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Yuu EY, Bührer C, Eckmanns T, Fulde M, Herz M, Kurzai O, Lindstedt C, Panagiotou G, Piro VC, Radonic A, Renard BY, Reuss A, Siliceo SL, Thielemann N, Thürmer A, Vorst KV, Wieler LH, Haller S. The gut microbiome, resistome, and mycobiome in preterm newborn infants and mouse pups: lack of lasting effects by antimicrobial therapy or probiotic prophylaxis. Gut Pathog 2024; 16:27. [PMID: 38735967 PMCID: PMC11089716 DOI: 10.1186/s13099-024-00616-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 04/13/2024] [Indexed: 05/14/2024] Open
Abstract
BACKGROUND Enhancing our understanding of the underlying influences of medical interventions on the microbiome, resistome and mycobiome of preterm born infants holds significant potential for advancing infection prevention and treatment strategies. We conducted a prospective quasi-intervention study to better understand how antibiotics, and probiotics, and other medical factors influence the gut development of preterm infants. A controlled neonatal mice model was conducted in parallel, designed to closely reflect and predict exposures. Preterm infants and neonatal mice were stratified into four groups: antibiotics only, probiotics only, antibiotics followed by probiotics, and none of these interventions. Stool samples from both preterm infants and neonatal mice were collected at varying time points and analyzed by 16 S rRNA amplicon sequencing, ITS amplicon sequencing and whole genome shotgun sequencing. RESULTS The human infant microbiomes showed an unexpectedly high degree of heterogeneity. Little impact from medical exposure (antibiotics/probiotics) was observed on the strain patterns, however, Bifidobacterium bifidum was found more abundant after exposure to probiotics, regardless of prior antibiotic administration. Twenty-seven antibiotic resistant genes were identified in the resistome. High intra-variability was evident within the different treatment groups. Lastly, we found significant effects of antibiotics and probiotics on the mycobiome but not on the microbiome and resistome of preterm infants. CONCLUSIONS Although our analyses showed transient effects, these results provide positive motivation to continue the research on the effects of medical interventions on the microbiome, resistome and mycobiome of preterm infants.
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Affiliation(s)
- Elizabeth Y Yuu
- Data Analytics & Computational Statistics, Hasso Plattner Institute, University of Potsdam, Prof.-Dr.-Helmert-Straße 2-3, 14482 , Potsdam, Germany
| | | | | | - Marcus Fulde
- Department of Mathematics and Computer Science, Freie Universität Berlin, 14195, Berlin, Germany
| | - Michaela Herz
- Institute for Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | - Oliver Kurzai
- Institute for Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
- Department of Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Beutenbergstraße 11A, 07745 , Jena, Germany
| | | | - Gianni Panagiotou
- Department of Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Beutenbergstraße 11A, 07745 , Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University, 07745, Jena, Germany
- Department of Medicine, The University of Hong Kong, Hong Kong, China
| | - Vitor C Piro
- Data Analytics & Computational Statistics, Hasso Plattner Institute, University of Potsdam, Prof.-Dr.-Helmert-Straße 2-3, 14482 , Potsdam, Germany
- Department of Mathematics and Computer Science, Freie Universität Berlin, 14195, Berlin, Germany
| | | | - Bernhard Y Renard
- Data Analytics & Computational Statistics, Hasso Plattner Institute, University of Potsdam, Prof.-Dr.-Helmert-Straße 2-3, 14482 , Potsdam, Germany
| | - Annicka Reuss
- Robert Koch Institute, Berlin, Germany
- Ministry of Justice and Health, Schleswig-Holstein, Kiel , Germany
| | - Sara Leal Siliceo
- Department of Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Beutenbergstraße 11A, 07745 , Jena, Germany
| | - Nadja Thielemann
- Institute for Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | | | - Kira van Vorst
- Department of Mathematics and Computer Science, Freie Universität Berlin, 14195, Berlin, Germany
| | - Lothar H Wieler
- Data Analytics & Computational Statistics, Hasso Plattner Institute, University of Potsdam, Prof.-Dr.-Helmert-Straße 2-3, 14482 , Potsdam, Germany
- Robert Koch Institute, Berlin, Germany
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Zhang L, Agrawal M, Ng SC, Jess T. Early-life exposures and the microbiome: implications for IBD prevention. Gut 2024; 73:541-549. [PMID: 38123972 PMCID: PMC11150004 DOI: 10.1136/gutjnl-2023-330002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 11/29/2023] [Indexed: 12/23/2023]
Abstract
The early-life period is one of microbiome establishment and immune maturation. Early-life exposures are increasingly being recognised to play an important role in IBD risk. The composition of functions of the gut microbiome in the prenatal, perinatal, and postnatal period may be crucial towards development of health or disease, including IBD, later in life. We herein present a comprehensive summary of the interplay between early-life factors and microbiome perturbations, and their association with risk of IBD. In addition, we provide an overview of host and external factors in early life that are known to impact gut microbiome maturation and exposures implicated in IBD risk. Considering the emerging concept of IBD prevention, we propose strategies to minimise maternal and offspring exposure to potentially harmful variables and recommend protective measures during pregnancy and the postpartum period. This holistic view of early-life factors and microbiome signatures among mothers and their offspring will help frame our current understanding of their importance towards IBD pathogenesis and frame the roadmap for preventive strategies.
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Affiliation(s)
- Lin Zhang
- Microbiota I-Center (MagIC), Hong Kong SAR, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Manasi Agrawal
- Center for Molecular Prediction of Inflammatory Bowel Disease (PREDICT), Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York NY, New York, USA
| | - Siew C Ng
- Microbiota I-Center (MagIC), Hong Kong SAR, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Tine Jess
- Center for Molecular Prediction of Inflammatory Bowel Disease (PREDICT), Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark
- Department of Gastroenterology & Hepatology, Aalborg University Hospital, Aalborg, Denmark
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Minot SS, Mayer-Blackwell K, Fiore-Gartland A, Johnson A, Self S, Bhatti P, Yao L, Liu L, Sun X, Jinfa Y, Kublin J. Strain-level characterization of health-associated bacterial consortia that colonize the human gut during infancy. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.12.16.23300077. [PMID: 38168439 PMCID: PMC10760300 DOI: 10.1101/2023.12.16.23300077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Background The human gut microbiome develops rapidly during infancy, a key window of development coinciding with maturation of the adaptive immune system. However, little is known of the microbiome growth dynamics over the first few months of life and whether there are any generalizable patterns across human populations. We performed metagenomic sequencing on stool samples (n=94) from a cohort of infants (n=15) at monthly intervals in the first six months of life, augmenting our dataset with seven published studies for a total of 4,441 metagenomes from 1,162 infants. Results Strain-level de novo analysis was used to identify 592 of the most abundant organisms in the infant gut microbiome. Previously unrecognized consortia were identified which exhibited highly correlated abundances across samples and were composed of diverse species spanning multiple genera. Analysis of a cohort of infants with cystic fibrosis identified one such novel consortium of diverse Enterobacterales which was positively correlated with weight gain. While all studies showed an increased community stability during the first year of life, microbial dynamics varied widely in the first few months of life, both by study and by individual. Conclusion By augmenting published metagenomic datasets with data from a newly established cohort we were able to identify novel groups of organisms that are correlated with measures of robust human development. We hypothesize that the presence of these groups may impact human health in aggregate in ways that individual species may not in isolation.
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Affiliation(s)
| | | | - Andrew Fiore-Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, USA
| | - Andrew Johnson
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, USA
| | - Steven Self
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, USA
| | - Parveen Bhatti
- Cancer Control Research, BC Cancer Research Institute, Vancouver, BC, Canada
- Epidemiology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, USA
- School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada
| | - Lena Yao
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, USA
| | - Lili Liu
- Key Laboratory of Occupational Disease Prevention and Treatment, Guangdong Province Hospital for Occupational Disease Prevention and Treatment, Guangzhou, China
| | - Xin Sun
- National Institute of Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yi Jinfa
- Nanhai Maternity and Child Healthcare Hospital of Foshan, Foshan, China
| | - James Kublin
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, USA
- HIV Vaccine Trials Network, Fred Hutchinson Cancer Center, Seattle, USA
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Martemucci G, Fracchiolla G, Muraglia M, Tardugno R, Dibenedetto RS, D’Alessandro AG. Metabolic Syndrome: A Narrative Review from the Oxidative Stress to the Management of Related Diseases. Antioxidants (Basel) 2023; 12:2091. [PMID: 38136211 PMCID: PMC10740837 DOI: 10.3390/antiox12122091] [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: 10/10/2023] [Revised: 11/15/2023] [Accepted: 11/27/2023] [Indexed: 12/24/2023] Open
Abstract
Metabolic syndrome (MS) is a growing disorder affecting thousands of people worldwide, especially in industrialised countries, increasing mortality. Oxidative stress, hyperglycaemia, insulin resistance, inflammation, dysbiosis, abdominal obesity, atherogenic dyslipidaemia and hypertension are important factors linked to MS clusters of different pathologies, such as diabesity, cardiovascular diseases and neurological disorders. All biochemical changes observed in MS, such as dysregulation in the glucose and lipid metabolism, immune response, endothelial cell function and intestinal microbiota, promote pathological bridges between metabolic syndrome, diabesity and cardiovascular and neurodegenerative disorders. This review aims to summarise metabolic syndrome's involvement in diabesity and highlight the link between MS and cardiovascular and neurological diseases. A better understanding of MS could promote a novel strategic approach to reduce MS comorbidities.
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Affiliation(s)
- Giovanni Martemucci
- Department of Agricultural and Environmental Sciences, University of Bari Aldo Moro, 70126 Bari, Italy;
| | - Giuseppe Fracchiolla
- Department of Pharmacy–Drug Sciences, University of Bari Aldo Moro, 70126 Bari, Italy; (M.M.); (R.T.); (R.S.D.)
| | - Marilena Muraglia
- Department of Pharmacy–Drug Sciences, University of Bari Aldo Moro, 70126 Bari, Italy; (M.M.); (R.T.); (R.S.D.)
| | - Roberta Tardugno
- Department of Pharmacy–Drug Sciences, University of Bari Aldo Moro, 70126 Bari, Italy; (M.M.); (R.T.); (R.S.D.)
| | - Roberta Savina Dibenedetto
- Department of Pharmacy–Drug Sciences, University of Bari Aldo Moro, 70126 Bari, Italy; (M.M.); (R.T.); (R.S.D.)
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Wilson A, Bogie B, Chaaban H, Burge K. The Nonbacterial Microbiome: Fungal and Viral Contributions to the Preterm Infant Gut in Health and Disease. Microorganisms 2023; 11:909. [PMID: 37110332 PMCID: PMC10144239 DOI: 10.3390/microorganisms11040909] [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: 03/03/2023] [Revised: 03/27/2023] [Accepted: 03/30/2023] [Indexed: 04/29/2023] Open
Abstract
The intestinal microbiome is frequently implicated in necrotizing enterocolitis (NEC) pathogenesis. While no particular organism has been associated with NEC development, a general reduction in bacterial diversity and increase in pathobiont abundance has been noted preceding disease onset. However, nearly all evaluations of the preterm infant microbiome focus exclusively on the bacterial constituents, completely ignoring any fungi, protozoa, archaea, and viruses present. The abundance, diversity, and function of these nonbacterial microbes within the preterm intestinal ecosystem are largely unknown. Here, we review findings on the role of fungi and viruses, including bacteriophages, in preterm intestinal development and neonatal intestinal inflammation, with potential roles in NEC pathogenesis yet to be determined. In addition, we highlight the importance of host and environmental influences, interkingdom interactions, and the role of human milk in shaping fungal and viral abundance, diversity, and function within the preterm intestinal ecosystem.
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Affiliation(s)
| | | | - Hala Chaaban
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Kathryn Burge
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
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Brusselaers N, Pereira M, Alm J, Engstrand L, Engstrand Lilja H. Effect of proton pump inhibitors in infants with esophageal atresia on the gut microbiome: a pilot cohort. Gut Pathog 2022; 14:47. [PMID: 36527125 PMCID: PMC9758939 DOI: 10.1186/s13099-022-00518-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 11/08/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The effects of proton-pump inhibitors (PPIs) on the infant microbiome remain unclear. Swedish pilot cohort study to assess the longitudinal effect of long-term PPI on the infant gut microbiome, including ten newborn infants operated for esophageal atresia exposed to PPIs (mean 57 weeks), compared to healthy one-year-old controls. All children were born vaginally and were otherwise healthy. Within- and between sample diversity of the fecal microbiome was assessed using untargeted whole genome Shotgun metagenomics which sequences all the DNA in the sample and can capture genes rather than a taxonomic fingerprint. RESULTS A longer duration of PPI-use was associated with considerable changes in evenness and high variation on diversity within samples compared to a shorter duration of use. The limited difference between baseline samples and controls suggests that this shift was most likely due to the drug exposure and not the underlying alterations on the microbiome. We found no associations with the number of antibiotic treatment episodes among the PPI-users. CONCLUSION Prolonged PPI-use may alter the early infant gut microbiome composition, especially those with the most prolonged duration of use.
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Affiliation(s)
- Nele Brusselaers
- grid.4714.60000 0004 1937 0626Centre for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solnavägen 9, 17165 Stockholm, Sweden ,grid.5284.b0000 0001 0790 3681Global Health Institute, University of Antwerp, B-2610 Antwerp, Belgium ,grid.5342.00000 0001 2069 7798Department of Head and Skin, Ghent University, B-9000 Ghent, Belgium
| | - Marcela Pereira
- grid.4714.60000 0004 1937 0626Centre for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solnavägen 9, 17165 Stockholm, Sweden
| | - Johan Alm
- grid.4714.60000 0004 1937 0626Department of Clinical Science, Karolinska Institutet, 17165 Stockholm, Sweden ,grid.416648.90000 0000 8986 2221Sachs’ Children and Youth Hospital, Södersjukhuset, 11883 Stockholm, Sweden
| | - Lars Engstrand
- grid.4714.60000 0004 1937 0626Centre for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solnavägen 9, 17165 Stockholm, Sweden
| | - Helene Engstrand Lilja
- grid.4714.60000 0004 1937 0626Department of Women’s and Children’s Health, Karolinska Institutet, 17165 Stockholm, Sweden
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Del Valle Penella A, Pretorius CC, Baker CJ, Rench MA, Healy CM, Edwards MS. Group B Streptococcal Cellulitis-Adenitis Syndrome in Infants: Insights From 24 Years of Experience. J Pediatric Infect Dis Soc 2022; 11:375-378. [PMID: 35552426 DOI: 10.1093/jpids/piac033] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 04/18/2022] [Indexed: 11/14/2022]
Abstract
This series of 28 infants with group B streptococcal (GBS) cellulitis-adenitis from a single institution over 24 years offers insights important to the early recognition, spectrum of findings, and optimal management of this rare manifestation of invasive GBS disease.
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Affiliation(s)
| | - Christopher C Pretorius
- Department of Pediatrics, Kaiser Permanente Medicine, Mid-Atlantic Permanente Medical Group, Washington, DC, USA
| | - Carol J Baker
- Department of Pediatrics, University of Texas Health Science Center, McGovern Medical School, Houston, Texas, USA
| | - Marcia A Rench
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | | | - Morven S Edwards
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
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Hill L, Sharma R, Hart L, Popov J, Moshkovich M, Pai N. The neonatal microbiome in utero and beyond: perinatal influences and long-term impacts. J LAB MED 2021. [DOI: 10.1515/labmed-2021-0131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
The neonatal microbiome offers a valuable model for studying the origins of human health and disease. As the field of metagenomics expands, we also increase our understanding of early life influences on its development. In this review we will describe common techniques used to define and measure the microbiome. We will review in utero influences, normal perinatal development, and known risk factors for abnormal neonatal microbiome development. Finally, we will summarize current evidence that links early life microbial impacts on the development of chronic inflammatory diseases, obesity, and atopy.
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Affiliation(s)
- Lee Hill
- Department of Paediatrics, Division of Gastroenterology, Hepatology and Nutrition , McMaster Children’s Hospital, McMaster University , Hamilton , Canada
- Department of Human Biology, Division of Exercise Science and Sports Medicine , University of Cape Town , Cape Town , South Africa
| | - Ruchika Sharma
- Department of Paediatrics, Division of Gastroenterology, Hepatology and Nutrition , McMaster Children’s Hospital, McMaster University , Hamilton , Canada
- McMaster University , Hamilton , Canada
| | - Lara Hart
- Department of Paediatrics, Division of Gastroenterology, Hepatology and Nutrition , McMaster Children’s Hospital, McMaster University , Hamilton , Canada
| | - Jelena Popov
- Department of Paediatrics, Division of Gastroenterology, Hepatology and Nutrition , McMaster Children’s Hospital, McMaster University , Hamilton , Canada
- University College Cork, College of Medicine and Health , Cork , Ireland
| | - Michal Moshkovich
- Department of Paediatrics, Division of Gastroenterology, Hepatology and Nutrition , McMaster Children’s Hospital, McMaster University , Hamilton , Canada
- Faculty of Health Sciences , McMaster University , Hamilton , Canada
| | - Nikhil Pai
- Department of Paediatrics, Division of Gastroenterology, Hepatology and Nutrition , McMaster Children’s Hospital, McMaster University , Hamilton , Canada
- Farncombe Family Digestive Health Research Institute , McMaster University , Hamilton , Canada
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Rajendiran E, Ramadass B, Ramprasath V. Understanding connections and roles of gut microbiome in cardiovascular diseases. Can J Microbiol 2020; 67:101-111. [PMID: 33079568 DOI: 10.1139/cjm-2020-0043] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The gut microbiome encompasses trillions of residing microbes, mainly bacteria, which play a crucial role in maintaining the physiological and metabolic health of the host. The gut microbiome has been associated with several diseases, including cardiovascular disease (CVD). A growing body of evidence suggests that an altered gut environment and gut-microbiome-derived metabolites are associated with CVD events. The gut microbiome communicates with host physiology through different mechanisms, including trimethylamine N-oxide generation, primary and secondary bile acid metabolism pathways, and short-chain fatty acids production. The main focus of this review is to understand the association of the gut microbiome with CVD and its implications on the interactions between the gut microbiome and the host. Manipulation of the gut microbiome through specific dietary intervention is a simple approach to identifying novel targets for therapy or better dietary recommendations, and new preventive measures for screening biomarkers to reduce CVD risk in humans.
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Affiliation(s)
- Ethendhar Rajendiran
- Richardson Centre for Functional Foods and Nutraceuticals (RCFFN), Department of Food and Human Nutritional Sciences, University of Manitoba, Winnipeg, MB R3T 6C5, Canada
| | - Balamurugan Ramadass
- Center of Excellence for Clinical Microbiome Research, Department of Biochemistry, All India Institute of Medical Sciences, Bhubaneswar, India
| | - Vanu Ramprasath
- Richardson Centre for Functional Foods and Nutraceuticals (RCFFN), Department of Food and Human Nutritional Sciences, University of Manitoba, Winnipeg, MB R3T 6C5, Canada
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