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Matharu D, Ponsero AJ, Lengyel M, Meszaros-Matwiejuk A, Kolho KL, de Vos WM, Molnar-Gabor D, Salonen A. Human milk oligosaccharide composition is affected by season and parity and associates with infant gut microbiota in a birth mode dependent manner in a Finnish birth cohort. EBioMedicine 2024; 104:105182. [PMID: 38838470 DOI: 10.1016/j.ebiom.2024.105182] [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: 01/08/2024] [Revised: 05/05/2024] [Accepted: 05/21/2024] [Indexed: 06/07/2024] Open
Abstract
BACKGROUND Human milk oligosaccharides (HMOs), their determinants, infant gut microbiota and health are under extensive research; however, seldom jointly addressed. Leveraging data from the HELMi birth cohort, we investigated them collectively, considering maternal and infant secretor status. METHODS HMO composition in breastmilk collected 3 months postpartum (n = 350 mothers) was profiled using high-performance liquid chromatography. Infant gut microbiota taxonomic and functional development was studied at 3, 6, and 12 months (n = 823 stool samples) via shotgun metagenomic sequencing, focusing on HMO metabolism via glycoside hydrolase (GH) analysis. Maternal and infant secretor statuses were identified through phenotyping and genotyping, respectively. Child health, emphasizing allergies and antibiotics as proxies for infectious diseases, was recorded until 2 years. FINDINGS Mother's parity, irritable bowel syndrome, gestational diabetes, and season of milk collection associated with HMO composition. Neither maternal nor infant secretor status associated with infant gut microbiota, except for a few taxa linked to individual HMOs. Analysis stratified for birth mode revealed distinct patterns between the infant gut microbiota and HMOs. Child health parameters were not associated to infant or maternal secretor status. INTERPRETATION This comprehensive exploration unveils intricate links between secretor genotype, maternal factors, HMO composition, infant microbiota, and child health. Understanding these nuanced relationships is paramount for refining strategies to optimize early life nutrition and its enduring impact on long-term health. FUNDING Sweet Crosstalk EU H2020 MSCA ITN, Academy of Finland, Mary and Georg C. Ehrnrooth Foundation, Päivikki and Sakari Sohlberg Foundation, and Tekes.
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Affiliation(s)
- Dollwin Matharu
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Alise J Ponsero
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Marton Lengyel
- DSM-Firmenich, (Formerly: Glycom A/S), Hørsholm, Denmark
| | | | - Kaija-Leena Kolho
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Children's Hospital, University of Helsinki and HUS, Helsinki, Finland
| | - Willem M de Vos
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Laboratory of Microbiology, Wageningen University, the Netherlands
| | | | - Anne Salonen
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
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2
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Shaw C, Weimer BC, Gann R, Desai PT, Shah JD. The Yin and Yang of pathogens and probiotics: interplay between Salmonella enterica sv. Typhimurium and Bifidobacterium infantis during co-infection. Front Microbiol 2024; 15:1387498. [PMID: 38812689 PMCID: PMC11133690 DOI: 10.3389/fmicb.2024.1387498] [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: 02/17/2024] [Accepted: 04/12/2024] [Indexed: 05/31/2024] Open
Abstract
Probiotic bacteria have been proposed as an alternative to antibiotics for the control of antimicrobial resistant enteric pathogens. The mechanistic details of this approach remain unclear, in part because pathogen reduction appears to be both strain and ecology dependent. Here we tested the ability of five probiotic strains, including some from common probiotic genera Lactobacillus and Bifidobacterium, to reduce binding of Salmonella enterica sv. Typhimurium to epithelial cells in vitro. Bifidobacterium longum subsp. infantis emerged as a promising strain; however, S. Typhimurium infection outcome in epithelial cells was dependent on inoculation order, with B. infantis unable to rescue host cells from preceding or concurrent infection. We further investigated the complex mechanisms underlying this interaction between B. infantis, S. Typhimurium, and epithelial cells using a multi-omics approach that included gene expression and altered metabolism via metabolomics. Incubation with B. infantis repressed apoptotic pathways and induced anti-inflammatory cascades in epithelial cells. In contrast, co-incubation with B. infantis increased in S. Typhimurium the expression of virulence factors, induced anaerobic metabolism, and repressed components of arginine metabolism as well as altering the metabolic profile. Concurrent application of the probiotic and pathogen notably generated metabolic profiles more similar to that of the probiotic alone than to the pathogen, indicating a central role for metabolism in modulating probiotic-pathogen-host interactions. Together these data imply crosstalk via small molecules between the epithelial cells, pathogen and probiotic that consistently demonstrated unique molecular mechanisms specific probiotic/pathogen the individual associations.
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Affiliation(s)
| | - Bart C. Weimer
- Department of Population Health and Reproduction, School of Veterinary Medicine, 100K Pathogen Genome Project, University of California, Davis, Davis, CA, United States
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3
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Hilliard MA, Sela DA. Transmission and Persistence of Infant Gut-Associated Bifidobacteria. Microorganisms 2024; 12:879. [PMID: 38792709 PMCID: PMC11124121 DOI: 10.3390/microorganisms12050879] [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: 03/22/2024] [Revised: 04/18/2024] [Accepted: 04/25/2024] [Indexed: 05/26/2024] Open
Abstract
Bifidobacterium infantis are the primary colonizers of the infant gut, yet scientific research addressing the transmission of the genus Bifidobacterium to infants remains incomplete. This review examines microbial reservoirs of infant-type Bifidobacterium that potentially contribute to infant gut colonization. Accordingly, strain inheritance from mother to infant via the fecal-oral route is likely contingent on the bifidobacterial strain and phenotype, whereas transmission via the vaginal microbiota may be restricted to Bifidobacterium breve. Additional reservoirs include breastmilk, horizontal transfer from the environment, and potentially in utero transfer. Given that diet is a strong predictor of Bifidobacterium colonization in early life and the absence of Bifidobacterium is observed regardless of breastfeeding, it is likely that additional factors are responsible for bifidobacterial colonization early in life.
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Affiliation(s)
- Margaret A. Hilliard
- Department of Food Science, University of Massachusetts, Amherst, MA 01003, USA;
- Organismic and Evolutionary Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA
| | - David A. Sela
- Department of Food Science, University of Massachusetts, Amherst, MA 01003, USA;
- Organismic and Evolutionary Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA
- Department of Nutrition, University of Massachusetts, Amherst, MA 01003, USA
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
- Department of Microbiology & Physiological Systems and Center for Microbiome Research, University of Massachusetts Medical School, Worcester, MA 01605, USA
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4
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Zhou Y, Liu X, Chen H, Zhao J, Zhang H, Chen W, Yang B. Isolation and Characterisation of Streptococcus spp. with Human Milk Oligosaccharides Utilization Capacity from Human Milk. Foods 2024; 13:1291. [PMID: 38731662 PMCID: PMC11083076 DOI: 10.3390/foods13091291] [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: 03/21/2024] [Revised: 04/18/2024] [Accepted: 04/20/2024] [Indexed: 05/13/2024] Open
Abstract
Human milk oligosaccharides (HMO) that promote the growth of beneficial gut microbes in infants are abundant in human milk. Streptococcus, one of the dominant genera in human milk microbiota, is also highly prevalent in the infant gut microbiota, possibly due to its adeptness at utilizing HMOs. While previous studies have mainly focused on HMO interactions with gut bacteria like Bifidobacterium and Bacteroides spp., the interaction with Streptococcus spp. has not been fully explored. In this study, Streptococcus spp. was isolated from human milk and identified to exhibit extensive capabilities in utilizing HMOs. Their consumption rates of 2'-fucosyllactose (2'-FL), 6'-sialyllactose (6'-SL), and lacto-N-tetraose (LNT) closely matched those of Bifidobacterium longum subsp. infantis ATCC 15697. Furthermore, we assessed the safety-related genes in the genomes of the Streptococcus species capable of utilizing HMOs, revealing potential virulence and resistance genes. In addition, no haemolytic activity was observed. These findings expand the knowledge of metabolic interactions and networks within the microbiota of human milk and the early life human gut.
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Affiliation(s)
- Ye Zhou
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (Y.Z.); (X.L.); (H.C.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Xiaoming Liu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (Y.Z.); (X.L.); (H.C.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Haiqin Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (Y.Z.); (X.L.); (H.C.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (Y.Z.); (X.L.); (H.C.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Institute of Food Biotechnology, Jiangnan University, Yangzhou 225004, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (Y.Z.); (X.L.); (H.C.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Institute of Food Biotechnology, Jiangnan University, Yangzhou 225004, China
| | - Wei Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (Y.Z.); (X.L.); (H.C.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
| | - Bo Yang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (Y.Z.); (X.L.); (H.C.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- International Joint Research Laboratory for Pharmabiotics & Antibiotic Resistance, Jiangnan University, Wuxi 214122, China
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5
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Pereira GV, Boudaud M, Wolter M, Alexander C, De Sciscio A, Grant ET, Trindade BC, Pudlo NA, Singh S, Campbell A, Shan M, Zhang L, Yang Q, Willieme S, Kim K, Denike-Duval T, Fuentes J, Bleich A, Schmidt TM, Kennedy L, Lyssiotis CA, Chen GY, Eaton KA, Desai MS, Martens EC. Opposing diet, microbiome, and metabolite mechanisms regulate inflammatory bowel disease in a genetically susceptible host. Cell Host Microbe 2024; 32:527-542.e9. [PMID: 38513656 PMCID: PMC11064055 DOI: 10.1016/j.chom.2024.03.001] [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: 06/30/2023] [Revised: 12/18/2023] [Accepted: 03/01/2024] [Indexed: 03/23/2024]
Abstract
Inflammatory bowel diseases (IBDs) are chronic conditions characterized by periods of spontaneous intestinal inflammation and are increasing in industrialized populations. Combined with host genetics, diet and gut bacteria are thought to contribute prominently to IBDs, but mechanisms are still emerging. In mice lacking the IBD-associated cytokine, interleukin-10, we show that a fiber-deprived gut microbiota promotes the deterioration of colonic mucus, leading to lethal colitis. Inflammation starts with the expansion of natural killer cells and altered immunoglobulin-A coating of some bacteria. Lethal colitis is then driven by Th1 immune responses to increased activities of mucin-degrading bacteria that cause inflammation first in regions with thinner mucus. A fiber-free exclusive enteral nutrition diet also induces mucus erosion but inhibits inflammation by simultaneously increasing an anti-inflammatory bacterial metabolite, isobutyrate. Our findings underscore the importance of focusing on microbial functions-not taxa-contributing to IBDs and that some diet-mediated functions can oppose those that promote disease.
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Affiliation(s)
| | - Marie Boudaud
- Department of Infection and Immunity, Luxembourg Institute of Health, 4354 Esch-sur-Alzette, Luxembourg
| | - Mathis Wolter
- Department of Infection and Immunity, Luxembourg Institute of Health, 4354 Esch-sur-Alzette, Luxembourg; Faculty of Science, Technology and Medicine, University of Luxembourg, 4365 Esch-sur-Alzette, Luxembourg
| | - Celeste Alexander
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Alessandro De Sciscio
- Department of Infection and Immunity, Luxembourg Institute of Health, 4354 Esch-sur-Alzette, Luxembourg
| | - Erica T Grant
- Department of Infection and Immunity, Luxembourg Institute of Health, 4354 Esch-sur-Alzette, Luxembourg; Faculty of Science, Technology and Medicine, University of Luxembourg, 4365 Esch-sur-Alzette, Luxembourg
| | | | - Nicholas A Pudlo
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Shaleni Singh
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Austin Campbell
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Mengrou Shan
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA; Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Li Zhang
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA; Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Qinnan Yang
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Stéphanie Willieme
- Department of Infection and Immunity, Luxembourg Institute of Health, 4354 Esch-sur-Alzette, Luxembourg
| | - Kwi Kim
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Trisha Denike-Duval
- Unit for Laboratory Animal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Jaime Fuentes
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - André Bleich
- Institute for Laboratory Animal Science, Hanover Medical School, Hanover, Germany
| | - Thomas M Schmidt
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA; Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Lucy Kennedy
- Unit for Laboratory Animal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Costas A Lyssiotis
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA; Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Grace Y Chen
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Kathryn A Eaton
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Mahesh S Desai
- Department of Infection and Immunity, Luxembourg Institute of Health, 4354 Esch-sur-Alzette, Luxembourg; Odense Research Center for Anaphylaxis, Department of Dermatology and Allergy Center, Odense University Hospital, University of Southern Denmark, Odense, Denmark.
| | - Eric C Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA.
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6
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Li S, Chen M, Wang Z, Abudourexiti W, Zhang L, Ding C, Ding L, Gong J. Ant may well destroy a whole dam: glycans of colonic mucus barrier disintegrated by gut bacteria. Microbiol Res 2024; 281:127599. [PMID: 38219635 DOI: 10.1016/j.micres.2023.127599] [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: 09/25/2023] [Revised: 12/29/2023] [Accepted: 12/30/2023] [Indexed: 01/16/2024]
Abstract
The colonic mucus layer plays a critical role in maintaining the integrity of the colonic mucosal barrier, serving as the primary defense against colonic microorganisms. Predominantly composed of mucin 2 (MUC2), a glycosylation-rich protein, the mucus layer forms a gel-like coating that covers the colonic epithelium surface. This layer provides a habitat for intestinal microorganisms, which can utilize mucin glycans present in the mucus layer as a sustainable source of nutrients. Additionally, metabolites produced by the microbiota during the metabolism of mucus glycans have a profound impact on host health. Under normal conditions, the production and consumption of mucus maintain a dynamic balance. However, several studies have demonstrated that certain factors, such as dietary fiber deficiency, can enhance the metabolism of mucus glycans by gut bacteria, thereby disturbing this balance and weakening the mucus barrier function of the mucus layer. To better understand the occurrence and development of colon-related diseases, it is crucial to investigate the complex metabolic patterns of mucus glycosylation by intestinal microorganisms. Our objective was to comprehensively review these patterns in order to clarify the effects of mucus layer glycan metabolism by intestinal microorganisms on the host.
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Affiliation(s)
- Song Li
- Department of General Surgery, Affiliated Jinling Hospital, Medical School, Nanjing University, Nanjing, China
| | - Mingfei Chen
- Department of General Surgery, Affiliated Jinling Hospital, Medical School, Nanjing University, Nanjing, China
| | - Zhongyuan Wang
- Department of General Surgery, Affiliated Jinling Hospital, Medical School, Nanjing University, Nanjing, China
| | - Waresi Abudourexiti
- Department of General Surgery, Affiliated Jinling Hospital, Medical School, Nanjing University, Nanjing, China
| | - Liang Zhang
- Department of Gastrointestinal Surgery, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical College, Jiangsu, China
| | - Chao Ding
- Department of General Surgery, Affiliated Drum Tower Hospital, Medical School, Nanjing University, Nanjing, China.
| | - Lin Ding
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China; Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China.
| | - Jianfeng Gong
- Department of General Surgery, Affiliated Jinling Hospital, Medical School, Nanjing University, Nanjing, China.
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7
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Lordan C, Roche AK, Delsing D, Nauta A, Groeneveld A, MacSharry J, Cotter PD, van Sinderen D. Linking human milk oligosaccharide metabolism and early life gut microbiota: bifidobacteria and beyond. Microbiol Mol Biol Rev 2024; 88:e0009423. [PMID: 38206006 PMCID: PMC10966949 DOI: 10.1128/mmbr.00094-23] [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] [Indexed: 01/12/2024] Open
Abstract
SUMMARYHuman milk oligosaccharides (HMOs) are complex, multi-functional glycans present in human breast milk. They represent an intricate mix of heterogeneous structures which reach the infant intestine in an intact form as they resist gastrointestinal digestion. Therefore, they confer a multitude of benefits, directly and/or indirectly, to the developing neonate. Certain bifidobacterial species, being among the earliest gut colonizers of breast-fed infants, have an adapted functional capacity to metabolize various HMO structures. This ability is typically observed in infant-associated bifidobacteria, as opposed to bifidobacteria associated with a mature microbiota. In recent years, information has been gleaned regarding how these infant-associated bifidobacteria as well as certain other taxa are able to assimilate HMOs, including the mechanistic strategies enabling their acquisition and consumption. Additionally, complex metabolic interactions occur between microbes facilitated by HMOs, including the utilization of breakdown products released from HMO degradation. Interest in HMO-mediated changes in microbial composition and function has been the focal point of numerous studies, in recent times fueled by the availability of individual biosynthetic HMOs, some of which are now commonly included in infant formula. In this review, we outline the main HMO assimilatory and catabolic strategies employed by infant-associated bifidobacteria, discuss other taxa that exhibit breast milk glycan degradation capacity, and cover HMO-supported cross-feeding interactions and related metabolites that have been described thus far.
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Affiliation(s)
- Cathy Lordan
- Teagasc Food Research Centre, Fermoy, Co Cork, Ireland
| | - Aoife K. Roche
- APC Microbiome Ireland, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | | | - Arjen Nauta
- FrieslandCampina, Amersfoort, the Netherlands
| | | | - John MacSharry
- APC Microbiome Ireland, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Paul D. Cotter
- Teagasc Food Research Centre, Fermoy, Co Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Douwe van Sinderen
- APC Microbiome Ireland, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
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8
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Guilfoyle MM. Ramadan fasting in the third trimester of pregnancy and postpartum colostrum cortisol concentrations in Morocco. Am J Hum Biol 2024:e24071. [PMID: 38497094 DOI: 10.1002/ajhb.24071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 03/07/2024] [Accepted: 03/08/2024] [Indexed: 03/19/2024] Open
Abstract
Breast milk cortisol concentration varies among and within lactating women, but the causes and consequences of variation are not yet fully understood. This study investigated whether maternal fasting from food and water for over 16 h per day during the third trimester of pregnancy was associated with increased concentrations of cortisol in colostrum during the month of Ramadan in a Moroccan sample. Participants were women who gave birth at the public maternity hospital in Rabat, Morocco throughout the month of and month following Ramadan. Participants completed interviews (N = 92), underwent anthropometric assessment (N = 73), and colostrum samples (N = 63) were collected approximately 48-72 h postpartum. Cortisol analysis was completed on a subset of colostrum samples (N = 43). Women were categorized as fasting every day of Ramadan before giving birth (N = 52/92, 57%), fasting some days (N = 29/92, 32%), and not fasting (N = 11/92, 11%). For women who fasted, average fasting duration was 19.5 days (range: 1-29 days), and average time between the last day of fasting and birth was 8.8 days (range: 0-43 days). The number of days of fasting was positively associated with cortisol concentrations in colostrum (p < .009) in a multivariate analysis controlling for maternal anthropometry, hypertension and/or diabetes, and reasons for opting out of fasting. Each day of fasting was associated with a 4.05% increase in colostrum cortisol. Results are consistent with the hypothesis that maternal fasting during the third trimester of pregnancy increases breast milk cortisol and thus alters the hormonal milieu to which the infant is exposed.
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9
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Wong JPH, Chillier N, Fischer-Stettler M, Zeeman SC, Battin TJ, Persat A. Bacteroides thetaiotaomicron metabolic activity decreases with polysaccharide molecular weight. mBio 2024; 15:e0259923. [PMID: 38376161 PMCID: PMC10936149 DOI: 10.1128/mbio.02599-23] [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: 09/26/2023] [Accepted: 01/26/2024] [Indexed: 02/21/2024] Open
Abstract
The human colon hosts hundreds of commensal bacterial species, many of which ferment complex dietary carbohydrates. To transform these fibers into metabolically accessible compounds, microbes often express a series of dedicated enzymes homologous to the starch utilization system (Sus) encoded in polysaccharide utilization loci (PULs). The genome of Bacteroides thetaiotaomicron (Bt), a common member of the human gut microbiota, encodes nearly 100 PULs, conferring a strong metabolic versatility. While the structures and functions of individual enzymes within the PULs have been investigated, little is known about how polysaccharide complexity impacts the function of Sus-like systems. We here show that the activity of Sus-like systems depends on polysaccharide size, ultimately impacting bacterial growth. We demonstrate the effect of size-dependent metabolism in the context of dextran metabolism driven by the specific utilization system PUL48. We find that as the molecular weight of dextran increases, Bt growth rate decreases and lag time increases. At the enzymatic level, the dextranase BT3087, a glycoside hydrolase (GH) belonging to the GH family 66, is the main GH for dextran utilization, and BT3087 and BT3088 contribute to Bt dextran metabolism in a size-dependent manner. Finally, we show that the polysaccharide size-dependent metabolism of Bt impacts its metabolic output in a way that modulates the composition of a producer-consumer community it forms with Bacteroides fragilis. Altogether, our results expose an overlooked aspect of Bt metabolism that can impact the composition and diversity of microbiota. IMPORTANCE Polysaccharides are complex molecules that are commonly found in our diet. While humans lack the ability to degrade many polysaccharides, their intestinal microbiota contain bacterial commensals that are versatile polysaccharide utilizers. The gut commensal Bacteroides thetaiotaomicron dedicates roughly 20% of their genomes to the expression of polysaccharide utilization loci for the broad range utilization of polysaccharides. Although it is known that different polysaccharide utilization loci are dedicated to the degradation of specific polysaccharides with unique glycosidic linkages and monosaccharide compositions, it is often overlooked that specific polysaccharides may also exist in various molecular weights. These different physical attributes may impact their processability by starch utilization system-like systems, leading to differing growth rates and nutrient-sharing properties at the community level. Therefore, understanding how molecular weight impacts utilization by gut microbe may lead to the potential design of novel precision prebiotics.
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Affiliation(s)
- Jeremy P. H. Wong
- Institute of Bioengineering and Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Sion, Switzerland
| | - Noémie Chillier
- Institute of Bioengineering and Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | | | | | - Tom J. Battin
- School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Sion, Switzerland
| | - Alexandre Persat
- Institute of Bioengineering and Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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10
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Padilla L, Fricker AD, Luna E, Choudhury B, Hughes ER, Panzetta ME, Valdivia RH, Flores GE. Mechanism of 2'-fucosyllactose degradation by human-associated Akkermansia. J Bacteriol 2024; 206:e0033423. [PMID: 38299857 PMCID: PMC10886448 DOI: 10.1128/jb.00334-23] [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: 10/14/2023] [Accepted: 01/04/2024] [Indexed: 02/02/2024] Open
Abstract
Among the first microorganisms to colonize the human gut of breastfed infants are bacteria capable of fermenting human milk oligosaccharides (HMOs). One of the most abundant HMOs, 2'-fucosyllactose (2'-FL), may specifically drive bacterial colonization of the intestine. Recently, differential growth has been observed across multiple species of Akkermansia on various HMOs including 2'-FL. In culture, we found growth of two species, A. muciniphila MucT and A. biwaensis CSUN-19,on HMOs corresponded to a decrease in the levels of 2'-FL and an increase in lactose, indicating that the first step in 2'-FL catabolism is the cleavage of fucose. Using phylogenetic analysis and transcriptional profiling, we found that the number and expression of fucosidase genes from two glycoside hydrolase (GH) families, GH29 and GH95, vary between these two species. During the mid-log phase of growth, the expression of several GH29 genes was increased by 2'-FL in both species, whereas the GH95 genes were induced only in A. muciniphila. We further show that one putative fucosidase and a β-galactosidase from A. biwaensis are involved in the breakdown of 2'-FL. Our findings indicate that the plasticity of GHs of human-associated Akkermansia sp. enables access to additional growth substrates present in HMOs, including 2'-FL. Our work highlights the potential for Akkermansia to influence the development of the gut microbiota early in life and expands the known metabolic capabilities of this important human symbiont.IMPORTANCEAkkermansia are mucin-degrading specialists widely distributed in the human population. Akkermansia biwaensis has recently been observed to have enhanced growth relative to other human-associated Akkermansia on multiple human milk oligosaccharides (HMOs). However, the mechanisms for enhanced growth are not understood. Here, we characterized the phylogenetic diversity and function of select genes involved in the growth of A. biwaensis on 2'-fucosyllactose (2'-FL), a dominant HMO. Specifically, we demonstrate that two genes in a genomic locus, a putative β-galactosidase and α-fucosidase, are likely responsible for the enhanced growth on 2'-FL. The functional characterization of A. biwaensis growth on 2'-FL delineates the significance of a single genomic locus that may facilitate enhanced colonization and functional activity of select Akkermansia early in life.
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Affiliation(s)
- Loren Padilla
- Department of Biology, California State University, Northridge, California, USA
| | - Ashwana D. Fricker
- Department of Biology, California State University, Northridge, California, USA
| | - Estefani Luna
- Department of Biology, California State University, Northridge, California, USA
| | - Biswa Choudhury
- GlycoAnalytics Core, UC San Diego, Health Sciences, La Jolla, California, USA
| | - Elizabeth R. Hughes
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Maria E. Panzetta
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Raphael H. Valdivia
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Gilberto E. Flores
- Department of Biology, California State University, Northridge, California, USA
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11
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Tarracchini C, Milani C, Lugli GA, Mancabelli L, Turroni F, van Sinderen D, Ventura M. The infant gut microbiota as the cornerstone for future gastrointestinal health. ADVANCES IN APPLIED MICROBIOLOGY 2024; 126:93-119. [PMID: 38637108 DOI: 10.1016/bs.aambs.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
The early postnatal period represents a critical window of time for the establishment and maturation of the human gut microbiota. The gut microbiota undergoes dramatic developmental changes during the first year of life, being influenced by a variety of external factors, with diet being a major player. Indeed, the introduction of complementary feeding provides novel nutritive substrates and triggers a shift from milk-adapted gut microbiota toward an adult-like bacterial composition, which is characterized by an enhancement in diversity and proportions of fiber-degrading bacterial genera like Ruminococcus, Prevotella, Eubacterium, and Bacteroides genera. Inadequate gut microbiota development in early life is frequently associated with concomitant and future adverse health conditions. Thus, understanding the processes that govern initial colonization and establishment of microbes in the gastrointestinal tract is of great importance. This review summarizes the actual understanding of the assembly and development of the microbial community associated with the infant gut, emphasizing the importance of mother-to-infant vertical transmission events as a fundamental arrival route for the first colonizers.
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Affiliation(s)
- Chiara Tarracchini
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy; Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy; Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy
| | - Leonardo Mancabelli
- Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy; 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; Interdepartmental Research Centre "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; Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy.
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12
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Buzun E, Hsu CY, Sejane K, Oles RE, Vasquez Ayala A, Loomis LR, Zhao J, Rossitto LA, McGrosso DM, Gonzalez DJ, Bode L, Chu H. A bacterial sialidase mediates early-life colonization by a pioneering gut commensal. Cell Host Microbe 2024; 32:181-190.e9. [PMID: 38228143 PMCID: PMC10922750 DOI: 10.1016/j.chom.2023.12.014] [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: 08/03/2023] [Revised: 11/14/2023] [Accepted: 12/19/2023] [Indexed: 01/18/2024]
Abstract
The early microbial colonization of the gastrointestinal tract can have long-term impacts on development and health. Keystone species, including Bacteroides spp., are prominent in early life and play crucial roles in maintaining the structure of the intestinal ecosystem. However, the process by which a resilient community is curated during early life remains inadequately understood. Here, we show that a single sialidase, NanH, in Bacteroides fragilis mediates stable occupancy of the intestinal mucosa in early life and regulates a commensal colonization program. This program is triggered by sialylated glycans, including those found in human milk oligosaccharides and intestinal mucus. NanH is required for vertical transmission from dams to pups and promotes B. fragilis dominance during early life. Furthermore, 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 microbiota mediated through host-derived glycans to promote stable colonization.
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Affiliation(s)
- Ekaterina Buzun
- Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Chia-Yun Hsu
- Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kristija Sejane
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Renee E Oles
- Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Adriana Vasquez Ayala
- Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Luke R Loomis
- Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jiaqi Zhao
- Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Leigh-Ana Rossitto
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Dominic M McGrosso
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - David J Gonzalez
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Lars Bode
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence (MOMI CORE), University of California, San Diego, La Jolla, CA 92093, USA; Human Milk Institute (HMI), University of California, San Diego, La Jolla, CA 92093, USA
| | - Hiutung Chu
- Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA; Human Milk Institute (HMI), University of California, San Diego, La Jolla, CA 92093, USA; Chiba University-UC San Diego Center for Mucosal Immunology, Allergy and Vaccines (cMAV), University of California, San Diego, La Jolla, CA 92093, USA; Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ON M5G 1M1, Canada.
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13
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Devarajalu P, Kumar J, Dutta S, Attri SV, Kabeerdoss J. Gut microbiota of preterm infants in the neonatal intensive care unit: a study from a tertiary care center in northern India. Front Microbiol 2024; 15:1329926. [PMID: 38389529 PMCID: PMC10881769 DOI: 10.3389/fmicb.2024.1329926] [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: 10/30/2023] [Accepted: 01/22/2024] [Indexed: 02/24/2024] Open
Abstract
Introduction Disruptions of the gut microbiota of preterm infants admitted to the neonatal intensive care unit (NICU) during the first 2 weeks of life are of critical importance. These infants are prone to various complications, including necrotizing enterocolitis (NEC) and sepsis. Studying the gut microbiota will improve outcomes in preterm infants. In the present study, we examined the gut microbiota of preterm infants admitted to the NICU in the first month of life. Methods Neonates admitted to the NICU were recruited, and stool samples were collected weekly from the seventh day of the infant's life until the 30th day of life. DNA was extracted using a DNeasy Powersoil DNA isolation kit. 16S rRNA gene sequencing targeting the V3-V4 region was performed using the MiSeq platform. Sequenced reads were processed on DADA2 pipeline to obtain an amplicon sequence variant (ASV) table. All bioinformatic and statistical analyses were performed using different packages in the R statistical framework. Results Fourteen preterm infants were recruited, and 48 samples were collected. Alpha diversity metrics, observed ASV count, and Shannon index were found to have no differences in any clinical variables. Permutational multivariate analysis of variance (PERMANOVA) showed discrimination of neonates by gestational age and administration of probiotics. Differential abundance analysis showed a decreased abundance of Bifidobacterium Breve in extremely preterm infants (gestational age <28 weeks) compared to moderate preterm infants (gestational age 29-32 weeks). Supplementation with probiotics decreased Acinetobacter and increased Bifidobacterium in the gut of preterm neonates regardless of gestational age. Conclusion Gestational age and probiotic supplementation alter the gut microbiota of preterm infants admitted to the NICU.
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Affiliation(s)
- Prabavathi Devarajalu
- Pediatric Biochemistry Unit, Department of Pediatrics, Post Graduate Institute of Medical Education & Research (PGIMER), Chandigarh, India
| | - Jogender Kumar
- Newborn Unit, Department of Pediatrics, Post Graduate Institute of Medical Education & Research (PGIMER), Chandigarh, India
| | - Sourabh Dutta
- Newborn Unit, Department of Pediatrics, Post Graduate Institute of Medical Education & Research (PGIMER), Chandigarh, India
| | - Savita Verma Attri
- Pediatric Biochemistry Unit, Department of Pediatrics, Post Graduate Institute of Medical Education & Research (PGIMER), Chandigarh, India
| | - Jayakanthan Kabeerdoss
- Pediatric Biochemistry Unit, Department of Pediatrics, Post Graduate Institute of Medical Education & Research (PGIMER), Chandigarh, India
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14
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Patangia DV, Grimaud G, O'Shea CA, Ryan CA, Dempsey E, Stanton C, Ross RP. Early life exposure of infants to benzylpenicillin and gentamicin is associated with a persistent amplification of the gut resistome. MICROBIOME 2024; 12:19. [PMID: 38310316 PMCID: PMC10837951 DOI: 10.1186/s40168-023-01732-6] [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: 05/09/2023] [Accepted: 11/24/2023] [Indexed: 02/05/2024]
Abstract
BACKGROUND Infant gut microbiota is highly malleable, but the long-term longitudinal impact of antibiotic exposure in early life, together with the mode of delivery on infant gut microbiota and resistome, is not extensively studied. METHODS Two hundred and eight samples from 45 infants collected from birth until 2 years of age over five time points (week 1, 4, 8, 24, year 2) were analysed. Based on shotgun metagenomics, the gut microbial composition and resistome profile were compared in the early life of infants divided into three groups: vaginal delivery/no-antibiotic in the first 4 days of life, C-section/no-antibiotic in the first 4 days of life, and C-section/antibiotic exposed in first 4 days of life. Gentamycin and benzylpenicillin were the most commonly administered antibiotics during this cohort's first week of life. RESULTS Newborn gut microbial composition differed in all three groups, with higher diversity and stable composition seen at 2 years of age, compared to week 1. An increase in microbial diversity from week 1 to week 4 only in the C-section/antibiotic-exposed group reflects the effect of antibiotic use in the first 4 days of life, with a gradual increase thereafter. Overall, a relative abundance of Actinobacteria and Bacteroides was significantly higher in vaginal delivery/no-antibiotic while Proteobacteria was higher in C-section/antibiotic-exposed infants. Strains from species belonging to Bifidobacterium and Bacteroidetes were generally persistent colonisers, with Bifidobacterium breve and Bifidobacterium bifidum species being the major persistent colonisers in all three groups. Bacteroides persistence was dominant in the vaginal delivery/no-antibiotic group, with species Bacteroides ovatus and Phocaeicola vulgatus found to be persistent colonisers in the no-antibiotic groups. Most strains carrying antibiotic-resistance genes belonged to phyla Proteobacteria and Firmicutes, with the C-section/antibiotic-exposed group presenting a higher frequency of antibiotic-resistance genes (ARGs). CONCLUSION These data show that antibiotic exposure has an immediate and persistent effect on the gut microbiome in early life. As such, the two antibiotics used in the study selected for strains (mainly Proteobacteria) which were multiple drug-resistant (MDR), presumably a reflection of their evolutionary lineage of historical exposures-leading to what can be an extensive and diverse resistome. Video Abstract.
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Affiliation(s)
- Dhrati V Patangia
- School of Microbiology, University College Cork, Cork, Ireland
- Teagasc Food Research Centre, Moorepark, Fermoy Co., Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Ghjuvan Grimaud
- Teagasc Food Research Centre, Moorepark, Fermoy Co., Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | | | - C A Ryan
- APC Microbiome Ireland, Cork, Ireland
| | - Eugene Dempsey
- APC Microbiome Ireland, Cork, Ireland
- Department of Paediatrics and Child Health, University College Cork, Cork, Ireland
- Infant Research Centre, University College Cork, Cork, Ireland
| | - Catherine Stanton
- Teagasc Food Research Centre, Moorepark, Fermoy Co., Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - R Paul Ross
- School of Microbiology, University College Cork, Cork, Ireland.
- APC Microbiome Ireland, Cork, Ireland.
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15
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Mienaltowski MJ, Callahan M, De La Torre U, Maga EA. Comparing microbiotas of foals and their mares' milk in the first two weeks after birth. BMC Vet Res 2024; 20:17. [PMID: 38191395 PMCID: PMC10775675 DOI: 10.1186/s12917-023-03864-1] [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: 05/04/2023] [Accepted: 12/21/2023] [Indexed: 01/10/2024] Open
Abstract
BACKGROUND The mare-foal relationship is essential for the well-being and growth of a foal. Mare's milk provides a foal with nutrients, protective immunity, and microbes. Within the first two weeks of life, there is a risk for a foal to suffer from diarrhea, particularly "foal heat diarrhea" which happens at about the time of a mare's estrus cycle but is more likely due to transitions in the microbiota in the foal's gastrointestinal (GI) tract. We hypothesized that this GI microbiota transition could be caused by changes in lysozyme and microbial populations in the mare's milk. To test this hypothesis, fifteen mare-foal pairs were followed in the first 15 days post-foaling. Every other day milk was collected from mares and rectal swabs were collected from foals. Lysozyme activity in the mare's milk was measured using a fluorescence assay. Microbial DNA was isolated from the milk and swabs and the V4 domain of 16 S rRNA genes were PCR amplified and sequenced using Illumina MiSeq technology. Microbial populations were analyzed using DADA2 and phyloseq within R. RESULTS Mare's milk lysozyme activity peaked for samples at Day 1 and levels dropped to 72.5% of Day 1 activity by Day 15; however, microbial populations in the mare's milk did not vary significantly over the two weeks. Furthermore, levels of microbial diversity found in foal rectal swabs were initially similar to microbial diversity seen in mare's milk; however, over the first fifteen days, diversity increased for the foal rectal swab microbiota and swab microbial populations differed from milk microbes. A transition occurred shifting from microbes from the phylum Proteobacteria early in rectal swabs to those primarily from the phyla Firmicutes and Bacteroidota after the first few days post-foaling. These phyla contained several families and genera of microbes that promote utilization of milk components in healthy gut transition. Microbial abundance levels correlated more with days post-parturition than with lysozyme activity and mare's milk microbial populations. CONCLUSIONS The findings suggest that much of the microbial populations responsible for the transition of the foal's gut comes from sources outside of mare's milk species and levels of lysozyme activity.
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Affiliation(s)
- Michael J Mienaltowski
- Department of Animal Science, University of California Davis, One Shields Avenue, 2251 Meyer Hall, Davis, CA, 95616, USA.
| | - Mitchell Callahan
- Department of Animal Science, University of California Davis, One Shields Avenue, 2251 Meyer Hall, Davis, CA, 95616, USA
| | - Ubaldo De La Torre
- Department of Animal Science, University of California Davis, One Shields Avenue, 2251 Meyer Hall, Davis, CA, 95616, USA
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, BRB 440, Portland, OR, 97239, USA
| | - Elizabeth A Maga
- Department of Animal Science, University of California Davis, One Shields Avenue, 2251 Meyer Hall, Davis, CA, 95616, USA
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16
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Kijner S, Ennis D, Shmorak S, Florentin A, Yassour M. CRISPR-Cas-based identification of a sialylated human milk oligosaccharides utilization cluster in the infant gut commensal Bacteroides dorei. Nat Commun 2024; 15:105. [PMID: 38167825 PMCID: PMC10761964 DOI: 10.1038/s41467-023-44437-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 12/13/2023] [Indexed: 01/05/2024] Open
Abstract
The infant gut microbiome is impacted by early-life feeding, as human milk oligosaccharides (HMOs) found in breastmilk cannot be digested by infants and serve as nutrients for their gut bacteria. While the vast majority of HMO-utilization research has focused on Bifidobacterium species, recent studies have suggested additional HMO-utilizers, mostly Bacteroides, yet their utilization mechanism is poorly characterized. Here, we investigate Bacteroides dorei isolates from breastfed-infants and identify that polysaccharide utilization locus (PUL) 33 enables B. dorei to utilize sialylated HMOs. We perform transcriptional profiling and identity upregulated genes when growing on sialylated HMOs. Using CRISPR-Cas12 to knock-out four PUL33 genes, combined with complementation assays, we identify GH33 as the critical gene in PUL33 for sialylated HMO-utilization. This demonstration of an HMO-utilization system by Bacteroides species isolated from infants opens the way to further characterization of additional such systems, to better understand HMO-utilization in the infant gut.
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Affiliation(s)
- Sivan Kijner
- Microbiology & Molecular Genetics Department, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Dena Ennis
- Microbiology & Molecular Genetics Department, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shimrit Shmorak
- Microbiology & Molecular Genetics Department, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Anat Florentin
- Microbiology & Molecular Genetics Department, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
- The Kuvin Center for the Study of Infectious and Tropical Diseases, Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Moran Yassour
- Microbiology & Molecular Genetics Department, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel.
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17
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Reens AL, Cosetta CM, Saur R, Trofimuk O, Brooker SL, Lee ML, Sun AK, McKenzie GJ, Button JE. Tunable control of B. infantis abundance and gut metabolites by co-administration of human milk oligosaccharides. Gut Microbes 2024; 16:2304160. [PMID: 38235736 PMCID: PMC10798361 DOI: 10.1080/19490976.2024.2304160] [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: 09/19/2023] [Accepted: 01/08/2024] [Indexed: 01/19/2024] Open
Abstract
Precision engineering of the gut microbiome holds promise as an effective therapeutic approach for diseases associated with a disruption in this microbial community. Engrafting a live biotherapeutic product (LBP) in a predictable, controllable manner is key to the consistent success of this approach and has remained a challenge for most LBPs under development. We recently demonstrated high-level engraftment of Bifidobacterium longum subsp. infantis (B. infantis) in adults when co-dosed with a specific prebiotic, human milk oligosaccharides (HMO). Here, we present a cellular kinetic-pharmacodynamic approach, analogous to pharmacokinetic-pharmacodynamic-based analyses of small molecule- and biologic-based drugs, to establish how HMO controls expansion, abundance, and metabolic output of B. infantis in a human microbiota-based model in gnotobiotic mice. Our data demonstrate that the HMO dose controls steady-state abundance of B. infantis in the microbiome, and that B. infantis together with HMO impacts gut metabolite levels in a targeted, HMO-dependent manner. We also found that HMO creates a privileged niche for B. infantis expansion across a 5-log range of bacterial inocula. These results demonstrate remarkable control of both B. infantis levels and the microbiome community metabolic outputs using this synbiotic approach, and pave the way for precision engineering of desirable microbes and metabolites to treat a range of diseases.
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Affiliation(s)
| | | | | | | | | | - Martin L. Lee
- Prolacta Bioscience, Duarte, CA, USA
- Department of Biostatistics, University of California Los Angeles Fielding School of Public Health, Los AngelesCA, USA
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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.
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Affiliation(s)
| | - Daniel Garrido
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Catolica de Chile, Santiago 7820436, Chile
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19
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Luo K, Chen GC, Zhang Y, Moon JY, Xing J, Peters BA, Usyk M, Wang Z, Hu G, Li J, Selvin E, Rebholz CM, Wang T, Isasi CR, Yu B, Knight R, Boerwinkle E, Burk RD, Kaplan RC, Qi Q. Variant of the lactase LCT gene explains association between milk intake and incident type 2 diabetes. Nat Metab 2024; 6:169-186. [PMID: 38253929 PMCID: PMC11097298 DOI: 10.1038/s42255-023-00961-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 12/04/2023] [Indexed: 01/24/2024]
Abstract
Cow's milk is frequently included in the human diet, but the relationship between milk intake and type 2 diabetes (T2D) remains controversial. Here, using data from the Hispanic Community Health Study/Study of Latinos, we show that in both sexes, higher milk intake is associated with lower risk of T2D in lactase non-persistent (LNP) individuals (determined by a variant of the lactase LCT gene, single nucleotide polymorphism rs4988235 ) but not in lactase persistent individuals. We validate this finding in the UK Biobank. Further analyses reveal that among LNP individuals, higher milk intake is associated with alterations in gut microbiota (for example, enriched Bifidobacterium and reduced Prevotella) and circulating metabolites (for example, increased indolepropionate and reduced branched-chain amino acid metabolites). Many of these metabolites are related to the identified milk-associated bacteria and partially mediate the association between milk intake and T2D in LNP individuals. Our study demonstrates a protective association between milk intake and T2D among LNP individuals and a potential involvement of gut microbiota and blood metabolites in this association.
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Affiliation(s)
- Kai Luo
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Guo-Chong Chen
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Nutrition and Food Hygiene, MOE Key Laboratory of Geriatric Diseases and Immunology, School of Public Health, Suzhou Medical College of Soochow University, Suzhou, China
| | - Yanbo Zhang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jee-Young Moon
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jiaqian Xing
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Brandilyn A Peters
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Mykhaylo Usyk
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Zheng Wang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Gang Hu
- Chronic Disease Epidemiology Laboratory, Pennington Biomedical Research Center, Baton Rouge, LA, USA
| | - Jun Li
- Division of Preventive Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Elizabeth Selvin
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Casey M Rebholz
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Tao Wang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Carmen R Isasi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Bing Yu
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Rob Knight
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Eric Boerwinkle
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Robert D Burk
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Obstetrics and Gynecology and Women's Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Robert C Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Qibin Qi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA.
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
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20
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Monaco MH, Wang M, Hauser J, Yan J, Dilger RN, Donovan SM. Formula supplementation with human and bovine milk oligosaccharides modulates blood IgG and T-helper cell populations, and ex vivo LPS-stimulated cytokine production in a neonatal preclinical model. Front Immunol 2023; 14:1327853. [PMID: 38179055 PMCID: PMC10765566 DOI: 10.3389/fimmu.2023.1327853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 12/06/2023] [Indexed: 01/06/2024] Open
Abstract
Introduction Human milk contains structurally diverse oligosaccharides (HMO), which are multifunctional modulators of neonatal immune development. Our objective was to investigate formula supplemented with fucosylated (2'FL) + neutral (lacto-N-neotetraose, LNnt) oligosaccharides and/or sialylated bovine milk oligosaccharides (BMOS) on immunological outcomes. Methods Pigs (n=46) were randomized at 48h of age to four diets: sow milk replacer formula (CON), BMOS (CON + 6.5 g/L BMOS), HMO (CON + 1.0 g/L 2'FL + 0.5 g/L LNnT), or BMOS+HMO (CON + 6.5 g/L BMOS + 1.0 g/L 2'FL + 0.5 g/L LNnT). Blood and tissues were collected on postnatal day 33 for measurement of cytokines and IgG, phenotypic identification of immune cells, and ex vivo lipopolysaccharide (LPS)-stimulation of immune cells. Results Serum IgG was significantly lower in the HMO group than BMOS+HMO but did not differ from CON or BMOS. The percentage of PBMC T-helper cells was lower in BMOS+HMO than the other groups. Splenocytes from the BMOS group secreted more IL-1β when stimulated ex vivo with LPS compared to CON or HMO groups. For PBMCs, a statistical interaction of BMOS*HMO was observed for IL-10 secretion (p=0.037), with BMOS+HMO and HMO groups differing at p=0.1. Discussion The addition of a mix of fucosylated and sialylated oligosaccharides to infant formula provides specific activities in the immune system that differ from formulations supplemented with one oligosaccharide structure.
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Affiliation(s)
- Marcia H. Monaco
- Department of Food Science and Human Nutrition, University of Illinois at Urbana Champaign, Urbana, IL, United States
| | - Mei Wang
- Department of Food Science and Human Nutrition, University of Illinois at Urbana Champaign, Urbana, IL, United States
| | - Jonas Hauser
- Brain Health Department, Nestlé Institute of Health Sciences, Société des Produits Nestlé SA, Lausanne, Switzerland
| | - Jian Yan
- Nestlé Product Technology Center Nutrition, Vevey, Switzerland
| | - Ryan N. Dilger
- Department of Animal Sciences, University of Illinois at Urbana Champaign, Urbana, IL, United States
| | - Sharon M. Donovan
- Department of Food Science and Human Nutrition, University of Illinois at Urbana Champaign, Urbana, IL, United States
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21
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Low KE, Tingley JP, Klassen L, King ML, Xing X, Watt C, Hoover SER, Gorzelak M, Abbott DW. Carbohydrate flow through agricultural ecosystems: Implications for synthesis and microbial conversion of carbohydrates. Biotechnol Adv 2023; 69:108245. [PMID: 37652144 DOI: 10.1016/j.biotechadv.2023.108245] [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: 08/04/2022] [Revised: 08/10/2023] [Accepted: 08/25/2023] [Indexed: 09/02/2023]
Abstract
Carbohydrates are chemically and structurally diverse biomolecules, serving numerous and varied roles in agricultural ecosystems. Crops and horticulture products are inherent sources of carbohydrates that are consumed by humans and non-human animals alike; however carbohydrates are also present in other agricultural materials, such as soil and compost, human and animal tissues, milk and dairy products, and honey. The biosynthesis, modification, and flow of carbohydrates within and between agricultural ecosystems is intimately related with microbial communities that colonize and thrive within these environments. Recent advances in -omics techniques have ushered in a new era for microbial ecology by illuminating the functional potential for carbohydrate metabolism encoded within microbial genomes, while agricultural glycomics is providing fresh perspective on carbohydrate-microbe interactions and how they influence the flow of functionalized carbon. Indeed, carbohydrates and carbohydrate-active enzymes are interventions with unrealized potential for improving carbon sequestration, soil fertility and stability, developing alternatives to antimicrobials, and circular production systems. In this manner, glycomics represents a new frontier for carbohydrate-based biotechnological solutions for agricultural systems facing escalating challenges, such as the changing climate.
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Affiliation(s)
- Kristin E Low
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Jeffrey P Tingley
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Leeann Klassen
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Marissa L King
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Xiaohui Xing
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Caitlin Watt
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Shelley E R Hoover
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada
| | - Monika Gorzelak
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - D Wade Abbott
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada.
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22
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Zhao L, Sui M, Zhang T, Zhang K. The interaction between ginseng and gut microbiota. Front Nutr 2023; 10:1301468. [PMID: 38045813 PMCID: PMC10690783 DOI: 10.3389/fnut.2023.1301468] [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: 09/25/2023] [Accepted: 11/02/2023] [Indexed: 12/05/2023] Open
Abstract
The importance of the gut microbiota to human health is attracting increasing attention. It is also involved in ginseng metabolism, mediating the bioactive metabolites of ginsenosides. In response, ginseng, known as the king of herbs, can regulate intestinal flora, including promoting probiotics and restricting the growth of harmful bacteria. Specifically, the interactions between ginseng or ginsenosides and gastrointestinal microbiota are complex. In this review, we summarized the effects of ginseng and ginsenosides on the composition of gut microbiota and discussed the gut microbiota-mediated biotransformation of ginsenosides. In particular, their therapeutic potential and clinical application in related diseases were also summarized.
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Affiliation(s)
| | | | | | - Kai Zhang
- Department of General Surgery, The Second Hospital of Jilin University, Changchun, China
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23
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Zhang M, Zhang K, Liu T, Wang L, Wu M, Gao S, Cai B, Zhang F, Su L, Wu J. High-Level Production of Lacto- N-neotetraose in Escherichia coli by Stepwise Optimization of the Biosynthetic Pathway. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:16212-16220. [PMID: 37851455 DOI: 10.1021/acs.jafc.3c04856] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2023]
Abstract
Lacto-N-neotetraose (LNnT), an abundant human milk oligosaccharide (HMO), has been approved as a novel functional additive for infant formulas. Therefore, LNnT biosynthesis has attracted extensive attention. Here, a high LNnT-producing, low lacto-N-triose II (LNT II)-residue Escherichia coli strain was constructed. First, an initial LNnT-producing chassis strain was constructed by blocking lactose, UDP-N-acetylglucosamine, and UDP-galactose competitive consumption pathways and introducing β-1,3-N-acetylglucosaminyltransferase LgtA and β-1,4-galactosyltransferase LgtB. Subsequently, the supply of LNnT precursors was increased by enhancing UDP-N-acetylglucosamine and UDP-galactose synthesis, inactivating LNT II extracellular transporter SetA, and improving UTP synthesis. Then, modular engineering strategy was used to optimize LNnT biosynthetic pathway fluxes. Moreover, pathway fluxes were fine-tuned by modulating translation initiation strength of essential genes lgtB, prs, and lacY. Finally, LNnT production reached 6.70 g/L in a shake flask and 19.40 g/L in a 3 L bioreactor with 0.47 g/(L h) productivity, with 1.79 g/L LNT II residue, highest productivity level, and lowest LNT II residue thus far.
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Affiliation(s)
- Mengwei Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Kang Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Tongle Liu
- State Key Laboratory of Food Science and Resources, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Luyao Wang
- State Key Laboratory of Food Science and Resources, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Mengping Wu
- State Key Laboratory of Food Science and Resources, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Shengqi Gao
- State Key Laboratory of Food Science and Resources, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Bohan Cai
- State Key Laboratory of Food Science and Resources, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Fengshan Zhang
- Shandong Huatai Paper Co., Ltd. and Shandong Yellow Triangle Biotechnology Industry Research Institute Co. LTD, Dongying 257335, China
| | - Lingqia Su
- State Key Laboratory of Food Science and Resources, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Jing Wu
- State Key Laboratory of Food Science and Resources, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
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24
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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: 3] [Impact Index Per Article: 3.0] [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.
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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
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25
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Liu B, Garza DR, Gonze D, Krzynowek A, Simoens K, Bernaerts K, Geirnaert A, Faust K. Starvation responses impact interaction dynamics of human gut bacteria Bacteroides thetaiotaomicron and Roseburia intestinalis. THE ISME JOURNAL 2023; 17:1940-1952. [PMID: 37670028 PMCID: PMC10579405 DOI: 10.1038/s41396-023-01501-1] [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: 03/16/2023] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 09/07/2023]
Abstract
Bacterial growth often alters the environment, which in turn can impact interspecies interactions among bacteria. Here, we used an in vitro batch system containing mucin beads to emulate the dynamic host environment and to study its impact on the interactions between two abundant and prevalent human gut bacteria, the primary fermenter Bacteroides thetaiotaomicron and the butyrate producer Roseburia intestinalis. By combining machine learning and flow cytometry, we found that the number of viable B. thetaiotaomicron cells decreases with glucose consumption due to acid production, while R. intestinalis survives post-glucose depletion by entering a slow growth mode. Both species attach to mucin beads, but only viable cell counts of B. thetaiotaomicron increase significantly. The number of viable co-culture cells varies significantly over time compared to those of monocultures. A combination of targeted metabolomics and RNA-seq showed that the slow growth mode of R. intestinalis represents a diauxic shift towards acetate and lactate consumption, whereas B. thetaiotaomicron survives glucose depletion and low pH by foraging on mucin sugars. In addition, most of the mucin monosaccharides we tested inhibited the growth of R. intestinalis but not B. thetaiotaomicron. We encoded these causal relationships in a kinetic model, which reproduced the observed dynamics. In summary, we explored how R. intestinalis and B. thetaiotaomicron respond to nutrient scarcity and how this affects their dynamics. We highlight the importance of understanding bacterial metabolic strategies to effectively modulate microbial dynamics in changing conditions.
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Affiliation(s)
- Bin Liu
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, B-3000, Leuven, Belgium
| | - Daniel Rios Garza
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, B-3000, Leuven, Belgium
| | - Didier Gonze
- Unité de Chronobiologie Théorique, Faculté des Sciences, CP 231, Université Libre de Bruxelles, Bvd du Triomphe, B-1050, Bruxelles, Belgium
| | - Anna Krzynowek
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, B-3000, Leuven, Belgium
| | - Kenneth Simoens
- Department of Chemical Engineering, Chemical and Biochemical Reactor Engineering and Safety (CREaS), KU Leuven, B-3001, Leuven, Belgium
| | - Kristel Bernaerts
- Department of Chemical Engineering, Chemical and Biochemical Reactor Engineering and Safety (CREaS), KU Leuven, B-3001, Leuven, Belgium
| | - Annelies Geirnaert
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zürich, CH-8092, Zürich, Switzerland
| | - Karoline Faust
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, B-3000, Leuven, Belgium.
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26
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Nishida AH, Ochman H. Origins and Evolution of Novel Bacteroides in Captive Apes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.20.563286. [PMID: 37961372 PMCID: PMC10634691 DOI: 10.1101/2023.10.20.563286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Bacterial strains evolve in response to the gut environment of their hosts, with genomic changes that influence their interactions with hosts as well as with other members of the gut community. Great apes in captivity have acquired strains of Bacteroides xylanisolvens, which are common within gut microbiome of humans but not typically found other apes, thereby enabling characterization of strain evolution following colonization. Here, we isolate, sequence and reconstruct the history of gene gain and loss events in numerous captive-ape-associated strains since their divergence from their closest human-associated strains. We show that multiple captive-ape-associated B. xylanisolvens lineages have independently acquired gene complexes that encode functions related to host mucin metabolism. Our results support the finding of high genome fluidity in Bacteroides, in that several strains, in moving from humans to captive apes, have rapidly gained large genomic regions that augment metabolic properties not previously present in their relatives.
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Affiliation(s)
- Alexandra H. Nishida
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712 USA
| | - Howard Ochman
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712 USA
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27
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Padilla L, Fricker AD, Luna E, Choudhury B, Hughes ER, Panzetta ME, Valdivia RH, Flores GE. Mechanism of 2'-Fucosyllactose degradation by Human-Associated Akkermansia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.17.562767. [PMID: 37904935 PMCID: PMC10614881 DOI: 10.1101/2023.10.17.562767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
Among the first microorganisms to colonize the human gut of breastfed infants are bacteria capable of fermenting human milk oligosaccharides (HMOs). One of the most abundant HMOs, 2'-fucosyllactose (2'-FL), may specifically drive bacterial colonization of the intestine. Recently, differential growth has been observed across multiple species of Akkermansia on various HMOs including 2'FL. In culture, we found growth of two species, A. muciniphila Muc T and A. biwaensis CSUN-19, in HMOS corresponded to a decrease in the levels of 2'-FL and an increase in lactose, indicating that the first step in 2'-FL catabolism is the cleavage of fucose. Using phylogenetic analysis and transcriptional profiling, we found that the number and expression of fucosidase genes from two glycoside hydrolase (GH) families, GH29 and GH95, varies between these two species. During mid-log phase growth, the expression of several GH29 genes was increased by 2'-FL in both species, whereas the GH95 genes were induced only in A. muciniphila . We further show that one putative fucosidase and a β-galactosidase from A. biwaensis are involved in the breakdown of 2'-FL. Our findings indicate that that plasticity of GHs of human associated Akkermansia sp. enable access to additional growth substrates present in HMOs, including 2'-FL. Our work highlights the potential for Akkermansia to influence the development of the gut microbiota early in life and expands the known metabolic capabilities of this important human symbiont. IMPORTANCE Akkermansia are mucin degrading specialists widely distributed in the human population. Akkermansia biwaensis has recently been observed to have enhanced growth relative to other human associated Akkermansia on multiple human milk oligosaccharides (HMOs). However, the mechanisms for enhanced growth are not understood. Here, we characterized the phylogenetic diversity and function of select genes involved in growth of A. biwaensis on 2'-fucosyllactose (2'-FL), a dominant HMO. Specifically, we demonstrate that two genes in a genomic locus, a putative β-galactosidase and α-fucosidase, are likely responsible for the enhanced growth on 2'-FL. The functional characterization of A. biwaensis growth on 2'-FL delineates the significance of a single genomic locus that may facilitate enhanced colonization and functional activity of select Akkermansia early in life.
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28
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Guo R, Zhang W, Shen W, Zhang G, Xie T, Li L, Jinmei J, Liu Y, Kong F, Guo B, Li B, Sun Y, Liu S. Analysis of gut microbiota in chinese donkey in different regions using metagenomic sequencing. BMC Genomics 2023; 24:524. [PMID: 37670231 PMCID: PMC10478257 DOI: 10.1186/s12864-023-09575-z] [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] [Accepted: 08/11/2023] [Indexed: 09/07/2023] Open
Abstract
BACKGROUND Gut microbiota plays a significant role in host survival, health, and diseases; however, compared to other livestock, research on the gut microbiome of donkeys is limited. RESULTS In this study, a total of 30 donkey samples of rectal contents from six regions, including Shigatse, Changdu, Yunnan, Xinjiang, Qinghai, and Dezhou, were collected for metagenomic sequencing. The results of the species annotation revealed that the dominant phyla were Firmicutes and Bacteroidetes, and the dominant genera were Bacteroides, unclassified_o_Clostridiales (short for Clostridiales) and unclassified_f_Lachnospiraceae (short for Lachnospiraceae). The dominant phyla, genera and key discriminators were Bacteroidetes, Clostridiales and Bacteroidetes in Tibet donkeys (Shigatse); Firmicutes, Clostridiales and Clostridiales in Tibet donkeys (Changdu); Firmicutes, Fibrobacter and Tenericutes in Qinghai donkeys; Firmicutes, Clostridiales and Negativicutes in Yunnan donkeys; Firmicutes, Fibrobacter and Fibrobacteres in Xinjiang donkeys; Firmicutes, Clostridiales and Firmicutes in Dezhou donkeys. In the functional annotation, it was mainly enriched in the glycolysis and gluconeogenesis of carbohydrate metabolism, and the abundance was the highest in Dezhou donkeys. These results combined with altitude correlation analysis demonstrated that donkeys in the Dezhou region exhibited strong glucose-conversion ability, those in the Shigatse region exhibited strong glucose metabolism and utilization ability, those in the Changdu region exhibited a strong microbial metabolic function, and those in the Xinjiang region exhibited the strongest ability to decompose cellulose and hemicellulose. CONCLUSION According to published literature, this is the first study to construct a dataset with multi-regional donkey breeds. Our study revealed the differences in the composition and function of gut microbes in donkeys from different geographic regions and environmental settings and is valuable for donkey gut microbiome research.
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Affiliation(s)
- Rong Guo
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Wei Zhang
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, Shandong, 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
| | - Taifeng Xie
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Ling Li
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Jiacuo Jinmei
- Tibet Autonomous Region Animal husbandry Station, Tibet, China
| | - Yiduan Liu
- Yunnan Provincial Animal Husbandry Station, Yunnan, China
| | - Fanyong Kong
- Honghe state animal husbandry technology extension station, Honghe, Yunnan, China
| | - Baozhu Guo
- Zhangjiakou City animal husbandry technology extension station, Zhangjiakou, Hebei, China
| | - Benke Li
- Binzhou City Agricultural Technology Extension Center, Binzhou, 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.
| | - Shuqin Liu
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, Shandong, China.
- Gene Bank of Equine Genetic Resources, Qingdao, Shandong, China.
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Wang X, Pei J, Hao D, Zhang Y, Liao Y, Wang Q, Fan J, Huang L, Wang Z. Online PGC-LC-ESI-MS/MS comparative analysis of variations in human milk O-glycopatterns from different secretor status. Carbohydr Polym 2023; 315:121004. [PMID: 37230641 DOI: 10.1016/j.carbpol.2023.121004] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/22/2023] [Accepted: 05/08/2023] [Indexed: 05/27/2023]
Abstract
O-glycome is one of the important components of glycoconjugates in human milk which is speculated to provide protective features similar to those observed in free oligosaccharides. The effects of maternal secretor status on free oligosaccharides and N-glycome in milk have been well researched and documented. Currently, milk O-glycome of secretors (Se+) and nonsecretors (Se-) was investigated through reductive β-elimination combined with porous graphitized carbon-liquid chromatography-electrospray ionization-tandem mass spectrometry. A total of 70 presumptive O-glycan structures were identified, of which 25 O-glycans (including 14 sulfated O-glycans) were reported for the first time. Notably, 23 O-glycans exhibited significant differences between Se+ and Se- samples (p < 0.05). Compared to Se- group, the O-glycans of the Se+ group was two times more abundant in the total glycosylation, sialylation, fucosylation, and sulfation (p < 0.01). In conclusion, approximately one-third of the milk O-glycosylation was influenced by maternal FUT2-related secretor status. Our data will lay a foundation for the study of O-glycans structure-function relationship.
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Affiliation(s)
- Xiaoqin Wang
- Shaanxi Natural Carbohydrate Resource Engineering Research Center, College of Food Science and Technology, Northwest University, Xi'an 710069, China
| | - Jiahuan Pei
- Shaanxi Natural Carbohydrate Resource Engineering Research Center, College of Food Science and Technology, Northwest University, Xi'an 710069, China
| | - Daokuan Hao
- Shaanxi Natural Carbohydrate Resource Engineering Research Center, College of Food Science and Technology, Northwest University, Xi'an 710069, China
| | - Yuyang Zhang
- Shaanxi Natural Carbohydrate Resource Engineering Research Center, College of Food Science and Technology, Northwest University, Xi'an 710069, China
| | - Yujie Liao
- Shaanxi Natural Carbohydrate Resource Engineering Research Center, College of Food Science and Technology, Northwest University, Xi'an 710069, China
| | - Qingling Wang
- Shaanxi Natural Carbohydrate Resource Engineering Research Center, College of Food Science and Technology, Northwest University, Xi'an 710069, China
| | - Jiangbo Fan
- The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710004, China
| | - Linjuan Huang
- Shaanxi Natural Carbohydrate Resource Engineering Research Center, College of Food Science and Technology, Northwest University, Xi'an 710069, China.
| | - Zhongfu Wang
- Shaanxi Natural Carbohydrate Resource Engineering Research Center, College of Food Science and Technology, Northwest University, Xi'an 710069, China.
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Chen L, Qin Y, Ma L, Meng D, You C. Biosynthesis of Lacto-N-biose I from starch and N-acetylglucosamine via an in vitro synthetic enzymatic biosystem. Synth Syst Biotechnol 2023; 8:555-562. [PMID: 37663063 PMCID: PMC10468323 DOI: 10.1016/j.synbio.2023.08.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 08/07/2023] [Accepted: 08/16/2023] [Indexed: 09/05/2023] Open
Abstract
Human milk oligosaccharides (HMOs) are very distinctive components in human milk and are beneficial for infant health. Lacto-N-biose I (LNB) is the core structural unit of HMOs, which could be used for the synthesis of other HMOs. In this study, an ATP-free in vitro synthetic enzymatic biosystem contained four thermostable enzymes (alpha-glucan phosphorylase from Thermococcus kodakarensis, UDP-glucose-hexose-1-phosphate uridylyltransferase from Thermotoga maritima, UDP-glucose 4-epimerase from T. maritima, lacto-N-biose phosphorylase from Clostridium thermobutyricum) were constructed for the biosynthesis of LNB from starch and N-acetylglucosamine (GlcNAc). Under the optimal conditions, 0.75 g/L and 2.23 g/L LNB was produced from 1.1 g/L and 4.4 g/L GlcNAc and excess starch, with the molar yield of 39% and 29% based on the GlcNAc concentration, respectively, confirming the feasibility of this in vitro synthetic enzymatic biosystem for LNB synthesis and shedding light on the biosynthesis of other HMOs using LNB as the core structural unit from low cost polysaccharides.
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Affiliation(s)
- Lijie Chen
- College of Bioengineering, Tianjin University of Science and Technology, Tianjin, 300457, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Yanmei Qin
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Long Ma
- College of Bioengineering, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Dongdong Meng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Chun You
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
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Liu G, Sun H, Liu C, Bai L, Yang L, Jiang W, Gao S. Impact of different dietary fibre sources on production performance, bacterial composition and metabolites in the caecal contents of rabbits. J Anim Physiol Anim Nutr (Berl) 2023; 107:1279-1293. [PMID: 37070489 DOI: 10.1111/jpn.13823] [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: 06/25/2022] [Revised: 12/10/2022] [Accepted: 04/01/2023] [Indexed: 04/19/2023]
Abstract
This study was conducted to investigate the effects of different dietary fibre sources on growth performance, gastrointestinal tract development, caecal fermentation and bacterial composition in the caecal contents of rabbits. A total of 120 35-day-old weaned Minxinan black rabbits were divided into three groups and fed a diet composed of peanut straw powder (Group A), alfalfa powder (Group B) and soybean straw powder (Group C) as the main fibre source. The final body weight and average daily gain in Group B were higher than those in Group C, and the average daily feed intake and feed conversion ratio in Group A were lower than those in Group C (p < 0.05). The relative weights of the stomach, small intestine and caecum of rabbits in Group C were higher than those in Groups of B and A, and the relative weights of the caecal contents in Group C were lower than those in Groups A or B (p < 0.05). The pH value and propionic acid, butyric acid and valeric acid concentrations in the caecum of Group C were lower than those in the caecum of Groups A or B, and the concentration of acetic acid in the caecum was lower (p < 0.05). The dominant microbes in the caecal contents of Minxinan black rabbits were Firmicutes, Bacteroidetes and Proteobacteria at the phylum level, and the number of species, Chao1 index and ACE index measured was different between the B-C and A-C groups (p < 0.05). Different dietary fibre sources could affect the growth performance, gastrointestinal tract development and intestinal microbiota of rabbits, and the nutritional value of alfalfa powder was better than that of peanut straw and soybean straw.
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Affiliation(s)
- Gongyan Liu
- Shandong Key Laboratory of Animal Disease Control and Breeding, Key Laboratory of Livestock and Poultry Multiomics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Haitao Sun
- Shandong Key Laboratory of Animal Disease Control and Breeding, Key Laboratory of Livestock and Poultry Multiomics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Ce Liu
- Shandong Key Laboratory of Animal Disease Control and Breeding, Key Laboratory of Livestock and Poultry Multiomics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Liya Bai
- Shandong Key Laboratory of Animal Disease Control and Breeding, Key Laboratory of Livestock and Poultry Multiomics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Liping Yang
- Shandong Key Laboratory of Animal Disease Control and Breeding, Key Laboratory of Livestock and Poultry Multiomics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Wenxue Jiang
- Shandong Key Laboratory of Animal Disease Control and Breeding, Key Laboratory of Livestock and Poultry Multiomics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Shuxia Gao
- Shandong Key Laboratory of Animal Disease Control and Breeding, Key Laboratory of Livestock and Poultry Multiomics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
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Larke JA, Heiss BE, Ehrlich AM, Taft DH, Raybould HE, Mills DA, Slupsky CM. Milk oligosaccharide-driven persistence of Bifidobacterium pseudocatenulatum modulates local and systemic microbial metabolites upon synbiotic treatment in conventionally colonized mice. MICROBIOME 2023; 11:194. [PMID: 37635250 PMCID: PMC10463478 DOI: 10.1186/s40168-023-01624-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 07/14/2023] [Indexed: 08/29/2023]
Abstract
BACKGROUND Bifidobacteria represent an important gut commensal in humans, particularly during initial microbiome assembly in the first year of life. Enrichment of Bifidobacterium is mediated though the utilization of human milk oligosaccharides (HMOs), as several human-adapted species have dedicated genomic loci for transport and metabolism of these glycans. This results in the release of fermentation products into the gut lumen which may offer physiological benefits to the host. Synbiotic pairing of probiotic species with a cognate prebiotic delivers a competitive advantage, as the prebiotic provides a nutrient niche. METHODS To determine the fitness advantage and metabolic characteristics of an HMO-catabolizing Bifidobacterium strain in the presence or absence of 2'-fucosyllactose (2'-FL), conventionally colonized mice were gavaged with either Bifidobacterium pseudocatenulatum MP80 (B.p. MP80) (as the probiotic) or saline during the first 3 days of the experiment and received water or water containing 2'-FL (as the prebiotic) throughout the study. RESULTS 16S rRNA gene sequencing revealed that mice provided only B.p. MP80 were observed to have a similar microbiota composition as control mice throughout the experiment with a consistently low proportion of Bifidobacteriaceae present. Using 1H NMR spectroscopy, similar metabolic profiles of gut luminal contents and serum were observed between the control and B.p. MP80 group. Conversely, synbiotic supplemented mice exhibited dramatic shifts in their community structure across time with an overall increased, yet variable, proportion of Bifidobacteriaceae following oral inoculation. Parsing the synbiotic group into high and moderate bifidobacterial persistence based on the median proportion of Bifidobacteriaceae, significant differences in gut microbial diversity and metabolite profiles were observed. Notably, metabolites associated with the fermentation of 2'-FL by bifidobacteria were significantly greater in mice with a high proportion of Bifidobacteriaceae in the gut suggesting metabolite production scales with population density. Moreover, 1,2-propanediol, a fucose fermentation product, was only observed in the liver and brain of mice harboring high proportions of Bifidobacteriaceae. CONCLUSIONS This study reinforces that the colonization of the gut with a commensal microorganism does not guarantee a specific functional output. Video Abstract.
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Affiliation(s)
- Jules A Larke
- Department of Nutrition, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Britta E Heiss
- Department of Food Science and Technology, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Amy M Ehrlich
- Department of Anatomy, Physiology, and Cell Biology, School of Veterinary Medicine, University of California, Davis, , Davis, CA, USA
| | - Diana H Taft
- Department of Food Science and Technology, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Helen E Raybould
- Department of Anatomy, Physiology, and Cell Biology, School of Veterinary Medicine, University of California, Davis, , Davis, CA, USA
| | - David A Mills
- Department of Food Science and Technology, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA.
| | - Carolyn M Slupsky
- Department of Nutrition, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA.
- Department of Food Science and Technology, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA.
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Jochum F, Meyer-Krott M, Hübler T, Lorenz M, Bedikian R, Zakarian J, Litzka A, Judex G, Hertzberg H, Klee D, Maurer L, Schacht M, Al-Radhi A, Maier J, Kröckel A, Faustmann C, Lavalle L, Dahbane S. Real-world evidence study on tolerance and growth in infants fed an infant formula with two human milk oligosaccharides vs mixed fed and exclusively breastfed infants. Mol Cell Pediatr 2023; 10:7. [PMID: 37597076 PMCID: PMC10439867 DOI: 10.1186/s40348-023-00162-6] [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: 02/27/2023] [Accepted: 08/04/2023] [Indexed: 08/21/2023] Open
Abstract
INTRODUCTION Human milk oligosaccharides (HMOs) are important components of human milk having diverse functions in the development of infants. Randomized controlled trials (RCTs) have demonstrated that infant formulas with the HMOs 2'-fucosyllactose (2'FL) and lacto-N-neotetraose (LNnT) are safe, well-tolerated, and support normal growth. This study aimed to generate real-world evidence (RWE) on growth and gastrointestinal (GI) tolerance in infants consuming a formula with 1 g/L 2'FL and 0.5 g/L LNnT, including a mixed feeding group not studied before in RCTs. PARTICIPANTS AND METHODS This 8-week open-label prospective multicenter study was conducted in Germany and Austria, and included groups of healthy, exclusively breastfed infants (BF), exclusively formula-fed infants (FF) who received the HMO-formula, and infants mixed fed with both HMO formula and human milk (MF). Co-primary outcomes were anthropometry and gastrointestinal tolerance via validated Infant Gastrointestinal Symptom Questionnaire (IGSQ). Secondary outcomes included formula satisfaction and adverse events (AEs). RESULTS One-hundred six infants completed the study (46 FF, 22 MF, and 38 BF). Mean anthropometric z-scores were comparable between groups and generally within ± 0.5 of WHO medians at week 8. IGSQ composite scores demonstrated good GI tolerance in all groups with no significant group differences at week 4 or 8. IGSQ composite scores in FF improved during the course of the study and parents provided high satisfaction ratings for the HMO-formula. Four potentially product-related AEs were reported in FF (no in MF). CONCLUSIONS In this RWE study examining an infant formula with HMOs, growth and GI tolerance outcomes were confirming the good tolerance and safety of this early feeding option previously reported in RCTs.
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Grants
- NCT05150288 Société des Produits Nestlé S.A., Vevey, Switzerland
- NCT05150288 Société des Produits Nestlé S.A., Vevey, Switzerland
- NCT05150288 Société des Produits Nestlé S.A., Vevey, Switzerland
- NCT05150288 Société des Produits Nestlé S.A., Vevey, Switzerland
- NCT05150288 Société des Produits Nestlé S.A., Vevey, Switzerland
- NCT05150288 Société des Produits Nestlé S.A., Vevey, Switzerland
- NCT05150288 Société des Produits Nestlé S.A., Vevey, Switzerland
- NCT05150288 Société des Produits Nestlé S.A., Vevey, Switzerland
- NCT05150288 Société des Produits Nestlé S.A., Vevey, Switzerland
- NCT05150288 Société des Produits Nestlé S.A., Vevey, Switzerland
- NCT05150288 Société des Produits Nestlé S.A., Vevey, Switzerland
- NCT05150288 Société des Produits Nestlé S.A., Vevey, Switzerland
- NCT05150288 Société des Produits Nestlé S.A., Vevey, Switzerland
- NCT05150288 Société des Produits Nestlé S.A., Vevey, Switzerland
- NCT05150288 Société des Produits Nestlé S.A., Vevey, Switzerland
- NCT05150288 Société des Produits Nestlé S.A., Vevey, Switzerland
- NCT05150288 Société des Produits Nestlé S.A., Vevey, Switzerland
- NCT05150288 Société des Produits Nestlé S.A., Vevey, Switzerland
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Affiliation(s)
- Frank Jochum
- Klinik für Kinder- und Jugendmedizin, Ev. Waldkrankenhaus Spandau Stadtrandstr. 555, 13589, Berlin und Medizinische Hochschule Brandenburg - Theodor Fontane (MHB), 16816, Neuruppin, Germany.
| | | | - Tina Hübler
- Gemeinschaftspraxis Kinder- und Jugendarztpraxis, Clemensstraße 4, 47608, Geldern, Germany
| | - Maja Lorenz
- Kinder- und Jugendarzt, Venloer Straße 67, 41751, Viersen, Germany
| | - Raffi Bedikian
- Kinder- und Jugendärztliche Gemeinschaftspraxis, Eugen-Zur-Nieden-Ring 1, 46145, Oberhausen, Germany
| | - Joseph Zakarian
- Kinderarztpraxis, Suitbertusstr. 31, 40223, Düsseldorf, Germany
| | - Anja Litzka
- Facharztpraxis für Kinder- und Jugendmedizin, Regensburger Str. 40, 93133, Burglengenfeld, Germany
| | - Guido Judex
- Zentrum für Kinder- und Jugendgesundheit Regensburg, Dr.-Leo-Ritter-Str. 4, 93049, Regensburg, Germany
| | - Holger Hertzberg
- Kinder- und Jugendarztpraxis, Ludwigstraße 4, 91126, Schwabach, Germany
| | - Daniela Klee
- Kinder- und Jugendarzt, Röntgen-Str. 6, 68642, Bürstadt, Germany
| | - Lothar Maurer
- Fachärzte für Säuglings-, Kinder- und Jugendmedizin, Welschgasse 39, 67227, Frankenthal, Germany
| | - Martin Schacht
- Facharzt für Säuglings-, Kinder- und Jugendmedizin, Schwachhauser Heerstr. 63a, 28211, Bremen, Germany
| | - Adnan Al-Radhi
- Kinder- und Jugendarzt Al-Radhi, Winckelhoferstrasse 3, 89584, Ehingen, Germany
| | - Jan Maier
- Kinder und Jugendarztpraxis, Geranienstr. 11, 70771, Leinfelden-Echterdingen, Germany
| | - Alexander Kröckel
- Kinder- und Jugendarztpraxis, Schwarzwurzelstraße 52/54, 12689, Berlin, Germany
| | - Christian Faustmann
- Facharzt für Kinder- und Jugendheilkunde, Wiener Strasse 8a, 7400, Oberwart, Austria
| | - Luca Lavalle
- Nestlé Research, Société des Produits Nestlé S.A., Lausanne, Switzerland
| | - Samir Dahbane
- Global Medical Affairs, Société des Produits Nestlé S.A., Vevey, Switzerland
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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.
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Devi R, Sharma E, Thakur R, Lal P, Kumar A, Altaf MA, Singh B, Tiwari RK, Lal MK, Kumar R. Non-dairy prebiotics: Conceptual relevance with nutrigenomics and mechanistic understanding of the effects on human health. Food Res Int 2023; 170:112980. [PMID: 37316060 DOI: 10.1016/j.foodres.2023.112980] [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: 01/15/2023] [Revised: 05/08/2023] [Accepted: 05/13/2023] [Indexed: 06/16/2023]
Abstract
The increasing health awareness of consumers has made a shift towards vegan and non-dairy prebiotics counterparts. Non-dairy prebiotics when fortified with vegan products have interesting properties and widely found its applications in food industry. The chief vegan products that have prebiotics added include water-soluble plant-based extracts (fermented beverages, frozen desserts), cereals (bread, cookies), and fruits (juices & jelly, ready to eat fruits). The main prebiotic components utilized are inulin, oligofructose, polydextrose, fructooligosaccharides, and xylooligosaccharides. Prebiotics' formulations, type and food matrix affect food products, host health, and technological attributes. Prebiotics from non-dairy sources have a variety of physiological effects that help to prevent and treat chronic metabolic diseases. This review focuses on mechanistic insight on non-dairy prebiotics affecting human health, how nutrigenomics is related to prebiotics development, and role of gene-microbes' interactions. The review will provide industries and researchers with important information about prebiotics, mechanism of non-dairy prebiotics and microbe interaction as well as prebiotic based vegan products.
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Affiliation(s)
- Rajni Devi
- Department of Microbiology, Punjab Agricultural University, Ludhiana 141004, India
| | - Eshita Sharma
- Department of Molecular Biology and Biochemistry, Guru Nanak Dev University, Amritsar 143005, India
| | - Richa Thakur
- Division of Silviculture and Forest Management, Himalayan Forest Research Institute, Conifer Campus, Shimla, India
| | - Priyanka Lal
- Department of Agricultural Economics and Extension, School of Agriculture, Lovely Professional University, Jalandhar GT Road (NH1), Phagwara, India
| | - Awadhesh Kumar
- Division of Crop Physiology and Biochemistry, ICAR-National Rice Research Institute, Cuttack, India
| | | | - Brajesh Singh
- ICAR-Central Potato Research Institute, Shimla 171001, India
| | | | - Milan Kumar Lal
- ICAR-Central Potato Research Institute, Shimla 171001, India.
| | - Ravinder Kumar
- ICAR-Central Potato Research Institute, Shimla 171001, India.
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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.
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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
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Bozorgmehr T, Boutin RCT, Woodward SE, Donald K, Chow JM, Buck RH, Finlay BB. Early Life Exposure to Human Milk Oligosaccharides Reduces Allergic Response in a Murine Asthma Model. J Immunol Res 2023; 2023:9603576. [PMID: 37545544 PMCID: PMC10404156 DOI: 10.1155/2023/9603576] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 06/27/2023] [Accepted: 06/29/2023] [Indexed: 08/08/2023] Open
Abstract
Background Studies suggest that early-life gut microbiota composition and intestinal short-chain fatty acids (SCFAs) are linked to future asthma susceptibility. Furthermore, infancy offers a critical time window to modulate the microbiota and associated metabolites through diet-microbe interactions to promote infant health. Human milk oligosaccharides (HMOs), nondigestible carbohydrates abundant in breast milk, are prebiotics selectively metabolized by gut microbiota that consequently modify microbiome composition and SCFA production. Methods Using a house dust mite mouse model of allergy, we investigated the impacts of early oral treatment of pups with biologically relevant doses of 2'-fucosyllactose (2'-FL) and 6'-sialyllactose (6'-SL), two of the most abundant HMOs in human milk, in amelioration of allergic airway disease severity. Results We found that administration of 2'-FL and 6'-SL during early life reduced lung histopathology scores, circulating IgE, cytokine levels, and inflammatory cell infiltration, all hallmark symptoms of allergic asthma. HMO supplementation also increased the relative abundance of intestinal Bacteroidetes and Clostridia, known SCFA producers within the gut. Indeed, we detected increased SCFA concentrations in both the intestine and blood of adult mice who received HMOs prior to weaning. Conclusion We propose a model in which orally administered HMOs delivered during early life shift the microbiota toward increased production of SCFAs, which dampens the allergic immune responses behind allergy and asthma. Overall, these data suggest the potential for HMO supplementation to protect infants against asthma development later in life, with possible benefits against additional atopic diseases such as eczema and food allergies.
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Affiliation(s)
- Tahereh Bozorgmehr
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Rozlyn C. T. Boutin
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Sarah E. Woodward
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Katherine Donald
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Jo May Chow
- Nutrition Division, Abbott Laboratories, Columbus, OH, USA
| | | | - B. Brett Finlay
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
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Luis AS, Hansson GC. Intestinal mucus and their glycans: A habitat for thriving microbiota. Cell Host Microbe 2023; 31:1087-1100. [PMID: 37442097 PMCID: PMC10348403 DOI: 10.1016/j.chom.2023.05.026] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/07/2023] [Accepted: 05/23/2023] [Indexed: 07/15/2023]
Abstract
The colon mucus layer is organized with an inner colon mucus layer that is impenetrable to bacteria and an outer mucus layer that is expanded to allow microbiota colonization. A major component of mucus is MUC2, a glycoprotein that is extensively decorated, especially with O-glycans. In the intestine, goblet cells are specialized in controlling glycosylation and making mucus. Some microbiota members are known to encode multiple proteins that are predicted to bind and/or cleave mucin glycans. The interactions between commensal microbiota and host mucins drive intestinal colonization, while at the same time, the microbiota can utilize the glycans on mucins and affect the colonic mucus properties. This review will examine this interaction between commensal microbes and intestinal mucins and discuss how this interplay affects health and disease.
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Affiliation(s)
- Ana S Luis
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Gunnar C Hansson
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 405 30 Gothenburg, Sweden.
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Holst AQ, Myers P, Rodríguez-García P, Hermes GDA, Melsaether C, Baker A, Jensen SR, Parschat K. Infant Formula Supplemented with Five Human Milk Oligosaccharides Shifts the Fecal Microbiome of Formula-Fed Infants Closer to That of Breastfed Infants. Nutrients 2023; 15:3087. [PMID: 37513505 PMCID: PMC10383262 DOI: 10.3390/nu15143087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 06/30/2023] [Accepted: 07/05/2023] [Indexed: 07/30/2023] Open
Abstract
Breastmilk is the optimal source of infant nutrition, with short-term and long-term health benefits. Some of these benefits are mediated by human milk oligosaccharides (HMOs), a unique group of carbohydrates representing the third most abundant solid component of human milk. We performed the first clinical study on infant formula supplemented with five different HMOs (5HMO-mix), comprising 2'-fucosyllactose, 3-fucosyllactose, lacto-N-tetraose, 3'-sialyllactose and 6'-sialyllactose at a natural total concentration of 5.75 g/L, and here report the analysis of the infant fecal microbiome. We found an increase in the relative abundance of bifidobacteria in the 5HMO-mix cohort compared with the formula-fed control, specifically affecting bifidobacteria that can produce aromatic lactic acids. 5HMO-mix influenced the microbial composition as early as Week 1, and the observed changes persisted to at least Week 16, including a relative decrease in species with opportunistic pathogenic strains down to the level observed in breastfed infants during the first 4 weeks. We further analyzed the functional potential of the microbiome and observed features shared between 5HMO-mix-supplemented and breastfed infants, such as a relative enrichment in mucus and tyrosine degradation, with the latter possibly being linked to the aromatic lactic acids. The 5HMO-mix supplement, therefore, shifts the infant fecal microbiome closer to that of breastfed infants.
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Affiliation(s)
| | | | | | | | | | - Adam Baker
- Chr. Hansen A/S, 2970 Hoersholm, Denmark
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40
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Chen X, Shi Y. Determinants of microbial colonization in the premature gut. Mol Med 2023; 29:90. [PMID: 37407941 DOI: 10.1186/s10020-023-00689-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 06/20/2023] [Indexed: 07/07/2023] Open
Abstract
Abnormal microbial colonization in the gut at an early stage of life affects growth, development, and health, resulting in short- and long-term adverse effects. Microbial colonization patterns of preterm infants differ from those of full-term infants in that preterm babies and their mothers have more complicated prenatal and postnatal medical conditions. Maternal complications, antibiotic exposure, delivery mode, feeding type, and the use of probiotics may significantly shape the gut microbiota of preterm infants at an early stage of life; however, these influences subside with age. Although some factors and processes are difficult to intervene in or avoid, understanding the potential factors and determinants will help in developing timely strategies for a healthy gut microbiota in preterm infants. This review discusses potential determinants of gut microbial colonization in preterm infants and their underlying mechanisms.
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Affiliation(s)
- Xiaoyu Chen
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, 110000, China
| | - Yongyan Shi
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, 110000, China.
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41
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St-Pierre B, Perez Palencia JY, Samuel RS. Impact of Early Weaning on Development of the Swine Gut Microbiome. Microorganisms 2023; 11:1753. [PMID: 37512925 PMCID: PMC10385335 DOI: 10.3390/microorganisms11071753] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 06/29/2023] [Accepted: 07/03/2023] [Indexed: 07/30/2023] Open
Abstract
Considering that pigs are naturally weaned between 12 and 18 weeks of age, the common practice in the modern swine industry of weaning as early as between two and four weeks of age increases challenges during this transition period. Indeed, young pigs with an immature gut are suddenly separated from the sow, switched from milk to a diet consisting of only solid ingredients, and subjected to a new social hierarchy from mixing multiple litters. From the perspective of host gut development, weaning under these conditions causes a regression in histological structure as well as in digestive and barrier functions. While the gut is the main center of immunity in mature animals, the underdeveloped gut of early weaned pigs has yet to contribute to this function until seven weeks of age. The gut microbiota or microbiome, an essential contributor to the health and nutrition of their animal host, undergoes dramatic alterations during this transition, and this descriptive review aims to present a microbial ecology-based perspective on these events. Indeed, as gut microbial communities are dependent on cross-feeding relationships, the change in substrate availability triggers a cascade of succession events until a stable composition is reached. During this process, the gut microbiota is unstable and prone to dysbiosis, which can devolve into a diseased state. One potential strategy to accelerate maturation of the gut microbiome would be to identify microbial species that are critical to mature swine gut microbiomes, and develop strategies to facilitate their establishment in early post-weaning microbial communities.
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Affiliation(s)
- Benoit St-Pierre
- Department of Animal Science, South Dakota State University, Animal Science Complex, Box 2170, Brookings, SD 57007, USA
| | - Jorge Yair Perez Palencia
- Department of Animal Science, South Dakota State University, Animal Science Complex, Box 2170, Brookings, SD 57007, USA
| | - Ryan S Samuel
- Department of Animal Science, South Dakota State University, Animal Science Complex, Box 2170, Brookings, SD 57007, USA
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Muñoz-Provencio D, Yebra MJ. Gut Microbial Sialidases and Their Role in the Metabolism of Human Milk Sialylated Glycans. Int J Mol Sci 2023; 24:9994. [PMID: 37373145 DOI: 10.3390/ijms24129994] [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: 04/21/2023] [Revised: 05/26/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Sialic acids (SAs) are α-keto-acid sugars with a nine-carbon backbone present at the non-reducing end of human milk oligosaccharides and the glycan moiety of glycoconjugates. SAs displayed on cell surfaces participate in the regulation of many physiologically important cellular and molecular processes, including signaling and adhesion. Additionally, sialyl-oligosaccharides from human milk act as prebiotics in the colon by promoting the settling and proliferation of specific bacteria with SA metabolism capabilities. Sialidases are glycosyl hydrolases that release α-2,3-, α-2,6- and α-2,8-glycosidic linkages of terminal SA residues from oligosaccharides, glycoproteins and glycolipids. The research on sialidases has been traditionally focused on pathogenic microorganisms, where these enzymes are considered virulence factors. There is now a growing interest in sialidases from commensal and probiotic bacteria and their potential transglycosylation activity for the production of functional mimics of human milk oligosaccharides to complement infant formulas. This review provides an overview of exo-alpha-sialidases of bacteria present in the human gastrointestinal tract and some insights into their biological role and biotechnological applications.
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Affiliation(s)
- Diego Muñoz-Provencio
- Department of Food Biotechnology, Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC), Av. Agustín Escardino 7, 46980 Paterna, Spain
| | - María J Yebra
- Department of Food Biotechnology, Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC), Av. Agustín Escardino 7, 46980 Paterna, Spain
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Hou P, Li B, Wang Y, Li D, Huang X, Sun W, Liang X, Zhang E. The Effect of Dietary Supplementation with Zinc Amino Acids on Immunity, Antioxidant Capacity, and Gut Microbiota Composition in Calves. Animals (Basel) 2023; 13:ani13091570. [PMID: 37174607 PMCID: PMC10177098 DOI: 10.3390/ani13091570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/02/2023] [Accepted: 05/05/2023] [Indexed: 05/15/2023] Open
Abstract
The aim of this study was to investigate the effect of dietary supplementation with zinc (Zn) amino acids at different concentrations on immunity, antioxidant capacity, and gut microbiota composition in calves. Twenty-four one-month-old healthy Angus calves of comparable body weight were randomly divided into three groups (four males and four females in each group) based on the amount of Zn supplementation added to the feed the animals received: group A, 40 mg/kg DM; group B, 80 mg/kg DM; and group C, 120 mg/kg DM. The experiment ended when calves reached three months of age (weaning period). The increase in dietary Zn amino acid content promoted the growth of calves, and the average daily weight gain increased by 36.58% (p < 0.05) in group C compared with group A. With the increase in the content of dietary Zn amino acids, the indexes of serum immune functions initially increased and then decreased; in particular, the content of immunoglobulin M in group A and group B was higher than that in group C (p < 0.05), whereas the content of interleukin-2 in group B was higher than that in the other two groups (p < 0.05). In addition, the content of superoxide dismutase and total antioxidant capacity in the serum of calves in group B was higher than that in group C (p < 0.05), and the MDA level was lower than in group C (p < 0.05). Moreover, alpha diversity in the gut microbiota of calves in group B was higher than that in group A and group C (p < 0.05); the dominant phyla were Firmicutes and Bacteroidota, whereas the dominant genera were Unclassified-Lachnospiraceae and Ruminococcus. Linear discriminant analysis showed that the relative abundance of Bacteroides in the gut microbiota of calves in group B was higher than that in group A, and the relative abundance of Prevotellaceae-UCG-003 was higher compared to that in experimental group C. Thus, dietary supplementation of 80 mg/kg of Zn amino acids to calves could improve the immune function and antioxidant capacity, as well as enrich and regulate the equilibrium of gut microbiota, thus promoting the healthy growth of calves.
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Affiliation(s)
- Pengxia Hou
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China
| | - Bo Li
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China
| | - Yan Wang
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China
| | - Dan Li
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China
| | - Xiaoyu Huang
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China
| | - Wenyang Sun
- Ningxia Academy of Agriculture and Forestry Science, Institute of Animal, Yinchuan 750002, China
| | - Xiaojun Liang
- Ningxia Academy of Agriculture and Forestry Science, Institute of Animal, Yinchuan 750002, China
| | - Enping Zhang
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China
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44
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Lin X, Hu T, Chen J, Liang H, Zhou J, Wu Z, Ye C, Jin X, Xu X, Zhang W, Jing X, Yang T, Wang J, Yang H, Kristiansen K, Xiao L, Zou Y. The genomic landscape of reference genomes of cultivated human gut bacteria. Nat Commun 2023; 14:1663. [PMID: 36966151 PMCID: PMC10039858 DOI: 10.1038/s41467-023-37396-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 03/14/2023] [Indexed: 03/27/2023] Open
Abstract
Culture-independent metagenomic studies have revolutionized our understanding of the gut microbiota. However, the lack of full genomes from cultured species is still a limitation for in-depth studies of the gut microbiota. Here we present a substantially expanded version of our Cultivated Genome Reference (CGR), termed CGR2, providing 3324 high-quality draft genomes from isolates selected from a large-scale cultivation of bacterial isolates from fecal samples of healthy Chinese individuals. The CGR2 classifies 527 species (179 previously unidentified species) from 8 phyla, and uncovers a genomic and functional diversity of Collinsella aerofaciens. The CGR2 genomes match 126 metagenome-assembled genomes without cultured representatives in the Unified Human Gastrointestinal Genome (UHGG) collection and harbor 3767 unidentified secondary metabolite biosynthetic gene clusters, providing a source of natural compounds with pharmaceutical potentials. We uncover accurate phage-bacterium linkages providing information on the evolutionary characteristics of interaction between bacteriophages and bacteria at the strain level.
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Affiliation(s)
- Xiaoqian Lin
- BGI-Shenzhen, Shenzhen, 518083, China
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | | | - Jianwei Chen
- BGI-Shenzhen, Shenzhen, 518083, China
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, 266555, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken 13, 2100, Copenhagen, Denmark
| | | | - Jianwei Zhou
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, 266555, China
| | - Zhinan Wu
- BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chen Ye
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Xin Jin
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, 518083, China
| | | | - Xiaohuan Jing
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Tao Yang
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, 518083, China
- James D. Watson Institute of Genome Sciences, Hangzhou, 310058, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, 518083, China
- James D. Watson Institute of Genome Sciences, Hangzhou, 310058, China
| | - Karsten Kristiansen
- BGI-Shenzhen, Shenzhen, 518083, China.
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, 266555, China.
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken 13, 2100, Copenhagen, Denmark.
- PREDICT, Center for Molecular Prediction of Inflammatory Bowel Disease, Faculty of Medicine, Aalborg University, 2450, Copenhagen, Denmark.
| | - Liang Xiao
- BGI-Shenzhen, Shenzhen, 518083, China.
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, 266555, China.
- Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI-Shenzhen, Shenzhen, China.
| | - Yuanqiang Zou
- BGI-Shenzhen, Shenzhen, 518083, China.
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, 266555, China.
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken 13, 2100, Copenhagen, Denmark.
- Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI-Shenzhen, Shenzhen, China.
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45
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Rahman T, Sarwar PF, Potter C, Comstock SS, Klepac-Ceraj V. Role of human milk oligosaccharide metabolizing bacteria in the development of atopic dermatitis/eczema. Front Pediatr 2023; 11:1090048. [PMID: 37020647 PMCID: PMC10069630 DOI: 10.3389/fped.2023.1090048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 02/23/2023] [Indexed: 04/07/2023] Open
Abstract
Despite affecting up to 20% of infants in the United States, there is no cure for atopic dermatitis (AD), also known as eczema. Atopy usually manifests during the first six months of an infant's life and is one predictor of later allergic health problems. A diet of human milk may offer protection against developing atopic dermatitis. One milk component, human milk oligosaccharides (HMOs), plays an important role as a prebiotic in establishing the infant gut microbiome and has immunomodulatory effects on the infant immune system. The purpose of this review is to summarize the available information about bacterial members of the intestinal microbiota capable of metabolizing HMOs, the bacterial genes or metabolic products present in the intestinal tract during early life, and the relationship of these genes and metabolic products to the development of AD/eczema in infants. We find that specific HMO metabolism gene sets and the metabolites produced by HMO metabolizing bacteria may enable the protective role of human milk against the development of atopy because of interactions with the immune system. We also identify areas for additional research to further elucidate the relationship between the human milk metabolizing bacteria and atopy. Detailed metagenomic studies of the infant gut microbiota and its associated metabolomes are essential for characterizing the potential impact of human milk-feeding on the development of atopic dermatitis.
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Affiliation(s)
- Trisha Rahman
- Department of Biological Sciences, Wellesley College, Wellesley, MA, United States
| | - Prioty F. Sarwar
- Department of Biological Sciences, Wellesley College, Wellesley, MA, United States
| | - Cassie Potter
- Department of Biological Sciences, Wellesley College, Wellesley, MA, United States
| | - Sarah S. Comstock
- Department of Food Science & Human Nutrition, Michigan State University, East Lansing, MI, United States
| | - Vanja Klepac-Ceraj
- Department of Biological Sciences, Wellesley College, Wellesley, MA, United States
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Mohamad-Fauzi N, Shaw C, Foutouhi SH, Hess M, Kong N, Kol A, Storey DB, Desai PT, Shah J, Borjesson D, Murray JD, Weimer BC. Salmonella enhances osteogenic differentiation in adipose-derived mesenchymal stem cells. Front Cell Dev Biol 2023; 11:1077350. [PMID: 37009487 PMCID: PMC10055666 DOI: 10.3389/fcell.2023.1077350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 02/17/2023] [Indexed: 03/17/2023] Open
Abstract
The potential of mesenchymal stem cells (MSCs) for tissue repair and regeneration has garnered great attention. While MSCs are likely to interact with microbes at sites of tissue damage and inflammation, like in the gastrointestinal system, the consequences of pathogenic association on MSC activities have yet to be elucidated. This study investigated the effects of pathogenic interaction on MSC trilineage differentiation paths and mechanisms using model intracellular pathogen Salmonella enterica ssp enterica serotype Typhimurium. The examination of key markers of differentiation, apoptosis, and immunomodulation demonstrated that Salmonella altered osteogenic and chondrogenic differentiation pathways in human and goat adipose-derived MSCs. Anti-apoptotic and pro-proliferative responses were also significantly upregulated (p < 0.05) in MSCs during Salmonella challenge. These results together indicate that Salmonella, and potentially other pathogenic bacteria, can induce pathways that influence both apoptotic response and functional differentiation trajectories in MSCs, highlighting that microbes have a potentially significant role as influencers of MSC physiology and immune activity.
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Affiliation(s)
- Nuradilla Mohamad-Fauzi
- Department of Animal Science, College of Agricultural and Environmental Sciences, University of California, Davis, Davis, CA, United States
| | - Claire Shaw
- Department of Animal Science, College of Agricultural and Environmental Sciences, University of California, Davis, Davis, CA, United States
| | - Soraya H. Foutouhi
- Department of Population Health and Reproduction, 100K Pathogen Genome Project, Davis, CA, United States
| | - Matthias Hess
- Department of Animal Science, College of Agricultural and Environmental Sciences, University of California, Davis, Davis, CA, United States
| | - Nguyet Kong
- Department of Population Health and Reproduction, 100K Pathogen Genome Project, Davis, CA, United States
| | - Amir Kol
- Department of Pathology, Microbiology and Immunology, University of California, Davis, Davis, CA, United States
| | - Dylan Bobby Storey
- Department of Population Health and Reproduction, 100K Pathogen Genome Project, Davis, CA, United States
| | - Prerak T. Desai
- Department of Population Health and Reproduction, 100K Pathogen Genome Project, Davis, CA, United States
| | - Jigna Shah
- Department of Population Health and Reproduction, 100K Pathogen Genome Project, Davis, CA, United States
| | - Dori Borjesson
- Department of Pathology, Microbiology and Immunology, University of California, Davis, Davis, CA, United States
| | - James D. Murray
- Department of Animal Science, College of Agricultural and Environmental Sciences, University of California, Davis, Davis, CA, United States
- Department of Population Health and Reproduction, 100K Pathogen Genome Project, Davis, CA, United States
- *Correspondence: James D. Murray, ; Bart C. Weimer,
| | - Bart C. Weimer
- Department of Population Health and Reproduction, 100K Pathogen Genome Project, Davis, CA, United States
- *Correspondence: James D. Murray, ; Bart C. Weimer,
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Nuñez S, Barra M, Garrido D. Developing a Fluorescent Inducible System for Free Fucose Quantification in Escherichia coli. BIOSENSORS 2023; 13:bios13030388. [PMID: 36979599 PMCID: PMC10046853 DOI: 10.3390/bios13030388] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 03/10/2023] [Accepted: 03/13/2023] [Indexed: 05/28/2023]
Abstract
L-Fucose is a monosaccharide abundant in mammalian glycoconjugates. In humans, fucose can be found in human milk oligosaccharides (HMOs), mucins, and glycoproteins in the intestinal epithelium. The bacterial consumption of fucose and fucosylated HMOs is critical in the gut microbiome assembly of infants, dominated by Bifidobacterium. Fucose metabolism is important for the production of short-chain fatty acids and is involved in cross-feeding microbial interactions. Methods for assessing fucose concentrations in complex media are lacking. Here we designed and developed a molecular quantification method of free fucose using fluorescent Escherichia coli. For this, low- and high-copy plasmids were evaluated with and without the transcription factor fucR and its respective fucose-inducible promoter controlling the reporter gene sfGFP. E. coli BL21 transformed with a high copy plasmid containing pFuc and fucR displayed a high resolution across increasing fucose concentrations and high fluorescence/OD values after 18 h. The molecular circuit was specific against other monosaccharides and showed a linear response in the 0-45 mM range. Adjusting data to the Hill equation suggested non-cooperative, simple regulation of FucR to its promoter. Finally, the biosensor was tested on different concentrations of free fucose and the supernatant of Bifidobacterium bifidum JCM 1254 supplemented with 2-fucosyl lactose, indicating the applicability of the method in detecting free fucose. In conclusion, a bacterial biosensor of fucose was validated with good sensitivity and precision. A biological method for quantifying fucose could be useful for nutraceutical and microbiological applications, as well as molecular diagnostics.
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48
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O-Mucin-degrading carbohydrate-active enzymes and their possible implication in inflammatory bowel diseases. Essays Biochem 2023; 67:331-344. [PMID: 36912232 PMCID: PMC10154620 DOI: 10.1042/ebc20220153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 03/14/2023]
Abstract
Inflammatory bowel diseases (IBD) are modern diseases, with incidence rising around the world. They are associated with perturbation of the intestinal microbiota, and with alteration and crossing of the mucus barrier by the commensal bacteria that feed on it. In the process of mucus catabolism and invasion by gut bacteria, carbohydrate-active enzymes (CAZymes) play a critical role since mucus is mainly made up by O- and N-glycans. Moreover, the occurrence of IBD seems to be associated with low-fiber diets. Conversely, supplementation with oligosaccharides, such as human milk oligosaccharides (HMOs), which are structurally similar to intestinal mucins and could thus compete with them towards bacterial mucus-degrading CAZymes, has been suggested to prevent inflammation. In this mini-review, we will establish the current state of knowledge regarding the identification and characterization of mucus-degrading enzymes from both cultured and uncultured species of gut commensals and enteropathogens, with a particular focus on the present technological opportunities available to further the discovery of mucus-degrading CAZymes within the entire gut microbiome, by coupling microfluidics with metagenomics and culturomics. Finally, we will discuss the challenges to overcome to better assess how CAZymes targeting specific functional oligosaccharides could be involved in the modulation of the mucus-driven cross-talk between gut bacteria and their host in the context of IBD.
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49
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Pereira GV, Boudaud M, Wolter M, Alexander C, De Sciscio A, Grant ET, Trindade BC, Pudlo NA, Singh S, Campbell A, Shan M, Zhang L, Willieme S, Kim K, Denike-Duval T, Bleich A, Schmidt TM, Kennedy L, Lyssiotis CA, Chen GY, Eaton KA, Desai MS, Martens EC. Unravelling specific diet and gut microbial contributions to inflammatory bowel disease. RESEARCH SQUARE 2023:rs.3.rs-2518251. [PMID: 36993463 PMCID: PMC10055531 DOI: 10.21203/rs.3.rs-2518251/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Inflammatory bowel disease (IBD) is a chronic condition characterized by periods of spontaneous intestinal inflammation and is increasing in industrialized populations. Combined with host genetic predisposition, diet and gut bacteria are thought to be prominent features contributing to IBD, but little is known about the precise mechanisms involved. Here, we show that low dietary fiber promotes bacterial erosion of protective colonic mucus, leading to lethal colitis in mice lacking the IBD-associated cytokine, interleukin-10. Diet-induced inflammation is driven by mucin-degrading bacteria-mediated Th1 immune responses and is preceded by expansion of natural killer T cells and reduced immunoglobulin A coating of some bacteria. Surprisingly, an exclusive enteral nutrition diet, also lacking dietary fiber, reduced disease by increasing bacterial production of isobutyrate, which is dependent on the presence of a specific bacterial species, Eubacterium rectale. Our results illuminate a mechanistic framework using gnotobiotic mice to unravel the complex web of diet, host and microbial factors that influence IBD.
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Affiliation(s)
| | - Marie Boudaud
- Department of Infection and Immunity, Luxembourg Institute of Health, 4354 Esch-sur-Alzette, Luxembourg
| | - Mathis Wolter
- Department of Infection and Immunity, Luxembourg Institute of Health, 4354 Esch-sur-Alzette, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, 4365 Esch-sur-Alzette, Luxembourg
| | - Celeste Alexander
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Alessandro De Sciscio
- Department of Infection and Immunity, Luxembourg Institute of Health, 4354 Esch-sur-Alzette, Luxembourg
| | - Erica. T. Grant
- Department of Infection and Immunity, Luxembourg Institute of Health, 4354 Esch-sur-Alzette, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, 4365 Esch-sur-Alzette, Luxembourg
| | | | - Nicholas A. Pudlo
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Shaleni Singh
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Austin Campbell
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Mengrou Shan
- Dept. of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Dept. of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA
| | - Li Zhang
- Dept. of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Dept. of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA
| | - Stéphanie Willieme
- Department of Infection and Immunity, Luxembourg Institute of Health, 4354 Esch-sur-Alzette, Luxembourg
| | - Kwi Kim
- Dept. of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Trisha Denike-Duval
- Unit for Laboratory Animal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - André Bleich
- Institute for Laboratory Animal Science, Hanover Medical School, Hanover, Germany
| | - Thomas M. Schmidt
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Dept. of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Dept. of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Lucy Kennedy
- Unit for Laboratory Animal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Costas A. Lyssiotis
- Dept. of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Dept. of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA
| | - Grace Y. Chen
- Dept. of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Kathryn A. Eaton
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Mahesh S. Desai
- Department of Infection and Immunity, Luxembourg Institute of Health, 4354 Esch-sur-Alzette, Luxembourg
- Odense Research Center for Anaphylaxis, Department of Dermatology and Allergy Center, Odense University Hospital, University of Southern Denmark, 5000 Odense, Denmark
| | - Eric C. Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
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50
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Therapeutic Potential of Gut Microbiota and Its Metabolite Short-Chain Fatty Acids in Neonatal Necrotizing Enterocolitis. Life (Basel) 2023; 13:life13020561. [PMID: 36836917 PMCID: PMC9959300 DOI: 10.3390/life13020561] [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: 12/19/2022] [Revised: 01/31/2023] [Accepted: 02/15/2023] [Indexed: 02/19/2023] Open
Abstract
Short chain fatty acids (SCFAs), the principle end-products produced by the anaerobic gut microbial fermentation of complex carbohydrates (CHO) in the colon perform beneficial roles in metabolic health. Butyrate, acetate and propionate are the main SCFA metabolites, which maintain gut homeostasis and host immune responses, enhance gut barrier integrity and reduce gut inflammation via a range of epigenetic modifications in DNA/histone methylation underlying these effects. The infant gut microbiota composition is characterized by higher abundances of SCFA-producing bacteria. A large number of in vitro/vivo studies have demonstrated the therapeutic implications of SCFA-producing bacteria in infant inflammatory diseases, such as obesity and asthma, but the application of gut microbiota and its metabolite SCFAs to necrotizing enterocolitis (NEC), an acute inflammatory necrosis of the distal small intestine/colon affecting premature newborns, is scarce. Indeed, the beneficial health effects attributed to SCFAs and SCFA-producing bacteria in neonatal NEC are still to be understood. Thus, this literature review aims to summarize the available evidence on the therapeutic potential of gut microbiota and its metabolite SCFAs in neonatal NEC using the PubMed/MEDLINE database.
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