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Xiao M, Zhang C, Duan H, Narbad A, Zhao J, Chen W, Zhai Q, Yu L, Tian F. Cross-feeding of bifidobacteria promotes intestinal homeostasis: a lifelong perspective on the host health. NPJ Biofilms Microbiomes 2024; 10:47. [PMID: 38898089 PMCID: PMC11186840 DOI: 10.1038/s41522-024-00524-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 06/07/2024] [Indexed: 06/21/2024] Open
Abstract
Throughout the life span of a host, bifidobacteria have shown superior colonization and glycan abilities. Complex glycans, such as human milk oligosaccharides and plant glycans, that reach the colon are directly internalized by the transport system of bifidobacteria, cleaved into simple structures by extracellular glycosyl hydrolase, and transported to cells for fermentation. The glycan utilization of bifidobacteria introduces cross-feeding activities between bifidobacterial strains and other microbiota, which are influenced by host nutrition and regulate gut homeostasis. This review discusses bifidobacterial glycan utilization strategies, focusing on the cross-feeding involved in bifidobacteria and its potential health benefits. Furthermore, the impact of cross-feeding on the gut trophic niche of bifidobacteria and host health is also highlighted. This review provides novel insights into the interactions between microbe-microbe and host-microbe.
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Affiliation(s)
- Meifang Xiao
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Chuan Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Hui Duan
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Arjan Narbad
- Quadram Institute Bioscience, Norwich Research Park Colney, Norwich, Norfolk, NR4 7UA, UK
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Wei Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Leilei Yu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China.
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China.
| | - Fengwei Tian
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China.
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China.
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2
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Yang X, Zhang J, Zhu J, Yang R, Tong Y. Molecular insights into FucR transcription factor to control the metabolism of L-fucose in Bifidobacterium longum subsp. infantis. Microbiol Res 2024; 283:127709. [PMID: 38593579 DOI: 10.1016/j.micres.2024.127709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 03/27/2024] [Accepted: 03/30/2024] [Indexed: 04/11/2024]
Abstract
Bifidobacterium longum subsp. infantis commonly colonizes the human gut and is capable of metabolizing L-fucose, which is abundant in the gut. Multiple studies have focused on the mechanisms of L-fucose utilization by B. longum subsp. infantis, but the regulatory pathways governing the expression of these catabolic processes are still unclear. In this study, we have conducted a structural and functional analysis of L-fucose metabolism transcription factor FucR derived from B. longum subsp. infantis Bi-26. Our results indicated that FucR is a L-fucose-sensitive repressor with more α-helices, fewer β-sheets, and β-turns. Transcriptional analysis revealed that FucR displays weak negative self-regulation, which is counteracted in the presence of L-fucose. Isothermal titration calorimetry indicated that FucR has a 2:1 stoichiometry with L-fucose. The key amino acid residues for FucR binding L-fucose are Asp280 and Arg331, with mutation of Asp280 to Ala resulting in a decrease in the affinity between FucR and L-fucose with the Kd value from 2.58 to 11.68 μM, and mutation of Arg331 to Ala abolishes the binding ability of FucR towards L-fucose. FucR specifically recognized and bound to a 20-bp incomplete palindrome sequence (5'-ACCCCAATTACGAAAATTTTT-3'), and the affinity of the L-fucose-loaded FucR for the DNA fragment was lower than apo-FucR. The results provided new insights into the regulating L-fucose metabolism by B. longum subsp. infantis.
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Affiliation(s)
- Xiaojun Yang
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Jing Zhang
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Jing Zhu
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Ruijin Yang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yanjun Tong
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China.
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3
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Borlandelli V, Offen W, Moroz O, Nin-Hill A, McGregor N, Binkhorst L, Ishiwata A, Armstrong Z, Artola M, Rovira C, Davies GJ, Overkleeft HS. β-l- Arabinofurano-cyclitol Aziridines Are Covalent Broad-Spectrum Inhibitors and Activity-Based Probes for Retaining β-l-Arabinofuranosidases. ACS Chem Biol 2023; 18:2564-2573. [PMID: 38051515 PMCID: PMC10728902 DOI: 10.1021/acschembio.3c00558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/14/2023] [Accepted: 11/17/2023] [Indexed: 12/07/2023]
Abstract
GH127 and GH146 microorganismal retaining β-l-arabinofuranosidases, expressed by human gut microbiomes, feature an atypical catalytic domain and an unusual mechanism of action. We recently reported that both Bacteroides thetaiotaomicron BtGH146 and Bifidobacterium longum HypBA1 are inhibited by β-l-arabinofuranosyl cyclophellitol epoxide, supporting the action of a zinc-coordinated cysteine as a catalytic nucleophile, where in most retaining GH families, an aspartate or glutamate is employed. This work presents a panel of β-l-arabinofuranosyl cyclophellitol epoxides and aziridines as mechanism-based BtGH146/HypBA1 inhibitors and activity-based probes. The β-l-arabinofuranosyl cyclophellitol aziridines both inhibit and label β-l-arabinofuranosidase efficiently (however with different activities), whereas the epoxide-derived probes favor BtGH146 over HypBA1. These findings are accompanied by X-ray structural analysis of the unmodified β-l-arabinofuranosyl cyclophellitol aziridine in complex with both isozymes, which were shown to react by nucleophilic opening of the aziridine, at the pseudoanomeric carbon, by the active site cysteine nucleophile to form a stable thioether bond. Altogether, our activity-based probes may serve as chemical tools for the detection and identification of low-abundance β-l-arabinofuranosidases in complex biological samples.
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Affiliation(s)
- Valentina Borlandelli
- Bio-organic
Synthesis, Leiden Institute of Chemistry (LIC), Leiden University, Gorlaeus Laboratories, Einsteinweg 55, 2333
CC Leiden, The Netherlands
| | - Wendy Offen
- Department
of Chemistry, York Structural Biology Laboratory, University of York, Heslington, York YO10
5DD, United Kingdom
| | - Olga Moroz
- Department
of Chemistry, York Structural Biology Laboratory, University of York, Heslington, York YO10
5DD, United Kingdom
| | - Alba Nin-Hill
- Departament
de Química Inorgànica i Orgànica (Secció
de Química Orgànica), Institut
de Química Teòrica i Computacional (IQTCUB), Universitat
de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Nicholas McGregor
- Department
of Chemistry, York Structural Biology Laboratory, University of York, Heslington, York YO10
5DD, United Kingdom
| | - Lars Binkhorst
- Bio-organic
Synthesis, Leiden Institute of Chemistry (LIC), Leiden University, Gorlaeus Laboratories, Einsteinweg 55, 2333
CC Leiden, The Netherlands
| | - Akihiro Ishiwata
- RIKEN
Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Zachary Armstrong
- Bio-organic
Synthesis, Leiden Institute of Chemistry (LIC), Leiden University, Gorlaeus Laboratories, Einsteinweg 55, 2333
CC Leiden, The Netherlands
| | - Marta Artola
- Bio-organic
Synthesis, Leiden Institute of Chemistry (LIC), Leiden University, Gorlaeus Laboratories, Einsteinweg 55, 2333
CC Leiden, The Netherlands
| | - Carme Rovira
- Departament
de Química Inorgànica i Orgànica (Secció
de Química Orgànica), Institut
de Química Teòrica i Computacional (IQTCUB), Universitat
de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Gideon J. Davies
- Department
of Chemistry, York Structural Biology Laboratory, University of York, Heslington, York YO10
5DD, United Kingdom
| | - Herman S. Overkleeft
- Bio-organic
Synthesis, Leiden Institute of Chemistry (LIC), Leiden University, Gorlaeus Laboratories, Einsteinweg 55, 2333
CC Leiden, The Netherlands
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4
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Yang X, Zeng D, Li C, Yu W, Xie G, Zhang Y, Lu W. Therapeutic potential and mechanism of functional oligosaccharides in inflammatory bowel disease: a review. FOOD SCIENCE AND HUMAN WELLNESS 2023. [DOI: 10.1016/j.fshw.2023.03.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
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5
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The Pleiotropic Effects of Carbohydrate-Mediated Growth Rate Modifications in Bifidobacterium longum NCC 2705. Microorganisms 2023; 11:microorganisms11030588. [PMID: 36985162 PMCID: PMC10059941 DOI: 10.3390/microorganisms11030588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 02/17/2023] [Accepted: 02/23/2023] [Indexed: 03/03/2023] Open
Abstract
Bifidobacteria are saccharolytic bacteria that are able to metabolize a relatively large range of carbohydrates through their unique central carbon metabolism known as the “bifid-shunt”. Carbohydrates have been shown to modulate the growth rate of bifidobacteria, but unlike for other genera (e.g., E. coli or L. lactis), the impact it may have on the overall physiology of the bacteria has not been studied in detail to date. Using glucose and galactose as model substrates in Bifidobacterium longum NCC 2705, we established that the strain displayed fast and slow growth rates on those carbohydrates, respectively. We show that these differential growth conditions are accompanied by global transcriptional changes and adjustments of central carbon fluxes. In addition, when grown on galactose, NCC 2705 cells were significantly smaller, exhibited an expanded capacity to import and metabolized different sugars and displayed an increased acid-stress resistance, a phenotypic signature associated with generalized fitness. We predict that part of the observed adaptation is regulated by the previously described bifidobacterial global transcriptional regulator AraQ, which we propose to reflect a catabolite-repression-like response in B. longum. With this manuscript, we demonstrate that not only growth rate but also various physiological characteristics of B. longum NCC 2705 are responsive to the carbon source used for growth, which is relevant in the context of its lifestyle in the human infant gut where galactose-containing oligosaccharides are prominent.
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6
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Bai Y, Zhou Y, Zhang R, Chen Y, Wang F, Zhang M. Gut microbial fermentation promotes the intestinal anti-inflammatory activity of Chinese yam polysaccharides. Food Chem 2023; 402:134003. [DOI: 10.1016/j.foodchem.2022.134003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 08/05/2022] [Accepted: 08/21/2022] [Indexed: 11/20/2022]
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Xie NN, Wu CY, Ge Q, Zhou J, Long F, Mao Q, Li SL, Shen H. Structure-specific antitumor effects and potential gut microbiota-involved mechanisms of ginseng polysaccharides on B16F10 melanoma-bearing mice. Food Funct 2023; 14:796-809. [PMID: 36607268 DOI: 10.1039/d2fo03383f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Ginseng polysaccharides (GPs) have shown gut microbiota-related antitumor effects. However, the relation between their structures and antitumor functions remains unknown. Here, crude polysaccharide (GP-c) and its fractions neutral polysaccharide (GP-n) and pectin (GP-a) were prepared for structure characterization and anti-B16F10 melanoma effect evaluation, and their influence on gut microbiota diversities and short-chain fatty acids (SCFAs) were also analyzed. Spearman correlations among the altered gut microbiota, SCFAs, and antitumor effects were conducted to elucidate the structure-function relationships. It was shown that the structures of GP-c, GP-n, and GP-a varied in monosaccharide composition and molecular weight distribution. GP-n and GP-c showed anti-melanoma effects, whereas GP-a promoted its growth slightly. GP-n and GP-c restored SCFAs levels such as acetic acid and butyric acid; moreover, it improved the gut microbiota ecosystem by upregulating the abundance of Allobaculum and Bifidobacterium. However, the restoration effect of GP-a was weak, or even worse. In addition, these two bacteria were negatively correlated with the tumor weight and related with the altered SCFAs. In conclusion, GP-n is essential for the anti-melanoma effects of GP, and the potential mechanisms might be related with its specific regulation of Allobaculum and Bifidobacterium abundance, and tumor-associated SCFAs levels. The outcomes highlighted here enable a deeper insight into the structure-function relationship of GP and propose new opinions on its antitumor effect.
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Affiliation(s)
- Ni-Na Xie
- Department of Pharmaceutical Analysis, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing 210028, People's Republic of China.
| | - Cheng-Ying Wu
- Department of Metabolomics, Jiangsu Province Academy of Traditional Chinese Medicine and Jiangsu Branch of China Academy of Chinese Medical Sciences, Nanjing 210028, People's Republic of China.
| | - Qiong Ge
- Department of Pharmaceutical Analysis, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing 210028, People's Republic of China.
| | - Jing Zhou
- Department of Metabolomics, Jiangsu Province Academy of Traditional Chinese Medicine and Jiangsu Branch of China Academy of Chinese Medical Sciences, Nanjing 210028, People's Republic of China.
| | - Fang Long
- Department of Metabolomics, Jiangsu Province Academy of Traditional Chinese Medicine and Jiangsu Branch of China Academy of Chinese Medical Sciences, Nanjing 210028, People's Republic of China.
| | - Qian Mao
- Department of Metabolomics, Jiangsu Province Academy of Traditional Chinese Medicine and Jiangsu Branch of China Academy of Chinese Medical Sciences, Nanjing 210028, People's Republic of China.
| | - Song-Lin Li
- Department of Metabolomics, Jiangsu Province Academy of Traditional Chinese Medicine and Jiangsu Branch of China Academy of Chinese Medical Sciences, Nanjing 210028, People's Republic of China.
| | - Hong Shen
- Department of Pharmaceutical Analysis, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing 210028, People's Republic of China.
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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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Effects of Lycium barbarum Polysaccharides on Immunity and Metabolic Syndrome Associated with the Modulation of Gut Microbiota: A Review. Foods 2022. [PMCID: PMC9602392 DOI: 10.3390/foods11203177] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Lycium barbarum polysaccharides (LBPs) have attracted increasing attention due to their multiple pharmacological activities and physiological functions. Recently, both in vitro and in vivo studies have demonstrated that the biological effects of dietary LBPs are related to the regulation of gut microbiota. Supplementation with LBPs could modulate the composition of microbial communities, and simultaneously influence the levels of active metabolites, thus exerting their beneficial effects on host health. Interestingly, LBPs with diverse chemical structures may enrich or reduce certain specific intestinal microbes. The present review summarizes the extraction, purification, and structural types of LBPs and the regulation effects of LBPs on the gut microbiome and their derived metabolites. Furthermore, the health promoting effects of LBPs on host bidirectional immunity (e.g., immune enhancement and immune inflammation suppression) and metabolic syndrome (e.g., obesity, type 2 diabetes, and nonalcoholic fatty liver disease) by targeting gut microbiota are also discussed based on their structural types. The contents presented in this review might help to better understand the health benefits of LBPs targeting gut microbiota and provide a scientific basis to further clarify the structure–function relationship of LBPs.
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10
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Arzamasov AA, Osterman AL. Milk glycan metabolism by intestinal bifidobacteria: insights from comparative genomics. Crit Rev Biochem Mol Biol 2022; 57:562-584. [PMID: 36866565 PMCID: PMC10192226 DOI: 10.1080/10409238.2023.2182272] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 01/11/2023] [Accepted: 02/15/2023] [Indexed: 03/04/2023]
Abstract
Bifidobacteria are early colonizers of the human neonatal gut and provide multiple health benefits to the infant, including inhibiting the growth of enteropathogens and modulating the immune system. Certain Bifidobacterium species prevail in the gut of breastfed infants due to the ability of these microorganisms to selectively forage glycans present in human milk, specifically human milk oligosaccharides (HMOs) and N-linked glycans. Therefore, these carbohydrates serve as promising prebiotic dietary supplements to stimulate the growth of bifidobacteria in the guts of children suffering from impaired gut microbiota development. However, the rational formulation of milk glycan-based prebiotics requires a detailed understanding of how bifidobacteria metabolize these carbohydrates. Accumulating biochemical and genomic data suggest that HMO and N-glycan assimilation abilities vary remarkably within the Bifidobacterium genus, both at the species and strain levels. This review focuses on the delineation and genome-based comparative analysis of differences in respective biochemical pathways, transport systems, and associated transcriptional regulatory networks, providing a foundation for genomics-based projection of milk glycan utilization capabilities across a rapidly growing number of sequenced bifidobacterial genomes and metagenomic datasets. This analysis also highlights remaining knowledge gaps and suggests directions for future studies to optimize the formulation of milk-glycan-based prebiotics that target bifidobacteria.
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Affiliation(s)
- Aleksandr A Arzamasov
- Infectious and Inflammatory Diseases Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Andrei L Osterman
- Infectious and Inflammatory Diseases Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
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11
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Tomioka S, Seki N, Sugiura Y, Akiyama M, Uchiyama J, Yamaguchi G, Yakabe K, Ejima R, Hattori K, Kimizuka T, Fujimura Y, Sato H, Gondo M, Ozaki S, Honme Y, Suematsu M, Kimura I, Inohara N, Núñez G, Hase K, Kim YG. Cooperative action of gut-microbiota-accessible carbohydrates improves host metabolic function. Cell Rep 2022; 40:111087. [PMID: 35858544 DOI: 10.1016/j.celrep.2022.111087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 03/17/2022] [Accepted: 06/22/2022] [Indexed: 12/31/2022] Open
Abstract
Microbiota-accessible carbohydrates (MACs) exert health-promoting effects, but how each MAC impacts gut microbiota and regulates host physiology remains unclear. Here, we show that l-arabinose and sucrose cooperatively act on gut microbiota and exert anti-obesogenic effects. Specifically, l-arabinose, a monosaccharide that is poorly absorbed in the gut and inhibits intestinal sucrase, suppresses diet-induced obesity in mice in the presence of sucrose. Additionally, the suppressive effect of l-arabinose on adiposity is abrogated in mice lacking the short-chain fatty acid (SCFA) receptors GPR43 and GPR41. Mechanistically, l-arabinose increases the relative abundance of acetate and propionate producers (e.g., Bacteroides), while sucrose enhances SCFA production. Furthermore, l-arabinose and sucrose activate the glycolytic and pentose phosphate pathways of Bacteroides, respectively, indicating that they synergistically promote acetate production through distinct pathways. These findings suggest that each MAC has a unique property and thus may serve as a precision gut-microbiota modulator to promote host homeostasis.
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Affiliation(s)
- Sawako Tomioka
- Research Center for Drug Discovery and Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan; Division of Biochemistry, Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan
| | - Natsumi Seki
- Research Center for Drug Discovery and Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan; Division of Biochemistry, Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan
| | - Yuki Sugiura
- Department of Biochemistry, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Masahiro Akiyama
- Research Center for Drug Discovery and Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan
| | - Jun Uchiyama
- Research Center for Drug Discovery and Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan; Division of Biochemistry, Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan
| | - Genki Yamaguchi
- Research Center for Drug Discovery and Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan; Division of Biochemistry, Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan
| | - Kyosuke Yakabe
- Research Center for Drug Discovery and Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan; Division of Biochemistry, Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan
| | - Ryuta Ejima
- Research Center for Drug Discovery and Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan; Division of Biochemistry, Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan
| | - Kouya Hattori
- Research Center for Drug Discovery and Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan; Division of Biochemistry, Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan
| | - Tatsuki Kimizuka
- Research Center for Drug Discovery and Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan; Division of Biochemistry, Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan
| | - Yumiko Fujimura
- Division of Biochemistry, Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan
| | - Hiroki Sato
- Research Center for Drug Discovery and Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan
| | - Monica Gondo
- Research Center for Drug Discovery and Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan; Division of Biochemistry, Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan
| | - Satoru Ozaki
- Co-Creation Center, Meiji Holdings Co., Ltd., Tokyo 192-0919, Japan
| | - Yoshiko Honme
- Co-Creation Center, Meiji Holdings Co., Ltd., Tokyo 192-0919, Japan
| | - Makoto Suematsu
- Department of Biochemistry, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Ikuo Kimura
- Laboratory of Molecular Neurobiology, Graduate School of Biostudies, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Naohiro Inohara
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Gabriel Núñez
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Koji Hase
- Division of Biochemistry, Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan
| | - Yun-Gi Kim
- Research Center for Drug Discovery and Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan.
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12
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Duboux S, Muller JA, De Franceschi F, Mercenier A, Kleerebezem M. Using fluorescent promoter-reporters to study sugar utilization control in Bifidobacterium longum NCC 2705. Sci Rep 2022; 12:10477. [PMID: 35729224 PMCID: PMC9213400 DOI: 10.1038/s41598-022-14638-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 06/09/2022] [Indexed: 02/01/2023] Open
Abstract
Bifidobacteria are amongst the first bacteria to colonize the human gastro-intestinal system and have been proposed to play a crucial role in the development of the infant gut since their absence is correlated to the development of diseases later in life. Bifidobacteria have the capacity to metabolize a diverse range of (complex) carbohydrates, reflecting their adaptation to the lower gastro-intestinal tract. Detailed understanding of carbohydrate metabolism regulation in this genus is of prime importance and availability of additional genetic tools easing such studies would be beneficial. To develop a fluorescent protein-based reporter system that can be used in B. longum NCC 2705, we first selected the most promising fluorescent protein out of the seven we tested (i.e., mCherry). This reporter protein was then used to study the carbohydrate mediated activation of PBl1518 and PBl1694, two promoters respectively predicted to be controlled by the transcriptional factors AraQ and AraU, previously suggested to regulate arabinose utilization and proposed to also act as global transcriptional regulators in bifidobacteria. We confirmed that in B. longum NCC 2705 the AraQ controlled promoter (PBl1518) is induced strongly by arabinose and established that the AraU controlled promoter (PBl1694) was mostly induced by the hexoses galactose and fructose. Combining the mCherry reporter system with flow cytometry, we established that NCC 2705 is able to co-metabolize arabinose and glucose while galactose was only consumed after glucose exhaustion, thus illustrating the complexity of different carbohydrate consumption patterns and their specific regulation in this strain.
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Affiliation(s)
- S Duboux
- Nestlé Research, Lausanne, Switzerland. .,Host-Microbe Interactomics Group, Wageningen University and Research, De Elst 1, 6708WD, Wageningen, The Netherlands.
| | | | | | - A Mercenier
- Host-Microbe Interactomics Group, Wageningen University and Research, De Elst 1, 6708WD, Wageningen, The Netherlands
| | - M Kleerebezem
- Host-Microbe Interactomics Group, Wageningen University and Research, De Elst 1, 6708WD, Wageningen, The Netherlands.
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13
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Kang JW, Tang X, Walton CJ, Brown MJ, Brewer RA, Maddela RL, Zheng JJ, Agus JK, Zivkovic AM. Multi-Omic Analyses Reveal Bifidogenic Effect and Metabolomic Shifts in Healthy Human Cohort Supplemented With a Prebiotic Dietary Fiber Blend. Front Nutr 2022; 9:908534. [PMID: 35782954 PMCID: PMC9248813 DOI: 10.3389/fnut.2022.908534] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 05/20/2022] [Indexed: 12/14/2022] Open
Abstract
Dietary fiber, a nutrient derived mainly from whole grains, vegetables, fruits, and legumes, is known to confer a number of health benefits, yet most Americans consume less than half of the daily recommended amount. Convenience and affordability are key factors determining the ability of individuals to incorporate fiber-rich foods into their diet, and many Americans struggle to access, afford, and prepare foods rich in fiber. The objective of this clinical study was to test the changes in microbial community composition, human metabolomics, and general health markers of a convenient, easy to use prebiotic supplement in generally healthy young participants consuming a diet low in fiber. Twenty healthy adults participated in this randomized, placebo-controlled, double-blind, crossover study which was registered at clinicaltrials.gov as NCT03785860. During the study participants consumed 12 g of a prebiotic fiber supplement and 12 g of placebo daily as a powder mixed with water as part of their habitual diet in randomized order for 4 weeks, with a 4-week washout between treatment arms. Fecal microbial DNA was extracted and sequenced by shallow shotgun sequencing on an Illumina NovaSeq. Plasma metabolites were detected using liquid chromatography–mass spectrometry with untargeted analysis. The phylum Actinobacteria, genus Bifidobacterium, and several Bifidobacterium species (B. bifidum, B. adolescentis, B. breve, B. catenulatum, and B. longum) significantly increased after prebiotic supplementation when compared to the placebo. The abundance of genes associated with the utilization of the prebiotic fiber ingredients (sacA, xfp, xpk) and the production of acetate (poxB, ackA) significantly changed with prebiotic supplementation. Additionally, the abundance of genes associated with the prebiotic utilization (xfp, xpk), acetate production (ackA), and choline to betaine oxidation (gbsB) were significantly correlated with changes in the abundance of the genus Bifidobacterium in the prebiotic group. Plasma concentrations of the bacterially produced metabolite indolepropionate significantly increased. The results of this study demonstrate that an easy to consume, low dose (12 g) of a prebiotic powder taken daily increases the abundance of beneficial bifidobacteria and the production of health-promoting bacteria-derived metabolites in healthy individuals with a habitual low-fiber diet.
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Affiliation(s)
- Jea Woo Kang
- Department of Nutrition, University of California, Davis, Davis, CA, United States
| | - Xinyu Tang
- Department of Nutrition, University of California, Davis, Davis, CA, United States
| | | | - Mark J. Brown
- USANA Health Sciences, Inc., Salt Lake City, UT, United States
| | | | | | - Jack Jingyuan Zheng
- Department of Nutrition, University of California, Davis, Davis, CA, United States
| | - Joanne K. Agus
- Department of Nutrition, University of California, Davis, Davis, CA, United States
| | - Angela M. Zivkovic
- Department of Nutrition, University of California, Davis, Davis, CA, United States
- *Correspondence: Angela M. Zivkovic
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14
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Yue F, Xu J, Zhang S, Hu X, Wang X, Lü X. Structural features and anticancer mechanisms of pectic polysaccharides: A review. Int J Biol Macromol 2022; 209:825-839. [PMID: 35447258 DOI: 10.1016/j.ijbiomac.2022.04.073] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 03/01/2022] [Accepted: 04/09/2022] [Indexed: 02/07/2023]
Abstract
The anticancer activity of pectic polysaccharides (PPs) was proved by numerous studies, and which also indicated that the bioactivity of PPs was closely related to its complicated structures. Based on the summary and analysis about structure characteristics and corresponding enzymatic process of the reported PPs, the anticancer mechanism and related structural features were systematically clarified. It was found that not only the direct effects on the cancer cells by proliferation inhibition or apoptosis, but also the regulation of immune system, gut microbiota and gut metabolism as indirect effects, jointly played important roles in the anticancer of PPs. Nevertheless, during the study of PPs as promising anticancer components, the exact structure-function relationship, digestion process in vivo, and comprehensive action mechanism are still not well understanding. With the unveiling of the proposed issues, it is believed that PPs are promising to be exploited as effective cancer therapy/adjunctive therapy drugs or functional foods.
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Affiliation(s)
- Fangfang Yue
- College of Food Science and Engineering, Northwest Agriculture and Forestry University, Yangling 712100, Shaanxi, China
| | - Jiaxin Xu
- College of Food Science and Engineering, Northwest Agriculture and Forestry University, Yangling 712100, Shaanxi, China
| | - Sitan Zhang
- College of Food Science and Engineering, Northwest Agriculture and Forestry University, Yangling 712100, Shaanxi, China
| | - Xinyu Hu
- College of Food Science and Engineering, Northwest Agriculture and Forestry University, Yangling 712100, Shaanxi, China
| | - Xin Wang
- College of Food Science and Engineering, Northwest Agriculture and Forestry University, Yangling 712100, Shaanxi, China.
| | - Xin Lü
- College of Food Science and Engineering, Northwest Agriculture and Forestry University, Yangling 712100, Shaanxi, China.
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15
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Barratt MJ, Nuzhat S, Ahsan K, Frese SA, Arzamasov AA, Sarker SA, Islam MM, Palit P, Islam MR, Hibberd MC, Nakshatri S, Cowardin CA, Guruge JL, Byrne AE, Venkatesh S, Sundaresan V, Henrick B, Duar RM, Mitchell RD, Casaburi G, Prambs J, Flannery R, Mahfuz M, Rodionov DA, Osterman AL, Kyle D, Ahmed T, Gordon JI. Bifidobacterium infantis treatment promotes weight gain in Bangladeshi infants with severe acute malnutrition. Sci Transl Med 2022; 14:eabk1107. [PMID: 35417188 PMCID: PMC9516695 DOI: 10.1126/scitranslmed.abk1107] [Citation(s) in RCA: 64] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Disrupted development of the gut microbiota is a contributing cause of childhood malnutrition. Bifidobacterium longum subspecies infantis is a prominent early colonizer of the infant gut that consumes human milk oligosaccharides (HMOs). We found that the absolute abundance of Bifidobacterium infantis is lower in 3- to 24-month-old Bangladeshi infants with severe acute malnutrition (SAM) compared to their healthy age-matched counterparts. A single-blind, placebo-controlled trial (SYNERGIE) was conducted in 2- to 6-month-old Bangladeshi infants with SAM. A commercial U.S. donor-derived B. infantis strain (EVC001) was administered daily with or without the HMO lacto-N-neotetraose for 28 days. This intervention increased fecal B. infantis abundance in infants with SAM, although to levels still 10- to 100-fold lower than in untreated healthy controls. EVC001 treatment promoted weight gain that was associated with reduced intestinal inflammation markers in infants with SAM. We cultured fecal B. infantis strains from Bangladeshi infants and colonized gnotobiotic mice with these cultured strains. The gnotobiotic mice were fed a diet representative of that consumed by 6-month-old Bangladeshi infants, with or without HMO supplementation. One B. infantis strain, Bg_2D9, expressing two gene clusters involved in uptake and utilization of N-glycans and plant-derived polysaccharides, exhibited superior fitness over EVC001. The fitness advantage of Bg_2D9 was confirmed in a gnotobiotic mouse model of mother-to-infant gut microbiota transmission where dams received a pretreatment fecal community from a SAM infant in the SYNERGIE trial. Whether Bg_2D9 is superior to EVC001 for treating malnourished infants who consume a diet with limited breastmilk requires further clinical testing.
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Affiliation(s)
- Michael J. Barratt
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Sharika Nuzhat
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Kazi Ahsan
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Steven A. Frese
- Evolve BioSystems, Inc., Davis, CA 95618 USA
- Department of Food Science and Technology, University of Nebraska, Lincoln, NE 68588 USA
| | - Aleksandr A. Arzamasov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037 USA
| | - Shafiqul Alam Sarker
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - M. Munirul Islam
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Parag Palit
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Md Ridwan Islam
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Matthew C. Hibberd
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Swetha Nakshatri
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Carrie A. Cowardin
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Janaki L. Guruge
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Alexandra E. Byrne
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Siddarth Venkatesh
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Vinaik Sundaresan
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Bethany Henrick
- Evolve BioSystems, Inc., Davis, CA 95618 USA
- Department of Food Science and Technology, University of Nebraska, Lincoln, NE 68588 USA
| | | | | | | | | | | | - Mustafa Mahfuz
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Dmitry A. Rodionov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037 USA
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127994 Russia
| | - Andrei L. Osterman
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037 USA
| | - David Kyle
- Evolve BioSystems, Inc., Davis, CA 95618 USA
| | - Tahmeed Ahmed
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Jeffrey I. Gordon
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110 USA
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16
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Pino A, Benkaddour B, Inturri R, Amico P, Vaccaro SC, Russo N, Vaccalluzzo A, Agolino G, Caggia C, Miloud H, Randazzo CL. Characterization of Bifidobacterium asteroides Isolates. Microorganisms 2022; 10:microorganisms10030655. [PMID: 35336230 PMCID: PMC8950671 DOI: 10.3390/microorganisms10030655] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/04/2022] [Accepted: 03/11/2022] [Indexed: 11/16/2022] Open
Abstract
Bifidobacteria have long been recognized as bacteria with probiotic and therapeutic features. The aim of this work is to characterize the Bifidobacterium asteroides BA15 and BA17 strains, isolated from honeybee gut, to evaluate its safety for human use. An in-depth assessment was carried out on safety properties (antibiotic resistance profiling, β-hemolytic, DNase and gelatinase activities and virulence factor presence) and other properties (antimicrobial activity, auto-aggregation, co-aggregation and hydrophobicity). Based on phenotypic and genotypic characterization, both strains satisfied all the safety requirements. More specifically, genome analysis showed the absence of genes encoding for glycopeptide (vanA, vanB, vanC-1, vanC-2, vanD, vanE, vanG), resistance to tetracycline (tetM, tetL and tetO) and virulence genes (asa1, gelE, cylA, esp, hyl).
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Affiliation(s)
- Alessandra Pino
- Department of Agricultural, Food and Environment, University of Catania, 95123 Catania, Italy; (A.P.); (N.R.); (A.V.); (G.A.); (C.C.)
- ProBioEtna S.r.l., Spin-Off of University of Catania, 95123 Catania, Italy
| | - Bachir Benkaddour
- Department of Biology, Faculty of Natural Sciences and Life, University of Oran1, Oran 31000, Algeria; (B.B.); (H.M.)
| | - Rosanna Inturri
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
- Department of R&D, Local Noto Unit, Fidia Farmaceutici S.p.A., 96017 Noto, Italy; (P.A.); (S.C.V.)
- Correspondence: (R.I.); (C.L.R.)
| | - Pietro Amico
- Department of R&D, Local Noto Unit, Fidia Farmaceutici S.p.A., 96017 Noto, Italy; (P.A.); (S.C.V.)
| | - Susanna C. Vaccaro
- Department of R&D, Local Noto Unit, Fidia Farmaceutici S.p.A., 96017 Noto, Italy; (P.A.); (S.C.V.)
| | - Nunziatina Russo
- Department of Agricultural, Food and Environment, University of Catania, 95123 Catania, Italy; (A.P.); (N.R.); (A.V.); (G.A.); (C.C.)
- ProBioEtna S.r.l., Spin-Off of University of Catania, 95123 Catania, Italy
| | - Amanda Vaccalluzzo
- Department of Agricultural, Food and Environment, University of Catania, 95123 Catania, Italy; (A.P.); (N.R.); (A.V.); (G.A.); (C.C.)
| | - Gianluigi Agolino
- Department of Agricultural, Food and Environment, University of Catania, 95123 Catania, Italy; (A.P.); (N.R.); (A.V.); (G.A.); (C.C.)
| | - Cinzia Caggia
- Department of Agricultural, Food and Environment, University of Catania, 95123 Catania, Italy; (A.P.); (N.R.); (A.V.); (G.A.); (C.C.)
- ProBioEtna S.r.l., Spin-Off of University of Catania, 95123 Catania, Italy
| | - Hadadji Miloud
- Department of Biology, Faculty of Natural Sciences and Life, University of Oran1, Oran 31000, Algeria; (B.B.); (H.M.)
| | - Cinzia L. Randazzo
- Department of Agricultural, Food and Environment, University of Catania, 95123 Catania, Italy; (A.P.); (N.R.); (A.V.); (G.A.); (C.C.)
- ProBioEtna S.r.l., Spin-Off of University of Catania, 95123 Catania, Italy
- Correspondence: (R.I.); (C.L.R.)
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17
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Zafar H, Saier MH. Comparative Analyses of the Transport Proteins Encoded within the Genomes of nine Bifidobacterium Species. Microb Physiol 2022; 32:30-44. [PMID: 34555832 PMCID: PMC8940750 DOI: 10.1159/000518954] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 08/02/2021] [Indexed: 01/03/2023]
Abstract
The human microbiome influences human health in both negative and positive ways. Studies on the transportomes of these organisms yield information that may be utilized for various purposes, including the identification of novel drug targets and the manufacture of improved probiotic strains. Moreover, these genomic analyses help to improve our understanding of the physiology and metabolic capabilities of these organisms. The present study is a continuation of our studies on the transport proteins of the major gut microbes. Bifidobacterium species are essential members of the human gut microbiome, and they initiate colonization of the gut at birth, providing health benefits that last a lifetime. In this study we analyze the transportomes of nine bifidobacterial species: B. adolescentis, B. animalis, B. bifidum, B. breve, B. catenulatum, B. dentium, B. longum subsp. infantis, B. longum subsp. longum, and B. pseudocatenulatum. All of these species have proven probiotic characteristics and exert beneficial effects on human health. Surprisingly, we found that all nine of these species have similar pore-forming toxins and drug exporters that may play roles in pathogenesis. These species have transporters for amino acids, carbohydrates, and proteins, essential for their organismal lifestyles and adaption to their respective ecological niches. The strictly probiotic species, B. bifidum, however, contains fewer such transporters, thus indicative of limited interactions with host cells and other gut microbial counterparts. The results of this study were compared with those of our previous studies on the transportomes of multiple species of Bacteroides, Escherichia coli/Salmonella, and Lactobacillus. Overall, bifidobacteria have larger transportomes (based on percentages of total proteins) than the previously examined groups of bacterial species, with a preference for primary active transport systems over secondary carriers. Taken together, these results provide useful information about the physiologies and pathogenic potentials of these probiotic organisms as reflected by their transportomes.
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Affiliation(s)
- Hassan Zafar
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116.,Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic.,Corresponding Authors HZ: Tel: +420773283624, ; MS: Tel: +1 858 534 4084, Fax: +1 858 534 7108,
| | - Milton H. Saier
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116.,Corresponding Authors HZ: Tel: +420773283624, ; MS: Tel: +1 858 534 4084, Fax: +1 858 534 7108,
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18
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Buckley D, Odamaki T, Xiao J, Mahony J, van Sinderen D, Bottacini F. Diversity of Human-Associated Bifidobacterial Prophage Sequences. Microorganisms 2021; 9:microorganisms9122559. [PMID: 34946160 PMCID: PMC8705816 DOI: 10.3390/microorganisms9122559] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/19/2021] [Accepted: 12/07/2021] [Indexed: 11/30/2022] Open
Abstract
Members of Bifidobacterium play an important role in the development of the immature gut and are associated with positive long-term health outcomes for their human host. It has previously been shown that intestinal bacteriophages are detected within hours of birth, and that induced prophages constitute a significant source of such gut phages. The gut phageome can be vertically transmitted from mother to newborn and is believed to exert considerable selective pressure on target prokaryotic hosts affecting abundance levels, microbiota composition, and host characteristics. The objective of the current study was to investigate prophage-like elements and predicted CRISPR-Cas viral immune systems present in publicly available, human-associated Bifidobacterium genomes. Analysis of 585 fully sequenced bifidobacterial genomes identified 480 prophage-like elements with an occurrence of 0.82 prophages per genome. Interestingly, we also detected the presence of very similar bifidobacterial prophages and corresponding CRISPR spacers across different strains and species, thus providing an initial exploration of the human-associated bifidobacterial phageome. Our analyses show that closely related and likely functional prophages are commonly present across four different species of human-associated Bifidobacterium. Further comparative analysis of the CRISPR-Cas spacer arrays against the predicted prophages provided evidence of historical interactions between prophages and different strains at an intra- and inter-species level. Clear evidence of CRISPR-Cas acquired immunity against infection by bifidobacterial prophages across several bifidobacterial strains and species was obtained. Notably, a spacer representing a putative major capsid head protein was found on different genomes representing multiple strains across B. adolescentis, B. breve, and B. bifidum, suggesting that this gene is a preferred target to provide bifidobacterial phage immunity.
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Affiliation(s)
- Darren Buckley
- INFANT Research Centre, University College Cork, Cork, Ireland;
| | - Toshitaka Odamaki
- Next Generation Science Institute, Morinaga Milk Industry Co., Ltd., Zama 252-8583, Japan; (T.O.); (J.X.)
| | - Jinzhong Xiao
- Next Generation Science Institute, Morinaga Milk Industry Co., Ltd., Zama 252-8583, Japan; (T.O.); (J.X.)
| | - Jennifer Mahony
- APC Microbiome Ireland, School of Microbiology, University College Cork, Cork, Ireland;
| | - Douwe van Sinderen
- APC Microbiome Ireland, School of Microbiology, University College Cork, Cork, Ireland;
- Correspondence: (D.v.S.); (F.B.)
| | - Francesca Bottacini
- APC Microbiome Ireland, School of Microbiology, University College Cork, Cork, Ireland;
- Biological Sciences, Munster Technological University, Cork, Ireland
- Correspondence: (D.v.S.); (F.B.)
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19
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Captive Common Marmosets (Callithrix jacchus) Are Colonized throughout Their Lives by a Community of Bifidobacterium Species with Species-Specific Genomic Content That Can Support Adaptation to Distinct Metabolic Niches. mBio 2021; 12:e0115321. [PMID: 34340536 PMCID: PMC8406136 DOI: 10.1128/mbio.01153-21] [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] [Indexed: 12/24/2022] Open
Abstract
The common marmoset (Callithrix jacchus) is an omnivorous New World primate whose diet in the wild includes large amounts of fruit, seeds, flowers, and a variety of lizards and invertebrates. Marmosets also feed heavily on tree gums and exudates, and they have evolved unique morphological and anatomical characteristics to facilitate gum feeding (gummivory). In this study, we characterized the fecal microbiomes of adult and infant animals from a captive population of common marmosets at the Callitrichid Research Center at the University of Nebraska at Omaha under their normal dietary and environmental conditions. The microbiomes of adult animals were dominated by species of Bifidobacterium, Bacteroides, Prevotella, Phascolarctobacterium, Megamonas, and Megasphaera. Culturing and genomic analysis of the Bifidobacterium populations from adult animals identified four known marmoset-associated species (B. reuteri, B. aesculapii, B. myosotis, and B. hapali) and three unclassified taxa of Bifidobacterium that are phylogenetically distinct. Species-specific quantitative PCR (qPCR) confirmed that these same species of Bifidobacterium are abundant members of the microbiome throughout the lives of the animals. Genomic loci in each Bifidobacterium species encode enzymes to support growth and major marmoset milk oligosaccharides during breastfeeding; however, metabolic islands that can support growth on complex polysaccharide substrates in the diets of captive adults (pectin, xyloglucan, and xylan), including loci in B. aesculapii that can support its unique ability to grow on arabinogalactan-rich tree gums, were species-specific.
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20
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Rodionov DA, Rodionova IA, Rodionov VA, Arzamasov AA, Zhang K, Rubinstein GM, Tanwee TNN, Bing RG, Crosby JR, Nookaew I, Basen M, Brown SD, Wilson CM, Klingeman DM, Poole FL, Zhang Y, Kelly RM, Adams MWW. Transcriptional Regulation of Plant Biomass Degradation and Carbohydrate Utilization Genes in the Extreme Thermophile Caldicellulosiruptor bescii. mSystems 2021; 6:e0134520. [PMID: 34060910 PMCID: PMC8579813 DOI: 10.1128/msystems.01345-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 05/04/2021] [Indexed: 11/20/2022] Open
Abstract
Extremely thermophilic bacteria from the genus Caldicellulosiruptor can degrade polysaccharide components of plant cell walls and subsequently utilize the constituting mono- and oligosaccharides. Through metabolic engineering, ethanol and other industrially important end products can be produced. Previous experimental studies identified a variety of carbohydrate-active enzymes in model species Caldicellulosiruptor saccharolyticus and Caldicellulosiruptor bescii, while prior transcriptomic experiments identified their putative carbohydrate uptake transporters. We investigated the mechanisms of transcriptional regulation of carbohydrate utilization genes using a comparative genomics approach applied to 14 Caldicellulosiruptor species. The reconstruction of carbohydrate utilization regulatory network includes the predicted binding sites for 34 mostly local regulators and point to the regulatory mechanisms controlling expression of genes involved in degradation of plant biomass. The Rex and CggR regulons control the central glycolytic and primary redox reactions. The identified transcription factor binding sites and regulons were validated with transcriptomic and transcription start site experimental data for C. bescii grown on cellulose, cellobiose, glucose, xylan, and xylose. The XylR and XynR regulons control xylan-induced transcriptional response of genes involved in degradation of xylan and xylose utilization. The reconstructed regulons informed the carbohydrate utilization reconstruction analysis and improved functional annotations of 51 transporters and 11 catabolic enzymes. Using gene deletion, we confirmed that the shared ATPase component MsmK is essential for growth on oligo- and polysaccharides but not for the utilization of monosaccharides. By elucidating the carbohydrate utilization framework in C. bescii, strategies for metabolic engineering can be pursued to optimize yields of bio-based fuels and chemicals from lignocellulose. IMPORTANCE To develop functional metabolic engineering platforms for nonmodel microorganisms, a comprehensive understanding of the physiological and metabolic characteristics is critical. Caldicellulosiruptor bescii and other species in this genus have untapped potential for conversion of unpretreated plant biomass into industrial fuels and chemicals. The highly interactive and complex machinery used by C. bescii to acquire and process complex carbohydrates contained in lignocellulose was elucidated here to complement related efforts to develop a metabolic engineering platform with this bacterium. Guided by the findings here, a clearer picture of how C. bescii natively drives carbohydrate utilization is provided and strategies to engineer this bacterium for optimal conversion of lignocellulose to commercial products emerge.
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Affiliation(s)
- Dmitry A. Rodionov
- Sanford-Burnhams-Prebys Medical Discovery Institute, La Jolla, California, USA
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Irina A. Rodionova
- Department of Bioengineering, University of California—San Diego, La Jolla, California, USA
| | - Vladimir A. Rodionov
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Aleksandr A. Arzamasov
- Sanford-Burnhams-Prebys Medical Discovery Institute, La Jolla, California, USA
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Ke Zhang
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Gabriel M. Rubinstein
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Tania N. N. Tanwee
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Ryan G. Bing
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - James R. Crosby
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Intawat Nookaew
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Mirko Basen
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Biowissenschaften, Mikrobiologie, Universität Rostock, Rostock, Germany
| | - Steven D. Brown
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Charlotte M. Wilson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- University of Otago, Dunedin, New Zealand
| | - Dawn M. Klingeman
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Farris L. Poole
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Ying Zhang
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Robert M. Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Michael W. W. Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
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21
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Sasaki K, Sasaki D, Sasaki K, Nishidono Y, Yamamori A, Tanaka K, Kondo A. Growth stimulation of Bifidobacterium from human colon using daikenchuto in an in vitro model of human intestinal microbiota. Sci Rep 2021; 11:4580. [PMID: 33633259 PMCID: PMC7907203 DOI: 10.1038/s41598-021-84167-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 12/28/2020] [Indexed: 12/11/2022] Open
Abstract
Daikenchuto (DKT) is a Japanese traditional herbal (Kampo) medicine containing ginseng, processed ginger, and Japanese or Chinese pepper. We aimed to determine how DKT affects human colonic microbiota. An in vitro microbiota model was established using fecal inocula collected from nine healthy volunteers, and each model was found to retain operational taxonomic units similar to the ones in the original human fecal samples. DKT was added to the in vitro microbiota model culture at a concentration of 0.5% by weight. Next-generation sequencing of bacterial 16S rRNA gene revealed a significant increase in the relative abundance of bacteria related to the Bifidobacterium genus in the model after incubation with DKT. In pure cultures, DKT significantly promoted the growth of Bifidobacterium adolescentis, but not that of Fusobacterium nucleatum or Escherichia coli. Additionally, in pure cultures, B. adolescentis transformed ginsenoside Rc to Rd, which was then probably utilized for its growth. Our study reveals the in vitro bifidogenic effect of DKT that likely contributes to its beneficial effects on the human colon.
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Affiliation(s)
- Kengo Sasaki
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo, 657-8501, Japan.
| | - Daisuke Sasaki
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo, 657-8501, Japan
| | - Katsunori Sasaki
- Sumitomo Chemical, Co., Ltd., 27-1 Shinkawa 2-chome, Chuo-ku, Tokyo, 104-8260, Japan
| | - Yuto Nishidono
- College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu, Shiga, 525-8577, Japan
| | - Akihiro Yamamori
- Sumitomo Chemical, Co., Ltd., 27-1 Shinkawa 2-chome, Chuo-ku, Tokyo, 104-8260, Japan
| | - Ken Tanaka
- College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu, Shiga, 525-8577, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo, 657-8501, Japan.,RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
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22
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Kelly SM, Munoz-Munoz J, van Sinderen D. Plant Glycan Metabolism by Bifidobacteria. Front Microbiol 2021; 12:609418. [PMID: 33613480 PMCID: PMC7889515 DOI: 10.3389/fmicb.2021.609418] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 01/04/2021] [Indexed: 12/18/2022] Open
Abstract
Members of the genus Bifidobacterium, of which the majority have been isolated as gut commensals, are Gram-positive, non-motile, saccharolytic, non-sporulating, anaerobic bacteria. Many bifidobacterial strains are considered probiotic and therefore are thought to bestow health benefits upon their host. Bifidobacteria are highly abundant among the gut microbiota of healthy, full term, breast-fed infants, yet the relative average abundance of bifidobacteria tends to decrease as the human host ages. Because of the inverse correlation between bifidobacterial abundance/prevalence and health, there has been an increasing interest in maintaining, increasing or restoring bifidobacterial populations in the infant, adult and elderly gut. In order to colonize and persist in the gastrointestinal environment, bifidobacteria must be able to metabolise complex dietary and/or host-derived carbohydrates, and be resistant to various environmental challenges of the gut. This is not only important for the autochthonous bifidobacterial species colonising the gut, but also for allochthonous bifidobacteria provided as probiotic supplements in functional foods. For example, Bifidobacterium longum subsp. longum is a taxon associated with the metabolism of plant-derived poly/oligosaccharides in the adult diet, being capable of metabolising hemicellulose and various pectin-associated glycans. Many of these plant glycans are believed to stimulate the metabolism and growth of specific bifidobacterial species and are for this reason classified as prebiotics. In this review, bifidobacterial carbohydrate metabolism, with a focus on plant poly-/oligosaccharide degradation and uptake, as well as its associated regulation, will be discussed.
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Affiliation(s)
- Sandra M Kelly
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Jose Munoz-Munoz
- Microbial Enzymology Group, Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Douwe van Sinderen
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
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23
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Peterson CT, Iablokov SN, Uchitel S, Chopra D, Perez-Santiago J, Rodionov DA, Peterson SN. Community Metabolic Interactions, Vitamin Production and Prebiotic Potential of Medicinal Herbs Used for Immunomodulation. Front Genet 2021; 12:584197. [PMID: 33613632 PMCID: PMC7886795 DOI: 10.3389/fgene.2021.584197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 01/13/2021] [Indexed: 12/12/2022] Open
Abstract
Historically, the health benefits and immunomodulatory potential of medicinal herbs have been considered an intrinsic quality of the herb itself. We have hypothesized that the health benefits of medicinal herbs may be partially due to their prebiotic potential that alter gut microbiota leading to changes in short chain fatty acids and vitamin production or biotransformation of herb encoded molecules and secondary metabolites. Accumulating studies emphasize the relationship between the gut microbiota and host immune function. While largely unknown, these interactions are mediated by secreted microbial products that activate or repress a variety of immune cell types. Here we evaluated the effect of immunomodulatory, medicinal Ayurvedic herbs on gut microbiota in vitro using 16S rRNA sequencing to assess changes in community composition and functional potential. All immunomodulatory herbs displayed substantial prebiotic potential, targeting unique taxonomic groups. Application of genome reconstruction and analysis of biosynthetic capacity of herb selected communities suggests that many of the 11 herbs tested altered the community metabolism as the result of differential glycan harvest and sugar utilization and secreted products including multiple vitamins, butyrate, and propionate that may impact host physiology and immune function. Taken together, these results provide a useful framework for the further evaluation of these immunomodulatory herbs in vivo to maintain immune homeostasis or achieve desired regulation of immune components in the context of disease.
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Affiliation(s)
- Christine T Peterson
- Department of Family Medicine and Public Health, Center of Excellence for Research and Training in Integrative Health, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Stanislav N Iablokov
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia.,Department of Theoretical Physics, P.G. Demidov Yaroslavl State University, Yaroslavl, Russia
| | - Sasha Uchitel
- Department of Biology, Washington University, St. Louis, MO, United States
| | - Deepak Chopra
- Department of Family Medicine and Public Health, Center of Excellence for Research and Training in Integrative Health, School of Medicine, University of California, San Diego, La Jolla, CA, United States.,Department of Ayurveda and Yoga Research, Chopra Foundation, Carlsbad, CA, United States
| | - Josue Perez-Santiago
- Puerto Rico Omic Center Genomics Core Division of Cancer Biology, University of Puerto Rico Comprehensive Cancer Center, San Juan, Puerto Rico
| | - Dmitry A Rodionov
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia.,Bioinformatics and Structural Biology Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - Scott N Peterson
- Puerto Rico Omic Center Genomics Core Division of Cancer Biology, University of Puerto Rico Comprehensive Cancer Center, San Juan, Puerto Rico.,Bioinformatics and Structural Biology Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
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24
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Iablokov SN, Klimenko NS, Efimova DA, Shashkova T, Novichkov PS, Rodionov DA, Tyakht AV. Metabolic Phenotypes as Potential Biomarkers for Linking Gut Microbiome With Inflammatory Bowel Diseases. Front Mol Biosci 2021; 7:603740. [PMID: 33537340 PMCID: PMC7848230 DOI: 10.3389/fmolb.2020.603740] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 12/09/2020] [Indexed: 12/13/2022] Open
Abstract
The gut microbiome is of utmost importance to human health. While a healthy microbiome can be represented by a variety of structures, its functional capacity appears to be more important. Gene content of the community can be assessed by “shotgun” metagenomics, but this approach is still too expensive. High-throughput amplicon-based surveys are a method of choice for large-scale surveys of links between microbiome, diseases, and diet, but the algorithms for predicting functional composition need to be improved to achieve good precision. Here we show how feature engineering based on microbial phenotypes, an advanced method for functional prediction from 16S rRNA sequencing data, improves identification of alterations of the gut microbiome linked to the disease. We processed a large collection of published gut microbial datasets of inflammatory bowel disease (IBD) patients to derive their community phenotype indices (CPI)—high-precision semiquantitative profiles aggregating metabolic potential of the community members based on genome-wide metabolic reconstructions. The list of selected metabolic functions included metabolism of short-chain fatty acids, vitamins, and carbohydrates. The machine-learning approach based on microbial phenotypes allows us to distinguish the microbiome profiles of healthy controls from patients with Crohn's disease and from ones with ulcerative colitis. The classifiers were comparable in quality to conventional taxonomy-based classifiers but provided new findings giving insights into possible mechanisms of pathogenesis. Feature-wise partial dependence plot (PDP) analysis of contribution to the classification result revealed a diversity of patterns. These observations suggest a constructive basis for defining functional homeostasis of the healthy human gut microbiome. The developed features are promising interpretable candidate biomarkers for assessing microbiome contribution to disease risk for the purposes of personalized medicine and clinical trials.
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Affiliation(s)
- Stanislav N Iablokov
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia.,P.G. Demidov Yaroslavl State University, Yaroslavl, Russia
| | - Natalia S Klimenko
- Atlas Biomed Group-Knomics LLC, London, United Kingdom.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | | | - Tatiana Shashkova
- Atlas Biomed Group-Knomics LLC, London, United Kingdom.,Moscow Institute of Physics and Technology, Moscow, Russia
| | - Pavel S Novichkov
- PhenoBiome Inc., San Francisco, CA, United States.,Lawrence Berkeley National Lab, Berkeley, CA, United States
| | - Dmitry A Rodionov
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia.,Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - Alexander V Tyakht
- Atlas Biomed Group-Knomics LLC, London, United Kingdom.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
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25
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Jones RB, Berger PK, Plows JF, Alderete TL, Millstein J, Fogel J, Iablokov SN, Rodionov DA, Osterman AL, Bode L, Goran MI. Lactose-reduced infant formula with added corn syrup solids is associated with a distinct gut microbiota in Hispanic infants. Gut Microbes 2020; 12:1813534. [PMID: 32887539 PMCID: PMC7524300 DOI: 10.1080/19490976.2020.1813534] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/23/2020] [Accepted: 08/11/2020] [Indexed: 02/03/2023] Open
Abstract
Infant formula feeding, compared with human milk, has been associated with development of a distinct infant gut microbiome, but no previous study has examined effects of formula with added sugars. This work examined differences in gut microbiota among 91 Hispanic infants who consumed human milk [at breast (BB) vs. pumped in bottle (BP)] and 2 kinds of infant formula [(traditional lactose-based (TF) vs. lactose-reduced with added sugar (ASF)]. At 1 and 6 months, infant stool was collected to characterize gut microbiota. At 6 months, mothers completed 24-hour dietary recalls and questionnaires to determine infant consumption of human milk (BB vs. BP) or formula (TF vs. ASF). Linear regression models were used to determine associations of milk consumption type and microbial features at 6 months. Infants in the formula groups exhibited a significantly more 'mature' microbiome than infants in the human milk groups with the most pronounced differences observed between the ASF vs. BB groups. In the ASF group, we observed reduced log-normalized abundance of Bifidobacteriaceae (TF-BB Mean Difference = -0.71, ASF-BB Mean Difference = -1.10), and increased abundance of Lachnospiraceae (TF-BB Mean Difference = +0.89, ASF-BB Mean Difference = +1.20). We also observed a higher Community Phenotype Index of propionate, most likely produced by Lachnospiraceae, in the ASF group (TF-BB Mean Difference = +0.27, ASF-BB Mean Difference = +0.36). This study provides the first evidence that consumption of infant formula with added sugar may have a stronger association than birth delivery mode, infant caloric intake, and maternal BMI on the infant's microbiome at 6 months of age.
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Affiliation(s)
- Roshonda B. Jones
- Department of Pediatrics, The Saban Research Institute, Children’s Hospital Los Angeles, University of Southern California, Los Angeles, CA, USA
| | - Paige K. Berger
- Department of Pediatrics, The Saban Research Institute, Children’s Hospital Los Angeles, University of Southern California, Los Angeles, CA, USA
| | - Jasmine F. Plows
- Department of Pediatrics, The Saban Research Institute, Children’s Hospital Los Angeles, University of Southern California, Los Angeles, CA, USA
| | - Tanya L. Alderete
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
| | - Joshua Millstein
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jennifer Fogel
- Department of Pediatrics, The Saban Research Institute, Children’s Hospital Los Angeles, University of Southern California, Los Angeles, CA, USA
| | - Stanislav N. Iablokov
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- P.G. Demidov Yaroslavl State University, Yaroslavl, Russia
| | - Dmitry A. Rodionov
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | | | - Lars Bode
- Department of Pediatrics and Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence, University of California, San Diego, CA, USA
| | - Michael I. Goran
- Department of Pediatrics, The Saban Research Institute, Children’s Hospital Los Angeles, University of Southern California, Los Angeles, CA, USA
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26
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Pérez-Escalante E, Alatorre-Santamaría S, Castañeda-Ovando A, Salazar-Pereda V, Bautista-Ávila M, Cruz-Guerrero AE, Flores-Aguilar JF, González-Olivares LG. Human milk oligosaccharides as bioactive compounds in infant formula: recent advances and trends in synthetic methods. Crit Rev Food Sci Nutr 2020; 62:181-214. [DOI: 10.1080/10408398.2020.1813683] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Emmanuel Pérez-Escalante
- Universidad Autónoma del Estado de Hidalgo, Área Académica de Química. Ciudad del Conocimiento, Carretera Pachuca-Tulancingo km 4.5, Colonia Carboneras. CP. 42184. Mineral de la Reforma, Hidalgo, México
| | - Sergio Alatorre-Santamaría
- Universidad Autónoma Metropolitana, Unidad Iztapalapa. División de Ciencias Biológicas y de la Salud. Departamento de Biotecnología, Colonia Vicentina AP 09340, Ciudad de México, México
| | - Araceli Castañeda-Ovando
- Universidad Autónoma del Estado de Hidalgo, Área Académica de Química. Ciudad del Conocimiento, Carretera Pachuca-Tulancingo km 4.5, Colonia Carboneras. CP. 42184. Mineral de la Reforma, Hidalgo, México
| | - Verónica Salazar-Pereda
- Universidad Autónoma del Estado de Hidalgo, Área Académica de Química. Ciudad del Conocimiento, Carretera Pachuca-Tulancingo km 4.5, Colonia Carboneras. CP. 42184. Mineral de la Reforma, Hidalgo, México
| | - Mirandeli Bautista-Ávila
- Universidad Autónoma del Estado de Hidalgo. Área Académica de Farmacia, Instituto de Ciencias de la Salud. Ex-Hacienda la Concepción. San Agustín Tlaxiaca, Hidalgo, México
| | - Alma Elizabeth Cruz-Guerrero
- Universidad Autónoma Metropolitana, Unidad Iztapalapa. División de Ciencias Biológicas y de la Salud. Departamento de Biotecnología, Colonia Vicentina AP 09340, Ciudad de México, México
| | - Juan Francisco Flores-Aguilar
- Universidad Autónoma del Estado de Hidalgo, Área Académica de Química. Ciudad del Conocimiento, Carretera Pachuca-Tulancingo km 4.5, Colonia Carboneras. CP. 42184. Mineral de la Reforma, Hidalgo, México
| | - Luis Guillermo González-Olivares
- Universidad Autónoma del Estado de Hidalgo, Área Académica de Química. Ciudad del Conocimiento, Carretera Pachuca-Tulancingo km 4.5, Colonia Carboneras. CP. 42184. Mineral de la Reforma, Hidalgo, México
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27
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Chen C, Wang L, Yu H, Tian H. The local transcriptional regulators SacR1 and SacR2 act as repressors of fructooligosaccharides metabolism in Lactobacillus plantarum. Microb Cell Fact 2020; 19:161. [PMID: 32778113 PMCID: PMC7419226 DOI: 10.1186/s12934-020-01403-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 07/13/2020] [Indexed: 11/25/2022] Open
Abstract
Background In Lactobacillus plantarum, fructooligosaccharides (FOS) metabolism is controlled by both global and local regulatory mechanisms. Although catabolite control protein A has been identified as a global regulator of FOS metabolism, the functions of local regulators remain unclear. This study aimed to elucidate the roles of two local regulators, SacR1 and SacR2, in the regulation of FOS metabolism in L. plantarum both in vitro and in vivo. Results The inactivation of sacR1 and sacR2 affected the growth and production of metabolites for strains grown on FOS or glucose, respectively. A reverse transcription-quantitative PCR analysis of one wild-type and two mutant strains (ΔsacR1 and ΔsacR2) of L. plantarum identified SacR1 and SacR2 as repressors of genes relevant to FOS metabolism in the absence of FOS, and these genes could be induced or derepressed by the addition of FOS. The analysis predicted four potential transcription factor binding sites (TFBSs) in the putative promoter regions of two FOS-related clusters. The binding of SacR1 and SacR2 to these TFBSs both in vitro and in vivo was verified using electrophoretic mobility shift assays and chromatin immunoprecipitation, respectively. A consensus sequence of WNNNNNAACGNNTTNNNNNW was deduced for the TFBSs of SacR1 and SacR2. Conclusion Our results identified SacR1 and SacR2 as local repressors for FOS metabolism in L. plantarum. The regulation is achieved by the binding of SacR1 and SacR2 to TFBSs in the promoter regions of FOS-related clusters. The results provide new insights into the complex network regulating oligosaccharide metabolism by lactic acid bacteria. ![]()
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Affiliation(s)
- Chen Chen
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, 201418, People's Republic of China
| | - Linlin Wang
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, 201418, People's Republic of China
| | - Haiyan Yu
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, 201418, People's Republic of China
| | - Huaixiang Tian
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, 201418, People's Republic of China.
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28
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Jiang J, Yang B, Ross RP, Stanton C, Zhao J, Zhang H, Chen W. Comparative Genomics of Pediococcus pentosaceus Isolated From Different Niches Reveals Genetic Diversity in Carbohydrate Metabolism and Immune System. Front Microbiol 2020; 11:253. [PMID: 32174896 PMCID: PMC7055311 DOI: 10.3389/fmicb.2020.00253] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 02/03/2020] [Indexed: 12/13/2022] Open
Abstract
Pediococcus pentosaceus isolated from fermented food and the gastrointestinal tracts of humans and animals have been widely identified, and some strains have been reported to reduce inflammation, encephalopathy, obesity and fatty liver in animals. In this study, the genomes of 65 P. pentosaceus strains isolated from human and animal feces and different fermented food were sequenced and comparative genomics analysis was performed on all strains along with nine sequenced representative strains to preliminarily reveal the lifestyle of P. pentosaceus, and investigate the genomic diversity within this species. The results reveal that P. pentosaceus is not host-specific, and shares core genes encoding proteins related to translation, ribosomal structure and biogenesis and signal transduction mechanisms, while its genetic diversity relates mainly to carbohydrate metabolism, and horizontally transferred DNA, especially prophages and bacteriocins encoded on plasmids. Additionally, this is the first report of a type IIA CRISPR/Cas system in P. pentosaceus. This work provides expanded resources of P. pentosaceus genomes, and offers a framework for understanding the biotechnological potential of this species.
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Affiliation(s)
- Jie Jiang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Bo Yang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Food Science and Technology, Jiangnan University, Wuxi, China.,International Joint Research Center for Probiotics and Gut Health, Jiangnan University, Wuxi, China
| | - R Paul Ross
- International Joint Research Center for Probiotics and Gut Health, Jiangnan University, Wuxi, China.,APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Catherine Stanton
- International Joint Research Center for Probiotics and Gut Health, Jiangnan University, Wuxi, China.,Moorepark Teagasc Food Research Centre, Cork, Ireland
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Food Science and Technology, Jiangnan University, Wuxi, China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Food Science and Technology, Jiangnan University, Wuxi, China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China.,Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Food Science and Technology, Jiangnan University, Wuxi, China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, China
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29
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Pan M, Barrangou R. Combining omics technologies with CRISPR-based genome editing to study food microbes. Curr Opin Biotechnol 2020; 61:198-208. [DOI: 10.1016/j.copbio.2019.12.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 12/23/2019] [Accepted: 12/25/2019] [Indexed: 12/22/2022]
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Ricke SC, Lee SI, Kim SA, Park SH, Shi Z. Prebiotics and the poultry gastrointestinal tract microbiome. Poult Sci 2020; 99:670-677. [PMID: 32029153 PMCID: PMC7587714 DOI: 10.1016/j.psj.2019.12.018] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Indexed: 12/16/2022] Open
Abstract
Feed additives that can modulate the poultry gastrointestinal tract and provide benefit to bird performance and health have recently received more interest for commercial applications. Such feed supplements offer an economic advantage because they may directly benefit poultry producers by either decreasing mortality rates of farm animals, increasing bird growth rates, or improve feed efficieny. They can also limit foodborne pathogen establishment in bird flocks by modifying the gastrointestinal microbial population. Prebiotics are known as non-digestible carbohydrates that selectively stimulate the growth of beneficial bacteria, thus improving the overall health of the host. Once prebiotics are introduced to the host, 2 major modes of action can potentially occur. Initially, the corresponding prebiotic reaches the intestine of the chicken without being digested in the upper part of the gastrointestinal tract but are selectively utilized by certain bacteria considered beneficial to the host. Secondly, other gut activities occur due to the presence of the prebiotic, including generation of short-chain fatty acids and lactic acid as microbial fermentation products, a decreased rate of pathogen colonization, and potential bird health benefits. In the current review, the effect of prebiotics on the gastrointestinal tract microbiome will be discussed as well as future directions for further research.
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Affiliation(s)
- Steven C Ricke
- Center of Food Safety, Department of Food Science, University of Arkansas, Fayetteville, AR 72704; Cell and Molecular Biology Graduate Program, Department of Food Science, University of Arkansas, Fayetteville, AR 72701.
| | - Sang In Lee
- Center of Food Safety, Department of Food Science, University of Arkansas, Fayetteville, AR 72704; Cell and Molecular Biology Graduate Program, Department of Food Science, University of Arkansas, Fayetteville, AR 72701
| | - Sun Ae Kim
- Center of Food Safety, Department of Food Science, University of Arkansas, Fayetteville, AR 72704
| | - Si Hong Park
- Center of Food Safety, Department of Food Science, University of Arkansas, Fayetteville, AR 72704
| | - Zhaohao Shi
- Center of Food Safety, Department of Food Science, University of Arkansas, Fayetteville, AR 72704
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31
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Lanigan N, Kelly E, Arzamasov AA, Stanton C, Rodionov DA, van Sinderen D. Transcriptional control of central carbon metabolic flux in Bifidobacteria by two functionally similar, yet distinct LacI-type regulators. Sci Rep 2019; 9:17851. [PMID: 31780796 PMCID: PMC6882875 DOI: 10.1038/s41598-019-54229-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 11/06/2019] [Indexed: 12/21/2022] Open
Abstract
Bifidobacteria resident in the gastrointestinal tract (GIT) are subject to constantly changing environmental conditions, which require rapid adjustments in gene expression. Here, we show that two predicted LacI-type transcription factors (TFs), designated AraQ and MalR1, are involved in regulating the central, carbohydrate-associated metabolic pathway (the so-called phosphoketolase pathway or bifid shunt) of the gut commensal Bifidobacterium breve UCC2003. These TFs appear to not only control transcription of genes involved in the bifid shunt and each other, but also seem to commonly and directly affect transcription of other TF-encoding genes, as well as genes related to uptake and metabolism of various carbohydrates. This complex and interactive network of AraQ/MalR1-mediated gene regulation provides previously unknown insights into the governance of carbon metabolism in bifidobacteria.
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Affiliation(s)
- Noreen Lanigan
- School of Microbiology & APC Microbiome Ireland, University College Cork, Ireland University College Cork, Cork, Ireland
| | - Emer Kelly
- School of Microbiology & APC Microbiome Ireland, University College Cork, Ireland University College Cork, Cork, Ireland
| | - Aleksandr A Arzamasov
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, United States.,A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | | | - Dmitry A Rodionov
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, United States.,A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Douwe van Sinderen
- School of Microbiology & APC Microbiome Ireland, University College Cork, Ireland University College Cork, Cork, Ireland.
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32
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Integrated Process for Sequential Extraction of Bioactive Phenolic Compounds and Proteins from Mill and Field Olive Leaves and Effects on the Lignocellulosic Profile. Foods 2019; 8:foods8110531. [PMID: 31671747 PMCID: PMC6915506 DOI: 10.3390/foods8110531] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 10/23/2019] [Accepted: 10/27/2019] [Indexed: 12/21/2022] Open
Abstract
The extraction of bioactive compounds in a biorefinery context could be a way to valorize agri-food byproducts, but there is a remaining part that also requires attention. Therefore, in this work the integrated extraction of phenolic compounds, including the bioactive oleuropein, and proteins from olive mill leaves was addressed following three schemes, including the use of ultrasound. This affected the total phenolic content (4475.5-6166.9 mg gallic acid equivalents/100 g), oleuropein content (675.3-1790.0 mg/100 g), and antioxidant activity (18,234.3-25,459.0 µmol trolox equivalents/100 g). No effect was observed on either the protein recovery or the content of sugars and lignin in the extraction residues. Concerning the recovery of proteins, three operational parameters were evaluated by response surface methodology. The optimum (63.1%) was achieved using NaOH 0.7 M at 100 °C for 240 min. Then, the selected scheme was applied to olive leaves from the field, observing differences in the content of some of the studied components. It also changed the lignocellulosic profile of the extraction residues of both leaf types, which were enriched in cellulose. Overall, these results could be useful to diversify the valorization chain in the olive sector.
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33
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Peterson CT, Sharma V, Iablokov SN, Albayrak L, Khanipov K, Uchitel S, Chopra D, Mills PJ, Fofanov Y, Rodionov DA, Peterson SN. 16S rRNA gene profiling and genome reconstruction reveal community metabolic interactions and prebiotic potential of medicinal herbs used in neurodegenerative disease and as nootropics. PLoS One 2019; 14:e0213869. [PMID: 30889210 PMCID: PMC6424447 DOI: 10.1371/journal.pone.0213869] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 03/01/2019] [Indexed: 12/31/2022] Open
Abstract
The prebiotic potential of nervine herbal medicines has been scarcely studied. We therefore used anaerobic human fecal cultivation to investigate whether medicinal herbs commonly used as treatment in neurological health and disease in Ayurveda and other traditional systems of medicine modulate gut microbiota. Profiling of fecal cultures supplemented with either Kapikacchu, Gotu Kola, Bacopa/Brahmi, Shankhapushpi, Boswellia/Frankincense, Jatamansi, Bhringaraj, Guduchi, Ashwagandha or Shatavari by 16S rRNA sequencing revealed profound changes in diverse taxa. Principal coordinate analysis highlights that each herb drives the formation of unique microbial communities predicted to display unique metabolic potential. The relative abundance of approximately one-third of the 243 enumerated species was altered by all herbs. Additional species were impacted in an herb-specific manner. In this study, we combine genome reconstruction of sugar utilization and short chain fatty acid (SCFA) pathways encoded in the genomes of 216 profiled taxa with monosaccharide composition analysis of each medicinal herb by quantitative mass spectrometry to enhance the interpretation of resulting microbial communities and discern potential drivers of microbiota restructuring. Collectively, our results indicate that gut microbiota engage in both protein and glycan catabolism, providing amino acid and sugar substrates that are consumed by fermentative species. We identified taxa that are efficient amino acid fermenters and those capable of both amino acid and sugar fermentation. Herb-induced microbial communities are predicted to alter the relative abundance of taxa encoding SCFA (butyrate and propionate) pathways. Co-occurrence network analyses identified a large number of taxa pairs in medicinal herb cultures. Some of these pairs displayed related culture growth relationships in replicate cultures highlighting potential functional interactions among medicinal herb-induced taxa.
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Affiliation(s)
- Christine Tara Peterson
- UC San Diego, School of Medicine, Center of Excellence for Research and Training in Integrative Health, Department of Family Medicine and Public Health, La Jolla, California, United States of America
- * E-mail:
| | - Vandana Sharma
- Sanford Burnham Prebys Medical Discovery Institute, Bioinformatics and Structural Biology Program, La Jolla, California, United States of America
| | - Stanislav N. Iablokov
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- P.G. Demidov Yaroslavl State University, Yaroslavl, Russia
| | - Levent Albayrak
- Department of Pharmacology and Toxicology, Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Kamil Khanipov
- Department of Pharmacology and Toxicology, Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Sasha Uchitel
- Washington University, Department of Biology, St. Louis, Missouri, United States of America
| | - Deepak Chopra
- UC San Diego, School of Medicine, Center of Excellence for Research and Training in Integrative Health, Department of Family Medicine and Public Health, La Jolla, California, United States of America
- Chopra Foundation, Department of Ayurveda and Yoga Research, Carlsbad, California, United States of America
| | - Paul J. Mills
- UC San Diego, School of Medicine, Center of Excellence for Research and Training in Integrative Health, Department of Family Medicine and Public Health, La Jolla, California, United States of America
| | - Yuriy Fofanov
- Department of Pharmacology and Toxicology, Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Dmitry A. Rodionov
- Sanford Burnham Prebys Medical Discovery Institute, Bioinformatics and Structural Biology Program, La Jolla, California, United States of America
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Scott N. Peterson
- Sanford Burnham Prebys Medical Discovery Institute, Bioinformatics and Structural Biology Program, La Jolla, California, United States of America
- Sanford Burnham Prebys Medical Discovery Institute, Tumor Microenvironment and Cancer Immunology Program, La Jolla, California, United States of America
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In vitro digestion under simulated saliva, gastric and small intestinal conditions and fermentation by human gut microbiota of polysaccharides from the fruits of Lycium barbarum. Int J Biol Macromol 2019; 125:751-760. [DOI: 10.1016/j.ijbiomac.2018.12.081] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 11/27/2018] [Accepted: 12/07/2018] [Indexed: 12/18/2022]
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35
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Kelly SM, O'Callaghan J, Kinsella M, van Sinderen D. Characterisation of a Hydroxycinnamic Acid Esterase From the Bifidobacterium longum subsp. longum Taxon. Front Microbiol 2018; 9:2690. [PMID: 30473685 PMCID: PMC6237967 DOI: 10.3389/fmicb.2018.02690] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 10/22/2018] [Indexed: 12/15/2022] Open
Abstract
Bifidobacterium longum subsp. longum, a common member of the human gut microbiota with perceived positive health effects, is capable of metabolising certain complex, plant-derived carbohydrates which are commonly found in the (adult) human diet. These plant glycans may be employed to favourably modulate the microbial communities in the intestine. Hydroxycinnamic acids (HCAs) are plant phenolic compounds, which are attached to glycans, and which are associated with anti-oxidant and other beneficial properties. However, very little information is available regarding metabolism of HCA-containing glycans by bifidobacteria. In the current study, a gene encoding a hydroxycinnamic acid esterase was found to be conserved across the B. longum subsp. longum taxon and was present in a conserved locus associated with plant carbohydrate utilisation. The esterase was shown to be active against various HCA-containing substrates and was biochemically characterised in terms of substrate preference, and pH and temperature optima of the enzyme. This novel hydroxycinnamic acid esterase is presumed to be responsible for the release of HCAs from plant-based dietary sources, a process that may have benefits for the gut environment and thus host health.
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Affiliation(s)
- Sandra M Kelly
- School of Microbiology, University College Cork, Cork, Ireland.,APC Microbiome Ireland, University College Cork, Cork, Ireland
| | | | - Mike Kinsella
- Pharmaceutical and Molecular Biotechnology Research Centre, Department of Science, Waterford Institute of Technology, Waterford, Ireland
| | - Douwe van Sinderen
- School of Microbiology, University College Cork, Cork, Ireland.,APC Microbiome Ireland, University College Cork, Cork, Ireland
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