their immunomodulatory effect, focusing on those with more solid scientific evidence.
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Affiliation(s)
- Susana Delgado
- Department of Microbiology and Biochemistry of Dairy Products, Dairy Research Institute of Asturias (IPLA)-Spanish National Research Council (CSIC), Villaviciosa, 33300 Asturias, Spain; (S.D.); (B.S.); (A.M.); (P.R.-M.)
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, 33011 Asturias, Spain
| | - Borja Sánchez
- Department of Microbiology and Biochemistry of Dairy Products, Dairy Research Institute of Asturias (IPLA)-Spanish National Research Council (CSIC), Villaviciosa, 33300 Asturias, Spain; (S.D.); (B.S.); (A.M.); (P.R.-M.)
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, 33011 Asturias, Spain
| | - Abelardo Margolles
- Department of Microbiology and Biochemistry of Dairy Products, Dairy Research Institute of Asturias (IPLA)-Spanish National Research Council (CSIC), Villaviciosa, 33300 Asturias, Spain; (S.D.); (B.S.); (A.M.); (P.R.-M.)
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, 33011 Asturias, Spain
| | - Patricia Ruas-Madiedo
- Department of Microbiology and Biochemistry of Dairy Products, Dairy Research Institute of Asturias (IPLA)-Spanish National Research Council (CSIC), Villaviciosa, 33300 Asturias, Spain; (S.D.); (B.S.); (A.M.); (P.R.-M.)
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, 33011 Asturias, Spain
| | - Lorena Ruiz
- Department of Microbiology and Biochemistry of Dairy Products, Dairy Research Institute of Asturias (IPLA)-Spanish National Research Council (CSIC), Villaviciosa, 33300 Asturias, Spain; (S.D.); (B.S.); (A.M.); (P.R.-M.)
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, 33011 Asturias, Spain
- Correspondence:
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17
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Hao H, Zhu L, Faden HS. The milk-based diet of infancy and the gut microbiome. Gastroenterol Rep (Oxf) 2019; 7:246-249. [PMID: 31413830 PMCID: PMC6688733 DOI: 10.1093/gastro/goz031] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 06/05/2019] [Accepted: 07/04/2019] [Indexed: 01/07/2023] Open
Abstract
The composition and the diversity of the gut microbiome play a major role in the health and well-being of humans beginning at birth. The impact of the diet on the structure and the function of the gut microbiome is evident by the changes in the gut microbiome concurrent with the transition from human milk to solid food. Complex oligosaccharides contained in milk are essential nutrients for commensal microbes in the infant gut. The most important commensal bacterium in the infant gut, bifidobacterium, requires α1, 2 fucosylated oligosaccharides for growth. Because not all humans are able to secrete α1, 2 fucosylated oligosaccharides into milk, the gut microbiome of infants and bifidobacteria, in particular, vary considerably between ‘secretors’ and ‘non-secretors’. A paucity of α1, 2 fucosylated oligosaccharides and bifidobacteria in the gut of infants may be associated with poor health.
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Affiliation(s)
- Hu Hao
- Division of Pediatrics, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, P. R. China
| | - Lixin Zhu
- Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, P. R. China.,Department of Biochemistry, Genome, Environment and Microbiome Community of Excellence, State University of New York at Buffalo, Buffalo, NY, USA
| | - Howard S Faden
- Division of Infectious Diseases, Department of Pediatrics, Jacobs School of Medicine and Biological Sciences, University at Buffalo, State University of New York at Buffalo, Buffalo, NY, USA
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18
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Zakharevich NV, Nezametdinova VZ, Averina OV, Chekalina MS, Alekseeva MG, Danilenko VN. Complete Genome Sequence of Bifidobacterium angulatum GT102: Potential Genes and Systems of Communication with Host. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419070160] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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19
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Duranti S, Lugli GA, Milani C, James K, Mancabelli L, Turroni F, Alessandri G, Mangifesta M, Mancino W, Ossiprandi MC, Iori A, Rota C, Gargano G, Bernasconi S, Di Pierro F, Sinderen D, Ventura M. Bifidobacterium bifidum
and the infant gut microbiota: an intriguing case of microbe‐host co‐evolution. Environ Microbiol 2019; 21:3683-3695. [DOI: 10.1111/1462-2920.14705] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 06/03/2019] [Accepted: 06/04/2019] [Indexed: 02/07/2023]
Affiliation(s)
- Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental SustainabilityUniversity of Parma Parma Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental SustainabilityUniversity of Parma Parma Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental SustainabilityUniversity of Parma Parma Italy
| | - Kieran James
- APC Microbiome Institute and School of Microbiology, Bioscience InstituteNational University of Ireland Cork Ireland
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental SustainabilityUniversity of Parma Parma Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental SustainabilityUniversity of Parma Parma Italy
- Microbiome Research HubUniversity of Parma Parma Italy
| | - Giulia Alessandri
- Department of Veterinary Medical ScienceUniversity of Parma Parma Italy
| | | | - Walter Mancino
- APC Microbiome Institute and School of Microbiology, Bioscience InstituteNational University of Ireland Cork Ireland
| | - Maria Cristina Ossiprandi
- Microbiome Research HubUniversity of Parma Parma Italy
- Department of Veterinary Medical ScienceUniversity of Parma Parma Italy
| | - Alexandra Iori
- Neonatal Intensive Care Unit, Obstetric and Pediatric Department, IRCCSArcispedale Santa Maria Nuova Reggio Emilia Italy
| | - Claudio Rota
- Neonatal Intensive Care Unit, Obstetric and Pediatric Department, IRCCSArcispedale Santa Maria Nuova Reggio Emilia Italy
| | - Giancarlo Gargano
- Neonatal Intensive Care Unit, Obstetric and Pediatric Department, IRCCSArcispedale Santa Maria Nuova Reggio Emilia Italy
| | | | | | - Douwe Sinderen
- APC Microbiome Institute and School of Microbiology, Bioscience InstituteNational University of Ireland Cork Ireland
- Department of Veterinary Medical ScienceUniversity of Parma Parma Italy
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental SustainabilityUniversity of Parma Parma Italy
- Microbiome Research HubUniversity of Parma Parma Italy
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20
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Bovine colostrum-driven modulation of intestinal epithelial cells for increased commensal colonisation. Appl Microbiol Biotechnol 2019; 103:2745-2758. [PMID: 30685814 DOI: 10.1007/s00253-019-09642-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 01/04/2019] [Accepted: 01/10/2019] [Indexed: 01/04/2023]
Abstract
Nutritional intake may influence the intestinal epithelial glycome and in turn the available attachment sites for bacteria. In this study, we tested the hypothesis that bovine colostrum may influence the intestinal cell surface and in turn the attachment of commensal organisms. Human HT-29 intestinal cells were exposed to a bovine colostrum fraction (BCF) rich in free oligosaccharides. The adherence of several commensal bacteria, comprising mainly bifidobacteria, to the intestinal cells was significantly enhanced (up to 52-fold) for all strains tested which spanned species that are found across the human lifespan. Importantly, the changes to the HT-29 cell surface did not support enhanced adhesion of the enteric pathogens tested. The gene expression profile of the HT-29 cells following treatment with the BCF was evaluated by microarray analysis. Many so called "glyco-genes" (glycosyltransferases and genes involved in the complex biosynthetic pathways of glycans) were found to be differentially regulated suggesting modulation of the enzymatic addition of sugars to glycoconjugate proteins. The microarray data was further validated by means of real-time PCR. The current findings provide an insight into how commensal microorganisms colonise the human gut and highlight the potential of colostrum and milk components as functional ingredients that can potentially increase commensal numbers in individuals with lower counts of health-promoting bacteria.
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Alberoni D, Gaggìa F, Baffoni L, Modesto MM, Biavati B, Di Gioia D. Bifidobacterium xylocopae sp. nov. and Bifidobacterium aemilianum sp. nov., from the carpenter bee (Xylocopa violacea) digestive tract. Syst Appl Microbiol 2018; 42:205-216. [PMID: 30551956 DOI: 10.1016/j.syapm.2018.11.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 11/09/2018] [Accepted: 11/21/2018] [Indexed: 12/17/2022]
Abstract
Social bees harbor a community of gut mutualistic bacteria, among which bifidobacteria occupy an important niche. Recently, four novel species have been isolated from guts of different bumblebees, thus allowing to suppose that a core bifidobacterial population may be present in wild solitary bees. To date there is sparse information about bifidobacteria in solitary bees such as Xylocopa and Osmia spp., this study is therefore focused on the isolation and characterization of bifidobacterial strains from solitary bees, in particular carpenter bee (Xylocopa violacea), builder bee (Osmia cornuta), and red mason bee (Osmia rufa). Among the isolates from Osmia spp. no new species have been detected whereas among Xylocopa isolates four strains (XV2, XV4, XV10, XV16) belonging to putative new species were found. Isolated strains are Gram-positive, lactate- and acetate-producing and possess the fructose-6-phosphate phosphoketolase enzyme. Full genome sequencing and genome annotation were performed for XV2 and XV10. Phylogenetic relationships were determined using partial and complete 16S rRNA sequences and hsp60 restriction analysis that confirmed the belonging of the new strains to Bifidobacterium genus and the relatedness of the strains XV2 and XV10 with XV16 and XV4, respectively. Phenotypic tests were performed for the proposed type strains, reference strains and their closest neighbor in the phylogenetic tree. The results support the proposal of two novel species Bifidobacterium xylocopae sp. nov. whose type strain is XV2 (=DSM 104955T=LMG 30142T), reference strain XV16 and Bifidobacterium aemilianum sp. nov. whose type strain is XV10 (=DSM 104956T=LMG 30143T), reference strain XV4.
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Affiliation(s)
- Daniele Alberoni
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, University of Bologna, Viale Fanin 44, 40127, Bologna, Italy
| | - Francesca Gaggìa
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, University of Bologna, Viale Fanin 44, 40127, Bologna, Italy
| | - Loredana Baffoni
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, University of Bologna, Viale Fanin 44, 40127, Bologna, Italy.
| | - Monica Marianna Modesto
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, University of Bologna, Viale Fanin 44, 40127, Bologna, Italy
| | - Bruno Biavati
- Institute of Earth Systems, Division of Rural Sciences Food Systems, University of Malta, Msida, Malta
| | - Diana Di Gioia
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, University of Bologna, Viale Fanin 44, 40127, Bologna, Italy
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22
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Whole fractions from probiotic bacteria induce in vitro Th17 responses in human peripheral blood mononuclear cells. J Funct Foods 2018. [DOI: 10.1016/j.jff.2018.07.038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
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23
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Turroni F, Milani C, Duranti S, Ferrario C, Lugli GA, Mancabelli L, van Sinderen D, Ventura M. Bifidobacteria and the infant gut: an example of co-evolution and natural selection. Cell Mol Life Sci 2018; 75:103-118. [PMID: 28983638 PMCID: PMC11105234 DOI: 10.1007/s00018-017-2672-0] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 09/29/2017] [Indexed: 12/16/2022]
Abstract
Throughout the human life, the gut microbiota interacts with us in a number of different ways, thereby influencing our health status. The acquisition of such an interactive gut microbiota commences at birth. Medical and environmental factors including diet, antibiotic exposure and mode of delivery are major factors that shape the composition of the microbial communities in the infant gut. Among the most abundant members of the infant microbiota are species belonging to the Bifidobacterium genus, which are believed to confer beneficial effects upon their host. Bifidobacteria may be acquired directly from the mother by vertical transmission and their persistence in the infant gut is associated with their saccharolytic activity toward glycans that are abundant in the infant gut. Here, we discuss the establishment of the infant gut microbiota and the contribution of bifidobacteria to this early life microbial consortium.
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Affiliation(s)
- Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Chiara Ferrario
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.
- Microbiome Research Hub, University of Parma, Parma, Italy.
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24
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Ruiz L, Delgado S, Ruas-Madiedo P, Sánchez B, Margolles A. Bifidobacteria and Their Molecular Communication with the Immune System. Front Microbiol 2017; 8:2345. [PMID: 29255450 PMCID: PMC5722804 DOI: 10.3389/fmicb.2017.02345] [Citation(s) in RCA: 186] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 11/15/2017] [Indexed: 12/16/2022] Open
Abstract
Bifidobacterium represents a genus within the phylum Actinobacteria which is one of the major phyla in the healthy intestinal tract of humans. Bifidobacterium is one of the most abundant genera in adults, but its predominance is even more pronounced in infants, especially during lactation, when they can constitute the majority of the total bacterial population. They are one of the pioneering colonizers of the early gut microbiota, and they are known to play important roles in the metabolism of dietary components, otherwise indigestible in the upper parts of the intestine, and in the maturation of the immune system. Bifidobacteria have been shown to interact with human immune cells and to modulate specific pathways, involving innate and adaptive immune processes. In this mini-review, we provide an overview of the current knowledge on the immunomodulatory properties of bifidobacteria and the mechanisms and molecular players underlying these processes, focusing on the corresponding implications for human health. We deal with in vitro models suitable for studying strain-specific immunomodulatory activities. These include peripheral blood mononuclear cells and T cell-mediated immune responses, both effector and regulatory cell responses, as well as the modulation of the phenotype of dendritic cells, among others. Furthermore, preclinical studies, mainly germ-free, gnotobiotic, and conventional murine models, and human clinical trials, are also discussed. Finally, we highlight evidence supporting the immunomodulatory effects of bifidobacterial molecules (proteins and peptides, exopolysaccharides, metabolites, and DNA), as well as the role of bifidobacterial metabolism in maintaining immune homeostasis through cross-feeding mechanisms.
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Affiliation(s)
- Lorena Ruiz
- Dairy Research Institute, Spanish National Research Council (Instituto de Productos Lácteos de Asturias - CSIC), Villaviciosa, Spain
| | - Susana Delgado
- Dairy Research Institute, Spanish National Research Council (Instituto de Productos Lácteos de Asturias - CSIC), Villaviciosa, Spain
| | - Patricia Ruas-Madiedo
- Dairy Research Institute, Spanish National Research Council (Instituto de Productos Lácteos de Asturias - CSIC), Villaviciosa, Spain
| | - Borja Sánchez
- Dairy Research Institute, Spanish National Research Council (Instituto de Productos Lácteos de Asturias - CSIC), Villaviciosa, Spain
| | - Abelardo Margolles
- Dairy Research Institute, Spanish National Research Council (Instituto de Productos Lácteos de Asturias - CSIC), Villaviciosa, Spain
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Exploring the role of the microbiota member Bifidobacterium in modulating immune-linked diseases. Emerg Top Life Sci 2017; 1:333-349. [PMID: 33525778 PMCID: PMC7288987 DOI: 10.1042/etls20170058] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Revised: 10/22/2017] [Accepted: 10/25/2017] [Indexed: 12/19/2022]
Abstract
The gut-associated microbiota is essential for multiple physiological processes, including immune development. Acquisition of our initial pioneer microbial communities, including the dominant early life genus Bifidobacterium, occurs at a critical period of immune maturation and programming. Bifidobacteria are resident microbiota members throughout our lifetime and have been shown to modulate specific immune cells and pathways. Notably, reductions in this genus have been associated with several diseases, including inflammatory bowel disease. In this review, we provide an overview of bifidobacteria profiles throughout life and how different strains of bifidobacteria have been implicated in immune modulation in disease states. The focus will be examining preclinical models and outcomes from clinical trials on immune-linked chronic conditions. Finally, we highlight some of the important unresolved questions in relation to Bifidobacterium-mediated immune modulation and implications for future directions, trials, and development of new therapies.
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Hidalgo-Cantabrana C, Moro-García MA, Blanco-Míguez A, Fdez-Riverola F, Lourenço A, Alonso-Arias R, Sánchez B. In Silico Screening of the Human Gut Metaproteome Identifies Th17-Promoting Peptides Encrypted in Proteins of Commensal Bacteria. Front Microbiol 2017; 8:1726. [PMID: 28943872 PMCID: PMC5596104 DOI: 10.3389/fmicb.2017.01726] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Accepted: 08/24/2017] [Indexed: 01/26/2023] Open
Abstract
Scientific studies focused on the role of the human microbiome over human health have generated billions of gigabits of genetic information during the last decade. Nowadays integration of all this information in public databases and development of pipelines allowing us to biotechnologically exploit this information are urgently needed. Prediction of the potential bioactivity of the products encoded by the human gut microbiome, or metaproteome, is the first step for identifying proteins responsible for the molecular interaction between microorganisms and the immune system. We have recently published the Mechanism of Action of the Human Microbiome (MAHMI) database (http://www.mahmi.org), conceived as a resource compiling peptide sequences with a potential immunomodulatory activity. Fifteen out of the 300 hundred million peptides contained in the MAHMI database were synthesized. These peptides were identified as being encrypted in proteins produced by gut microbiota members, they do not contain cleavage points for the major intestinal endoproteases and displayed high probability to have immunomodulatory bioactivity. The bacterial peptides FR-16 and LR-17 encrypted in proteins from Bifidobacterium longum DJ010A and Bifidobacterium fragilis YCH46 respectively, showed the higher immune modulation capability over human peripheral blood mononuclear cells. Both peptides modulated the immune response toward increases in the Th17 and decreases in the Th1 cell response, together with an induction of IL-22 production. These results strongly suggest the combined use of bioinformatics and in vitro tools as a first stage in the screening of bioactive peptides encrypted in the human gut metaproteome.
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Affiliation(s)
- Claudio Hidalgo-Cantabrana
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones CientíficasVillaviciosa, Spain.,Department of Immunology, Hospital Universitario Central de AsturiasOviedo, Spain
| | - Marco A Moro-García
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones CientíficasVillaviciosa, Spain.,Department of Immunology, Hospital Universitario Central de AsturiasOviedo, Spain
| | - Aitor Blanco-Míguez
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones CientíficasVillaviciosa, Spain.,Escuela Superior de Ingeniería Informática - Department of Computer Science, University of VigoVigo, Spain.,Centro de Investigaciones Biomédicas, University of VigoVigo, Spain
| | - Florentino Fdez-Riverola
- Escuela Superior de Ingeniería Informática - Department of Computer Science, University of VigoVigo, Spain.,Centro de Investigaciones Biomédicas, University of VigoVigo, Spain
| | - Anália Lourenço
- Escuela Superior de Ingeniería Informática - Department of Computer Science, University of VigoVigo, Spain.,Centro de Investigaciones Biomédicas, University of VigoVigo, Spain.,Centre of Biological Engineering, University of MinhoBraga, Portugal
| | - Rebeca Alonso-Arias
- Department of Immunology, Hospital Universitario Central de AsturiasOviedo, Spain
| | - Borja Sánchez
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones CientíficasVillaviciosa, Spain
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Thomson P, Medina DA, Garrido D. Human milk oligosaccharides and infant gut bifidobacteria: Molecular strategies for their utilization. Food Microbiol 2017; 75:37-46. [PMID: 30056961 DOI: 10.1016/j.fm.2017.09.001] [Citation(s) in RCA: 139] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 08/30/2017] [Accepted: 09/02/2017] [Indexed: 02/08/2023]
Abstract
Breast milk is the gold standard in infant nutrition. In addition to provide essential nutrients for the newborn, it contains multiple bioactive molecules that provide protection and stimulate proper development. Human milk oligosaccharides (HMO) are complex carbohydrates abundant in breast milk. Intriguingly, these molecules do not provide energy to the infant. Instead, these oligosaccharides are key to guide and support the assembly of a healthy gut microbiome in the infant, dominated by beneficial gut microbes such as Bifidobacterium. New analytical methods for glycan analysis, and next-generation sequencing of microbial communities, have been instrumental in advancing our understanding of the positive role of breast milk oligosaccharides on the gut microbiome, and the genomics and molecular strategies of Bifidobacterium to utilize these oligosaccharides. Moreover, novel approaches to simulate the impact of HMO on the gut microbiome have been described and successfully validated, including the incorporation of synthetic HMO and bovine milk oligosaccharides to infant formula. This review discusses recent advances regarding the influence of HMO in promoting a healthy gut microbiome, with emphasis in the molecular basis of the enrichment in beneficial Bifidobacterium, and novel approaches to replicate the effect of HMO using synthetic or bovine oligosaccharides.
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Affiliation(s)
- Pamela Thomson
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Santiago, Chile
| | - Daniel A Medina
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Santiago, Chile
| | - Daniel Garrido
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Santiago, Chile.
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Hidalgo-Cantabrana C, O’Flaherty S, Barrangou R. CRISPR-based engineering of next-generation lactic acid bacteria. Curr Opin Microbiol 2017. [DOI: 10.1016/j.mib.2017.05.015] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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