1
|
Bai G, Ye M, Yu L, Yang M, Wang Y, Chen S. Purification, characterization, simulated gastrointestinal digestion and gut microbiota fermentation of a Bifidobacterium-directed mannoglucan from Lilium brownii var. viridulum. Food Chem X 2024; 23:101671. [PMID: 39139491 PMCID: PMC11321392 DOI: 10.1016/j.fochx.2024.101671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 02/26/2024] [Accepted: 07/16/2024] [Indexed: 08/15/2024] Open
Abstract
Lilium brownii var. viridulum (Longya lily) is an edible vegetable and medicinal plant with the effects of moistening lungs, relieving coughs, and removing phlegm. In this study, a homogenous mannoglucan LLP11 was purified from Longya lily using membrane ultrafiltration followed by ion exchange chromatography. The M w of LLP11 was 12.0 kDa. LLP11 exhibited a backbone of →4)-α-D-Glcp-(1 → and →4)-β-D-Manp-(1 → with a branch of T-α-D-Glcp-(1 → substituted at C-6 of →4,6)-α-D-Glcp-(1→. During the simulated digestion, LLP11 remained indigestible to digestive enzymes. Furthermore, through its interaction with the gut microbiota, LLP11 was able to significantly boost Bifidobacterium and decrease the harmful bacteria Klebsiella, that was linked to pneumonia. Additionally, LLP11 promoted the growth of B. pseudocatenulatum and B. longum and was utilized to produce acetic acid. Our findings introduced an alternative approach for the investigation of microbiota-targeted polysaccharides and underscored the potential of LLP11 as a prebiotic for supplementary treatment in respiratory diseases.
Collapse
Affiliation(s)
- Guangjian Bai
- Key Laboratory of Modern Preparation of TCM, Ministry of Education, Jiangxi University of Chinese Medicine, Nanchang 330004, China
- National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Miaoyun Ye
- Key Laboratory of Modern Preparation of TCM, Ministry of Education, Jiangxi University of Chinese Medicine, Nanchang 330004, China
| | - Li Yu
- Key Laboratory of Modern Preparation of TCM, Ministry of Education, Jiangxi University of Chinese Medicine, Nanchang 330004, China
| | - Ming Yang
- Key Laboratory of Modern Preparation of TCM, Ministry of Education, Jiangxi University of Chinese Medicine, Nanchang 330004, China
| | - Yaqi Wang
- Key Laboratory of Modern Preparation of TCM, Ministry of Education, Jiangxi University of Chinese Medicine, Nanchang 330004, China
| | - Shaodan Chen
- National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| |
Collapse
|
2
|
Sanchez-Gallardo R, Bottacini F, Friess L, Esteban-Torres M, Somers C, Moore RL, McAuliffe FM, Cotter PD, van Sinderen D. Unveiling metabolic pathways of selected plant-derived glycans by Bifidobacterium pseudocatenulatum. Front Microbiol 2024; 15:1414471. [PMID: 39081887 PMCID: PMC11286577 DOI: 10.3389/fmicb.2024.1414471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 06/25/2024] [Indexed: 08/02/2024] Open
Abstract
Bifidobacteria are commonly encountered members of the human gut microbiota that possess the enzymatic machinery necessary for the metabolism of certain plant-derived, complex carbohydrates. In the current study we describe differential growth profiles elicited by a panel of 21 newly isolated Bifidobacterium pseudocatenulatum strains on various plant-derived glycans. Using a combination of gene-trait matching and comparative genome analysis, we identified two distinct xylanases responsible for the degradation of xylan. Furthermore, three distinct extracellular α-amylases were shown to be involved in starch degradation by certain strains of B. pseudocatenulatum. Biochemical characterization showed that all three α-amylases can cleave the related substrates amylose, amylopectin, maltodextrin, glycogen and starch. The genes encoding these enzymes are variably found in the species B. pseudocatenulatum, therefore constituting a strain-specific adaptation to the gut environment as these glycans constitute common plant-derived carbohydrates present in the human diet. Overall, our study provides insights into the metabolism of these common dietary carbohydrates by a human-derived bifidobacterial species.
Collapse
Affiliation(s)
- Rocio Sanchez-Gallardo
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Francesca Bottacini
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Biological Sciences, Munster Technological University, Cork, Ireland
| | - Lisa Friess
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Maria Esteban-Torres
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Clarissa Somers
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Rebecca L. Moore
- UCD Perinatal Research Centre, School of Medicine, National Maternity Hospital, University College Dublin, Dublin, Ireland
| | - Fionnuala M. McAuliffe
- UCD Perinatal Research Centre, School of Medicine, National Maternity Hospital, University College Dublin, Dublin, Ireland
| | - Paul D. Cotter
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Teagasc Food Research Centre Moorepark, Cork, Ireland
| | - Douwe van Sinderen
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| |
Collapse
|
3
|
Chac D, Slater DM, Guillaume Y, Dunmire CN, Ternier R, Vissières K, Juin S, Lucien MAB, Boncy J, Sanchez VM, Dumayas MG, Augustin GC, Bhuiyan TR, Qadri F, Chowdhury F, Khan AI, Weil AA, Ivers LC, Harris JB. Association between chlorine-treated drinking water, the gut microbiome, and enteric pathogen burden in young children in Haiti: An observational study. Int J Infect Dis 2024; 147:107165. [PMID: 38977240 DOI: 10.1016/j.ijid.2024.107165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 06/18/2024] [Accepted: 07/03/2024] [Indexed: 07/10/2024] Open
Abstract
OBJECTIVE The effects of sanitation and hygiene interventions on the gut microbiome and enteric pathogen burden are not well understood. We measured the association between free chlorine residue (FCR) levels in drinking water, microbiome composition, and stool enteric pathogens in infants and young children in Haiti. METHODS FCR levels were measured in household drinking water and enteric pathogen burden was evaluated using multiplex RT-PCR of stool among 131 children from one month to five years of age living in Mirebalais, Haiti. Microbiome profiling was performed using metagenomic sequencing. RESULTS Most individuals lived in households with undetectable FCR measured in the drinking water (112/131, 86%). Detection of enteric pathogen DNA in stool was common and did not correlate with household water FCR. The infant microbiome in households with detectable FCR demonstrated reduced richness (fewer total number of species, P = 0.04 Kruskall-Wallis test) and less diversity by Inverse Simpson measures (P = 0.05) than households with undetectable FCR. Infants in households with a detectable FCR were more likely to have abundant Bifidobacterium. Using in vitro susceptibility testing, we found that some Bifidobacterium species were resistant to chlorine. CONCLUSIONS FCR in household drinking water did not correlate with enteric pathogen burden in our study.
Collapse
Affiliation(s)
- Denise Chac
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Damien M Slater
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Yodeline Guillaume
- Center for Global Health, Massachusetts General Hospital, Boston, MA, USA
| | | | - Ralph Ternier
- Partners In Health/Zanmi Lasante, Croix des Bouquets, Haiti
| | | | - Stanley Juin
- United States Centers for Disease Control and Prevention, Port-au-Prince, Haiti
| | | | - Jacques Boncy
- National Laboratory of Public Health, Port-au-Prince, Haiti
| | - Vanessa M Sanchez
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Mia G Dumayas
- Department of Medicine, University of Washington, Seattle, WA, USA
| | | | - Taufiqur R Bhuiyan
- International Center for Diarrheal Disease Research, Bangladesh, Vaccine Sciences, Dhaka, Bangladesh
| | - Firdausi Qadri
- International Center for Diarrheal Disease Research, Bangladesh, Vaccine Sciences, Dhaka, Bangladesh
| | - Fahima Chowdhury
- International Center for Diarrheal Disease Research, Bangladesh, Vaccine Sciences, Dhaka, Bangladesh
| | - Ashraful I Khan
- International Center for Diarrheal Disease Research, Bangladesh, Vaccine Sciences, Dhaka, Bangladesh
| | - Ana A Weil
- Department of Medicine, University of Washington, Seattle, WA, USA; Department of Global Health, University of Washington, Seattle, WA, USA.
| | - Louise C Ivers
- Center for Global Health, Massachusetts General Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Jason B Harris
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA; Center for Global Health, Massachusetts General Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| |
Collapse
|
4
|
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.
Collapse
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.
| |
Collapse
|
5
|
Zhang X, Wang J, Zhang T, Li S, Liu J, Li M, Lu J, Zhang M, Chen H. Updated Progress on Polysaccharides with Anti-Diabetic Effects through the Regulation of Gut Microbiota: Sources, Mechanisms, and Structure-Activity Relationships. Pharmaceuticals (Basel) 2024; 17:456. [PMID: 38675416 PMCID: PMC11053653 DOI: 10.3390/ph17040456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 03/28/2024] [Accepted: 03/29/2024] [Indexed: 04/28/2024] Open
Abstract
Diabetes mellitus (DM) is a common chronic metabolic disease worldwide. The disturbance of the gut microbiota has a complex influence on the development of DM. Polysaccharides are one type of the most important natural components with anti-diabetic effects. Gut microbiota can participate in the fermentation of polysaccharides, and through this, polysaccharides regulate the gut microbiota and improve DM. This review begins by a summary of the sources, anti-diabetic effects and the gut microbiota regulation functions of natural polysaccharides. Then, the mechanisms of polysaccharides in regulating the gut microbiota to exert anti-diabetic effects and the structure-activity relationship are summarized. It is found that polysaccharides from plants, fungi, and marine organisms show great hypoglycemic activities and the gut microbiota regulation functions. The mechanisms mainly include repairing the gut burrier, reshaping gut microbiota composition, changing the metabolites, regulating anti-inflammatory activity and immune function, and regulating the signal pathways. Structural characteristics of polysaccharides, such as monosaccharide composition, molecular weight, and type of glycosidic linkage, show great influence on the anti-diabetic activity of polysaccharides. This review provides a reference for the exploration and development of the anti-diabetic effects of polysaccharides.
Collapse
Affiliation(s)
- Xiaoyu Zhang
- Tianjin Key Laboratory for Modern Drug Delivery and High-Efficiency, School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin 300072, China; (X.Z.); (J.W.); (T.Z.); (S.L.); (J.L.); (M.L.); (J.L.)
| | - Jia Wang
- Tianjin Key Laboratory for Modern Drug Delivery and High-Efficiency, School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin 300072, China; (X.Z.); (J.W.); (T.Z.); (S.L.); (J.L.); (M.L.); (J.L.)
| | - Tingting Zhang
- Tianjin Key Laboratory for Modern Drug Delivery and High-Efficiency, School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin 300072, China; (X.Z.); (J.W.); (T.Z.); (S.L.); (J.L.); (M.L.); (J.L.)
| | - Shuqin Li
- Tianjin Key Laboratory for Modern Drug Delivery and High-Efficiency, School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin 300072, China; (X.Z.); (J.W.); (T.Z.); (S.L.); (J.L.); (M.L.); (J.L.)
| | - Junyu Liu
- Tianjin Key Laboratory for Modern Drug Delivery and High-Efficiency, School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin 300072, China; (X.Z.); (J.W.); (T.Z.); (S.L.); (J.L.); (M.L.); (J.L.)
| | - Mingyue Li
- Tianjin Key Laboratory for Modern Drug Delivery and High-Efficiency, School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin 300072, China; (X.Z.); (J.W.); (T.Z.); (S.L.); (J.L.); (M.L.); (J.L.)
| | - Jingyang Lu
- Tianjin Key Laboratory for Modern Drug Delivery and High-Efficiency, School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin 300072, China; (X.Z.); (J.W.); (T.Z.); (S.L.); (J.L.); (M.L.); (J.L.)
| | - Min Zhang
- China-Russia Agricultural Processing Joint Laboratory, Tianjin Agricultural University, Tianjin 300384, China;
- State Key Laboratory of Nutrition and Safety, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Haixia Chen
- Tianjin Key Laboratory for Modern Drug Delivery and High-Efficiency, School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin 300072, China; (X.Z.); (J.W.); (T.Z.); (S.L.); (J.L.); (M.L.); (J.L.)
| |
Collapse
|
6
|
Kebbe M, Shankar K, Redman LM, Andres A. Human Milk Components and the Infant Gut Microbiome at 6 Months: Understanding the Interconnected Relationship. J Nutr 2024; 154:1200-1208. [PMID: 38442855 DOI: 10.1016/j.tjnut.2024.02.029] [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: 12/18/2023] [Revised: 01/29/2024] [Accepted: 02/26/2024] [Indexed: 03/07/2024] Open
Abstract
BACKGROUND Human milk oligosaccharides have been shown to relate to the infant gut microbiome. However, the impact of other human milk components on infant gut bacterial colonization remains unexplored. OBJECTIVES Our cross-sectional analysis aimed to investigate associations between human milk components (energy, macronutrients, free amino acids, inflammatory markers, and hormones) and infant gut microbiome diversity and composition (phylum, family, and genus) at 6 mo of age. METHODS Human milk and infant stool samples were collected at 6 mo postpartum. The infant gut microbiome was profiled using 16S rRNA sequencing. Linear regression models were performed to examine associations, adjusting for pregravid BMI (kg/m2), delivery mode, duration of human milk feeding, and infant sex, with q < 0.2 considered significant. RESULTS This analysis included a total of 54 mothers (100% exclusively feeding human milk) and infants (n = 28 male; 51.9%). Total energy in human milk showed a negative association with α-diversity measures (Chao1 and Shannon). Interleukin (IL)-8 in human milk was positively associated with Chao1 and observed operational taxonomic units. At the family level, human milk glutamine and serine levels showed a negative association with the abundance of Veillonellaceae, whereas isoleucine showed a positive association with Bacteroidaceae. Human milk IL-8 and IL-6 concentrations were positively associated with Bacteroidaceae abundance. IL-8 also had a positive relationship with Bifidobacteriaceae, whereas it had a negative relationship with Streptococcacea and Clostridiaceae. Human milk IL-8 was positively associated with the phylum Bacteroidetes, and negatively associated with Proteobacteria. At the genus level, human milk IL-8 exhibited a positive relationship with Bacteroides, whereas human milk isoleucine had a negative relationship with Bacteroides and Ruminococcus. Pregravid BMI and sex effects were observed. CONCLUSIONS IL-8 in human milk could potentially prepare the infant's immune system to respond effectively to various microorganisms, potentially promoting the growth of beneficial gut bacteria and protecting against pathogens.
Collapse
Affiliation(s)
- Maryam Kebbe
- Faculty of Kinesiology, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - Kartik Shankar
- Department of Pediatrics, University of Colorado, Denver, CO, United States
| | - Leanne M Redman
- Pennington Biomedical Research Center, Louisiana State University, Baton Rouge, LA, United States
| | - Aline Andres
- Arkansas Children's Nutrition Center, Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, United States.
| |
Collapse
|
7
|
Argentini C, Lugli GA, Tarracchini C, Fontana F, Mancabelli L, Viappiani A, Anzalone R, Angelini L, Alessandri G, Bianchi MG, Taurino G, Bussolati O, Milani C, van Sinderen D, Turroni F, Ventura M. Ecology- and genome-based identification of the Bifidobacterium adolescentis prototype of the healthy human gut microbiota. Appl Environ Microbiol 2024; 90:e0201423. [PMID: 38294252 PMCID: PMC10880601 DOI: 10.1128/aem.02014-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 11/20/2023] [Indexed: 02/01/2024] Open
Abstract
Bifidobacteria are among the first microbial colonizers of the human gut, being frequently associated with human health-promoting activities. In the current study, an in silico methodology based on an ecological and phylogenomic-driven approach allowed the selection of a Bifidobacterium adolescentis prototype strain, i.e., B. adolescentis PRL2023, which best represents the overall genetic content and functional features of the B. adolescentis taxon. Such features were confirmed by in vitro experiments aimed at evaluating the ability of this strain to survive in the gastrointestinal tract of the host and its ability to interact with human intestinal cells and other microbial gut commensals. In this context, co-cultivation of B. adolescentis PRL2023 and several gut commensals revealed various microbe-microbe interactions and indicated co-metabolism of particular plant-derived glycans, such as xylan.IMPORTANCEThe use of appropriate bacterial strains in experimental research becomes imperative in order to investigate bacterial behavior while mimicking the natural environment. In the current study, through in silico and in vitro methodologies, we were able to identify the most representative strain of the Bifidobacterium adolescentis species. The ability of this strain, B. adolescentis PRL2023, to cope with the environmental challenges imposed by the gastrointestinal tract, together with its ability to switch its carbohydrate metabolism to compete with other gut microorganisms, makes it an ideal choice as a B. adolescentis prototype and a member of the healthy microbiota of adults. This strain possesses a genetic blueprint appropriate for its exploitation as a candidate for next-generation probiotics.
Collapse
Affiliation(s)
- Chiara Argentini
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
| | - Chiara Tarracchini
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Federico Fontana
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
- GenProbio srl, Parma, Italy
| | - Leonardo Mancabelli
- Microbiome Research Hub, University of Parma, Parma, Italy
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | | | | | | | - Giulia Alessandri
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Massimiliano G. Bianchi
- Microbiome Research Hub, University of Parma, Parma, Italy
- Department of Medicine and Surgery, Laboratory of General Pathology, University of Parma, Parma, Italy
| | - Giuseppe Taurino
- Microbiome Research Hub, University of Parma, Parma, Italy
- Department of Medicine and Surgery, Laboratory of General Pathology, University of Parma, Parma, Italy
| | - Ovidio Bussolati
- Microbiome Research Hub, University of Parma, Parma, Italy
- Department of Medicine and Surgery, Laboratory of General Pathology, University of Parma, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
| |
Collapse
|
8
|
Gao X, Xu F, Li T, Huang P, Yu L, Tian F, Zhao J, Chen W, Zhai Q. CAZymes-associated method to explore glycans that mitigate DSS-induced colitis via targeting Bacteroides cellulosilyticus. Int J Biol Macromol 2024; 258:128694. [PMID: 38096941 DOI: 10.1016/j.ijbiomac.2023.128694] [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: 10/05/2023] [Revised: 11/27/2023] [Accepted: 12/07/2023] [Indexed: 12/29/2023]
Abstract
Improving Bacteroides cellulosilyticus abundance is a feasible approach to treating inflammatory bowel disease (IBD). Although B. cellulosilyticus is responsive to dietary components, untargeted manipulation cannot focus on target microbe and lead to an increase in harmful bacteria in the microbiota. Breakthroughs in methods for regulating specific microbes, but the protocols are expensive, time-consuming, and difficult to follow. Glycans based on microbial-carbohydrate-active enzymes (CAZymes) would provide a potential solution. We propose a method based on CAZymes to explore polysaccharides that target specific gut microbes and alleviate diseases. The designed polysaccharides (Arabinogalactan, AG) enrich the abundance of B. cellulosilyticus in single-strain co-cultures, fermentation in vitro, and mouse models in vivo. Supplementation with AG relieved mice from colitis and clinical symptoms. We reveal that AG directly alters B. cellulosilyticus level and cooperative microbes, resulting in remission of colitis. Our glycan design pipeline is a promising way to improve disease through the targeted enhancement of specific microbes.
Collapse
Affiliation(s)
- Xiaoxiang Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - FuSheng Xu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Tangjun Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Pan Huang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Leilei Yu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Fengwei Tian
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China.
| |
Collapse
|
9
|
Rizzo SM, Vergna LM, Alessandri G, Lee C, Fontana F, Lugli GA, Carnevali L, Bianchi MG, Barbetti M, Taurino G, Sgoifo A, Bussolati O, Turroni F, van Sinderen D, Ventura M. GH136-encoding gene (perB) is involved in gut colonization and persistence by Bifidobacterium bifidum PRL2010. Microb Biotechnol 2024; 17:e14406. [PMID: 38271233 PMCID: PMC10884991 DOI: 10.1111/1751-7915.14406] [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: 09/07/2023] [Revised: 12/21/2023] [Accepted: 12/26/2023] [Indexed: 01/27/2024] Open
Abstract
Bifidobacteria are commensal microorganisms that typically inhabit the mammalian gut, including that of humans. As they may be vertically transmitted, they commonly colonize the human intestine from the very first day following birth and may persist until adulthood and old age, although generally at a reduced relative abundance and prevalence compared to infancy. The ability of bifidobacteria to persist in the human intestinal environment has been attributed to genes involved in adhesion to epithelial cells and the encoding of complex carbohydrate-degrading enzymes. Recently, a putative mucin-degrading glycosyl hydrolase belonging to the GH136 family and encoded by the perB gene has been implicated in gut persistence of certain bifidobacterial strains. In the current study, to better characterize the function of this gene, a comparative genomic analysis was performed, revealing the presence of perB homologues in just eight bifidobacterial species known to colonize the human gut, including Bifidobacterium bifidum and Bifidobacterium longum subsp. longum strains, or in non-human primates. Mucin-mediated growth and adhesion to human intestinal cells, in addition to a rodent model colonization assay, were performed using B. bifidum PRL2010 as a perB prototype and its isogenic perB-insertion mutant. These results demonstrate that perB inactivation reduces the ability of B. bifidum PRL2010 to grow on and adhere to mucin, as well as to persist in the rodent gut niche. These results corroborate the notion that the perB gene is one of the genetic determinants involved in the persistence of B. bifidum PRL2010 in the human gut.
Collapse
Affiliation(s)
- Sonia Mirjam Rizzo
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental SustainabilityUniversity of ParmaParmaItaly
| | - Laura Maria Vergna
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental SustainabilityUniversity of ParmaParmaItaly
| | - Giulia Alessandri
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental SustainabilityUniversity of ParmaParmaItaly
| | - Ciaran Lee
- APC Microbiome Institute and School of Microbiology, Bioscience InstituteNational University of IrelandCorkIreland
| | - Federico Fontana
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental SustainabilityUniversity of ParmaParmaItaly
- GenProbio srlParmaItaly
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental SustainabilityUniversity of ParmaParmaItaly
- Interdepartmental Research Centre “Microbiome Research Hub”University of ParmaParmaItaly
| | - Luca Carnevali
- Interdepartmental Research Centre “Microbiome Research Hub”University of ParmaParmaItaly
- Stress Physiology Lab, Department of Chemistry, Life Sciences and Environmental SustainabilityUniversity of ParmaParmaItaly
| | - Massimiliano G. Bianchi
- Interdepartmental Research Centre “Microbiome Research Hub”University of ParmaParmaItaly
- Laboratory of General Pathology, Department of Medicine and SurgeryUniversity of ParmaParmaItaly
| | - Margherita Barbetti
- Stress Physiology Lab, Department of Chemistry, Life Sciences and Environmental SustainabilityUniversity of ParmaParmaItaly
| | - Giuseppe Taurino
- Interdepartmental Research Centre “Microbiome Research Hub”University of ParmaParmaItaly
- Laboratory of General Pathology, Department of Medicine and SurgeryUniversity of ParmaParmaItaly
| | - Andrea Sgoifo
- Interdepartmental Research Centre “Microbiome Research Hub”University of ParmaParmaItaly
- Stress Physiology Lab, Department of Chemistry, Life Sciences and Environmental SustainabilityUniversity of ParmaParmaItaly
| | - Ovidio Bussolati
- Interdepartmental Research Centre “Microbiome Research Hub”University of ParmaParmaItaly
- Laboratory of General Pathology, Department of Medicine and SurgeryUniversity of ParmaParmaItaly
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental SustainabilityUniversity of ParmaParmaItaly
- Interdepartmental Research Centre “Microbiome Research Hub”University of ParmaParmaItaly
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, Bioscience InstituteNational University of IrelandCorkIreland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental SustainabilityUniversity of ParmaParmaItaly
- Interdepartmental Research Centre “Microbiome Research Hub”University of ParmaParmaItaly
| |
Collapse
|
10
|
Ding H, Liu J, Chen Z, Huang S, Yan C, Kwek E, He Z, Zhu H, Chen ZY. Protocatechuic acid alleviates TMAO-aggravated atherosclerosis via mitigating inflammation, regulating lipid metabolism, and reshaping gut microbiota. Food Funct 2024; 15:881-893. [PMID: 38165856 DOI: 10.1039/d3fo04396g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2024]
Abstract
Trimethylamine-N-oxide (TMAO) is a risk factor for atherosclerosis. As a natural phenolic acid, protocatechuic acid (PCA) is abundant in various plant foods. The present study investigated the effect of PCA on TMAO-aggravated atherosclerosis in ApoE-/- mice. The mice were randomly divided into five groups and fed one of the following five diets for 12 weeks: namely a low-fat diet (LFD), a western diet (WD), a WD + 0.2% TMAO diet (WDT), a WDT + 0.5% PCA diet (WDT + LPCA), and a WDT + 1.0% PCA diet (WDT + HPCA). Results demonstrated that dietary TMAO exacerbated the development of atherosclerosis by eliciting inflammation and disturbing lipid metabolism. The diet with PCA at 1% reduced TMAO-induced aortic plaque by 30% and decreased the levels of plasma pro-inflammatory cytokines. PCA also improved lipid metabolism by up-regulating the hepatic gene expression of peroxisome proliferator-activated receptor alpha (PPARα). In addition, PCA supplementation enhanced fecal excretion of fatty acids and decreased hepatic fat accumulation. PCA supplementation favorably modulated gut microbiota by increasing the α-diversity with an increase in the abundance of beneficial genera (Rikenella, Turicibacter, Clostridium_sensu_stricto and Bifidobacterium) and a decrease in the abundance of the harmful Helicobacter genus. In summary, PCA could alleviate the TMAO-exacerbated atherosclerosis and inflammation, improve the lipid metabolism, and modulate gut microbiota.
Collapse
Affiliation(s)
- Huafang Ding
- Food & Nutritional Sciences Programme, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong 999077, China.
| | - Jianhui Liu
- Food & Nutritional Sciences Programme, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong 999077, China.
- College of Food Science and Engineering, Nanjing University of Finance and Economics, Collaborative Innovation Center for Modern Grain Circulation and Safety, Jiangsu Province Engineering Research Center of Edible Fungus Preservation and Intensive Processing, Nanjing 210023, China
| | - Zixing Chen
- Food & Nutritional Sciences Programme, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong 999077, China.
| | - Shouhe Huang
- Food & Nutritional Sciences Programme, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong 999077, China.
| | - Chi Yan
- Food & Nutritional Sciences Programme, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong 999077, China.
| | - Erika Kwek
- Food & Nutritional Sciences Programme, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong 999077, China.
| | - Zouyan He
- Food & Nutritional Sciences Programme, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong 999077, China.
| | - Hanyue Zhu
- Food & Nutritional Sciences Programme, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong 999077, China.
| | - Zhen-Yu Chen
- Food & Nutritional Sciences Programme, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong 999077, China.
| |
Collapse
|
11
|
Díaz R, Garrido D. Screening competition and cross-feeding interactions during utilization of human milk oligosaccharides by gut microbes. MICROBIOME RESEARCH REPORTS 2024; 3:12. [PMID: 38455082 PMCID: PMC10917614 DOI: 10.20517/mrr.2023.61] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/30/2023] [Accepted: 12/07/2023] [Indexed: 03/09/2024]
Abstract
Background: The infant gut microbiome is a complex community that influences short- and long-term health. Its assembly and composition are governed by variables such as the feeding type. Breast milk provides infants an important supply of human milk oligosaccharides (HMO), a broad family of carbohydrates comprising neutral, fucosylated, and sialylated molecules. There is a positive association between HMOs and the overrepresentation of Bifidobacterium species in the infant gut, which is sustained by multiple molecular determinants present in the genomes of these species. Infant-gut-associated Bifidobacterium species usually share a similar niche and display similar HMO inclinations, suggesting they compete for these resources. There is also strong evidence of cross-feeding interactions between HMO-derived molecules and bifidobacteria. Methods: In this study, we screened for unidirectional and bidirectional interactions between Bifidobacterium and other species using individual HMO. Bifidobacterium bifidum and Bacteroides thetaiotaomicron increased the growth of several other species when their supernatants were used, probably mediated by the partial degradation of HMO. In contrast, Bifidobacterium longum subsp. infantis. supernatants did not exhibit positive growth. Results: Bifidobacterium species compete for lacto-N-tetraose, which is associated with reduced bidirectional growth. The outcome of these interactions was HMO-dependent, in which the two species could compete for one substrate but cross-feed on another. 2'-fucosyllactose and lacto-N-neotetraose are associated with several positive interactions that generally originate from the partial degradation of these HMOs. Conclusion: This study presents evidence for complex interactions during HMO utilization, which can be cooperative or competitive, depending on the nature of the HMO. This information could be useful for understanding how breast milk supports the growth of some Bifidobacterium species, shaping the ecology of this important microbial community.
Collapse
Affiliation(s)
| | - Daniel Garrido
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Catolica de Chile, Santiago 7820436, Chile
| |
Collapse
|
12
|
Wang S, Mu L, Yu C, He Y, Hu X, Jiao Y, Xu Z, You S, Liu SL, Bao H. Microbial collaborations and conflicts: unraveling interactions in the gut ecosystem. Gut Microbes 2024; 16:2296603. [PMID: 38149632 PMCID: PMC10761165 DOI: 10.1080/19490976.2023.2296603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 12/14/2023] [Indexed: 12/28/2023] Open
Abstract
The human gut microbiota constitutes a vast and complex community of microorganisms. The myriad of microorganisms present in the intestinal tract exhibits highly intricate interactions, which play a crucial role in maintaining the stability and balance of the gut microbial ecosystem. These interactions, in turn, influence the overall health of the host. The mammalian gut microbes have evolved a wide range of mechanisms to suppress or even eliminate their competitors for nutrients and space. Simultaneously, extensive cooperative interactions exist among different microbes to optimize resource utilization and enhance their own fitness. This review will focus on the competitive mechanisms among members of the gut microorganisms and discuss key modes of actions, including bacterial secretion systems, bacteriocins, membrane vesicles (MVs) etc. Additionally, we will summarize the current knowledge of the often-overlooked positive interactions within the gut microbiota, and showcase representative machineries. This information will serve as a reference for better understanding the complex interactions occurring within the mammalian gut environment. Understanding the interaction dynamics of competition and cooperation within the gut microbiota is crucial to unraveling the ecology of the mammalian gut microbial communities. Targeted interventions aimed at modulating these interactions may offer potential therapeutic strategies for disease conditions.
Collapse
Affiliation(s)
- Shuang Wang
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- Department of Biopharmaceutical Sciences (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), College of Pharmacy, Harbin Medical University, Harbin, China
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD) College of Pharmacy, Harbin Medical University, Harbin, China
| | - Lingyi Mu
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
| | - Chong Yu
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD) College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Yuting He
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD) College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Xinliang Hu
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD) College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Yanlei Jiao
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD) College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Ziqiong Xu
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD) College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Shaohui You
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD) College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Shu-Lin Liu
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD) College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Hongxia Bao
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD) College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| |
Collapse
|
13
|
Kim N, Kim CY, Ma J, Yang S, Park DJ, Ha SJ, Belenky P, Lee I. MRGM: an enhanced catalog of mouse gut microbial genomes substantially broadening taxonomic and functional landscapes. Gut Microbes 2024; 16:2393791. [PMID: 39230075 PMCID: PMC11376411 DOI: 10.1080/19490976.2024.2393791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 08/12/2024] [Accepted: 08/13/2024] [Indexed: 09/05/2024] Open
Abstract
Mouse gut microbiome research is pivotal for understanding the human gut microbiome, providing insights into disease modeling, host-microbe interactions, and the dietary influence on the gut microbiome. To enhance the translational value of mouse gut microbiome studies, we need detailed and high-quality catalogs of mouse gut microbial genomes. We introduce the Mouse Reference Gut Microbiome (MRGM), a comprehensive catalog with 42,245 non-redundant mouse gut bacterial genomes across 1,524 species. MRGM marks a 40% increase in the known taxonomic diversity of mouse gut microbes, capturing previously underrepresented lineages through refined genome quality assessment techniques. MRGM not only broadens the taxonomic landscape but also enriches the functional landscape of the mouse gut microbiome. Using deep learning, we have elevated the Gene Ontology annotation rate for mouse gut microbial proteins from 3.2% with orthology to 60%, marking an over 18-fold increase. MRGM supports both DNA- and marker-based taxonomic profiling by providing custom databases, surpassing previous catalogs in performance. Finally, taxonomic and functional comparisons between human and mouse gut microbiota reveal diet-driven divergences in their taxonomic composition and functional enrichment. Overall, our study highlights the value of high-quality microbial genome catalogs in advancing our understanding of the co-evolution between gut microbes and their host.
Collapse
Affiliation(s)
- Nayeon Kim
- Department of Biotechnology, College of Life Science & Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Chan Yeong Kim
- Department of Biotechnology, College of Life Science & Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Junyeong Ma
- Department of Biotechnology, College of Life Science & Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Sunmo Yang
- Department of Biotechnology, College of Life Science & Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Dong Jin Park
- Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Sang-Jun Ha
- Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Peter Belenky
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, USA
| | - Insuk Lee
- Department of Biotechnology, College of Life Science & Biotechnology, Yonsei University, Seoul, Republic of Korea
- POSTECH Biotech Center, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| |
Collapse
|
14
|
Duan H, Yu Q, Ni Y, Li J, Yu L, Fan L. Interactions between wheat germ polysaccharide and gut microbiota through in vitro batch fecal fermentation and an aging mice model: Targeting enrichment of Bacteroides uniformis and Bifidobacterium pseudocatenulatum. Int J Biol Macromol 2023; 253:127559. [PMID: 37865367 DOI: 10.1016/j.ijbiomac.2023.127559] [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: 08/04/2023] [Revised: 09/23/2023] [Accepted: 10/18/2023] [Indexed: 10/23/2023]
Abstract
The interaction between wheat germ polysaccharide (WGP) and gut microbiota remains relatively less investigated. Thus, this study explored their interaction via in vitro batch fecal fermentation. WGP elevated dramatically the relative abundances of Bacteroides (especially Ba. xylanisolvens, Ba. uniformis, and Ba. intestinalis), Bifidobacterium (especially Bi. pseudocatenulatum) and Eubacterium, and decreased Alistipes, Klebsiella, Bilophila and Sutterella. Moreover, the metabolomics and Spearman correlation results showed that these alterations in gut microbiota gave rise to over 13-fold augmentation in the quantities of short-chain fatty acids (SCFAs) and indole-3-lactic acid, as well as 7.17- and 4.23-fold increase in acetylcholine and GABA, respectively, at 24 h of fermentation. Interestingly, PICRUSt analysis showed that WGP markedly reduced aging pathway, and enriched nervous system pathway. Therefore, the D-gal-induced aging mice model was used to further verify these effects. The results demonstrated that WGP had a protective effect on D-gal-induced behavioral deficits, particularly in locomotor activity, and spatial and recognition memory. WGP elevated dramatically the relative abundances of Bacteroides (especially Ba. sartorii and Ba. uniformis), Bifidobacterium (especially Bi. pseudocatenulatum) and Parabacteroides, and decreased Alistipes and Candidatus Arthromitus. These findings highlight the potential utility of WGP as a dietary supplement for retarding the aging process and mitigating age-associated learning and memory decline via the targeted enrichment of Bacteroides and Bifidobacterium and the related metabolites.
Collapse
Affiliation(s)
- Hui Duan
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Qun Yu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yang Ni
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Jinwei Li
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Leilei Yu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, China.
| | - Liuping Fan
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, China.
| |
Collapse
|
15
|
Lu J, Zhang L, Zhang H, Chen Y, Zhao J, Chen W, Lu W, Li M. Population-level variation in gut bifidobacterial composition and association with geography, age, ethnicity, and staple food. NPJ Biofilms Microbiomes 2023; 9:98. [PMID: 38086914 PMCID: PMC10716157 DOI: 10.1038/s41522-023-00467-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
Bifidobacteria are key gut commensals that confer various health benefits and are commonly used as probiotics. However, little is known about the population-level variation in gut bifidobacterial composition and its affecting factors. Therefore, we analyzed Bifidobacterium species with amplicon sequencing of the groEL gene on fecal samples of 1674 healthy individuals, who belonged to eight ethnic groups and resided in 60 counties/cities of 28 provinces across China. We found that the composition of the bifidobacterial community was associated with geographical factors, demographic characteristics, staple food type, and urbanization. First, geography, which reflects a mixed effect of other variables, explained the largest variation in the bifidobacterial profile. Second, middle adolescence (age 14-17) and age 30 were two key change points in the bifidobacterial community development, and a bifidobacterial community resembling that of adults occurred in middle adolescence, which is much later than the maturation of the whole gut microbial community at approximately age 3. Third, each ethnicity showed a distinct bifidobacterial profile, and the remarkable amount of unknown Bifidobacterium species in the Tibetan gut suggested undiscovered biodiversity. Fourth, wheat as the main staple food promoted the flourish of B. adolescentis and B. longum. Fifth, alpha diversity of the bifidobacterial community decreased with urbanization. Collectively, our findings provide insight into the environmental and host factors that shape the human gut bifidobacterial community, which is fundamental for precision probiotics.
Collapse
Affiliation(s)
- Jing Lu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Li Zhang
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, 101300, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, China
| | - Yutao Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, China
- International Joint Research Laboratory for Pharmabiotics & Antibiotic Resistance, Jiangnan University, Wuxi, 214122, China
| | - Wenwei Lu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, China.
- International Joint Research Laboratory for Pharmabiotics & Antibiotic Resistance, Jiangnan University, Wuxi, 214122, China.
| | - Mingkun Li
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, 101300, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| |
Collapse
|
16
|
Yin P, Du T, Yi S, Zhang C, Yu L, Tian F, Chen W, Zhai Q. Response differences of gut microbiota in oligofructose and inulin are determined by the initial gut Bacteroides/Bifidobacterium ratios. Food Res Int 2023; 174:113598. [PMID: 37986462 DOI: 10.1016/j.foodres.2023.113598] [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: 07/30/2023] [Revised: 10/07/2023] [Accepted: 10/13/2023] [Indexed: 11/22/2023]
Abstract
Prebiotics are known to modulate the gut microbiota, but there is host variability, mainly due to differences in carbohydrate-utilisation by gut microbiota. Bifidobacterium and Bacteroides are powerful carbohydrate-utilising bacteria, and the ratio of both is closely related to the utilisation of prebiotics. However, the differential impact of prebiotics on the composition and function of the gut microbiota and its metabolites in participants with different Bacteroides/Bifidobacterium (Ba/Bi) ratios have not been studied. Here, we conducted a 4-week randomised double-blind, parallel four-arm trial using two prebiotics (oligofructose and inulin) in two populations with high Ba/Bi (H) and low Ba/Bi (L). The response to prebiotics in both populations was influenced by the baseline microbiota background specificity. Notably, at an overall level, FOS was slightly better than inulin in modulating the gut microbiota. Difference in gut microbiota regulation by FOS across microbiota contexts were significant between the two groups. Butyric acid-producing bacteria were significantly more abundant in H and further elevated butyric acid and related metabolite levels, with H more likely to benefit from the FOS intervention. The two groups showed only metabolic differences in their response to inulin, with L showing a significant increase in propionic acid and being enriched in glycolysis functions, whereas H was enriched in amino acids and aminoglycolysis functions. Overall, these results provide a basis for selecting appropriate prebiotics for participants with different gut backgrounds.
Collapse
Affiliation(s)
- Pingping Yin
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Ting Du
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Shanrong Yi
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Chengcheng Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Leilei Yu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Fengwei Tian
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wei Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China.
| |
Collapse
|
17
|
Lou YC, Rubin BE, Schoelmerich MC, DiMarco KS, Borges AL, Rovinsky R, Song L, Doudna JA, Banfield JF. Infant microbiome cultivation and metagenomic analysis reveal Bifidobacterium 2'-fucosyllactose utilization can be facilitated by coexisting species. Nat Commun 2023; 14:7417. [PMID: 37973815 PMCID: PMC10654741 DOI: 10.1038/s41467-023-43279-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023] Open
Abstract
The early-life gut microbiome development has long-term health impacts and can be influenced by factors such as infant diet. Human milk oligosaccharides (HMOs), an essential component of breast milk that can only be metabolized by some beneficial gut microorganisms, ensure proper gut microbiome establishment and infant development. However, how HMOs are metabolized by gut microbiomes is not fully elucidated. Isolate studies have revealed the genetic basis for HMO metabolism, but they exclude the possibility of HMO assimilation via synergistic interactions involving multiple organisms. Here, we investigate microbiome responses to 2'-fucosyllactose (2'FL), a prevalent HMO and a common infant formula additive, by establishing individualized microbiomes using fecal samples from three infants as the inocula. Bifidobacterium breve, a prominent member of infant microbiomes, typically cannot metabolize 2'FL. Using metagenomic data, we predict that extracellular fucosidases encoded by co-existing members such as Ruminococcus gnavus initiate 2'FL breakdown, thus critical for B. breve's growth. Using both targeted co-cultures and by supplementation of R. gnavus into one microbiome, we show that R. gnavus can promote extensive growth of B. breve through the release of lactose from 2'FL. Overall, microbiome cultivation combined with genome-resolved metagenomics demonstrates that HMO utilization can vary with an individual's microbiome.
Collapse
Affiliation(s)
- Yue Clare Lou
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Benjamin E Rubin
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Marie C Schoelmerich
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Environmental Systems Sciences, ETH Zurich, Zurich, Switzerland
| | - Kaden S DiMarco
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Adair L Borges
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Rachel Rovinsky
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Leo Song
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Jennifer A Doudna
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Jillian F Banfield
- Innovative Genomics Institute, University of California, Berkeley, CA, USA.
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA.
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA.
| |
Collapse
|
18
|
Fan L, Xia Y, Wang Y, Han D, Liu Y, Li J, Fu J, Wang L, Gan Z, Liu B, Fu J, Zhu C, Wu Z, Zhao J, Han H, Wu H, He Y, Tang Y, Zhang Q, Wang Y, Zhang F, Zong X, Yin J, Zhou X, Yang X, Wang J, Yin Y, Ren W. Gut microbiota bridges dietary nutrients and host immunity. SCIENCE CHINA. LIFE SCIENCES 2023; 66:2466-2514. [PMID: 37286860 PMCID: PMC10247344 DOI: 10.1007/s11427-023-2346-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 04/05/2023] [Indexed: 06/09/2023]
Abstract
Dietary nutrients and the gut microbiota are increasingly recognized to cross-regulate and entrain each other, and thus affect host health and immune-mediated diseases. Here, we systematically review the current understanding linking dietary nutrients to gut microbiota-host immune interactions, emphasizing how this axis might influence host immunity in health and diseases. Of relevance, we highlight that the implications of gut microbiota-targeted dietary intervention could be harnessed in orchestrating a spectrum of immune-associated diseases.
Collapse
Affiliation(s)
- Lijuan Fan
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Yaoyao Xia
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Youxia Wang
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Dandan Han
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yanli Liu
- College of Animal Science and Technology, Northwest A&F University, Xi'an, 712100, China
| | - Jiahuan Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jie Fu
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Leli Wang
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
| | - Zhending Gan
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Bingnan Liu
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Jian Fu
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Congrui Zhu
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Zhenhua Wu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jinbiao Zhao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Hui Han
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hao Wu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yiwen He
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Yulong Tang
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
| | - Qingzhuo Zhang
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Yibin Wang
- College of Animal Science and Technology, Northwest A&F University, Xi'an, 712100, China
| | - Fan Zhang
- College of Animal Science and Technology, Northwest A&F University, Xi'an, 712100, China
| | - Xin Zong
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Jie Yin
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, 410128, China.
| | - Xihong Zhou
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China.
| | - Xiaojun Yang
- College of Animal Science and Technology, Northwest A&F University, Xi'an, 712100, China.
| | - Junjun Wang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| | - Yulong Yin
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China.
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, 410128, China.
| | - Wenkai Ren
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China.
| |
Collapse
|
19
|
Kiely LJ, Busca K, Lane JA, van Sinderen D, Hickey RM. Molecular strategies for the utilisation of human milk oligosaccharides by infant gut-associated bacteria. FEMS Microbiol Rev 2023; 47:fuad056. [PMID: 37793834 PMCID: PMC10629584 DOI: 10.1093/femsre/fuad056] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 09/14/2023] [Accepted: 10/03/2023] [Indexed: 10/06/2023] Open
Abstract
A number of bacterial species are found in high abundance in the faeces of healthy breast-fed infants, an occurrence that is understood to be, at least in part, due to the ability of these bacteria to metabolize human milk oligosaccharides (HMOs). HMOs are the third most abundant component of human milk after lactose and lipids, and represent complex sugars which possess unique structural diversity and are resistant to infant gastrointestinal digestion. Thus, these sugars reach the infant distal intestine intact, thereby serving as a fermentable substrate for specific intestinal microbes, including Firmicutes, Proteobacteria, and especially infant-associated Bifidobacterium spp. which help to shape the infant gut microbiome. Bacteria utilising HMOs are equipped with genes associated with their degradation and a number of carbohydrate-active enzymes known as glycoside hydrolase enzymes have been identified in the infant gut, which supports this hypothesis. The resulting degraded HMOs can also be used as growth substrates for other infant gut bacteria present in a microbe-microbe interaction known as 'cross-feeding'. This review describes the current knowledge on HMO metabolism by particular infant gut-associated bacteria, many of which are currently used as commercial probiotics, including the distinct strategies employed by individual species for HMO utilisation.
Collapse
Affiliation(s)
- Leonie Jane Kiely
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork P61C996, Ireland
- Health and Happiness Group, H&H Research, National Food Innovation Hub, Teagasc Moorepark, Fermoy, Co. Cork P61K202, Ireland
- APC Microbiome Ireland, Biosciences Institute, University College Cork, Cork T12 YT20, Ireland
- School of Microbiology, University College Cork, Cork T12 YN60, Ireland
| | - Kizkitza Busca
- Health and Happiness Group, H&H Research, National Food Innovation Hub, Teagasc Moorepark, Fermoy, Co. Cork P61K202, Ireland
| | - Jonathan A Lane
- Health and Happiness Group, H&H Research, National Food Innovation Hub, Teagasc Moorepark, Fermoy, Co. Cork P61K202, Ireland
| | - Douwe van Sinderen
- APC Microbiome Ireland, Biosciences Institute, University College Cork, Cork T12 YT20, Ireland
- School of Microbiology, University College Cork, Cork T12 YN60, Ireland
| | - Rita M Hickey
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork P61C996, Ireland
- APC Microbiome Ireland, Biosciences Institute, University College Cork, Cork T12 YT20, Ireland
| |
Collapse
|
20
|
Lehman PC, Ghimire S, Price JD, Ramer-Tait AE, Mangalam AK. Diet-microbiome-immune interplay in multiple sclerosis: Understanding the impact of phytoestrogen metabolizing gut bacteria. Eur J Immunol 2023; 53:e2250236. [PMID: 37673213 DOI: 10.1002/eji.202250236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 07/19/2023] [Accepted: 09/05/2023] [Indexed: 09/08/2023]
Abstract
Multiple sclerosis (MS) is a chronic and progressive autoimmune disease of the central nervous system (CNS), with both genetic and environmental factors contributing to the pathobiology of the disease. Although HLA genes have emerged as the strongest genetic factor linked to MS, consensus on the environmental risk factors is lacking. Recently, the gut microbiota has garnered increasing attention as a potential environmental factor in MS, as mounting evidence suggests that individuals with MS exhibit microbial dysbiosis (changes in the gut microbiome). Thus, there has been a strong emphasis on understanding the role of the gut microbiome in the pathobiology of MS, specifically, factors regulating the gut microbiota and the mechanism(s) through which gut microbes may contribute to MS. Among all factors, diet has emerged to have the strongest influence on the composition and function of gut microbiota. As MS patients lack gut bacteria capable of metabolizing dietary phytoestrogen, we will specifically discuss the role of a phytoestrogen diet and phytoestrogen metabolizing gut bacteria in the pathobiology of MS. A better understanding of these mechanisms will help to harness the enormous potential of the gut microbiota as potential therapeutics to treat MS and other autoimmune diseases.
Collapse
Affiliation(s)
- Peter C Lehman
- Department of Pathology, University of Iowa, Iowa City, IA, USA
- Department of Pathology Graduate Program, University of Iowa, Iowa City, IA, USA
| | - Sudeep Ghimire
- Department of Pathology, University of Iowa, Iowa City, IA, USA
| | - Jeffrey D Price
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Amanda E Ramer-Tait
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Ashutosh K Mangalam
- Department of Pathology, University of Iowa, Iowa City, IA, USA
- Department of Pathology Graduate Program, University of Iowa, Iowa City, IA, USA
- Graduate Program in Immunology, University of Iowa, Iowa City, IA, USA
- Iowa City VA Healthcare System, Iowa City, IA, USA
| |
Collapse
|
21
|
Li L, Yan S, Liu S, Wang P, Li W, Yi Y, Qin S. In-depth insight into correlations between gut microbiota and dietary fiber elucidates a dietary causal relationship with host health. Food Res Int 2023; 172:113133. [PMID: 37689844 DOI: 10.1016/j.foodres.2023.113133] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/09/2023] [Accepted: 06/10/2023] [Indexed: 09/11/2023]
Abstract
Dietary fiber exerts a wide range of biological benefits on host health, which not only provides a powerful source of nutrition for gut microbiota but also supplies key microbial metabolites that directly affect host health. This review mainly focuses on the decomposition and metabolism of dietary fiber and the essential genera Bacteroides and Bifidobacterium in dietary fiber fermentation. Dietary fiber plays an essential role in host health by impacting outcomes related to obesity, enteritis, immune health, cancer and neurodegenerative diseases. Additionally, the gut microbiota-independent pathway of dietary fiber affecting host health is also discussed. Personalized dietary fiber intake combined with microbiome, genetics, epigenetics, lifestyle and other factors has been highlighted for development in the future. A higher level of evidence is needed to demonstrate which microbial phenotype benefits from which kind of dietary fiber. In-depth insights into the correlation between gut microbiota and dietary fiber provide strong theoretical support for the precise application of dietary fiber, which elucidates a dietary causal relationship with host health.
Collapse
Affiliation(s)
- Lili Li
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China.
| | - Shuling Yan
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuangjiang Liu
- Shandong University, Qingdao 266237, China; Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Ping Wang
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China; Shandong University of Traditional Chinese Medicine, Jinan 250355, China.
| | - Wenjun Li
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China.
| | - Yuetao Yi
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China.
| | - Song Qin
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China.
| |
Collapse
|
22
|
Cao W, Guan S, Yuan Y, Wang Y, Mst Nushrat Y, Liu Y, Tong Y, Yu S, Hua X. The digestive behavior of pectin in human gastrointestinal tract: a review on fermentation characteristics and degradation mechanism. Crit Rev Food Sci Nutr 2023:1-24. [PMID: 37665605 DOI: 10.1080/10408398.2023.2253547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Pectin is widely spread in nature and it develops an extremely complex structure in terms of monosaccharide composition, glycosidic linkage types, and non-glycosidic substituents. As a non-digestible polysaccharide, pectin exhibits resistance to human digestive enzymes, however, it is easily utilized by gut microbiota in the large intestine. Currently, pectin has been exploited as a novel functional component with numerous physiological benefits, and it shows a promising prospect in promoting human health. In this review, we introduce the regulatory effects of pectin on intestinal inflammation and metabolic syndromes. Subsequently, the digestive behavior of pectin in the upper gastrointestinal tract is summarized, and then it will be focused on pectin's fermentation characteristics in the large intestine. The fermentation selectivity of pectin by gut bacteria and the effects of pectin structure on intestinal microecology were discussed to highlight the interaction between pectin and bacterial community. Meanwhile, we also offer information on how gut bacteria orchestrate enzymes to degrade pectin. All of these findings provide insights into pectin digestion and advance the application of pectin in human health.
Collapse
Affiliation(s)
- Weichao Cao
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Shuyi Guan
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Yuying Yuan
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Yuhang Wang
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | | | - Yaxian Liu
- Department of Biotechnology and Enzyme Science, University of Hohenheim, Institute of Food Science and Biotechnology, Stuttgart, Germany
| | - Yanjun Tong
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Shuhuai Yu
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Xiao Hua
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| |
Collapse
|
23
|
Buzun E, Hsu CY, Sejane K, Oles RE, Ayala AV, Loomis LR, Zhao J, Rossitto LA, McGrosso D, Gonzalez DJ, Bode L, Chu H. A bacterial sialidase mediates early life colonization by a pioneering gut commensal. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.08.552477. [PMID: 37609270 PMCID: PMC10441351 DOI: 10.1101/2023.08.08.552477] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
The early microbial colonization of the gastrointestinal tract can lead to long-term impacts in development and overall human health. Keystone species, including Bacteroides spp ., play a crucial role in maintaining the structure, diversity, and function of the intestinal ecosystem. However, the process by which a defined and resilient community is curated and maintained during early life remains inadequately understood. Here, we show that a single sialidase, NanH, in Bacteroides fragilis mediates stable occupancy of the intestinal mucosa and regulates the commensal colonization program during the first weeks of life. This program is triggered by sialylated glycans, including those found in human milk oligosaccharides and intestinal mucus. After examining the dynamics between pioneer gut Bacteroides species in the murine gut, we discovered that NanH enables vertical transmission from dams to pups and promotes B. fragilis dominance during early life. Furthermore, we demonstrate that NanH facilitates commensal resilience and recovery after antibiotic treatment in a defined microbial community. Collectively, our study reveals a co-evolutionary mechanism between the host and the microbiota mediated through host-derived glycans to promote stable intestinal colonization.
Collapse
|
24
|
Horrocks V, King OG, Yip AYG, Marques IM, McDonald JAK. Role of the gut microbiota in nutrient competition and protection against intestinal pathogen colonization. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001377. [PMID: 37540126 PMCID: PMC10482380 DOI: 10.1099/mic.0.001377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 07/25/2023] [Indexed: 08/05/2023]
Abstract
The human gut microbiota can restrict the growth of pathogens to prevent them from colonizing the intestine ('colonization resistance'). However, antibiotic treatment can kill members of the gut microbiota ('gut commensals') and reduce competition for nutrients, making these nutrients available to support the growth of pathogens. This disturbance can lead to the growth and expansion of pathogens within the intestine (including antibiotic-resistant pathogens), where these pathogens can exploit the absence of competitors and the nutrient-enriched gut environment. In this review, we discuss nutrient competition between the gut microbiota and pathogens. We also provide an overview of how nutrient competition can be harnessed to support the design of next-generation microbiome therapeutics to restrict the growth of pathogens and prevent the development of invasive infections.
Collapse
Affiliation(s)
- Victoria Horrocks
- Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Olivia G. King
- Centre for Bacterial Resistance Biology, Department of Infectious Disease, Imperial College London, London SW7 2AZ, UK
| | - Alexander Y. G. Yip
- Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Inês Melo Marques
- Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Julie A. K. McDonald
- Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| |
Collapse
|
25
|
Yin P, Zhang C, Du T, Yi S, Yu L, Tian F, Chen W, Zhai Q. Meta-analysis reveals different functional characteristics of human gut Bifidobacteria associated with habitual diet. Food Res Int 2023; 170:112981. [PMID: 37316017 DOI: 10.1016/j.foodres.2023.112981] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 05/03/2023] [Accepted: 05/13/2023] [Indexed: 06/16/2023]
Abstract
Dietary habits contribute to the composition and function of the gut microbiota. Different dietary structures, including vegan, vegetarian, and omnivorous diets, affect intestinal Bifidobacteria; however, the relationship between Bifidobacterial function and host metabolism in subjects with different dietary patterns is unclear. Here, we analyzed five metagenomics studies and six 16S sequencing studies, including 206 vegetarians (VG), 249 omnivores (O), and 270 vegans (V), through an unbiased theme-level meta-analysis framework and discovered that diet significantly affects the composition and functionality of intestinal Bifidobacteria. The relative abundance of Bifidobacterium pseudocatenulatum was significantly higher in V than in O and Bifidobacterium longum, Bifidobacterium adolescentis, and B. pseudocatenulatum differed significantly in carbohydrate transport and metabolism in subjects with different diet types. Diets high in fiber were associated with B. longum with increased capacity for carbohydrate catabolism and genes encoding GH29 and GH43_27 were significantly enriched in V. Bifidobacterium adolescentis and B. pseudocatenulatum, associated with O, had a higher prevalence of the genes related to carbohydrate transport and metabolism, which showed the enrichment of GH26 and GH27 families. The same Bifidobacterium species has different functions in subjects with different diet types, resulting in different physiological significance. The diversification and functionalities of Bifidobacterial species in the gut microbiome can be influenced by the host diet and this aspect should be considered when studying host-microbe associations.
Collapse
Affiliation(s)
- Pingping Yin
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Chengcheng Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Ting Du
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Shanrong Yi
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Leilei Yu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Fengwei Tian
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wei Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China.
| |
Collapse
|
26
|
Yamaguchi M, Yamamoto K. Mucin glycans and their degradation by gut microbiota. Glycoconj J 2023; 40:493-512. [PMID: 37318672 DOI: 10.1007/s10719-023-10124-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 03/13/2023] [Accepted: 05/22/2023] [Indexed: 06/16/2023]
Abstract
The human intestinal tract is inhabited by a tremendous number of microorganisms, which are collectively termed "the gut microbiota". The intestinal epithelium is covered with a dense layer of mucus that prevents penetration of the gut microbiota into underlying tissues of the host. Recent studies have shown that the maturation and function of the mucus layer are strongly influenced by the gut microbiota, and alteration in the structure and function of the gut microbiota is implicated in several diseases. Because the intestinal mucus layer is at a crucial interface between microbes and their host, its breakdown leads to gut bacterial invasion that can eventually cause inflammation and infection. The mucus is composed of mucin, which is rich in glycans, and the various structures of the complex carbohydrates of mucins can select for distinct mucosa-associated bacteria that are able to bind mucin glycans, and sometimes degrade them as a nutrient source. Mucin glycans are diverse molecules, and thus mucin glycan degradation is a complex process that requires a broad range of glycan-degrading enzymes. Because of the increased recognition of the role of mucus-associated microbes in human health, how commensal bacteria degrade and use host mucin glycans has become of increased interest. This review provides an overview of the relationships between the mucin glycan of the host and gut commensal bacteria, with a focus on mucin degradation.
Collapse
Affiliation(s)
- Masanori Yamaguchi
- Department of Organic Bio Chemistry, Faculty of Education, Wakayama University, 930, Sakaedani, Wakayama, 640-8510, Japan.
| | - Kenji Yamamoto
- Center for Innovative and Joint Research, Wakayama University, 930, Sakaedani, Wakayama, 640-8510, Japan
| |
Collapse
|
27
|
Cheong KL, Chen S, Teng B, Veeraperumal S, Zhong S, Tan K. Oligosaccharides as Potential Regulators of Gut Microbiota and Intestinal Health in Post-COVID-19 Management. Pharmaceuticals (Basel) 2023; 16:860. [PMID: 37375807 DOI: 10.3390/ph16060860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
The COVID-19 pandemic has had a profound impact worldwide, resulting in long-term health effects for many individuals. Recently, as more and more people recover from COVID-19, there is an increasing need to identify effective management strategies for post-COVID-19 syndrome, which may include diarrhea, fatigue, and chronic inflammation. Oligosaccharides derived from natural resources have been shown to have prebiotic effects, and emerging evidence suggests that they may also have immunomodulatory and anti-inflammatory effects, which could be particularly relevant in mitigating the long-term effects of COVID-19. In this review, we explore the potential of oligosaccharides as regulators of gut microbiota and intestinal health in post-COVID-19 management. We discuss the complex interactions between the gut microbiota, their functional metabolites, such as short-chain fatty acids, and the immune system, highlighting the potential of oligosaccharides to improve gut health and manage post-COVID-19 syndrome. Furthermore, we review evidence of gut microbiota with angiotensin-converting enzyme 2 expression for alleviating post-COVID-19 syndrome. Therefore, oligosaccharides offer a safe, natural, and effective approach to potentially improving gut microbiota, intestinal health, and overall health outcomes in post-COVID-19 management.
Collapse
Affiliation(s)
- Kit-Leong Cheong
- Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Guangdong Provincial Science and Technology Innovation Center for Subtropical Fruit and Vegetable Processing, College of Food Science and Technology, Guangdong Ocean University, Zhanjiang 524088, China
| | - Shutong Chen
- Department of Biology, College of Science, Shantou University, Shantou 515063, China
| | - Bo Teng
- Department of Biology, College of Science, Shantou University, Shantou 515063, China
| | - Suresh Veeraperumal
- Department of Biology, College of Science, Shantou University, Shantou 515063, China
| | - Saiyi Zhong
- Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Guangdong Provincial Science and Technology Innovation Center for Subtropical Fruit and Vegetable Processing, College of Food Science and Technology, Guangdong Ocean University, Zhanjiang 524088, China
| | - Karsoon Tan
- Guangxi Key Laboratory of Beibu Gulf Biodiversity Conservation, Beibu Gulf University, Qinzhou 535000, China
| |
Collapse
|
28
|
Dedon LR, Hilliard MA, Rani A, Daza-Merchan ZT, Story G, Briere CE, Sela DA. Fucosylated Human Milk Oligosaccharides Drive Structure-Specific Syntrophy between Bifidobacterium infantis and Eubacterium hallii within a Modeled Infant Gut Microbiome. Mol Nutr Food Res 2023; 67:e2200851. [PMID: 36938958 PMCID: PMC11010582 DOI: 10.1002/mnfr.202200851] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 03/23/2023] [Indexed: 03/21/2023]
Abstract
SCOPE Fucosylated human milk oligosaccharides (fHMOs) are metabolized by Bifidobacterium infantis and promote syntrophic interactions between microbiota that colonize the infant gut. The role of fHMO structure on syntrophic interactions and net microbiome function is not yet fully understood. METHODS AND RESULTS Metabolite production and microbial populations are tracked during mono- and co-culture fermentations of 2'fucosyllactose (2'FL) and difucosyllactose (DFL) by two B. infantis strains and Eubacterium hallii. This is also conducted in an in vitro modeled microbiome supplemented by B. infantis and/or E. hallii. Metabolites are quantified by high performance liquid chromatography. Total B. infantis and E. hallii populations are quantified through qRT-PCR and community composition through 16S amplicon sequencing. Differential metabolism of 2'FL and DFL by B. infantis strains gives rise to strain- and fHMO structure-specific syntrophy with E. hallii. Within the modeled microbial community, fHMO structure does not strongly alter metabolite production in aggregate, potentially due to functional redundancy within the modeled community. In contrast, community composition is dependent on fHMO structure. CONCLUSION Whereas short chain fatty acid production is not significantly altered by the specific fHMO structure introduced to the modeled community, specific fHMO structure influences the composition of the gut microbiome.
Collapse
Affiliation(s)
- Liv R. Dedon
- Department of Food Science, University of Massachusetts Amherst, Amherst, MA United States
| | - Margaret A. Hilliard
- Department of Food Science, University of Massachusetts Amherst, Amherst, MA United States
- Organismic and Evolutionary Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA United States
| | - Asha Rani
- Department of Food Science, University of Massachusetts Amherst, Amherst, MA United States
| | | | - Galaxie Story
- Department of Food Science, University of Massachusetts Amherst, Amherst, MA United States
| | - Carrie-Ellen Briere
- Elaine Marieb College of Nursing, University of Massachusetts Amherst, Amherst, MA, United States
| | - David A. Sela
- Department of Food Science, University of Massachusetts Amherst, Amherst, MA United States
- Department of Nutrition, University of Massachusetts Amherst, Amherst, MA, United States
- Department of Microbiology and Physiological Systems and Center for Microbiome Research, University of Massachusetts Medical School, Worcester, MA, United States
| |
Collapse
|
29
|
Development of the Anaerobic Microbiome in the Infant Gut. Pediatr Infect Dis J 2023:00006454-990000000-00384. [PMID: 36917032 DOI: 10.1097/inf.0000000000003905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Ninety-five percent of gut microbiota are anaerobes and vary according to age and diet. Complex carbohydrates in human milk enhance the growth of Bifidobacterium and Bacteroides in the first year. Complex carbohydrates in solid foods enhance the growth of Bacteroides and Clostridium in the second year. Short-chain fatty acids produced by Akkermansia and Faecalibacterium may reduce obesity, diabetes and IBD.
Collapse
|
30
|
Advances and challenges in interaction between heteroglycans and Bifidobacterium: Utilization strategies, intestinal health and future perspectives. Trends Food Sci Technol 2023. [DOI: 10.1016/j.tifs.2023.02.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
|
31
|
Wei X, Yu L, Zhang C, Ni Y, Zhang H, Zhai Q, Tian F. Genetic-Phenotype Analysis of Bifidobacterium bifidum and Its Glycoside Hydrolase Gene Distribution at Different Age Groups. Foods 2023; 12:foods12050922. [PMID: 36900439 PMCID: PMC10000437 DOI: 10.3390/foods12050922] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 02/18/2023] [Accepted: 02/20/2023] [Indexed: 02/24/2023] Open
Abstract
Human gut microbiota interfere with host development and aging. Bifidobacterium is a microbial genus found in the human digestive tract that has probiotic activities such as improving constipation and enhancing immunity. The species and numbers present change with age, but there has been limited research on probiotic gut microbiota at specific ages. This study analyzed the distribution of 610 bifidobacteria in subjects in several age groups (0-17, 18-65, and 66-108 y) using 486 fecal samples and determined the distribution of glycoside hydrolases based on genetic analysis of strains representing 85% of the Bifidobacterium species abundance in each age group. 6'-Sialyllactose is a major component of acidic breast milk oligosaccharides, which can promote human neurogenesis and bifidobacteria growth. Using genotypic and phenotypic association analysis, we investigated the utilization of 6'-sialyllactose by six B. bifidum strains isolated from subjects 0-17 and 18-65 y. A comparative genomic analysis of the six B. bifidum strains revealed differences in genomic features across age groups. Finally, the safety of these strains was evaluated by antibiotic gene and drug resistance phenotype analysis. Our results reveal that the distribution of glycoside hydrolase genes in B. bifidum varies with age, thus affecting the phenotypic results. This provides important insights for the design and application of probiotic products for different ages.
Collapse
Affiliation(s)
- Xiaojing Wei
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Leilei Yu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
- Correspondence: ; Tel./Fax: +86-510-85912155
| | - Chuan Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Yongqing Ni
- School of Food Science and Technology, Shihezi University, Shihezi 832000, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
| | - Fengwei Tian
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
| |
Collapse
|
32
|
Effect of Agaricus bisporus Polysaccharides on Human Gut Microbiota during In Vitro Fermentation: An Integrative Analysis of Microbiome and Metabolome. Foods 2023; 12:foods12040859. [PMID: 36832934 PMCID: PMC9957339 DOI: 10.3390/foods12040859] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/05/2023] [Accepted: 02/14/2023] [Indexed: 02/19/2023] Open
Abstract
Agaricus bisporus polysaccharide (ABP) is an important active component in edible mushrooms, but its interaction with gut microbiota is unclear. Therefore, this study evaluated the effect of ABP on the composition and metabolites of human gut microbiota by in vitro batch fermentation. The main degrading bacteria for ABP were Bacteroides, Streptococcus, Enterococcus, Paraprevotella, Bifidobacterium, Lactococcus, Megamonas, and Eubacterium, whose relative abundances increased during 24 h of in vitro fermentation. The short-chain fatty acids (SCFAs) content also increased more than 15-fold, accordingly. Moreover, the effects of ABP on the relative abundance of Bacteroides (Ba.) and Bifidobacterium (Bi.) at the species level were further determined. ABP can enrich Ba. thetaiotaomicron, Ba. intestinalis, Ba. uniformis, and Bi. longum. PICRUSt analysis revealed that the catabolism of ABP was accompanied by changes in the metabolism of carbohydrates, nucleotides, lipids and amino acids, which were also supported by metabonomic results. It is worth mentioning that, after 24 h fermentation, the relative amounts of gamma-aminobutyric acid (GABA), nicotinamide and nicotinamide adenine dinucleotide (NAD+) had 14.43-, 11.34- and 15.36-fold increases, respectively, which were positively related to Bacteroides (Ba. thetaiotaomicron, Ba. intestinalis), Streptococcus, and Bi. longum (|r| > 0.98). These results laid the research foundation for exploring ABP as a potential prebiotic or dietary supplement for the targeted regulation of gut microbiota or metabolites.
Collapse
|
33
|
Alessandri G, Fontana F, Tarracchini C, Rizzo SM, Bianchi MG, Taurino G, Chiu M, Lugli GA, Mancabelli L, Argentini C, Longhi G, Anzalone R, Viappiani A, Milani C, Turroni F, Bussolati O, van Sinderen D, Ventura M. Identification of a prototype human gut Bifidobacterium longum subsp. longum strain based on comparative and functional genomic approaches. Front Microbiol 2023; 14:1130592. [PMID: 36846784 PMCID: PMC9945282 DOI: 10.3389/fmicb.2023.1130592] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 01/17/2023] [Indexed: 02/10/2023] Open
Abstract
Bifidobacteria are extensively exploited for the formulation of probiotic food supplements due to their claimed ability to exert health-beneficial effects upon their host. However, most commercialized probiotics are tested and selected for their safety features rather than for their effective abilities to interact with the host and/or other intestinal microbial players. In this study, we applied an ecological and phylogenomic-driven selection to identify novel B. longum subsp. longum strains with a presumed high fitness in the human gut. Such analyses allowed the identification of a prototype microorganism to investigate the genetic traits encompassed by the autochthonous bifidobacterial human gut communities. B. longum subsp. longum PRL2022 was selected due to its close genomic relationship with the calculated model representative of the adult human-gut associated B. longum subsp. longum taxon. The interactomic features of PRL2022 with the human host as well as with key representative intestinal microbial members were assayed using in vitro models, revealing how this bifidobacterial gut strain is able to establish extensive cross-talk with both the host and other microbial residents of the human intestine.
Collapse
Affiliation(s)
- Giulia Alessandri
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Federico Fontana
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy,GenProbio srl, Parma, Italy
| | - Chiara Tarracchini
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Sonia Mirjam Rizzo
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Massimiliano G. Bianchi
- Department of Medicine and Surgery, University of Parma, Parma, Italy,Microbiome Research Hub, University of Parma, Parma, Italy
| | - Giuseppe Taurino
- Department of Medicine and Surgery, University of Parma, Parma, Italy,Microbiome Research Hub, University of Parma, Parma, Italy
| | - Martina Chiu
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Leonardo Mancabelli
- Department of Medicine and Surgery, University of Parma, Parma, Italy,Microbiome Research Hub, University of Parma, Parma, Italy
| | - Chiara Argentini
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Giulia Longhi
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy,GenProbio srl, Parma, Italy
| | | | | | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy,Microbiome Research Hub, University of Parma, Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy,Microbiome Research Hub, University of Parma, Parma, Italy
| | - Ovidio Bussolati
- Department of Medicine and Surgery, University of Parma, Parma, Italy,Microbiome Research Hub, University of Parma, Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy,Microbiome Research Hub, University of Parma, Parma, Italy,*Correspondence: Marco Ventura, ✉
| |
Collapse
|
34
|
Zhao J, Hu Y, Qian C, Hussain M, Liu S, Zhang A, He R, Sun P. The Interaction between Mushroom Polysaccharides and Gut Microbiota and Their Effect on Human Health: A Review. BIOLOGY 2023; 12:biology12010122. [PMID: 36671814 PMCID: PMC9856211 DOI: 10.3390/biology12010122] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 12/23/2022] [Accepted: 01/04/2023] [Indexed: 01/13/2023]
Abstract
Mushroom polysaccharides are a kind of biological macromolecule extracted from the fruiting body, mycelium or fermentation liquid of edible fungi. In recent years, the research on mushroom polysaccharides for alleviating metabolic diseases, inflammatory bowel diseases, cancers and other symptoms by changing the intestinal microenvironment has been increasing. Mushroom polysaccharides could promote human health by regulating gut microbiota, increasing the production of short-chain fatty acids, improving intestinal mucosal barrier, regulating lipid metabolism and activating specific signaling pathways. Notably, these biological activities are closely related to the molecular weight, monosaccharide composition and type of the glycosidic bond of mushroom polysaccharide. This review aims to summarize the latest studies: (1) Regulatory effects of mushroom polysaccharides on gut microbiota; (2) The effect of mushroom polysaccharide structure on gut microbiota; (3) Metabolism of mushroom polysaccharides by gut microbiota; and (4) Effects of mushroom polysaccharides on gut microbe-mediated diseases. It provides a theoretical basis for further exploring the mechanism of mushroom polysaccharides for regulating gut microbiota and gives a reference for developing and utilizing mushroom polysaccharides as promising prebiotics in the future.
Collapse
Affiliation(s)
- Jiahui Zhao
- College of Food Science and Technology, Zhejiang University of Technology, Hangzhou 310014, China
| | - Yixin Hu
- College of Food Science and Technology, Zhejiang University of Technology, Hangzhou 310014, China
| | - Chao Qian
- College of Food Science and Technology, Zhejiang University of Technology, Hangzhou 310014, China
| | - Muhammad Hussain
- College of Food Science and Technology, Zhejiang University of Technology, Hangzhou 310014, China
| | - Shizhu Liu
- Zhejiang Fangge Pharmaceutical Co., Ltd., Qingyuan 323800, China
| | - Anqiang Zhang
- College of Food Science and Technology, Zhejiang University of Technology, Hangzhou 310014, China
| | - Rongjun He
- College of Food Science and Technology, Zhejiang University of Technology, Hangzhou 310014, China
- Zhejiang Fangge Pharmaceutical Co., Ltd., Qingyuan 323800, China
- Bioactives and Functional Foods Research Center, China National Light Industry, Hangzhou 310014, China
- Correspondence: (R.H.); (P.S.)
| | - Peilong Sun
- College of Food Science and Technology, Zhejiang University of Technology, Hangzhou 310014, China
- Zhejiang Fangge Pharmaceutical Co., Ltd., Qingyuan 323800, China
- Key Laboratory of Food Macromolecular Resources Processing Technology Research, China National Light Industry, Hangzhou 310014, China
- Correspondence: (R.H.); (P.S.)
| |
Collapse
|
35
|
Analysis of Fecal Short-Chain Fatty Acids (SCFAs) in Healthy Children during the First Two Years of Life: An Observational Prospective Cohort Study. Nutrients 2023; 15:nu15020367. [PMID: 36678236 PMCID: PMC9864378 DOI: 10.3390/nu15020367] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 01/06/2023] [Accepted: 01/07/2023] [Indexed: 01/15/2023] Open
Abstract
Short-chain fatty acids (SCFAs) are important metabolites of the gut microbiota. The aim is to analyze the influence of perinatal factors, which can affect the gut microbiota, on the concentrations of fecal SCFAs over the first two years of life. Gas chromatography was used to analyze SCFA in a total of 456 fecal samples from 86 children. Total SCFA concentrations increased until 12 months and stabilized after that. Antibiotic treatment during pregnancy was associated with an increase in acetic acid, propionic acid and total SCFA in meconium and a decrease in the same SCFAs at 6 months. Butyric acid was increased after Caesarean delivery until 1 month. In formula-fed children, propionic acid (at 1 month) and butyric acid and total SCFA (at 12 months) were increased. Acetic and linear butyric acids and total SCFAs were also increased at 12 months in children born vaginally that were also formula-fed. Higher butyric acid was observed in children of mothers with normal pre-pregnancy weight and adequate weight gain during pregnancy. Butyric acid was also elevated in 6-month-old infants with a higher body weight (≥85th percentile). Acetic acid concentrations were significantly higher in 2-year-old females vs. males. We conclude that perinatal factors are linked to changes in fecal SCFAs and further long-term epidemiological studies are warranted.
Collapse
|
36
|
Zhao Q, Ren H, Yang N, Xia X, Chen Q, Zhou D, Liu Z, Chen X, Chen Y, Huang W, Zhou H, Xu H, Zhang W. Bifidobacterium pseudocatenulatum-Mediated Bile Acid Metabolism to Prevent Rheumatoid Arthritis via the Gut-Joint Axis. Nutrients 2023; 15:nu15020255. [PMID: 36678126 PMCID: PMC9861548 DOI: 10.3390/nu15020255] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 01/06/2023] Open
Abstract
Early intervention in rheumatoid arthritis (RA) is critical for optimal treatment, but initiation of pharmacotherapy to prevent damage remains unsatisfactory currently. Manipulation of the gut microbiome and microbial metabolites can be effective in protecting against RA. Thus, probiotics can be utilized to explore new strategies for preventing joint damage. The aim of this study was to explore the metabolites and mechanisms by which Bifidobacterium pseudocatenulatum affects RA. Based on 16S rRNA sequencing and UPLC-MS/MS assays, we focused on bile acid (BA) metabolism. In a collagen-induced arthritis (CIA) mouse model, B. pseudocatenulatum prevented joint damage by protecting the intestinal barrier and reshaped gut microbial composition, thereby elevating bile salt hydrolase (BSH) enzyme activity and increasing the levels of unconjugated secondary BAs to suppress aberrant T-helper 1/17-type immune responses; however, these benefits were eliminated by the Takeda G protein-coupled receptor 5 (TGR5) antagonist SBI-115. The results suggested that a single bacterium, B. pseudocatenulatum, can prevent RA, indicating that prophylactic administration of probiotics may be an effective therapy.
Collapse
Affiliation(s)
- Qing Zhao
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha 410008, China
- Hunan Key Laboratory of Pharmacogenetics, Institute of Clinical Pharmacology, Central South University, 110 Xiangya Road, Changsha 410078, China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha 410078, China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha 410008, China
| | - Huan Ren
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha 410008, China
- Hunan Key Laboratory of Pharmacogenetics, Institute of Clinical Pharmacology, Central South University, 110 Xiangya Road, Changsha 410078, China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha 410078, China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha 410008, China
| | - Nian Yang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha 410008, China
- Hunan Key Laboratory of Pharmacogenetics, Institute of Clinical Pharmacology, Central South University, 110 Xiangya Road, Changsha 410078, China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha 410078, China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha 410008, China
| | - Xuyang Xia
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Qifeng Chen
- Department of Pathology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha 410008, China
| | - Dingding Zhou
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha 410008, China
- Hunan Key Laboratory of Pharmacogenetics, Institute of Clinical Pharmacology, Central South University, 110 Xiangya Road, Changsha 410078, China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha 410078, China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha 410008, China
| | - Zhaoqian Liu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha 410008, China
- Hunan Key Laboratory of Pharmacogenetics, Institute of Clinical Pharmacology, Central South University, 110 Xiangya Road, Changsha 410078, China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha 410078, China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha 410008, China
| | - Xiaoping Chen
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha 410008, China
- Hunan Key Laboratory of Pharmacogenetics, Institute of Clinical Pharmacology, Central South University, 110 Xiangya Road, Changsha 410078, China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha 410078, China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha 410008, China
| | - Yao Chen
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha 410008, China
- Hunan Key Laboratory of Pharmacogenetics, Institute of Clinical Pharmacology, Central South University, 110 Xiangya Road, Changsha 410078, China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha 410078, China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha 410008, China
| | - Weihua Huang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha 410008, China
- Hunan Key Laboratory of Pharmacogenetics, Institute of Clinical Pharmacology, Central South University, 110 Xiangya Road, Changsha 410078, China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha 410078, China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha 410008, China
| | - Honghao Zhou
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha 410008, China
- Hunan Key Laboratory of Pharmacogenetics, Institute of Clinical Pharmacology, Central South University, 110 Xiangya Road, Changsha 410078, China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha 410078, China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha 410008, China
| | - Heng Xu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Wei Zhang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha 410008, China
- Hunan Key Laboratory of Pharmacogenetics, Institute of Clinical Pharmacology, Central South University, 110 Xiangya Road, Changsha 410078, China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha 410078, China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha 410008, China
- Correspondence: ; Tel.: +86-731-84805380
| |
Collapse
|
37
|
Li X, Chen W, Gao J, Gao W, Zhang Y, Zeng H, Zheng B. Structural changes of butyrylated lotus seed starch and its impact on the gut microbiota of rat in vitro fermentation. Food Hydrocoll 2023. [DOI: 10.1016/j.foodhyd.2023.108501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
|
38
|
Abstract
Gut microbiome maturation in infants born prematurely is uniquely influenced by the physiological, clinical, and environmental factors surrounding preterm birth and early life, leading to altered patterns of microbial succession relative to term infants during the first months of life. These differences in microbiome composition are implicated in acute clinical conditions that disproportionately affect preterm infants, including necrotizing enterocolitis (NEC) and late-onset sepsis (LOS). Probiotic supplementation initiated early in life is an effective prophylactic measure for preventing NEC, LOS, and other clinical concerns relevant to preterm infants. In parallel, reported benefits of probiotics on the preterm gut microbiome, metabolome, and immune function are beginning to emerge. This review summarizes the current literature on the influence of probiotics on the gut microbiome of preterm infants, outlines potential mechanisms by which these effects are exerted, and highlights important clinical considerations for determining the best practices for probiotic use in premature infants.
Collapse
Affiliation(s)
- Emily M Mercer
- Department of Physiology and Pharmacology, University of Calgary, Calgary, Alberta, Canada
- Department of Pediatrics, University of Calgary, Calgary, Alberta, Canada
- International Microbiome Center, University of Calgary, Calgary, Alberta, Canada
| | - Marie-Claire Arrieta
- Department of Physiology and Pharmacology, University of Calgary, Calgary, Alberta, Canada
- Department of Pediatrics, University of Calgary, Calgary, Alberta, Canada
- International Microbiome Center, University of Calgary, Calgary, Alberta, Canada
| |
Collapse
|
39
|
Mills DA, German JB, Lebrilla CB, Underwood MA. Translating neonatal microbiome science into commercial innovation: metabolism of human milk oligosaccharides as a basis for probiotic efficacy in breast-fed infants. Gut Microbes 2023; 15:2192458. [PMID: 37013357 PMCID: PMC10075334 DOI: 10.1080/19490976.2023.2192458] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 03/13/2023] [Indexed: 04/05/2023] Open
Abstract
For over a century, physicians have witnessed a common enrichment of bifidobacteria in the feces of breast-fed infants that was readily associated with infant health status. Recent advances in bacterial genomics, metagenomics, and glycomics have helped explain the nature of this unique enrichment and enabled the tailored use of probiotic supplementation to restore missing bifidobacterial functions in at-risk infants. This review documents a 20-year span of discoveries that set the stage for the current use of human milk oligosaccharide-consuming bifidobacteria to beneficially colonize, modulate, and protect the intestines of at-risk, human milk-fed, neonates. This review also presents a model for probiotic applications wherein bifidobacterial functions, in the form of colonization and HMO-related catabolic activity in situ, represent measurable metabolic outcomes by which probiotic efficacy can be scored toward improving infant health.
Collapse
Affiliation(s)
- David A. Mills
- Department of Food Science and Technology, University of California-Davis, Davis, CA, United States
- Department of Viticulture and Enology, University of California-Davis, Davis, CA, United States
- Foods for Health Institute, University of California-Davis, Davis, CA, United States
| | - J. Bruce German
- Department of Food Science and Technology, University of California-Davis, Davis, CA, United States
- Foods for Health Institute, University of California-Davis, Davis, CA, United States
| | - Carlito B. Lebrilla
- Foods for Health Institute, University of California-Davis, Davis, CA, United States
- Department of Chemistry, University of California-Davis, Davis, CA, United States
- Department of Biochemistry and Molecular Medicine, University of California-Davis, Davis, CA, United States
| | - Mark A. Underwood
- Foods for Health Institute, University of California-Davis, Davis, CA, United States
- Division of Neonatology, Department of Pediatrics, University of California-Davis, Sacramento, CA, United States
| |
Collapse
|
40
|
Dietary Fiber Intake and Gut Microbiota in Human Health. Microorganisms 2022; 10:microorganisms10122507. [PMID: 36557760 PMCID: PMC9787832 DOI: 10.3390/microorganisms10122507] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/11/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
Dietary fiber is fermented by the human gut microbiota, producing beneficial microbial metabolites, such as short-chain fatty acids. Over the last few centuries, dietary fiber intake has decreased tremendously, leading to detrimental alternations in the gut microbiota. Such changes in dietary fiber consumption have contributed to the global epidemic of obesity, type 2 diabetes, and other metabolic disorders. The responses of the gut microbiota to the dietary changes are specific to the type, amount, and duration of dietary fiber intake. The intricate interplay between dietary fiber and the gut microbiota may provide clues for optimal intervention strategies for patients with type 2 diabetes and other noncommunicable diseases. In this review, we summarize current evidence regarding dietary fiber intake, gut microbiota modulation, and modification in human health, highlighting the type-specific cutoff thresholds of dietary fiber for gut microbiota and metabolic outcomes.
Collapse
|
41
|
Fontana F, Alessandri G, Tarracchini C, Bianchi MG, Rizzo SM, Mancabelli L, Lugli GA, Argentini C, Vergna LM, Anzalone R, Longhi G, Viappiani A, Taurino G, Chiu M, Turroni F, Bussolati O, van Sinderen D, Milani C, Ventura M. Designation of optimal reference strains representing the infant gut bifidobacterial species through a comprehensive multi-omics approach. Environ Microbiol 2022; 24:5825-5839. [PMID: 36123315 PMCID: PMC10092070 DOI: 10.1111/1462-2920.16205] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 09/10/2022] [Indexed: 01/12/2023]
Abstract
The genomic era has resulted in the generation of a massive amount of genetic data concerning the genomic diversity of bacterial taxa. As a result, the microbiological community is increasingly looking for ways to define reference bacterial strains to perform experiments that are representative of the entire bacterial species. Despite this, there is currently no established approach allowing a reliable identification of reference strains based on a comprehensive genomic, ecological, and functional context. In the current study, we developed a comprehensive multi-omics approach that will allow the identification of the optimal reference strains using the Bifidobacterium genus as test case. Strain tracking analysis based on 1664 shotgun metagenomics datasets of healthy infant faecal samples were employed to identify bifidobacterial strains suitable for in silico and in vitro analyses. Subsequently, an ad hoc bioinformatic tool was developed to screen local strain collections for the most suitable species-representative strain alternative. The here presented approach was validated using in vitro trials followed by metagenomics and metatranscriptomics analyses. Altogether, these results demonstrated the validity of the proposed model for reference strain selection, thus allowing improved in silico and in vitro investigations both in terms of cross-laboratory reproducibility and relevance of research findings.
Collapse
Affiliation(s)
- Federico Fontana
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy.,GenProbio srl, Parma, Italy
| | - Giulia Alessandri
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Chiara Tarracchini
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | | | - Sonia Mirjam Rizzo
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Chiara Argentini
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Laura Maria Vergna
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | | | - Giulia Longhi
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy.,GenProbio srl, Parma, Italy
| | | | - Giuseppe Taurino
- Laboratory of General Pathology, Department of Medicine and Surgery, University of Parma, Parma, Italy.,Microbiome Research Hub, University of Parma, Parma, Italy
| | - Martina Chiu
- Laboratory of General Pathology, Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy.,Microbiome Research Hub, University of Parma, Parma, Italy
| | - Ovidio Bussolati
- Laboratory of General Pathology, Department of Medicine and Surgery, University of Parma, Parma, Italy.,Microbiome Research Hub, University of Parma, Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy.,Microbiome Research Hub, University of Parma, Parma, Italy
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy.,Microbiome Research Hub, University of Parma, Parma, Italy
| |
Collapse
|
42
|
Mary PR, Kapoor M. Co-culture fermentations suggest cross-feeding among Bacteroides ovatus DSMZ 1896, Lactiplantibacillus plantarum WCFS1 and Bifidobacterium adolescentis DSMZ 20083 for utilizing dietary galactomannans. Food Res Int 2022; 162:111942. [DOI: 10.1016/j.foodres.2022.111942] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/27/2022] [Accepted: 09/12/2022] [Indexed: 02/08/2023]
|
43
|
Wang H, Huang X, Tan H, Chen X, Chen C, Nie S. Interaction between dietary fiber and bifidobacteria in promoting intestinal health. Food Chem 2022; 393:133407. [PMID: 35696956 DOI: 10.1016/j.foodchem.2022.133407] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 06/01/2022] [Accepted: 06/03/2022] [Indexed: 01/10/2023]
Abstract
Bifidobacteria are considered as probiotics due to their role in promoting intestinal health, including regulating intestinal flora, controlling glycolipid metabolism, anti-colitis effects. Dietary fiber is considered as prebiotic favoring gut health. It also can be used as carbon source to support the growth and colonization of probiotics like bifidobacteria. However, because of genetic diversity, different bifidobacterial species differ in their ability to utilize dietary fiber. Meanwhile, dietary fiber with different structural properties has different effects on the bifidobacteria proliferation. The interaction between dietary fiber and bifidobacteria will consequently lead to a synergistic or antagonistic function in promoting intestinal health, therefore affecting the application of combined use of dietary fiber and bifidobacteria. In this case, we summarize the biological function of bifidobacteria, and their interaction with different dietary fiber in promoting gut health, and finally provide several strategies about their combined use.
Collapse
Affiliation(s)
- Hui Wang
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang 330047, China
| | - Xiaojun Huang
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang 330047, China.
| | - Huizi Tan
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang 330047, China
| | - Xiaomin Chen
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang 330047, China
| | - Chunhua Chen
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang 330047, China
| | - Shaoping Nie
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang 330047, China
| |
Collapse
|
44
|
Recent advances in targeted manipulation of the gut microbiome by prebiotics: from taxonomic composition to metabolic function. Curr Opin Food Sci 2022. [DOI: 10.1016/j.cofs.2022.100959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
45
|
Exploring species-level infant gut bacterial biodiversity by meta-analysis and formulation of an optimized cultivation medium. NPJ Biofilms Microbiomes 2022; 8:88. [PMID: 36316342 PMCID: PMC9622858 DOI: 10.1038/s41522-022-00349-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022] Open
Abstract
In vitro gut cultivation models provide host-uncoupled, fast, and cost-efficient solutions to investigate the effects of intrinsic and extrinsic factors impacting on both composition and functionality of the intestinal microbial ecosystem. However, to ensure the maintenance and survival of gut microbial players and preserve their functions, these systems require close monitoring of several variables, including oxygen concentration, pH, and temperature, as well as the use of a culture medium satisfying the microbial nutritional requirements. In this context, in order to identify the macro- and micro-nutrients necessary for in vitro cultivation of the infant gut microbiota, a meta-analysis based on 1669 publicly available shotgun metagenomic samples corresponding to fecal samples of healthy, full-term infants aged from a few days to three years was performed to define the predominant species characterizing the “infant-like” gut microbial ecosystem. A subsequent comparison of growth performances was made using infant fecal samples that contained the most abundant bacterial taxa of the infant gut microbiota, when cultivated on 18 different culture media. This growth analysis was performed by means of flow cytometry-based bacterial cell enumeration and shallow shotgun sequencing, which allowed the formulation of an optimized growth medium, i.e., Infant Gut Super Medium (IGSM), which maintains and sustains the infant gut microbial biodiversity under in vitro growth conditions. Furthermore, this formulation was used to evaluate the in vitro effect of two drugs commonly used in pediatrics, i.e., acetaminophen and simethicone, on the taxonomic composition of the infant gut microbiota.
Collapse
|
46
|
Jin Z, Ma Q, Chen X, Wang H, Zhu J, Lee YK, Zhang H, Zhao J, Lu W, Chen W. An α type gluco-oligosaccharide from brown algae Laminaria japonica stimulated the growth of lactic acid bacteria encoding specific ABC transport system components. Food Funct 2022; 13:11153-11168. [PMID: 36205751 DOI: 10.1039/d2fo01981g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Glucan is the most widely distributed glycan. Many probiotics such as lactic acid bacteria (LAB) encoded corresponding hydrolytic enzymes, which could use these glucans as energy substances. Brown alga is rich in glucan and has high edible and medicinal value, but research on its regulation to probiotics is not detailed enough. In this study, we determined a novel neutral α type gluco-oligosaccharide from the brown alga Laminaria japonica with a degree of polymerization (DP) of 2-8 and a structure that mainly consists of α-(1→4)-linked glycosidic bonds called Laminaria japonica gluco-oligosaccharide (LJGO). Fermentation in vitro and gene-phenotype correlation analyses revealed that LJGO selectively stimulated the growth of the LAB strain encoding a specific ATP-binding cassette (ABC) transport system in a GH13 gene cluster, with apparent differences among 14 tested species. Comparative genomics further revealed that this transport system is species-specific, implying a potential contribution to species evolution. Transcriptomic analysis based on LAB strains cultured on LJGO and 1H-NMR findings of LJGO residues after strain utilization showed that the GH13 gene cluster contains functional LAB genes involved in LJGO utilization. Further verification by gene knockout studies is needed to expand our findings.
Collapse
Affiliation(s)
- Zhen Jin
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
| | - Qingqing Ma
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
| | - Xuemei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
| | - Hongchao Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
| | - Jinlin Zhu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
| | - Yuan-Kun Lee
- Department of Microbiology & Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
- (Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou 225004, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
- (Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou 225004, China
| | - Wenwei Lu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
- (Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou 225004, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
| |
Collapse
|
47
|
Drey E, Kok CR, Hutkins R. Role of Bifidobacterium pseudocatenulatum in Degradation and Consumption of Xylan-Derived Carbohydrates. Appl Environ Microbiol 2022; 88:e0129922. [PMID: 36200766 PMCID: PMC9599329 DOI: 10.1128/aem.01299-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/16/2022] [Indexed: 11/20/2022] Open
Abstract
Xylans, a family of xylose-based polysaccharides, are dietary fibers resistant to digestion. They therefore reach the large intestine intact; there, they are utilized by members of the gut microbiota. They are initially broken down by primary degraders that utilize extracellular xylanases to cleave xylan into smaller oligomers. The resulting xylooligosaccharides (XOS) can either be further metabolized directly by primary degraders or cross-feed secondary consumers, including Bifidobacterium. While several Bifidobacterium species have metabolic systems for XOS, most grow poorly on longer-chain XOS and xylan substrates. In this study, we isolated strains of Bifidobacterium pseudocatenulatum and observed that some, including B. pseudocatenulatum ED02, displayed growth on XOS with a high degree of polymerization (DP) and straight-chain xylan, suggesting a primary degrader phenotype that is rare in Bifidobacterium. In silico analyses revealed that only the genomes of these xylan-fermenting (xylan+) strains contained an extracellular GH10 endo-β-1.4 xylanase, a key enzyme for primary degradation of xylan. The presence of an extracellular xylanase was confirmed by the appearance of xylan hydrolysis products in cell-free supernatants. Extracellular xylanolytic activity was only detected in xylan+ strains, as indicated by the production of XOS fragments with a DP of 2 to 6, identified by thin-layer chromatography (TLC) and high-performance liquid chromatography (HPLC). Additionally, in vitro fecal fermentations revealed that strains with a xylan+ phenotype can persist with xylan supplementation. These results indicate that xylan+ B. pseudocatenulatum strains may have a competitive advantage in the complex environment of the gastrointestinal tract, due to their ability to act as primary degraders of xylan through extracellular enzymatic degradation. IMPORTANCE The beneficial health effects of dietary fiber are now well established. Moreover, low fiber consumption is associated with increased risks of metabolic and systemic diseases. This so-called "fiber gap" also has a profound impact on the composition of the gut microbiome, leading to a disrupted or dysbiotic microbiota. Therefore, understanding the mechanisms by which keystone bacterial species in the gut utilize xylans and other dietary fibers may provide a basis for developing strategies to restore gut microbiome function. The results described here provide biochemical and genetic evidence for primary xylan utilization by human-derived Bifidobacterium pseudocatenulatum and show also that cooperative utilization of xylans occurs among other members of this species.
Collapse
Affiliation(s)
- Elizabeth Drey
- Department of Food Science and Technology, Food Innovation Center, University of Nebraska—Lincoln, Lincoln, Nebraska, USA
- Nebraska Food for Health Center, University of Nebraska—Lincoln, Lincoln, Nebraska, USA
| | - Car Reen Kok
- Nebraska Food for Health Center, University of Nebraska—Lincoln, Lincoln, Nebraska, USA
- Complex Biosystems, University of Nebraska—Lincoln, Lincoln, Nebraska, USA
| | - Robert Hutkins
- Department of Food Science and Technology, Food Innovation Center, University of Nebraska—Lincoln, Lincoln, Nebraska, USA
- Nebraska Food for Health Center, University of Nebraska—Lincoln, Lincoln, Nebraska, USA
| |
Collapse
|
48
|
Mancin L, Amatori S, Caprio M, Sattin E, Bertoldi L, Cenci L, Sisti D, Bianco A, Paoli A. Effect of 30 days of ketogenic Mediterranean diet with phytoextracts on athletes' gut microbiome composition. Front Nutr 2022; 9:979651. [DOI: 10.3389/fnut.2022.979651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/21/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundRecent research suggest that gut microbiome may play a fundamental role in athlete's health and performance. Interestingly, nutrition can affect athletic performance by influencing the gut microbiome composition. Among different dietary patterns, ketogenic diet represents an efficient nutritional approach to get adequate body composition in athletes, however, some concerns have been raised about its potential detrimental effect on gut microbiome. To the best of our knowledge, only one study investigated the effect of ketogenic diet on the gut microbiome in athletes (elite race walkers), whilst no studies are available in a model of mixed endurance/power sport such as soccer. This study aimed to investigate the influence of a ketogenic Mediterranean diet with phytoextracts (KEMEPHY) diet on gut microbiome composition in a cohort of semi-professional soccer players.Methods16 male soccer players were randomly assigned to KEMEPHY diet (KDP n = 8) or western diet (WD n = 8). Body composition, performance measurements and gut microbiome composition were measured before and after 30 days of intervention by 16S rRNA amplicon sequencing. Alpha-diversity measures and PERMANOVA was used to investigate pre-post differences in the relative abundance of all taxonomic levels (from phylum to genus) and Spearman's correlations was used to investigate associations between microbial composition and macronutrient intake. Linear discriminant analysis was also performed at the different taxonomic levels on the post-intervention data.ResultsNo differences were found between pre and post- dietary intervention for microbial community diversity: no significant effects of time (p = 0.056, ES = 0.486 and p = 0.129, ES = 0.388, respectively for OTUs number and Shannon's ENS), group (p = 0.317, ES = 0.180 and p = 0.809, ES = 0.047) or time × group (p = 0.999, ES = 0.01 and p = 0.230, ES = 0.315). Post-hoc paired Wilcoxon test showed a significant time × group effect for Actinobacteriota (p = 0.021, ES = 0.578), which increased in the WD group (median pre: 1.7%; median post: 2.3%) and decreased in the KEMEPHY group (median pre: 4.3%; median post: 1.7%). At genus level, the linear discriminant analysis in the post intervention differentiated the two groups for Bifidobacterium genus (pertaining to the Actinobacteria phylum), Butyricicoccus and Acidaminococcus genera, all more abundant in the WD group, and for Clostridia UCG-014 (order, family, and genus), Butyricimonas, Odoribacterter genera (pertaining to the Marinifilaceae family), and Ruminococcus genus, all more abundant in the KEMEPHY group.ConclusionsOur results demonstrate that 30 days of KEMEPHY intervention, in contrast with previous research on ketogenic diet and gut microbiome, do not modify the overall composition of gut microbiome in a cohort of athletes. KEMEPHY dietary pattern may represent an alternative and safety tool for maintaining and/or regulating the composition of gut microbiome in athletes practicing regular exercise. Due to the fact that not all ketogenic diets are equal, we hypothesized that each version of ketogenic diet, with different kind of nutrients or macronutrients partitioning, may differently affect the human gut microbiome.
Collapse
|
49
|
Guo R, Zhang S, Chen J, Shen W, Zhang G, Wang J, Zhang F, Pan Q, Xie T, Ai D, Dong J, Suo J, Sun Y, Liu S. Comparison of gut microflora of donkeys in high and low altitude areas. Front Microbiol 2022; 13:964799. [PMID: 36225357 PMCID: PMC9549287 DOI: 10.3389/fmicb.2022.964799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 08/11/2022] [Indexed: 11/13/2022] Open
Abstract
Donkeys’ gut microbe is critical for their health and adaptation to the environment. Little research has been conducted on the donkey gut microbiome compared with other domestic animals. The Tibetan Plateau is an extreme environment. In this study, 6 Qinghai donkeys (QH) from the Tibetan Plateau and 6 Dezhou donkeys (DZ) were investigated, and the contents of 4 parts—stomach, small intestine, cecum, and rectum—were collected. 16S rRNA sequencing and metagenomic sequencing were used to analyze the composition and diversity of gut microbial communities in donkeys. The results showed that the flora diversity and richness of the hindgut were significantly higher than those of the foregut (p < 0.01), with no sex differences, and the community structure and composition of the same or adjacent regions (stomach, small intestine, cecum, and rectum) were similar. Besides, the flora diversity and richness of QH on the Tibetan Plateau were significantly higher than those of DZ (p < 0.05). The major pathways associated with QH were signal transduction mechanisms and carbohydrate transport and metabolism, and Bacteroidales were the major contributors to these functions. Our study provides novel insights into the contribution of microbiomes to the adaptive evolution of donkeys.
Collapse
Affiliation(s)
- Rong Guo
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Shuer Zhang
- Shandong Animal Husbandry General Station, Jinan, Shandong, China
| | - Jianxing Chen
- College of Chemistry and Life Science, Chifeng University, Chifeng, Inner Mongolia, China
| | - Wei Shen
- Gene Bank of Equine Genetic Resources, Qingdao, Shandong, China
- College of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Guoliang Zhang
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, Shandong, China
- Gene Bank of Equine Genetic Resources, Qingdao, Shandong, China
| | - Junjie Wang
- Gene Bank of Equine Genetic Resources, Qingdao, Shandong, China
- College of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Fali Zhang
- Gene Bank of Equine Genetic Resources, Qingdao, Shandong, China
- College of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Qingjie Pan
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Taifeng Xie
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Deqiang Ai
- Qinghai Sheep Breeding and Extension Service Center, Gangcha County, Haibei Prefecture, Qinghai, China
| | - Jianbao Dong
- Department of Veterinary Medical Science, Shandong Vocational Animal Science and Veterinary College, Weifang, Shandong, China
| | - Jiajia Suo
- Department of Veterinary Medical Science, Shandong Vocational Animal Science and Veterinary College, Weifang, Shandong, China
| | - Yujiang Sun
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, Shandong, China
- Gene Bank of Equine Genetic Resources, Qingdao, Shandong, China
- Vocational College of Dongying, Dongying, Shandong, China
- *Correspondence: Yujiang Sun,
| | - Shuqin Liu
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, Shandong, China
- Gene Bank of Equine Genetic Resources, Qingdao, Shandong, China
- Shuqin Liu,
| |
Collapse
|
50
|
Baniel A, Petrullo L, Mercer A, Reitsema L, Sams S, Beehner JC, Bergman TJ, Snyder-Mackler N, Lu A. Maternal effects on early-life gut microbiota maturation in a wild nonhuman primate. Curr Biol 2022; 32:4508-4520.e6. [PMID: 36099914 DOI: 10.1016/j.cub.2022.08.037] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 06/14/2022] [Accepted: 08/15/2022] [Indexed: 11/25/2022]
Abstract
Early-life microbial colonization is an important process shaping host physiology,1-3 immunity,4-6 and long-term health outcomes7-10 in humans. However, our understanding of this dynamic process remains poorly investigated in wild animals,11-13 where developmental mechanisms can be better understood within ecological and evolutionarily relevant contexts.11,12 Using one of the largest developmental datasets on a wild primate-the gelada (Theropithecus gelada)-we used 16S rRNA amplicon sequencing to characterize gut microbiota maturation during the first 3 years of life and assessed the role of maternal effects in shaping offspring microbiota assembly. In contrast to recent data on chimpanzees, postnatal microbial colonization in geladas was highly similar to humans:14 microbial alpha diversity increased rapidly following birth, followed by gradual changes in composition until weaning. Dietary changes associated with weaning (from milk- to plant-based diet) were the main drivers of shifts in taxonomic composition and microbial predicted functional pathways. Maternal effects were also an important factor influencing the offspring gut microbiota. During nursing (<12 months), offspring of experienced (multi-time) mothers exhibited faster functional microbial maturation, likely reflecting the general faster developmental pace of infants born to these mothers. Following weaning (>18 months), the composition of the juvenile microbiota tended to be more similar to the maternal microbiota than to the microbiota of other adult females, highlighting that maternal effects may persist even after nursing cessation.15,16 Together, our findings highlight the dynamic nature of early-life gut colonization and the role of maternal effects in shaping this trajectory in a wild primate.
Collapse
Affiliation(s)
- Alice Baniel
- Center for Evolution and Medicine, Arizona State University, E Tyler Mall, Tempe, AZ 85281, USA; School of Life Sciences, Arizona State University, E Tyler Mall, Tempe, AZ 85287, USA.
| | - Lauren Petrullo
- Department of Psychology, University of Michigan, Church St., Ann Arbor, MI 48109, USA
| | - Arianne Mercer
- Department of Psychology, University of Washington, Okanogan Ln., Seattle, WA 98195, USA
| | - Laurie Reitsema
- Department of Anthropology, University of Georgia, Jackson St., Athens, GA 30602, USA
| | - Sierra Sams
- Department of Psychology, University of Washington, Okanogan Ln., Seattle, WA 98195, USA
| | - Jacinta C Beehner
- Department of Psychology, University of Michigan, Church St., Ann Arbor, MI 48109, USA; Department of Anthropology, University of Michigan, S University Ave., Ann Arbor, MI 48109, USA
| | - Thore J Bergman
- Department of Psychology, University of Michigan, Church St., Ann Arbor, MI 48109, USA; Department of Ecology and Evolutionary Biology, University of Michigan, N University Ave., Ann Arbor, MI 48109, USA
| | - Noah Snyder-Mackler
- Center for Evolution and Medicine, Arizona State University, E Tyler Mall, Tempe, AZ 85281, USA; School of Life Sciences, Arizona State University, E Tyler Mall, Tempe, AZ 85287, USA; Department of Psychology, University of Washington, Okanogan Ln., Seattle, WA 98195, USA; School for Human Evolution and Social Change, Arizona State University, Cady Mall, Tempe, AZ 85287, USA.
| | - Amy Lu
- Department of Anthropology, Stony Brook University, Circle Rd., Stony Brook, NY 11794, USA.
| |
Collapse
|