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Chen J, Gao Y, Zhang Y, Wang M. Research progress in the treatment of inflammatory bowel disease with natural polysaccharides and related structure-activity relationships. Food Funct 2024; 15:5680-5702. [PMID: 38738935 DOI: 10.1039/d3fo04919a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Abstract
Inflammatory bowel disease (IBD) comprises a group of highly prevalent and chronic inflammatory intestinal tract diseases caused by multiple factors. Despite extensive research into the causes of the disease, IBD's pathogenic mechanisms remain unclear. Moreover, side effects of current IBD therapies restrict their long-term clinical use. In contrast, natural polysaccharides exert beneficial anti-IBD effects and offer advantages over current anti-IBD drugs, including enhanced safety and straightforward isolation from abundant and reliable sources, and thus may serve as components of functional foods and health products for use in IBD prevention and treatment. However, few reviews have explored natural polysaccharides with anti-IBD activities or the relationship between polysaccharide conformation and anti-IBD biological activity. Therefore, this review aims to summarize anti-IBD activities and potential clinical applications of polysaccharides isolated from plant, animal, microorganismal, and algal sources, while also exploring the relationship between polysaccharide conformation and anti-IBD bioactivity for the first time. Furthermore, potential mechanisms underlying polysaccharide anti-IBD effects are summarized, including intestinal microbiota modulation, intestinal inflammation alleviation, and intestinal barrier protection from IBD-induced damage. Ultimately, this review provides a theoretical foundation and valuable insights to guide the development of natural polysaccharide-containing functional foods and nutraceuticals for use as dietary IBD therapies.
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Affiliation(s)
- Jiaqi Chen
- Affiliated Hospital, Changchun University of Chinese Medicine, Changchun, 130021, China.
- College of Pharmacy, Changchun University of Chinese Medicine, Changchun, 130021, China
| | - Yanan Gao
- Affiliated Hospital, Changchun University of Chinese Medicine, Changchun, 130021, China.
- College of Pharmacy, Changchun University of Chinese Medicine, Changchun, 130021, China
| | - Yanqiu Zhang
- Affiliated Hospital, Changchun University of Chinese Medicine, Changchun, 130021, China.
| | - Mingxing Wang
- Affiliated Hospital, Changchun University of Chinese Medicine, Changchun, 130021, China.
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Ratiner K, Ciocan D, Abdeen SK, Elinav E. Utilization of the microbiome in personalized medicine. Nat Rev Microbiol 2024; 22:291-308. [PMID: 38110694 DOI: 10.1038/s41579-023-00998-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/17/2023] [Indexed: 12/20/2023]
Abstract
Inter-individual human variability, driven by various genetic and environmental factors, complicates the ability to develop effective population-based early disease detection, treatment and prognostic assessment. The microbiome, consisting of diverse microorganism communities including viruses, bacteria, fungi and eukaryotes colonizing human body surfaces, has recently been identified as a contributor to inter-individual variation, through its person-specific signatures. As such, the microbiome may modulate disease manifestations, even among individuals with similar genetic disease susceptibility risks. Information stored within microbiomes may therefore enable early detection and prognostic assessment of disease in at-risk populations, whereas microbiome modulation may constitute an effective and safe treatment tailored to the individual. In this Review, we explore recent advances in the application of microbiome data in precision medicine across a growing number of human diseases. We also discuss the challenges, limitations and prospects of analysing microbiome data for personalized patient care.
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Affiliation(s)
- Karina Ratiner
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Dragos Ciocan
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Suhaib K Abdeen
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel.
| | - Eran Elinav
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel.
- Division of Cancer-Microbiome Research, DKFZ, Heidelberg, Germany.
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Wen C, Chen D, Zhong R, Peng X. Animal models of inflammatory bowel disease: category and evaluation indexes. Gastroenterol Rep (Oxf) 2024; 12:goae021. [PMID: 38634007 PMCID: PMC11021814 DOI: 10.1093/gastro/goae021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 02/12/2024] [Accepted: 02/29/2024] [Indexed: 04/19/2024] Open
Abstract
Inflammatory bowel disease (IBD) research often relies on animal models to study the etiology, pathophysiology, and management of IBD. Among these models, rats and mice are frequently employed due to their practicality and genetic manipulability. However, for studies aiming to closely mimic human pathology, non-human primates such as monkeys and dogs offer valuable physiological parallels. Guinea pigs, while less commonly used, present unique advantages for investigating the intricate interplay between neurological and immunological factors in IBD. Additionally, New Zealand rabbits excel in endoscopic biopsy techniques, providing insights into mucosal inflammation and healing processes. Pigs, with their physiological similarities to humans, serve as ideal models for exploring the complex relationships between nutrition, metabolism, and immunity in IBD. Beyond mammals, non-mammalian organisms including zebrafish, Drosophila melanogaster, and nematodes offer specialized insights into specific aspects of IBD pathology, highlighting the diverse array of model systems available for advancing our understanding of this multifaceted disease. In this review, we conduct a thorough analysis of various animal models employed in IBD research, detailing their applications and essential experimental parameters. These include clinical observation, Disease Activity Index score, pathological assessment, intestinal barrier integrity, fibrosis, inflammatory markers, intestinal microbiome, and other critical parameters that are crucial for evaluating modeling success and drug efficacy in experimental mammalian studies. Overall, this review will serve as a valuable resource for researchers in the field of IBD, offering insights into the diverse array of animal models available and their respective applications in studying IBD.
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Affiliation(s)
- Changlin Wen
- Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, Sichuan, P. R. China
| | - Dan Chen
- Acupuncture and Moxibustion School of Teaching, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, P. R. China
| | - Rao Zhong
- Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, Sichuan, P. R. China
| | - Xi Peng
- Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, Sichuan, P. R. China
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Mukherjee S, Chopra A, Karmakar S, Bhat SG. Periodontitis increases the risk of gastrointestinal dysfunction: an update on the plausible pathogenic molecular mechanisms. Crit Rev Microbiol 2024:1-31. [PMID: 38602474 DOI: 10.1080/1040841x.2024.2339260] [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: 11/04/2023] [Accepted: 04/01/2024] [Indexed: 04/12/2024]
Abstract
Periodontitis is an immuno-inflammatory disease of the soft tissues surrounding the teeth. Periodontitis is linked to many communicable and non-communicable diseases such as diabetes, cardiovascular disease, rheumatoid arthritis, and cancers. The oral-systemic link between periodontal disease and systemic diseases is attributed to the spread of inflammation, microbial products and microbes to distant organ systems. Oral bacteria reach the gut via swallowed saliva, whereby they induce gut dysbiosis and gastrointestinal dysfunctions. Some periodontal pathogens like Porphyromonas. gingivalis, Klebsiella, Helicobacter. Pylori, Streptococcus, Veillonella, Parvimonas micra, Fusobacterium nucleatum, Peptostreptococcus, Haemophilus, Aggregatibacter actinomycetomcommitans and Streptococcus mutans can withstand the unfavorable acidic, survive in the gut and result in gut dysbiosis. Gut dysbiosis increases gut inflammation, and induce dysplastic changes that lead to gut dysfunction. Various studies have linked oral bacteria, and oral-gut axis to various GIT disorders like inflammatory bowel disease, liver diseases, hepatocellular and pancreatic ductal carcinoma, ulcerative colitis, and Crohn's disease. Although the correlation between periodontitis and GIT disorders is well established, the intricate molecular mechanisms by which oral microflora induce these changes have not been discussed extensively. This review comprehensively discusses the intricate and unique molecular and immunological mechanisms by which periodontal pathogens can induce gut dysbiosis and dysfunction.
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Affiliation(s)
- Sayantan Mukherjee
- Department of Periodontology, Manipal College of Dental Sciences, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Aditi Chopra
- Department of Periodontology, Manipal College of Dental Sciences, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Shaswata Karmakar
- Department of Periodontology, Manipal College of Dental Sciences, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Subraya Giliyar Bhat
- Department of Preventive Dental Sciences, Division of Periodontology, College of Dental Surgery, Iman Abdulrahman Bin Faizal University, Dammam, Saudi Arabia
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Luo M, Zhu J, Jia J, Zhang H, Zhao J. Progress on network modeling and analysis of gut microecology: a review. Appl Environ Microbiol 2024; 90:e0009224. [PMID: 38415584 DOI: 10.1128/aem.00092-24] [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: 02/29/2024] Open
Abstract
The gut microecological network is a complex microbial community within the human body that plays a key role in linking dietary nutrition and host physiology. To understand the complex relationships among microbes and their functions within this community, network analysis has emerged as a powerful tool. By representing the interactions between microbes and their associated omics data as a network, we can gain a comprehensive understanding of the ecological mechanisms that drive the human gut microbiota. In addition, the network-based approach provides a more intuitive analysis of the gut microbiota, simplifying the study of its complex dynamics and interdependencies. This review provides a comprehensive overview of the methods used to construct and analyze networks in the context of gut microecological background. We discuss various types of network modeling approaches, including co-occurrence networks, causal networks, dynamic networks, and multi-omics networks, and describe the analytical techniques used to identify important network properties. We also highlight the challenges and limitations of network modeling in this area, such as data scarcity and heterogeneity, and provide future research directions to overcome these limitations. By exploring these network-based methods, researchers can gain valuable insights into the intricate relationships and functional roles of microbial communities within the gut, ultimately advancing our understanding of the gut microbiota's impact on human health.
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Affiliation(s)
- Meng Luo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Jinlin Zhu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Jiajia Jia
- Key Laboratory of Advanced Process Control for Light Industry (Ministry of Education), Jiangnan University, Wuxi, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu, China
- Wuxi Translational Medicine Research Center, Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi, China
- (Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- Wuxi Translational Medicine Research Center, Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi, China
- (Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou, China
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Browning BD, Kirkland AE, Green R, Engevik M, Alekseyenko AV, Leggio L, Tomko RL, Squeglia LM. The adolescent and young adult microbiome and its association with substance use: a scoping review. Alcohol Alcohol 2024; 59:agad055. [PMID: 37665023 PMCID: PMC10979412 DOI: 10.1093/alcalc/agad055] [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: 02/22/2023] [Revised: 07/18/2023] [Accepted: 08/07/2023] [Indexed: 09/05/2023] Open
Abstract
AIMS The microbiome is a critical factor in health throughout human development. The aims of this scoping review are to (i) elucidate the differences between the youth (post-natal day 21-65 for rodents, 2-7 years for non-human primates, and 10-25 years for humans) microbiome with other life stages and (ii) identify youth-specific microbial changes associated with substance use. METHODS Peer-reviewed studies published up to May 2023 were identified in PubMed and SCOPUS and included gut and oral microbiome studies from rodents, non-human primates, and humans (N = 1733). Twenty-six articles were determined eligible based on inclusion criteria (aim 1: n = 19, aim 2: n = 7). RESULTS The adolescent and young adult oral and gut microbiomes are distinct compared to other life stages, within both non-human and human models. While there is limited research in this area, the microbiome appears to be vulnerable to substance use exposure earlier in life, including substances commonly initiated and escalated during adolescence and young adulthood (i.e. alcohol, cannabis, and tobacco). CONCLUSIONS Studies across the lifespan indicate that adolescence and young adulthood are distinct periods of development, where the microbiome is sensitive to exposures, including substance use. There is a need for more studies focused on the adolescent and young adult microbiome and substance use, as well as focused on the oral microbiome during this developmental period. Understanding the gut and oral microbiome during adolescence and young adulthood may provide insight into the pathophysiology of substance use disorders.
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Affiliation(s)
- Brittney D Browning
- Department of Psychiatry and Behavioral Sciences, Medical University of South Carolina, 67 President St., Charleston, SC 29425, United States
- Department of Neuroscience, Medical University of South Carolina, 173 Ashley Ave., Charleston, SC 29425, United States
| | - Anna E Kirkland
- Department of Psychiatry and Behavioral Sciences, Medical University of South Carolina, 67 President St., Charleston, SC 29425, United States
| | - Rejoyce Green
- Department of Psychiatry and Behavioral Sciences, Medical University of South Carolina, 67 President St., Charleston, SC 29425, United States
| | - Melinda Engevik
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, 173 Ashley Ave., Charleston SC, 29425, United States
| | - Alexander V Alekseyenko
- Department of Public Health Sciences, Biomedical Informatics Center, Medical University of South Carolina, 135 Cannon St., Charleston, SC 29425, United States
| | - Lorenzo Leggio
- Clinical Psychoneuroendocrinology and Neuropsychopharmacology Section, Translational Addiction Medicine Branch, National Institute on Drug Abuse Intramural Research Program and National Institute on Alcohol Abuse and Alcoholism Division of Intramural Clinical and Biological Research, National Institutes of Health, Baltimore, Maryland, USA
| | - Rachel L Tomko
- Department of Psychiatry and Behavioral Sciences, Medical University of South Carolina, 67 President St., Charleston, SC 29425, United States
| | - Lindsay M Squeglia
- Department of Psychiatry and Behavioral Sciences, Medical University of South Carolina, 67 President St., Charleston, SC 29425, United States
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Troci A, Philippen S, Rausch P, Rave J, Weyland G, Niemann K, Jessen K, Schmill LP, Aludin S, Franke A, Berg D, Bang C, Bartsch T. Disease- and stage-specific alterations of the oral and fecal microbiota in Alzheimer's disease. PNAS NEXUS 2024; 3:pgad427. [PMID: 38205031 PMCID: PMC10776369 DOI: 10.1093/pnasnexus/pgad427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 11/30/2023] [Indexed: 01/12/2024]
Abstract
Microbial communities in the intestinal tract are suggested to impact the ethiopathogenesis of Alzheimer's disease (AD). The human microbiome might modulate neuroinflammatory processes and contribute to neurodegeneration in AD. However, the microbial compositions in patients with AD at different stages of the disease are still not fully characterized. We used 16S rRNA analyses to investigate the oral and fecal microbiota in patients with AD and mild cognitive impairment (MCI; n = 84), at-risk individuals (APOE4 carriers; n = 17), and healthy controls (n = 50) and investigated the relationship of microbial communities and disease-specific markers via multivariate- and network-based approaches. We found a slightly decreased diversity in the fecal microbiota of patients with AD (average Chao1 diversity for AD = 212 [SD = 66]; for controls = 215 [SD = 55]) and identified differences in bacterial abundances including Bacteroidetes, Ruminococcus, Sutterella, and Porphyromonadaceae. The diversity in the oral microbiota was increased in patients with AD and at-risk individuals (average Chao1 diversity for AD = 174 [SD = 60], for at-risk group = 195 [SD = 49]). Gram-negative proinflammatory bacteria including Haemophilus, Neisseria, Actinobacillus, and Porphyromonas were dominant oral bacteria in patients with AD and MCI and the abundance correlated with the cerebrospinal fluid biomarker. Taken together, we observed a strong shift in the fecal and the oral communities of patients with AD already prominent in prodromal and, in case of the oral microbiota, in at-risk stages. This indicates stage-dependent alterations in oral and fecal microbiota in AD which may contribute to the pathogenesis via a facilitated intestinal and systemic inflammation leading to neuroinflammation and neurodegeneration.
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Affiliation(s)
- Alba Troci
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Sarah Philippen
- Department of Neurology, Memory Disorders and Plasticity Group, University Hospital Schleswig-Holstein, Kiel 24105, Germany
| | - Philipp Rausch
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Julius Rave
- Department of Neurology, Memory Disorders and Plasticity Group, University Hospital Schleswig-Holstein, Kiel 24105, Germany
| | - Gina Weyland
- Department of Neurology, Memory Disorders and Plasticity Group, University Hospital Schleswig-Holstein, Kiel 24105, Germany
| | - Katharina Niemann
- Department of Neurology, Memory Disorders and Plasticity Group, University Hospital Schleswig-Holstein, Kiel 24105, Germany
| | - Katharina Jessen
- Department of Neurology, Memory Disorders and Plasticity Group, University Hospital Schleswig-Holstein, Kiel 24105, Germany
| | - Lars-Patrick Schmill
- Department of Radiology and Neuroradiology, University Hospital Schleswig-Holstein, Kiel 24105, Germany
| | - Schekeb Aludin
- Department of Radiology and Neuroradiology, University Hospital Schleswig-Holstein, Kiel 24105, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Daniela Berg
- Department of Neurology, Memory Disorders and Plasticity Group, University Hospital Schleswig-Holstein, Kiel 24105, Germany
| | - Corinna Bang
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Thorsten Bartsch
- Department of Neurology, Memory Disorders and Plasticity Group, University Hospital Schleswig-Holstein, Kiel 24105, Germany
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Tortora SC, Agurto MG, Martello LA. The oral-gut-circulatory axis: from homeostasis to colon cancer. Front Cell Infect Microbiol 2023; 13:1289452. [PMID: 38029267 PMCID: PMC10663299 DOI: 10.3389/fcimb.2023.1289452] [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: 09/05/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
The human microbiota is widely recognized as providing crucial health benefits to its host, specifically by modulating immune homeostasis. Microbial imbalance, known as dysbiosis, is linked to several conditions in the body. The oral cavity and gut host the two largest microbial communities playing a major role in microbial-associated diseases. While the oral-gut axis has been previously explored, our review uniquely highlights the significance of incorporating the circulatory system into this axis. The interaction between immune cells, inflammatory factors, circulating bacteria, and microbial metabolites influences the homeostasis of both the oral and gut microbiota in a bidirectional manner. In this comprehensive review, we aim to describe the bacterial components of the oral-gut-circulatory axis in both health and disease, with a specific focus on colon cancer.
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Affiliation(s)
- Sofia C. Tortora
- Department of Medicine and Division of Gastroenterology & Hepatology, SUNY Downstate Health Sciences University, Brooklyn, NY, United States
| | - Maria Gonzalez Agurto
- Departamento de Rehabilitación Craneofacial Integral, Universidad de Los Andes, Santiago, Chile
| | - Laura A. Martello
- Department of Medicine and Division of Gastroenterology & Hepatology, SUNY Downstate Health Sciences University, Brooklyn, NY, United States
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Gomez D, Toribio R, Caddey B, Costa M, Vijan S, Dembek K. Longitudinal effects of oral administration of antimicrobial drugs on fecal microbiota of horses. J Vet Intern Med 2023; 37:2562-2572. [PMID: 37681574 PMCID: PMC10658497 DOI: 10.1111/jvim.16853] [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: 08/23/2023] [Indexed: 09/09/2023] Open
Abstract
BACKGROUND Antimicrobial drug-associated diarrhea (AAD) is the most common adverse effect in horses receiving antimicrobials. Little information on how oral administration of antimicrobials alters intestinal microbiota in horses is available. OBJECTIVE Investigate changes of the fecal microbiota in response to oral administration of antimicrobials. ANIMALS Twenty healthy horses. METHODS Prospective, longitudinal study. Horses were randomly assigned to 4 groups comprising 4 horses each: group 1 (metronidazole); group 2 (erythromycin); group 3 (doxycycline); group 4 (sulfadiazine/trimethoprim, SMZ-TMP); and group 5 (control). Antimicrobials were administered for 5 days. Fecal samples were obtained before (day 0) and at 1, 2, 3, 4, 5, 6, and 30 days of the study period. Fecal microbiota was characterized by high throughput sequencing of the V4 region of the 16S rRNA. RESULTS Horses remained healthy throughout the study. Richness and diversity in doxycycline, erythromycin, and metronidazole, but not SMZ-TMP groups, was significantly lower (P < .05) at multiple time points after administration of antimicrobials compared with samples from day 0. Main changes in the microbiota were observed during the time of antimicrobial administration (day 2-5; weighted and unweighted UniFrac PERMANOVA P < .05). Administration of erythromycin, doxycycline and, to a lesser extent, metronidazole produced a pronounced alteration in the microbiota compared with day 0 samples by decreasing the abundance of Treponema, Fibrobacter, and Lachnospiraceae and increasing Fusobacterium and Escherichia-Shigella. CONCLUSIONS AND CLINICAL IMPORTANCE Oral administration of antimicrobials alters the intestinal microbiota of healthy horses resembling horses with dysbiosis, potentially resulting in intestinal inflammation and predisposition to diarrhea.
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Affiliation(s)
- Diego Gomez
- Department of Clinical Studies, Ontario Veterinary CollegeUniversity of GuelphGuelphOntarioCanada
| | - Ramiro Toribio
- Department of Clinical SciencesThe Ohio State University, College of Veterinary MedicineColumbusOhioUSA
| | - Benjamin Caddey
- Faculty of Veterinary MedicineUniversity of CalgaryCalgaryAlbertaCanada
| | - Marcio Costa
- Faculté de Médecine Vétérinaire – Département de Biomédecine VétérinaireUniversity of MontrealSaint‐HyacintheQuebecCanada
| | - Stephanie Vijan
- Department of Clinical SciencesThe Ohio State University, College of Veterinary MedicineColumbusOhioUSA
| | - Katarzyna Dembek
- Department of Clinical Sciences, College of Veterinary MedicineNorth Carolina State UniversityRaleighNorth CarolinaUSA
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Korobeinikova AV, Zlobovskaya OA, Sheptulina AF, Ashniev GA, Bobrova MM, Yafarova AA, Akasheva DU, Kabieva SS, Bakoev SY, Zagaynova AV, Lukashina MV, Abramov IA, Pokrovskaya MS, Doludin YV, Tolkacheva LR, Kurnosov AS, Zyatenkova EV, Lavrenova EA, Efimova IA, Glazunova EV, Kiselev AR, Shipulin GA, Kontsevaya AV, Keskinov AA, Yudin VS, Makarov VV, Drapkina OM, Yudin SM. Gut Microbiota Patterns in Patients with Non-Alcoholic Fatty Liver Disease: A Comprehensive Assessment Using Three Analysis Methods. Int J Mol Sci 2023; 24:15272. [PMID: 37894951 PMCID: PMC10607775 DOI: 10.3390/ijms242015272] [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: 08/17/2023] [Revised: 09/01/2023] [Accepted: 09/05/2023] [Indexed: 10/29/2023] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is considered the most common chronic liver disease worldwide, affecting nearly 25% of the global adult population. Increasing evidence suggests that functional and compositional changes in the gut microbiota may contribute to the development and promote the progression of NAFLD. 16S rRNA gene next-generation sequencing is widely used to determine specific features of the NAFLD microbiome, but a complex system such as the gut microbiota requires a comprehensive approach. We used three different approaches: MALDI-TOF-MS of bacterial cultures, qPCR, and 16S NGS sequencing, as well as a wide variety of statistical methods to assess the differences in gut microbiota composition between NAFLD patients without significant fibrosis and the control group. The listed methods showed enrichment in Collinsella sp. and Oscillospiraceae for the control samples and enrichment in Lachnospiraceae (and in particular Dorea sp.) and Veillonellaceae in NAFLD. The families, Bifidobacteriaceae, Lactobacillaceae, and Enterococcaceae (particularly Enterococcus faecium and Enterococcus faecalis), were also found to be important taxa for NAFLD microbiome evaluation. Considering individual method observations, an increase in Candida krusei and a decrease in Bacteroides uniformis for NAFLD patients were detected using MALDI-TOF-MS. An increase in Gracilibacteraceae, Chitinophagaceae, Pirellulaceae, Erysipelatoclostridiaceae, Muribaculaceae, and Comamonadaceae, and a decrease in Acidaminococcaceae in NAFLD were observed with 16S NGS, and enrichment in Fusobacterium nucleatum was shown using qPCR analysis. These findings confirm that NAFLD is associated with changes in gut microbiota composition. Further investigations are required to determine the cause-and-effect relationships and the impact of microbiota-derived compounds on the development and progression of NAFLD.
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Affiliation(s)
- Anna V. Korobeinikova
- Centre for Strategic Planning and Management of Biomedical Health Risks of Federal Medical Biological Agency, Pogodinskaya Str., 10/1, 119121 Moscow, Russia; (A.V.K.); (S.S.K.); (S.Y.B.); (M.V.L.); (A.S.K.)
| | - Olga A. Zlobovskaya
- Centre for Strategic Planning and Management of Biomedical Health Risks of Federal Medical Biological Agency, Pogodinskaya Str., 10/1, 119121 Moscow, Russia; (A.V.K.); (S.S.K.); (S.Y.B.); (M.V.L.); (A.S.K.)
| | - Anna F. Sheptulina
- National Medical Research Center for Therapy and Preventive Medicine, Petroverigskyj Lane 10, bld.3, 101990 Moscow, Russia; (A.F.S.); (A.A.Y.); (D.U.A.)
| | - German A. Ashniev
- Centre for Strategic Planning and Management of Biomedical Health Risks of Federal Medical Biological Agency, Pogodinskaya Str., 10/1, 119121 Moscow, Russia; (A.V.K.); (S.S.K.); (S.Y.B.); (M.V.L.); (A.S.K.)
| | - Maria M. Bobrova
- Centre for Strategic Planning and Management of Biomedical Health Risks of Federal Medical Biological Agency, Pogodinskaya Str., 10/1, 119121 Moscow, Russia; (A.V.K.); (S.S.K.); (S.Y.B.); (M.V.L.); (A.S.K.)
| | - Adel A. Yafarova
- National Medical Research Center for Therapy and Preventive Medicine, Petroverigskyj Lane 10, bld.3, 101990 Moscow, Russia; (A.F.S.); (A.A.Y.); (D.U.A.)
| | - Dariga U. Akasheva
- National Medical Research Center for Therapy and Preventive Medicine, Petroverigskyj Lane 10, bld.3, 101990 Moscow, Russia; (A.F.S.); (A.A.Y.); (D.U.A.)
| | - Shuanat Sh. Kabieva
- Centre for Strategic Planning and Management of Biomedical Health Risks of Federal Medical Biological Agency, Pogodinskaya Str., 10/1, 119121 Moscow, Russia; (A.V.K.); (S.S.K.); (S.Y.B.); (M.V.L.); (A.S.K.)
| | - Siroj Yu. Bakoev
- Centre for Strategic Planning and Management of Biomedical Health Risks of Federal Medical Biological Agency, Pogodinskaya Str., 10/1, 119121 Moscow, Russia; (A.V.K.); (S.S.K.); (S.Y.B.); (M.V.L.); (A.S.K.)
| | - Anjelica V. Zagaynova
- Centre for Strategic Planning and Management of Biomedical Health Risks of Federal Medical Biological Agency, Pogodinskaya Str., 10/1, 119121 Moscow, Russia; (A.V.K.); (S.S.K.); (S.Y.B.); (M.V.L.); (A.S.K.)
| | - Maria V. Lukashina
- Centre for Strategic Planning and Management of Biomedical Health Risks of Federal Medical Biological Agency, Pogodinskaya Str., 10/1, 119121 Moscow, Russia; (A.V.K.); (S.S.K.); (S.Y.B.); (M.V.L.); (A.S.K.)
| | - Ivan A. Abramov
- Centre for Strategic Planning and Management of Biomedical Health Risks of Federal Medical Biological Agency, Pogodinskaya Str., 10/1, 119121 Moscow, Russia; (A.V.K.); (S.S.K.); (S.Y.B.); (M.V.L.); (A.S.K.)
| | - Mariya S. Pokrovskaya
- National Medical Research Center for Therapy and Preventive Medicine, Petroverigskyj Lane 10, bld.3, 101990 Moscow, Russia; (A.F.S.); (A.A.Y.); (D.U.A.)
| | - Yurii V. Doludin
- National Medical Research Center for Therapy and Preventive Medicine, Petroverigskyj Lane 10, bld.3, 101990 Moscow, Russia; (A.F.S.); (A.A.Y.); (D.U.A.)
| | - Larisa R. Tolkacheva
- Centre for Strategic Planning and Management of Biomedical Health Risks of Federal Medical Biological Agency, Pogodinskaya Str., 10/1, 119121 Moscow, Russia; (A.V.K.); (S.S.K.); (S.Y.B.); (M.V.L.); (A.S.K.)
| | - Alexander S. Kurnosov
- Centre for Strategic Planning and Management of Biomedical Health Risks of Federal Medical Biological Agency, Pogodinskaya Str., 10/1, 119121 Moscow, Russia; (A.V.K.); (S.S.K.); (S.Y.B.); (M.V.L.); (A.S.K.)
| | - Elena V. Zyatenkova
- National Medical Research Center for Therapy and Preventive Medicine, Petroverigskyj Lane 10, bld.3, 101990 Moscow, Russia; (A.F.S.); (A.A.Y.); (D.U.A.)
| | - Evgeniya A. Lavrenova
- National Medical Research Center for Therapy and Preventive Medicine, Petroverigskyj Lane 10, bld.3, 101990 Moscow, Russia; (A.F.S.); (A.A.Y.); (D.U.A.)
| | - Irina A. Efimova
- National Medical Research Center for Therapy and Preventive Medicine, Petroverigskyj Lane 10, bld.3, 101990 Moscow, Russia; (A.F.S.); (A.A.Y.); (D.U.A.)
| | - Evgeniya V. Glazunova
- Centre for Strategic Planning and Management of Biomedical Health Risks of Federal Medical Biological Agency, Pogodinskaya Str., 10/1, 119121 Moscow, Russia; (A.V.K.); (S.S.K.); (S.Y.B.); (M.V.L.); (A.S.K.)
| | - Anton R. Kiselev
- National Medical Research Center for Therapy and Preventive Medicine, Petroverigskyj Lane 10, bld.3, 101990 Moscow, Russia; (A.F.S.); (A.A.Y.); (D.U.A.)
| | - German A. Shipulin
- Centre for Strategic Planning and Management of Biomedical Health Risks of Federal Medical Biological Agency, Pogodinskaya Str., 10/1, 119121 Moscow, Russia; (A.V.K.); (S.S.K.); (S.Y.B.); (M.V.L.); (A.S.K.)
| | - Anna V. Kontsevaya
- National Medical Research Center for Therapy and Preventive Medicine, Petroverigskyj Lane 10, bld.3, 101990 Moscow, Russia; (A.F.S.); (A.A.Y.); (D.U.A.)
| | - Anton A. Keskinov
- Centre for Strategic Planning and Management of Biomedical Health Risks of Federal Medical Biological Agency, Pogodinskaya Str., 10/1, 119121 Moscow, Russia; (A.V.K.); (S.S.K.); (S.Y.B.); (M.V.L.); (A.S.K.)
| | - Vladimir S. Yudin
- Centre for Strategic Planning and Management of Biomedical Health Risks of Federal Medical Biological Agency, Pogodinskaya Str., 10/1, 119121 Moscow, Russia; (A.V.K.); (S.S.K.); (S.Y.B.); (M.V.L.); (A.S.K.)
| | - Valentin V. Makarov
- Centre for Strategic Planning and Management of Biomedical Health Risks of Federal Medical Biological Agency, Pogodinskaya Str., 10/1, 119121 Moscow, Russia; (A.V.K.); (S.S.K.); (S.Y.B.); (M.V.L.); (A.S.K.)
| | - Oxana M. Drapkina
- National Medical Research Center for Therapy and Preventive Medicine, Petroverigskyj Lane 10, bld.3, 101990 Moscow, Russia; (A.F.S.); (A.A.Y.); (D.U.A.)
| | - Sergey M. Yudin
- Centre for Strategic Planning and Management of Biomedical Health Risks of Federal Medical Biological Agency, Pogodinskaya Str., 10/1, 119121 Moscow, Russia; (A.V.K.); (S.S.K.); (S.Y.B.); (M.V.L.); (A.S.K.)
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11
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Dregelies T, Haumaier F, Sterlacci W, Backert S, Vieth M. Detection of Fusobacterium nucleatum in Patients with Colitis-Associated Colorectal Cancer. Curr Microbiol 2023; 80:293. [PMID: 37468740 PMCID: PMC10356651 DOI: 10.1007/s00284-023-03398-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 06/30/2023] [Indexed: 07/21/2023]
Abstract
Fusobacterium nucleatum is supposed to play a critical role in the development of colorectal cancer. The species has also been associated with ulcerative colitis (UC) that can progress into colorectal cancer, however, the involvement of bacteria in this process remains unclear. We analysed 177 colon biopsies obtained from patients during screening, including 20 healthy controls, 56 UC cases and 69 cases at different stages of progression to colitis-associated cancer (CAC); 32 samples of sporadic colorectal carcinoma (sCRC) were also included. The presence of F. nucleatum was detected by quantitative real-time PCR (qPCR). Our data show an association between the presence of the bacteria and the progression of carcinogenesis in UC patients. In 39.5% of CAC samples F. nucleatum was detected, compared to only 1.8% in UC cases. The bacteria were detected in 6.3% of samples with initial neoplastic transformation, so-called low-grade dysplasia (LGD), whereas high-grade dysplasia (HGD) resulted in 33.3% of samples positive for F. nucleatum. The fraction of F. nucleatum-positive samples from sCRC cases was 56.3%, which was not significantly different to the CAC group. We conclude that F. nucleatum is associated with the occurrence and progression of colon carcinogenesis, rather than with UC itself.
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Affiliation(s)
- Theresa Dregelies
- Institut für Mikrobiologie, Friedrich-Alexander-Universität, Staudtstr. 5, 91058, Erlangen, Germany
- Institut für Pathologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Klinikum Bayreuth, Preuschwitzer Str. 101, 95445, Bayreuth, Germany
| | - Franziska Haumaier
- Institut für Pathologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Klinikum Bayreuth, Preuschwitzer Str. 101, 95445, Bayreuth, Germany
| | - William Sterlacci
- Institut für Pathologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Klinikum Bayreuth, Preuschwitzer Str. 101, 95445, Bayreuth, Germany
| | - Steffen Backert
- Institut für Mikrobiologie, Friedrich-Alexander-Universität, Staudtstr. 5, 91058, Erlangen, Germany
| | - Michael Vieth
- Institut für Pathologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Klinikum Bayreuth, Preuschwitzer Str. 101, 95445, Bayreuth, Germany.
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12
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Frioux C, Ansorge R, Özkurt E, Ghassemi Nedjad C, Fritscher J, Quince C, Waszak SM, Hildebrand F. Enterosignatures define common bacterial guilds in the human gut microbiome. Cell Host Microbe 2023; 31:1111-1125.e6. [PMID: 37339626 DOI: 10.1016/j.chom.2023.05.024] [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: 01/26/2023] [Revised: 04/03/2023] [Accepted: 05/23/2023] [Indexed: 06/22/2023]
Abstract
The human gut microbiome composition is generally in a stable dynamic equilibrium, but it can deteriorate into dysbiotic states detrimental to host health. To disentangle the inherent complexity and capture the ecological spectrum of microbiome variability, we used 5,230 gut metagenomes to characterize signatures of bacteria commonly co-occurring, termed enterosignatures (ESs). We find five generalizable ESs dominated by either Bacteroides, Firmicutes, Prevotella, Bifidobacterium, or Escherichia. This model confirms key ecological characteristics known from previous enterotype concepts, while enabling the detection of gradual shifts in community structures. Temporal analysis implies that the Bacteroides-associated ES is "core" in the resilience of westernized gut microbiomes, while combinations with other ESs often complement the functional spectrum. The model reliably detects atypical gut microbiomes correlated with adverse host health conditions and/or the presence of pathobionts. ESs provide an interpretable and generic model that enables an intuitive characterization of gut microbiome composition in health and disease.
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Affiliation(s)
- Clémence Frioux
- Food, Microbiome, and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, NR4 7UQ Norwich, Norfolk, UK; Digital Biology, Earlham Institute NR4 7UZ Norwich, Norfolk, UK; Inria, University of Bordeaux, INRAE, 33400 Talence, France.
| | - Rebecca Ansorge
- Food, Microbiome, and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, NR4 7UQ Norwich, Norfolk, UK; Digital Biology, Earlham Institute NR4 7UZ Norwich, Norfolk, UK
| | - Ezgi Özkurt
- Food, Microbiome, and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, NR4 7UQ Norwich, Norfolk, UK; Digital Biology, Earlham Institute NR4 7UZ Norwich, Norfolk, UK
| | | | - Joachim Fritscher
- Food, Microbiome, and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, NR4 7UQ Norwich, Norfolk, UK; Digital Biology, Earlham Institute NR4 7UZ Norwich, Norfolk, UK
| | - Christopher Quince
- Food, Microbiome, and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, NR4 7UQ Norwich, Norfolk, UK; Digital Biology, Earlham Institute NR4 7UZ Norwich, Norfolk, UK
| | - Sebastian M Waszak
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, Oslo 0318, Norway; Department of Neurology, University of California, San Francisco, San Francisco, CA 94148, USA; Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Falk Hildebrand
- Food, Microbiome, and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, NR4 7UQ Norwich, Norfolk, UK; Digital Biology, Earlham Institute NR4 7UZ Norwich, Norfolk, UK.
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13
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Strauss JC, Haskey N, Ramay HR, Ghosh TS, Taylor LM, Yousuf M, Ohland C, McCoy KD, Ingram RJM, Ghosh S, Panaccione R, Raman M. Weighted Gene Co-Expression Network Analysis Identifies a Functional Guild and Metabolite Cluster Mediating the Relationship between Mucosal Inflammation and Adherence to the Mediterranean Diet in Ulcerative Colitis. Int J Mol Sci 2023; 24:ijms24087323. [PMID: 37108484 PMCID: PMC10138710 DOI: 10.3390/ijms24087323] [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: 03/07/2023] [Revised: 04/09/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Diet influences the pathogenesis and clinical course of inflammatory bowel disease (IBD). The Mediterranean diet (MD) is linked to reductions in inflammatory biomarkers and alterations in microbial taxa and metabolites associated with health. We aimed to identify features of the gut microbiome that mediate the relationship between the MD and fecal calprotectin (FCP) in ulcerative colitis (UC). Weighted gene co-expression network analysis (WGCNA) was used to identify modules of co-abundant microbial taxa and metabolites correlated with the MD and FCP. The features considered were gut microbial taxa, serum metabolites, dietary components, short-chain fatty acid and bile acid profiles in participants that experienced an increase (n = 13) or decrease in FCP (n = 16) over eight weeks. WGCNA revealed ten modules containing sixteen key features that acted as key mediators between the MD and FCP. Three taxa (Faecalibacterium prausnitzii, Dorea longicatena, Roseburia inulinivorans) and a cluster of four metabolites (benzyl alcohol, 3-hydroxyphenylacetate, 3-4-hydroxyphenylacetate and phenylacetate) demonstrated a strong mediating effect (ACME: -1.23, p = 0.004). This study identified a novel association between diet, inflammation and the gut microbiome, providing new insights into the underlying mechanisms of how a MD may influence IBD. See clinicaltrials.gov (NCT04474561).
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Affiliation(s)
- Jaclyn C Strauss
- Department of Medicine, Cumming School of Medicine, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
| | - Natasha Haskey
- Department of Biology, Irving K Barber Faculty of Science, University of British Columbia-Okanagan, 3137 University Way, Kelowna, BC V1V 1V7, Canada
| | - Hena R Ramay
- International Microbiome Centre, HRIC 4AA08 Foothills Campus, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Tarini Shankar Ghosh
- APC Microbiome Ireland, College of Medicine and Health, University College Cork, College Road, National University of Ireland, T12 K8AF Cork, Ireland
| | - Lorian M Taylor
- Department of Medicine, Cumming School of Medicine, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
| | - Munazza Yousuf
- Department of Medicine, Cumming School of Medicine, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
| | - Christina Ohland
- International Microbiome Centre, HRIC 4AA08 Foothills Campus, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Kathy D McCoy
- International Microbiome Centre, HRIC 4AA08 Foothills Campus, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Richard J M Ingram
- Department of Medicine, Cumming School of Medicine, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
| | - Subrata Ghosh
- APC Microbiome Ireland, College of Medicine and Health, University College Cork, College Road, National University of Ireland, T12 K8AF Cork, Ireland
| | - Remo Panaccione
- Department of Medicine, Cumming School of Medicine, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
| | - Maitreyi Raman
- Department of Medicine, Cumming School of Medicine, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
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14
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Chen W, Wang J, Song J, Sun Q, Zhu B, Qin L. Exogenous and Endophytic Fungal Communities of Dendrobium nobile Lindl. across Different Habitats and Their Enhancement of Host Plants' Dendrobine Content and Biomass Accumulation. ACS OMEGA 2023; 8:12489-12500. [PMID: 37033800 PMCID: PMC10077458 DOI: 10.1021/acsomega.3c00608] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/15/2023] [Indexed: 06/19/2023]
Abstract
Both the biosynthesis and array of bioactive and medicinal compounds in plants can be influenced by interactions with endophytic and exogenous fungi. However, the composition of endophytic and exogenous fungal communities associated with many medicinal plants is unknown, and the mechanism by which these fungi stimulate the secondary metabolism of host plants is unclear. In this study, we conducted a correlative analysis between endophytic and exogenous fungi and dendrobine and biomass accumulation in Dendrobium nobile across five Chinese habitats: wild Danxia rock, greenhouse-associated large Danxia stone, broken Danxia stone, broken coarse sandstone, and wood spile. Across habitats, fungal communities exhibited significant differences. The abundances of Phyllosticta, Trichoderma, and Hydropus were higher in wild habitats than in greenhouse habitats. Wild habitats were host to a higher diversity and richness of exogenous fungi than were greenhouse habitats. However, there was no significant difference in endophytic fungal diversity between habitats. The differences between the fungal communities' effects on the dendrobine content and biomass of D. nobile were attributable to the composition of endophytic and exogenous fungi. Exogenous fungi had a greater impact than endophytic fungi on the accumulation of fresh weight (FW) and dendrobine in D. nobile. Furthermore, D. nobile samples with higher exogenous fungal richness and diversity exhibited higher dendrobine content and FW. Phyllosticta was the only genus to be significantly positively correlated with both FW and dendrobine content. A total of 86 strains of endophytic fungi were isolated from the roots, stems, and leaves of D. nobile, of which 8 strains were found to be symbiotic with D. nobile tissue-cultured seedlings. The strain DN14 (Phyllosticta fallopiae) was found to promote not only biomass accumulation (11.44%) but also dendrobine content (33.80%) in D. nobile tissue-cultured seedlings. The results of this study will aid in the development of strategies to increase the production of dendrobine in D. nobile. This work could also facilitate the screening of beneficial endophytic and exogenous fungal probiotics for use as biofertilizers in D. nobile.
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15
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Haskey N, Gold SL, Faith JJ, Raman M. To Fiber or Not to Fiber: The Swinging Pendulum of Fiber Supplementation in Patients with Inflammatory Bowel Disease. Nutrients 2023; 15:nu15051080. [PMID: 36904081 PMCID: PMC10005525 DOI: 10.3390/nu15051080] [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: 01/29/2023] [Revised: 02/18/2023] [Accepted: 02/20/2023] [Indexed: 02/24/2023] Open
Abstract
Evidence-based dietary guidance around dietary fiber in inflammatory bowel disease (IBD) has been limited owing to insufficient reproducibility in intervention trials. However, the pendulum has swung because of our increased understanding of the importance of fibers in maintaining a health-associated microbiome. Preliminary evidence suggests that dietary fiber can alter the gut microbiome, improve IBD symptoms, balance inflammation, and enhance health-related quality of life. Therefore, it is now more vital than ever to examine how fiber could be used as a therapeutic strategy to manage and prevent disease relapse. At present, there is limited knowledge about which fibers are optimal and in what form and quantity they should be consumed to benefit patients with IBD. Additionally, individual microbiomes play a strong role in determining the outcomes and necessitate a more personalized nutritional approach to implementing dietary changes, as dietary fiber may not be as benign as once thought in a dysbiotic microbiome. This review describes dietary fibers and their mechanism of action within the microbiome, details novel fiber sources, including resistant starches and polyphenols, and concludes with potential future directions in fiber research, including the move toward precision nutrition.
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Affiliation(s)
- Natasha Haskey
- Department of Biology, The Irving K. Barber Faculty of Science, University of British Columbia—Okanagan, 3187 University Way, Kelowna, BC V1V 1V7, Canada
- Division of Gastroenterology, Cumming School of Medicine, University of Calgary, 6D33 TRW Building, 3280 Hospital Drive NW, Calgary, AB T2N 4N1, Canada
| | - Stephanie L. Gold
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA
| | - Jeremiah J. Faith
- Precision Immunology Institute and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA
| | - Maitreyi Raman
- Division of Gastroenterology, Cumming School of Medicine, University of Calgary, 6D33 TRW Building, 3280 Hospital Drive NW, Calgary, AB T2N 4N1, Canada
- Correspondence:
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16
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Louis-Jean SF, Agrawal N, Bisht S. Fusobacterium nucleatum Pyogenic Liver Abscess and the Role of Bacterial Virulence and Gut Microbiota Dysbiosis. Cureus 2023; 15:e34548. [PMID: 36879688 PMCID: PMC9985409 DOI: 10.7759/cureus.34548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/02/2023] [Indexed: 02/05/2023] Open
Abstract
In the United States, pyogenic liver abscesses are often due to monomicrobial infection and are rarely documented to be a consequence of Fusobacterium infection, a common cause of Lemierre's syndrome. Recent advances in gut microbial studies have identified Fusobacterium as a commensal gut flora that becomes pathogenic in the setting of dysbiosis resulting from colorectal diseases, such as diverticulitis. While the bacteria's tropism for the liver remains to be elucidated, the virulence pattern of Fusobacterium and the portal venous drainage system have allowed us to understand the bacterium's propensity for causing right hepatic abscesses. In this case report, we detail an immunocompetent man with a history of sigmoid diverticulitis who developed a right hepatic abscess due to Fusobacterium nucleatum, while delineating a review of the literature on the virulent properties of the bacterium and the impact of gut microbiota dysbiosis in its pathogenicity. A descriptive analysis was also performed to identify the characteristics of patients who are at risk in hopes of further improving the clinical diagnostic schema for this condition.
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Affiliation(s)
| | - Nirav Agrawal
- Internal Medicine, Anne Arundel Medical Center, Annapolis, USA
| | - Sushrit Bisht
- Internal Medicine, Anne Arundel Medical Center, Annapolis, USA
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17
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Optimized Antimicrobial Peptide Jelleine-I Derivative Br-J-I Inhibits Fusobacterium Nucleatum to Suppress Colorectal Cancer Progression. Int J Mol Sci 2023; 24:ijms24021469. [PMID: 36674985 PMCID: PMC9865857 DOI: 10.3390/ijms24021469] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/16/2022] [Accepted: 12/22/2022] [Indexed: 01/15/2023] Open
Abstract
Colorectal cancer (CRC) is a major health burden worldwide due to its high morbidity, mortality, and complex etiology. Fusobacterium nucleatum (Fn), a Gram-negative anaerobe found in 30% of CRC patients, promotes CRC carcinogenesis, metastasis, and chemoresistance. Effective antimicrobial treatment is an unmet need for the rising CRC burden. Antimicrobial peptides (AMPs) represent a new class of antimicrobial drugs. In our previous study, we did the structure-activity study of Jelleine-I (J-I) and identified several halogenated J-I derivatives Cl-J-I, Br-J-I, and I-J-I. To determine whether those J-I derivatives can be a new therapy for bacterial-associated CRC, here we tested the antibacterial activities of these AMPs against Fn and their effects on CRC development. We found that Br-J-I showed the highest anti-Fn activity and Br-J-I may target membrane-associated FadA for Fn membrane disruption. More importantly, Fn promoted the growth of CRC cells-derived xenograft tumors. Br-J-I suppressed Fn load, colon inflammation, and Fn-induced CRC growth. Of note, Br-J-I induced better anti-CRC effects than common antibiotic metronidazole and Br-J-I sensitized the cancer-killing effect of chemotherapy drug 5-fluorouracil. These results suggest that Br-J-I could be considered as an adjunctive agent for CRC treatment and AMPs-based combination treatment is a new strategy for CRC in the future.
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18
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Di Stefano M, Santonocito S, Polizzi A, Mauceri R, Troiano G, Lo Giudice A, Romano A, Mascitti M, Isola G. A Reciprocal Link between Oral, Gut Microbiota during Periodontitis: The Potential Role of Probiotics in Reducing Dysbiosis-Induced Inflammation. Int J Mol Sci 2023; 24:ijms24021084. [PMID: 36674600 PMCID: PMC9867370 DOI: 10.3390/ijms24021084] [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: 10/24/2022] [Revised: 12/08/2022] [Accepted: 12/28/2022] [Indexed: 01/09/2023] Open
Abstract
Human body is colonized by a florid microbial community of bacteria, archaea, fungi, protists, helminths, and viruses, known as microbiota, which co-evolves with the host and influences its health through all stages of its life. It is well known that oral microorganisms form highly structurally and functionally organized multi-species biofilms and establish a network of complex mutual inter-species interactions having a primary function in synergy, signaling, or antagonism. This ecological model allows the microorganisms to increase their resistance to antimicrobial agents and settle a balanced microbes-host symbiotic relationship that ensures oral and global health status in humans. The host-associated microbiome is an important factor in human health and disease. Therefore, to develop novel diagnostic, therapeutic, and preventive strategies, microbiome's functions and the reciprocal interactions every microbiome entertains with other microbial communities in the human body are being investigated. This review provides an analysis of the literature about the close connection between the two largest microbial communities in humans: the oral and the gut microbiomes. Furthermore, it focuses on how the alteration of their microbial and functional characteristics can lead to and reciprocally influence the onset of both oral and intestinal microbiome-associated illness, along with the potential role of probiotics in ameliorating inflammation and microbial dysbiosis.
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Affiliation(s)
- Mattia Di Stefano
- Department of General Surgery and Surgical-Medical Specialties, School of Dentistry, University of Catania, 95124 Catania, Italy
| | - Simona Santonocito
- Department of General Surgery and Surgical-Medical Specialties, School of Dentistry, University of Catania, 95124 Catania, Italy
| | - Alessandro Polizzi
- Department of General Surgery and Surgical-Medical Specialties, School of Dentistry, University of Catania, 95124 Catania, Italy
| | - Rodolfo Mauceri
- Department of Surgical, Oncological and Oral Sciences (Di.Chir.On.S.), University of Palermo, 90127 Palermo, Italy
| | - Giuseppe Troiano
- Department of Clinical and Experimental Medicine, University of Foggia, Via Rovelli 50, 71122 Foggia, Italy
| | - Antonino Lo Giudice
- Department of General Surgery and Surgical-Medical Specialties, School of Dentistry, University of Catania, 95124 Catania, Italy
| | - Alessandra Romano
- Department of General Surgery and Surgical-Medical Specialties, School of Dentistry, University of Catania, 95124 Catania, Italy
| | - Marco Mascitti
- Department of Clinical Specialistic and Dental Sciences, Marche Polytechnic University, Via Tronto 10/A, 60126 Ancona, Italy
- Correspondence: (M.M.); (G.I.)
| | - Gaetano Isola
- Department of General Surgery and Surgical-Medical Specialties, School of Dentistry, University of Catania, 95124 Catania, Italy
- Correspondence: (M.M.); (G.I.)
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19
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Wiredu Ocansey DK, Hang S, Yuan X, Qian H, Zhou M, Valerie Olovo C, Zhang X, Mao F. The diagnostic and prognostic potential of gut bacteria in inflammatory bowel disease. Gut Microbes 2023; 15:2176118. [PMID: 36794838 PMCID: PMC9980661 DOI: 10.1080/19490976.2023.2176118] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/17/2023] Open
Abstract
The gut microbiome serves as a signaling hub that integrates environmental inputs with genetic and immune signals to influence the host's metabolism and immunity. Gut bacteria are intricately connected with human health and disease state, with specific bacteria species driving the characteristic dysbiosis found in gastrointestinal conditions such as inflammatory bowel disease (IBD); thus, gut bacteria changes could be harnessed to improve IBD diagnosis, prognosis, and treatment. The advancement in next-generation sequencing techniques such as 16S rRNA and whole-genome shotgun sequencing has allowed the exploration of the complexity of the gut microbial ecosystem with high resolution. Current microbiome data is promising and appears to perform better in some studies than the currently used fecal inflammation biomarker, calprotectin, in predicting IBD from healthy controls and irritable bowel syndrome (IBS). This study reviews current data on the differential potential of gut bacteria within IBD cohorts, and between IBD and other gastrointestinal diseases.
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Affiliation(s)
- Dickson Kofi Wiredu Ocansey
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang, P.R. China,Directorate of University Health Services, University of Cape Coast, PMB, Cape Coast, Ghana
| | - Sanhua Hang
- The People’s Hospital of Danyang, Affiliated Danyang Hospital of Nantong University, Zhenjiang, P.R. China
| | - Xinyi Yuan
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang, P.R. China
| | - Hua Qian
- Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, P.R. China
| | - Mengjiao Zhou
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang, P.R. China
| | - Chinasa Valerie Olovo
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang, P.R. China,Department of Microbiology, University of Nigeria, Nsukka, Nigeria
| | - Xu Zhang
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang, P.R. China
| | - Fei Mao
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang, P.R. China,CONTACT Fei Mao Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu212013, China
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20
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Abdelbary MMH, Hatting M, Bott A, Dahlhausen A, Keller D, Trautwein C, Conrads G. The oral-gut axis: Salivary and fecal microbiome dysbiosis in patients with inflammatory bowel disease. Front Cell Infect Microbiol 2022; 12:1010853. [PMID: 36275026 PMCID: PMC9585322 DOI: 10.3389/fcimb.2022.1010853] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 09/16/2022] [Indexed: 11/24/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a group of chronic inflammatory disorders that fall into two main categories: Crohn’s disease (CD) and ulcerative colitis (UC). The gastrointestinal tract extends from the mouth to the anus and harbors diverse bacterial communities. Several sequencing-based studies have identified an intestinal enrichment of oral-associated bacteria and demonstrated their ability to induce intestinal inflammation in mice, suggesting that intestinal pathobionts originate from the oral cavity, particularly members of the genus Streptococcus. This study aimed to investigate the composition of the salivary and fecal microbiome of IBD patients (n = 14) compared to healthy controls (n = 12) and to determine the abundance of common bacterial taxa in both niches. Metagenomic DNA was extracted from saliva and fecal samples, and the 16S rRNA gene was targeted for sequencing. Our results revealed that the overall microbial composition of saliva was significantly altered in the IBD patients compared to the control subjects (p = 0.038). At the genus level, Veillonella and Prevotella were highly abundant in IBD (median: 25.4% and 22.2%, respectively) compared to the control group (17.9% and 13.4%, respectively). In contrast, Neisseria, Streptococcus, Haemophilus, and Fusobacterium were associated with a healthy gut state. Regarding the fecal microbiome, the IBD group had a significantly higher abundance of Clostridium sensu stricto 1 and Escherichia-Shigella (both comprising pathogenic bacteria) compared with the control group. Members of both bacterial groups have previously been shown to positively correlate with intestinal inflammation and high expression of pro-inflammatory cytokines that disrupt intestinal barrier integrity. In addition, we demonstrate that the increased abundance of Clostridium sensu stricto 1 and Escherichia-Shigella has also been associated with significant upregulation of certain metabolic pathways in the feces of the IBD group, including bacterial invasion of epithelial cells. Streptococcus was the only common genus detected in both the salivary and fecal microbiome and represented the oral-gut axis in our study. Using culture-based methods, we isolated 57 and 91 Streptococcus strains from saliva as well as 40 and 31 strains from fecal samples of the controls and IBD patients, respectively. The phylogenetic tree of streptococci based on sodA sequences revealed several patient-specific clusters comprising salivary and fecal streptococcal isolates from the same patient and belonging to the same species, suggesting that the oral cavity is an endogenous reservoir for intestinal strains.
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Affiliation(s)
- Mohamed M. H. Abdelbary
- Division of Oral Microbiology and Immunology, Department of Operative Dentistry, Periodontology and Preventive Dentistry, Rheinisch-Westfälische Technische Hochschule (RWTH) University Hospital, Aachen, Germany
- *Correspondence: Mohamed M. H. Abdelbary,
| | | | - Alexandra Bott
- Division of Oral Microbiology and Immunology, Department of Operative Dentistry, Periodontology and Preventive Dentistry, Rheinisch-Westfälische Technische Hochschule (RWTH) University Hospital, Aachen, Germany
| | - Andrea Dahlhausen
- University Medical Center for Occupational Medicine, RWTH University, Aachen, Germany
| | - Doris Keller
- University Medical Center for Occupational Medicine, RWTH University, Aachen, Germany
| | | | - Georg Conrads
- Division of Oral Microbiology and Immunology, Department of Operative Dentistry, Periodontology and Preventive Dentistry, Rheinisch-Westfälische Technische Hochschule (RWTH) University Hospital, Aachen, Germany
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21
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Wang Z, Peters BA, Usyk M, Xing J, Hanna DB, Wang T, Post WS, Landay AL, Hodis HN, Weber K, French A, Golub ET, Lazar J, Gustafson D, Kassaye S, Aouizerat B, Haberlen S, Malvestutto C, Budoff M, Wolinsky SM, Sharma A, Anastos K, Clish CB, Kaplan RC, Burk RD, Qi Q. Gut Microbiota, Plasma Metabolomic Profiles, and Carotid Artery Atherosclerosis in HIV Infection. Arterioscler Thromb Vasc Biol 2022; 42:1081-1093. [PMID: 35678187 PMCID: PMC9339474 DOI: 10.1161/atvbaha.121.317276] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Alterations in gut microbiota and blood metabolomic profiles have been implicated in HIV infection and cardiovascular disease. However, it remains unclear whether alterations in gut microbiota may contribute to disrupted host blood metabolomic profiles in relation to atherosclerosis, especially in the context of HIV infection. METHODS We analyzed cross-sectional associations between gut microbiota features and carotid artery plaque in 361 women with or at high risk of HIV (67% HIV+), and further integrated plaque-associated microbial features with plasma lipidomic/metabolomic profiles. Furthermore, in 737 women and men, we examined prospective associations of baseline gut bacteria-associated lipidomic and metabolomic profiles with incident carotid artery plaque over 7-year follow-up. RESULTS We found 2 potentially pathogenic bacteria, Fusobacterium and Proteus, were associated with carotid artery plaque; while the beneficial butyrate producer Odoribacter was inversely associated with plaque. Fusobacterium and Proteus were associated with multiple lipids/metabolites which were clustered into 8 modules in network. A module comprised of 9 lysophosphatidylcholines and lysophosphatidylethanolamines and a module comprised of 9 diglycerides were associated with increased risk of carotid artery plaque (risk ratio [95% CI], 1.34 [1.09-1.64] and 1.24 [1.02-1.51] per SD increment, respectively). Functional analyses identified bacterial enzymes in lipid metabolism associated with these plasma lipids. In particular, phospholipase A1 and A2 are the key enzymes in the reactions producing lysophosphatidylcholines and lysophosphatidylethanolamines. CONCLUSIONS Among individuals with or at high risk of HIV infection, we identified altered gut microbiota and related functional capacities in the lipid metabolism associated with disrupted plasma lipidomic profiles and carotid artery atherosclerosis.
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Affiliation(s)
- Zheng Wang
- Department of Epidemiology and Population Health (Z.W., B.A.P., J.X., D.B.H., T.W., K.A., R.C.K., R.D.B., Q.Q.), Albert Einstein College of Medicine, Bronx, New York
| | - Brandilyn A Peters
- Department of Epidemiology and Population Health (Z.W., B.A.P., J.X., D.B.H., T.W., K.A., R.C.K., R.D.B., Q.Q.), Albert Einstein College of Medicine, Bronx, New York
| | - Mykhaylo Usyk
- Department of Pediatrics (M.U., R.D.B.), Albert Einstein College of Medicine, Bronx, New York
| | - Jiaqian Xing
- Department of Epidemiology and Population Health (Z.W., B.A.P., J.X., D.B.H., T.W., K.A., R.C.K., R.D.B., Q.Q.), Albert Einstein College of Medicine, Bronx, New York
| | - David B Hanna
- Department of Epidemiology and Population Health (Z.W., B.A.P., J.X., D.B.H., T.W., K.A., R.C.K., R.D.B., Q.Q.), Albert Einstein College of Medicine, Bronx, New York
| | - Tao Wang
- Department of Epidemiology and Population Health (Z.W., B.A.P., J.X., D.B.H., T.W., K.A., R.C.K., R.D.B., Q.Q.), Albert Einstein College of Medicine, Bronx, New York
| | - Wendy S Post
- Department of Medicine, Johns Hopkins University, Baltimore, MD (W.S.P.)
| | - Alan L Landay
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL (A.L.L)
| | - Howard N Hodis
- Atherosclerosis Research Unit, Keck School of Medicine, University of Southern California, Los Angeles (H.N.H.)
| | | | - Audrey French
- Department of Internal Medicine, John H. Stroger Jr Hospital of Cook County, Chicago, IL (A.F.)
| | - Elizabeth T Golub
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD (E.T.G., S.H.)
| | - Jason Lazar
- Department of Medicine (J.L.), State University of New York Downstate Medical Center, Brooklyn
| | - Deborah Gustafson
- Department of Neurology (D.G.), State University of New York Downstate Medical Center, Brooklyn
| | - Seble Kassaye
- Department of Medicine, Georgetown University, Washington DC (S.K.)
| | | | - Sabina Haberlen
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD (E.T.G., S.H.)
| | | | - Matthew Budoff
- David Geffen School of Medicine, University of California, Los Angeles (M.B.)
| | - Steven M Wolinsky
- Department of Medicine, Feinberg School of Medicine, Northwestern University Chicago, IL (S.M.W.)
| | - Anjali Sharma
- Department of Medicine (A.S., K.A.), Albert Einstein College of Medicine, Bronx, New York
| | - Kathryn Anastos
- Department of Epidemiology and Population Health (Z.W., B.A.P., J.X., D.B.H., T.W., K.A., R.C.K., R.D.B., Q.Q.), Albert Einstein College of Medicine, Bronx, New York.,Department of Medicine (A.S., K.A.), Albert Einstein College of Medicine, Bronx, New York
| | - Clary B Clish
- Broad Institute of MIT and Harvard, Cambridge, MA (C.B.C.)
| | - Robert C Kaplan
- Department of Epidemiology and Population Health (Z.W., B.A.P., J.X., D.B.H., T.W., K.A., R.C.K., R.D.B., Q.Q.), Albert Einstein College of Medicine, Bronx, New York.,Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA (R.C.K.)
| | - Robert D Burk
- Department of Epidemiology and Population Health (Z.W., B.A.P., J.X., D.B.H., T.W., K.A., R.C.K., R.D.B., Q.Q.), Albert Einstein College of Medicine, Bronx, New York.,Department of Pediatrics (M.U., R.D.B.), Albert Einstein College of Medicine, Bronx, New York.,Department of Microbiology & Immunology (R.D.B.), Albert Einstein College of Medicine, Bronx, New York
| | - Qibin Qi
- Department of Epidemiology and Population Health (Z.W., B.A.P., J.X., D.B.H., T.W., K.A., R.C.K., R.D.B., Q.Q.), Albert Einstein College of Medicine, Bronx, New York.,Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA (Q.Q.)
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22
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Periodontitis may induce gut microbiota dysbiosis via salivary microbiota. Int J Oral Sci 2022; 14:32. [PMID: 35732628 PMCID: PMC9217941 DOI: 10.1038/s41368-022-00183-3] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 05/23/2022] [Accepted: 05/28/2022] [Indexed: 12/17/2022] Open
Abstract
The aim of this study was to identify whether periodontitis induces gut microbiota dysbiosis via invasion by salivary microbes. First, faecal and salivary samples were collected from periodontally healthy participants (PH group, n = 16) and patients with severe periodontitis (SP group, n = 21) and analysed by 16S ribosomal RNA sequencing. Significant differences were observed in both the faecal and salivary microbiota between the PH and SP groups. Notably, more saliva-sourced microbes were observed in the faecal samples of the SP group. Then, the remaining salivary microbes were transplanted into C57BL6/J mice (the C-PH group and the C-SP group), and it was found that the composition of the gut microbiota of the C-SP group was significantly different from that of the C-PH group, with Porphyromonadaceae and Fusobacterium being significantly enriched in the C-SP group. In the colon, the C-SP group showed significantly reduced crypt depth and zonula occludens-1 expression. The mRNA expression levels of pro-inflammatory cytokines, chemokines and tight junction proteins were significantly higher in the C-SP group. To further investigate whether salivary bacteria could persist in the intestine, the salivary microbiota was stained with carboxyfluorescein diacetate succinimidyl ester and transplanted into mice. We found that salivary microbes from both the PH group and the SP group could persist in the gut for at least 24 h. Thus, our data demonstrate that periodontitis may induce gut microbiota dysbiosis through the influx of salivary microbes.
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23
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Franklin S, Aitken SL, Shi Y, Sahasrabhojane PV, Robinson S, Peterson CB, Daver N, Ajami NA, Kontoyiannis DP, Shelburne SA, Galloway-Peña J. Oral and Stool Microbiome Coalescence and Its Association With Antibiotic Exposure in Acute Leukemia Patients. Front Cell Infect Microbiol 2022; 12:848580. [PMID: 35433514 PMCID: PMC9010033 DOI: 10.3389/fcimb.2022.848580] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 03/08/2022] [Indexed: 11/16/2022] Open
Abstract
Failure to maintain segregation of oral and gut microbial communities has been linked to several diseases. We sought to characterize oral-fecal microbiome community coalescence, ectopic extension of oral bacteria, clinical variables contributing to this phenomenon, and associated infectious consequences by analyzing the 16S rRNA V4 sequences of longitudinal fecal (n=551) and oral (n=737) samples from 97 patients with acute myeloid leukemia (AML) receiving induction chemotherapy (IC). Clustering observed in permutation based multivariate analysis of variance (PERMANOVA) of Bray-Curtis dissimilarity and PCoA plot of UniFrac distances between intra-patient longitudinal oral-stool sample pairs suggested potential oral-stool microbial community coalescence. Bray-Curtis dissimilarities and UniFrac distances were used to create an objective definition of microbial community coalescence. We determined that only 23 of the 92 patients exhibited oral-stool community coalescence. This was validated through a linear mixed model which determined that patients who experienced coalescence had an increased proportion of shared to unique OTUs between their oral-stool sample pairs over time compared to non-coalesced patients. Evaluation of longitudinal microbial characteristics revealed that patients who experienced coalescence had increased stool abundance of Streptococcus and Stenotrophomonas compared to non-coalesced patients. When treated as a time-varying covariate, each additional day of linezolid (HR 1.15, 95% CI 1.06 – 1.24, P <0.001), meropenem (HR 1.13, 95% CI 1.05 – 1.21, P = 0.001), metronidazole (HR 1.13, 95% CI 1.05 – 1.21, P = 0.001), and cefepime (HR 1.10, 95% CI 1.01 – 1.18, P = 0.021) increased the hazard of oral-stool microbial community coalescence. Levofloxacin receipt was associated with a lower risk of microbiome community coalescence (HR 0.75, 95% CI 0.61 – 0.93, P = 0.009). By the time of neutrophil recovery, the relative abundance of Bacteroidia (P<0.001), Fusobacteria (P=0.012), and Clostridia (P=0.013) in the stool were significantly lower in patients with oral-gut community coalescence. Exhibiting oral-stool community coalescence was associated with the occurrence of infections prior to neutrophil recovery (P=0.002), as well as infections during the 90 days post neutrophil recovery (P=0.027). This work elucidates specific antimicrobial effects on microbial ecology and furthers the understanding of oral/intestinal microbial biogeography and its implications for adverse clinical outcomes.
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Affiliation(s)
- Samantha Franklin
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX, United States
- Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, College Station, TX, United States
| | - Samuel L. Aitken
- Department of Pharmacy, Michigan Medicine, Ann Arbor, MI, United States
| | - Yushi Shi
- Department of Statistics and Center for Biomedical Informatics, University of Missouri, Columbia, MO, United States
| | - Pranoti V. Sahasrabhojane
- Department of Infectious Disease, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Sarah Robinson
- Department of Statistics, Rice University, Houston, TX, United States
| | - Christine B. Peterson
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Naval Daver
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Nadim A. Ajami
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Dimitrios P. Kontoyiannis
- Department of Infectious Disease, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Samuel A. Shelburne
- Department of Infectious Disease, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Jessica Galloway-Peña
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX, United States
- Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, College Station, TX, United States
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
- *Correspondence: Jessica Galloway-Peña,
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24
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Molinero N, Taladrid D, Zorraquín-Peña I, de Celis M, Belda I, Mira A, Bartolomé B, Moreno-Arribas MV. Ulcerative Colitis Seems to Imply Oral Microbiome Dysbiosis. Curr Issues Mol Biol 2022; 44:1513-1527. [PMID: 35723361 PMCID: PMC9164047 DOI: 10.3390/cimb44040103] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/19/2022] [Accepted: 03/29/2022] [Indexed: 12/12/2022] Open
Abstract
Ulcerative colitis (UC) is a recurrent pathology of complex etiology that has been occasionally associated with oral lesions, but the overall composition of the oral microbiome in UC patients and its role in the pathogenesis of the disease are still poorly understood. In this study, the oral microbiome of UC patients and healthy individuals was compared to ascertain the possible changes in the oral microbial communities associated with UC. For this, the salivary microbiota of 10 patients diagnosed with an active phase of UC and 11 healthy controls was analyzed by 16S rRNA gene sequencing (trial ref. ISRCTN39987). Metataxonomic analysis revealed a decrease in the alpha diversity and an imbalance in the relative proportions of some key members of the oral core microbiome in UC patients. Additionally, Staphylococcus members and four differential species or phylotypes were only present in UC patients, not being detected in healthy subjects. This study provides a global snapshot of the existence of oral dysbiosis associated with UC, and the possible presence of potential oral biomarkers.
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Affiliation(s)
- Natalia Molinero
- Institute of Food Science Research (CIAL), CSIC-UAM, Campus de Cantoblanco, Nicolás Cabrera 9, 28049 Madrid, Spain; (N.M.); (D.T.); (I.Z.-P.); (B.B.)
| | - Diego Taladrid
- Institute of Food Science Research (CIAL), CSIC-UAM, Campus de Cantoblanco, Nicolás Cabrera 9, 28049 Madrid, Spain; (N.M.); (D.T.); (I.Z.-P.); (B.B.)
| | - Irene Zorraquín-Peña
- Institute of Food Science Research (CIAL), CSIC-UAM, Campus de Cantoblanco, Nicolás Cabrera 9, 28049 Madrid, Spain; (N.M.); (D.T.); (I.Z.-P.); (B.B.)
| | - Miguel de Celis
- Department of Genetics, Physiology and Microbiology, Complutense University of Madrid, 28040 Madrid, Spain; (M.d.C.); (I.B.)
| | - Ignacio Belda
- Department of Genetics, Physiology and Microbiology, Complutense University of Madrid, 28040 Madrid, Spain; (M.d.C.); (I.B.)
| | - Alex Mira
- Center for Advanced Research in Public Health, Department of Health and Genomics, FISABIO Foundation, 46020 Valencia, Spain;
| | - Begoña Bartolomé
- Institute of Food Science Research (CIAL), CSIC-UAM, Campus de Cantoblanco, Nicolás Cabrera 9, 28049 Madrid, Spain; (N.M.); (D.T.); (I.Z.-P.); (B.B.)
| | - M. Victoria Moreno-Arribas
- Institute of Food Science Research (CIAL), CSIC-UAM, Campus de Cantoblanco, Nicolás Cabrera 9, 28049 Madrid, Spain; (N.M.); (D.T.); (I.Z.-P.); (B.B.)
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25
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Chandra H, Sharma KK, Tuovinen OH, Sun X, Shukla P. Pathobionts: mechanisms of survival, expansion, and interaction with host with a focus on Clostridioides difficile. Gut Microbes 2022; 13:1979882. [PMID: 34724858 PMCID: PMC8565823 DOI: 10.1080/19490976.2021.1979882] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Pathobionts are opportunistic microbes that emerge as a result of perturbations in the healthy microbiome due to complex interactions of various genetic, exposomal, microbial, and host factors that lead to their selection and expansion. Their proliferations can aggravate inflammatory manifestations, trigger autoimmune diseases, and lead to severe life-threatening conditions. Current surge in microbiome research is unwinding these complex interplays between disease development and protection against pathobionts. This review summarizes the current knowledge of pathobiont emergence with a focus on Clostridioides difficile and the recent findings on the roles of immune cells such as iTreg cells, Th17 cells, innate lymphoid cells, and cytokines in protection against pathobionts. The review calls for adoption of innovative tools and cutting-edge technologies in clinical diagnostics and therapeutics to provide insights in identification and quantification of pathobionts.
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Affiliation(s)
- Harish Chandra
- Department of Environmental Microbiology, School of Earth and Environmental Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow, Uttar Pradesh, India,Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Krishna Kant Sharma
- Laboratory of Enzymology and Recombinant DNA Technology, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Olli H. Tuovinen
- Department of Microbiology, Ohio State University, Columbus, OH, USA
| | - Xingmin Sun
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA,Xingmin Sun Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Pratyoosh Shukla
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India,Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India,CONTACT Pratyoosh Shukla School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, India
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26
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Xu HM, Huang HL, Liu YD, Zhu JQ, Zhou YL, Chen HT, Xu J, Zhao HL, Guo X, Shi W, Nie YQ, Zhou YJ. Selection strategy of dextran sulfate sodium-induced acute or chronic colitis mouse models based on gut microbial profile. BMC Microbiol 2021; 21:279. [PMID: 34654370 PMCID: PMC8520286 DOI: 10.1186/s12866-021-02342-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 10/06/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Dextran sulfate sodium (DSS) replicates ulcerative colitis (UC)-like colitis in murine models. However, the microbial characteristics of DSS-triggered colitis require further clarification. To analyze the changes in gut microbiota associated with DSS-induced acute and chronic colitis. METHODS Acute colitis was induced in mice by administering 3% DSS for 1 week in the drinking water, and chronic colitis was induced by supplementing drinking water with 2.5% DSS every other week for 5 weeks. Control groups received the same drinking water without DSS supplementation. The histopathological score and length of the colons, and disease activity index (DAI) were evaluated to confirm the presence of experimental colitis. Intestinal microbiota was profiled by 16S rDNA sequencing of cecal content. RESULTS Mice with both acute and chronic DSS-triggered colitis had significantly higher DAI and colon histopathological scores in contrast to the control groups (P < 0.0001, P < 0.0001), and the colon was remarkably shortened (P < 0.0001, P < 0.0001). The gut microbiota α-diversity was partly downregulated in both acute and chronic colitis groups in contrast to their respective control groups (Pielou index P = 0.0022, P = 0.0649; Shannon index P = 0.0022, P = 0.0931). The reduction in the Pielou and Shannon indices were more obvious in mice with acute colitis (P = 0.0022, P = 0.0043). The relative abundance of Bacteroides and Turicibacter was increased (all P < 0.05), while that of Lachnospiraceae, Ruminococcaceae, Ruminiclostridium, Rikenella, Alistipes, Alloprevotella, and Butyricicoccus was significantly decreased after acute DSS induction (all P < 0.05). The relative abundance of Bacteroides, Akkermansia, Helicobacter, Parabacteroides, Erysipelatoclostridium, Turicibacter and Romboutsia was also markedly increased (all P < 0.05), and that of Lachnospiraceae_NK4A136_group, Alistipes, Enterorhabdus, Prevotellaceae_UCG-001, Butyricicoccus, Ruminiclostridium_6, Muribaculum, Ruminococcaceae_NK4A214_group, Family_XIII_UCG-001 and Flavonifractor was significantly decreased after chronic DSS induction (all P < 0.05). CONCLUSION DSS-induced acute and chronic colitis demonstrated similar symptoms and histopathological changes. The changes in the gut microbiota of the acute colitis model were closer to that observed in UC. The acute colitis model had greater abundance of SCFAs-producing bacteria and lower α-diversity compared to the chronic colitis model.
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Affiliation(s)
- Hao-Ming Xu
- Department of Gastroenterology and Hepatology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, No. 1 Panfu Road, Guangzhou, 510180, China
| | - Hong-Li Huang
- Department of Gastroenterology and Hepatology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, No. 1 Panfu Road, Guangzhou, 510180, China
| | - Yan-Di Liu
- Department of Gastroenterology and Hepatology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, No. 1 Panfu Road, Guangzhou, 510180, China
| | - Jia-Qi Zhu
- Department of Gastroenterology and Hepatology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, No. 1 Panfu Road, Guangzhou, 510180, China
| | - You-Lian Zhou
- Department of Gastroenterology and Hepatology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, No. 1 Panfu Road, Guangzhou, 510180, China
| | - Hui-Ting Chen
- Department of Gastroenterology and Hepatology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, No. 1 Panfu Road, Guangzhou, 510180, China
| | - Jing Xu
- Department of Gastroenterology and Hepatology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, No. 1 Panfu Road, Guangzhou, 510180, China
| | - Hai-Lan Zhao
- Department of Gastroenterology and Hepatology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, No. 1 Panfu Road, Guangzhou, 510180, China
| | - Xue Guo
- Department of Gastroenterology and Hepatology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, No. 1 Panfu Road, Guangzhou, 510180, China
| | - Wei Shi
- Department of Geriatrics, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, 510180, China
| | - Yu-Qiang Nie
- Department of Gastroenterology and Hepatology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, No. 1 Panfu Road, Guangzhou, 510180, China.
| | - Yong-Jian Zhou
- Department of Gastroenterology and Hepatology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, No. 1 Panfu Road, Guangzhou, 510180, China.
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Cai Z, Zhu T, Liu F, Zhuang Z, Zhao L. Co-pathogens in Periodontitis and Inflammatory Bowel Disease. Front Med (Lausanne) 2021; 8:723719. [PMID: 34616755 PMCID: PMC8488124 DOI: 10.3389/fmed.2021.723719] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 08/27/2021] [Indexed: 02/05/2023] Open
Abstract
Localized inflammatory lesions in one area of the body may affect other distant organs through various modes of transmission thus initiating secondary inflammatory infections. Periodontal disease (PD) and inflammatory bowel disease (IBD) have been shown to coexist. Periodontitis is a multifactorial inflammatory disease, and dental plaque is considered to be the initial risk factor. Individuals with genetic susceptibility are more likely to develop periodontitis when exposed to external stimuli. IBD is affected by host genetics, immunoregulation, daily diet, and the gut microbiota, and its risk factors appear to be shared with those of PD. However, the key etiologies of both diseases remain unclear, thus hindering the exploration of possible links between IBD and PD. Recent studies and systematic reviews have focused on evidence-based statistics of the prevalence and clinical manifestations of both diseases, but discussions of the microbial etiological correlation between periodontitis and intestinal inflammation are scarce. Here, we summarize the potential common pathogenic microorganisms that may serve as bridges between the two diseases. Studies have shown that invasive microorganisms such as Porphyromonas gingivalis, Fusobacterium nucleatum, Klebsiella spp. and Campylobacter spp. play key roles in the comorbidity of PD and IBD.
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Affiliation(s)
- Zhengwen Cai
- State Key Laboratory of Oral Diseases, West China College of Stomatology, Sichuan University, Chengdu, China
| | - Tao Zhu
- State Key Laboratory of Oral Diseases, West China College of Stomatology, Sichuan University, Chengdu, China
| | - Fengshuo Liu
- State Key Laboratory of Oral Diseases, West China College of Stomatology, Sichuan University, Chengdu, China
| | - Zixuan Zhuang
- Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Lei Zhao
- State Key Laboratory of Oral Diseases, West China College of Stomatology, Sichuan University, Chengdu, China.,Department of Periodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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Celik D, Kantarci A. Vascular Changes and Hypoxia in Periodontal Disease as a Link to Systemic Complications. Pathogens 2021; 10:1280. [PMID: 34684229 PMCID: PMC8541389 DOI: 10.3390/pathogens10101280] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/27/2021] [Accepted: 10/02/2021] [Indexed: 12/13/2022] Open
Abstract
The hypoxic microenvironment caused by oral pathogens is the most important cause of the disruption of dynamic hemostasis between the oral microbiome and the immune system. Periodontal infection exacerbates the inflammatory response with increased hypoxia and causes vascular changes. The chronicity of inflammation becomes systemic as a link between oral and systemic diseases. The vascular network plays a central role in controlling infection and regulating the immune response. In this review, we focus on the local and systemic vascular network change mechanisms of periodontal inflammation and the pathological processes of inflammatory diseases. Understanding how the vascular network influences the pathology of periodontal diseases and the systemic complication associated with this pathology is essential for the discovery of both local and systemic proactive control mechanisms.
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Affiliation(s)
- Dilek Celik
- Immunology Division, Health Sciences Institute, Trakya University, Edirne 22100, Turkey;
| | - Alpdogan Kantarci
- Forsyth Institute, Cambridge, MA 02142, USA
- School of Dental Medicine, Harvard University, Boston, MA 02142, USA
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29
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Toro‐Valdivieso C, Toro F, Stubbs S, Castro‐Nallar E, Blacklaws B. Patterns of the fecal microbiota in the Juan Fernández fur seal (Arctocephalus philippii). Microbiologyopen 2021; 10:e1215. [PMID: 34459554 PMCID: PMC8302013 DOI: 10.1002/mbo3.1215] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/26/2021] [Accepted: 06/03/2021] [Indexed: 12/13/2022] Open
Abstract
As apex predators, pinnipeds are considered to be useful bioindicators of marine and coastal environments. Endemic to a small archipelago in the South Pacific, the Juan Fernandez fur seal (JFFS) is one of the less-studied members of the pinniped family Otariidae. This study aimed to characterize the fecal microbiome of the JFFS for the first time, to establish a baseline for future studies of host-microbial-environment interactions and monitoring programs. During two consecutive reproductive seasons, 57 fecal samples were collected from seven different JFFS colonies within the Juan Fernandez Archipelago, Chile. Bacterial composition and abundance were characterized by sequencing the V4 region of the 16S rRNA gene. The overall microbiome composition was dominated by five phyla: Firmicutes (40% ±24), Fusobacteria (30% ±17), Bacteroidetes (22% ±10), Proteobacteria (6% ±4), and Actinobacteria (2% ±3). Alpha diversity was higher in Tierras Blancas. However, location was not found to be a dominant driver of microbial composition. Interestingly, the strongest signal in the data was a negative association between the genera Peptoclostridium and Fusobacterium, which explained 29.7% of the total microbial composition variability between samples. The genus Peptoclostridium has not been reported in other pinniped studies, and its role here is unclear, with interpretation challenging due to a lack of information regarding microbiome functionality in marine mammals. As a first insight into the JFFS fecal microbiome, these results contribute towards our understanding of the natural microbial diversity and composition in free-ranging pinnipeds.
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Affiliation(s)
| | - Frederick Toro
- Facultad de Ciencias de la VidaUniversidad Andres BelloSantiagoChile
- Escuela de Medicina VeterinariaFacultad de Recursos Naturales y Medicina VeterinariaUniversidad Santo TomásViña del MarChile
- ONG PanthalassaRed de Estudios de Vertebrados Marinos en ChileSantiagoChile
- Ph.D. Program in Conservation MedicineFacultad de Ecología y Recursos NaturalesUniversidad Andrés BelloSantiagoChile
| | - Samuel Stubbs
- Department of Infectious Disease EpidemiologyLondon School of Hygiene and Tropical MedicineLondonUK
| | - Eduardo Castro‐Nallar
- Center for Bioinformatics and Integrative BiologyUniversidad Andres BelloSantiagoChile
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Thomas C, Minty M, Vinel A, Canceill T, Loubières P, Burcelin R, Kaddech M, Blasco-Baque V, Laurencin-Dalicieux S. Oral Microbiota: A Major Player in the Diagnosis of Systemic Diseases. Diagnostics (Basel) 2021; 11:1376. [PMID: 34441309 PMCID: PMC8391932 DOI: 10.3390/diagnostics11081376] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 07/28/2021] [Accepted: 07/28/2021] [Indexed: 02/06/2023] Open
Abstract
The oral cavity is host to a complex and diverse microbiota community which plays an important role in health and disease. Major oral infections, i.e., caries and periodontal diseases, are both responsible for and induced by oral microbiota dysbiosis. This dysbiosis is known to have an impact on other chronic systemic diseases, whether triggering or aggravating them, making the oral microbiota a novel target in diagnosing, following, and treating systemic diseases. In this review, we summarize the major roles that oral microbiota can play in systemic disease development and aggravation and also how novel tools can help investigate this complex ecosystem. Finally, we describe new therapeutic approaches based on oral bacterial recolonization or host modulation therapies. Collaboration in diagnosis and treatment between oral specialists and general health specialists is of key importance in bridging oral and systemic health and disease and improving patients' wellbeing.
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Affiliation(s)
- Charlotte Thomas
- INSERM UMR 1297 Inserm, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Avenue Jean Poulhès 1, CEDEX 4, 31432 Toulouse, France; (A.V.); (P.L.); (R.B.); (V.B.-B.)
- Faculté de Chirurgie Dentaire, Université Paul Sabatier III (UPS), 118 Route de Narbonne, CEDEX 9, 31062 Toulouse, France; (T.C.); (M.K.); (S.L.-D.)
- Service d’Odontologie Rangueil, CHU de Toulouse, 3 Chemin des Maraîchers, CEDEX 9, 31062 Toulouse, France
| | - Matthieu Minty
- INSERM UMR 1297 Inserm, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Avenue Jean Poulhès 1, CEDEX 4, 31432 Toulouse, France; (A.V.); (P.L.); (R.B.); (V.B.-B.)
- Faculté de Chirurgie Dentaire, Université Paul Sabatier III (UPS), 118 Route de Narbonne, CEDEX 9, 31062 Toulouse, France; (T.C.); (M.K.); (S.L.-D.)
- Service d’Odontologie Rangueil, CHU de Toulouse, 3 Chemin des Maraîchers, CEDEX 9, 31062 Toulouse, France
| | - Alexia Vinel
- INSERM UMR 1297 Inserm, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Avenue Jean Poulhès 1, CEDEX 4, 31432 Toulouse, France; (A.V.); (P.L.); (R.B.); (V.B.-B.)
- Faculté de Chirurgie Dentaire, Université Paul Sabatier III (UPS), 118 Route de Narbonne, CEDEX 9, 31062 Toulouse, France; (T.C.); (M.K.); (S.L.-D.)
- Service d’Odontologie Rangueil, CHU de Toulouse, 3 Chemin des Maraîchers, CEDEX 9, 31062 Toulouse, France
| | - Thibault Canceill
- Faculté de Chirurgie Dentaire, Université Paul Sabatier III (UPS), 118 Route de Narbonne, CEDEX 9, 31062 Toulouse, France; (T.C.); (M.K.); (S.L.-D.)
- Service d’Odontologie Rangueil, CHU de Toulouse, 3 Chemin des Maraîchers, CEDEX 9, 31062 Toulouse, France
- UMR CNRS 5085, Centre Interuniversitaire de Recherche et d’Ingénierie des Matériaux (CIRIMAT), Université Paul Sabatier, 35 Chemin des Maraichers, CEDEX 9, 31062 Toulouse, France
| | - Pascale Loubières
- INSERM UMR 1297 Inserm, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Avenue Jean Poulhès 1, CEDEX 4, 31432 Toulouse, France; (A.V.); (P.L.); (R.B.); (V.B.-B.)
- Faculté de Chirurgie Dentaire, Université Paul Sabatier III (UPS), 118 Route de Narbonne, CEDEX 9, 31062 Toulouse, France; (T.C.); (M.K.); (S.L.-D.)
| | - Remy Burcelin
- INSERM UMR 1297 Inserm, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Avenue Jean Poulhès 1, CEDEX 4, 31432 Toulouse, France; (A.V.); (P.L.); (R.B.); (V.B.-B.)
- Faculté de Chirurgie Dentaire, Université Paul Sabatier III (UPS), 118 Route de Narbonne, CEDEX 9, 31062 Toulouse, France; (T.C.); (M.K.); (S.L.-D.)
| | - Myriam Kaddech
- Faculté de Chirurgie Dentaire, Université Paul Sabatier III (UPS), 118 Route de Narbonne, CEDEX 9, 31062 Toulouse, France; (T.C.); (M.K.); (S.L.-D.)
- Service d’Odontologie Rangueil, CHU de Toulouse, 3 Chemin des Maraîchers, CEDEX 9, 31062 Toulouse, France
| | - Vincent Blasco-Baque
- INSERM UMR 1297 Inserm, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Avenue Jean Poulhès 1, CEDEX 4, 31432 Toulouse, France; (A.V.); (P.L.); (R.B.); (V.B.-B.)
- Faculté de Chirurgie Dentaire, Université Paul Sabatier III (UPS), 118 Route de Narbonne, CEDEX 9, 31062 Toulouse, France; (T.C.); (M.K.); (S.L.-D.)
- Service d’Odontologie Rangueil, CHU de Toulouse, 3 Chemin des Maraîchers, CEDEX 9, 31062 Toulouse, France
| | - Sara Laurencin-Dalicieux
- Faculté de Chirurgie Dentaire, Université Paul Sabatier III (UPS), 118 Route de Narbonne, CEDEX 9, 31062 Toulouse, France; (T.C.); (M.K.); (S.L.-D.)
- Service d’Odontologie Rangueil, CHU de Toulouse, 3 Chemin des Maraîchers, CEDEX 9, 31062 Toulouse, France
- INSERM UMR 1295, Centre d’Epidémiologie et de Recherche en Santé des Populations de Toulouse (CERPOP), Epidémiologie et Analyse en Santé Publique, Risques, Maladies Chroniques et Handicaps, 37 Allées Jules Guesdes, 31000 Toulouse, France
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Liu Y, Huang W, Wang J, Ma J, Zhang M, Lu X, Liu J, Kou Y. Multifaceted Impacts of Periodontal Pathogens in Disorders of the Intestinal Barrier. Front Immunol 2021; 12:693479. [PMID: 34386004 PMCID: PMC8353228 DOI: 10.3389/fimmu.2021.693479] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 07/12/2021] [Indexed: 12/12/2022] Open
Abstract
Periodontal disease, a common inflammatory disease, is considered a hazardous factor that contributes to the development of diseases of the digestive system as well as other systems. The bridge between periodontitis and systemic diseases is believed to be periodontal pathogens. The intestine, as part of the lower gastrointestinal tract, has a close connection with the oral cavity. Within the intestine, the intestinal barrier acts as a multifunctional system including microbial, mucous, physical and immune barrier. The intestinal barrier forms the body's first line of defense against external pathogens; its breakdown can lead to pathological changes in the gut and other organs or systems. Reports in the literature have described how oral periodontal pathogens and pathobiont-reactive immune cells can transmigrate to the intestinal mucosa, causing the destruction of intestinal barrier homeostasis. Such findings might lead to novel ideas for investigating the relationship between periodontal disease and other systemic diseases. This review summarizes studies on the effects of periodontal pathogens on the intestinal barrier, which might contribute to understanding the link between periodontitis and gastrointestinal diseases.
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Affiliation(s)
- Yingman Liu
- Department of Periodontics, School and Hospital of Stomatology, China Medical University, Liaoning Provincial Key Laboratory of Oral Diseases, Shenyang, China
| | - Wenxuan Huang
- School of Stomatology, Shenyang Medical College, Shenyang, China
| | - Jiaqi Wang
- Department of Periodontics, School and Hospital of Stomatology, China Medical University, Liaoning Provincial Key Laboratory of Oral Diseases, Shenyang, China
| | - Jiaojiao Ma
- Department of Periodontics, School and Hospital of Stomatology, China Medical University, Liaoning Provincial Key Laboratory of Oral Diseases, Shenyang, China
| | - Manman Zhang
- Department of Oral Biology, School and Hospital of Stomatology, China Medical University, Liaoning Provincial Key Laboratory of Oral Diseases, Shenyang, China
| | - Xiaoying Lu
- Department of Oral Biology, School and Hospital of Stomatology, China Medical University, Liaoning Provincial Key Laboratory of Oral Diseases, Shenyang, China
| | - Jie Liu
- Science Experiment Center, China Medical University, Shenyang, China
| | - Yurong Kou
- Department of Periodontics, School and Hospital of Stomatology, China Medical University, Liaoning Provincial Key Laboratory of Oral Diseases, Shenyang, China
- Department of Oral Biology, School and Hospital of Stomatology, China Medical University, Liaoning Provincial Key Laboratory of Oral Diseases, Shenyang, China
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Virgínio Júnior GF, Coelho MG, de Toledo AF, Montenegro H, Coutinho LL, Bittar CMM. The Liquid Diet Composition Affects the Fecal Bacterial Community in Pre-weaning Dairy Calves. FRONTIERS IN ANIMAL SCIENCE 2021. [DOI: 10.3389/fanim.2021.649468] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Feeding a liquid diet to the newborn calf has considerable implications for developing the intestinal microbiota, as its composition can shift the population to a highly adapted microbiota. The present work evaluated 15 Holstein calves individually housed and fed one of the three liquid diets: I – whole milk (n = 5), II – milk replacer (22.9% CP; 16.2% fat; diluted to 14% solids; n = 5) and III – acidified whole milk to pH 4.5 with formic acid (n = 5). All animals received 6 L of liquid diet, divided into two meals, being weaned at week 8 of life. Calves also had free access to water and starter concentrate. After weaning, all calves were grouped on pasture, fed with starter concentrate, and hay ad libitum. The fecal samples were collected at birth (0) and at weeks 1, 2, 4, 8, and 10 of life. The bacterial community was assessed the through sequencing of the V3-V4 region of the 16S rRNA gene on the Illumina MiSeq platform and analyzed using the DADA2 pipeline. Diversity indices were not affected by the liquid diets, but by age (P < 0.001) with weeks 1 and 2 presenting lower diversity, evenness, and richness values. The bacterial community structure was affected by diet, age, and the interaction of these factors (P < 0.01). Twenty-eight bacterial phyla were identified in the fecal samples, and the most predominant phyla were Firmicutes (42.35%), Bacteroidota (39.37%), and Proteobacteria (9.36%). The most prevalent genera were Bacteroides (10.71%), Lactobacillus (8.11%), Alloprevotella (6.20%). Over the weeks, different genera were predominant, with some showing significant differences among treatments. The different liquid diets altered the fecal bacterial community during the pre-weaning period. However, differences in the initial colonization due to different liquid diets are alleviated after weaning, when animals share a common environment and solid diet composition.
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33
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Park SY, Hwang BO, Lim M, Ok SH, Lee SK, Chun KS, Park KK, Hu Y, Chung WY, Song NY. Oral-Gut Microbiome Axis in Gastrointestinal Disease and Cancer. Cancers (Basel) 2021; 13:2124. [PMID: 33924899 PMCID: PMC8125773 DOI: 10.3390/cancers13092124] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/05/2021] [Accepted: 03/09/2021] [Indexed: 02/07/2023] Open
Abstract
It is well-known that microbiota dysbiosis is closely associated with numerous diseases in the human body. The oral cavity and gut are the two largest microbial habitats, playing a major role in microbiome-associated diseases. Even though the oral cavity and gut are continuous regions connected through the gastrointestinal tract, the oral and gut microbiome profiles are well-segregated due to the oral-gut barrier. However, the oral microbiota can translocate to the intestinal mucosa in conditions of the oral-gut barrier dysfunction. Inversely, the gut-to-oral microbial transmission occurs as well in inter- and intrapersonal manners. Recently, it has been reported that oral and gut microbiomes interdependently regulate physiological functions and pathological processes. Oral-to-gut and gut-to-oral microbial transmissions can shape and/or reshape the microbial ecosystem in both habitats, eventually modulating pathogenesis of disease. However, the oral-gut microbial interaction in pathogenesis has been underappreciated to date. Here, we will highlight the oral-gut microbiome crosstalk and its implications in the pathogenesis of the gastrointestinal disease and cancer. Better understanding the role of the oral-gut microbiome axis in pathogenesis will be advantageous for precise diagnosis/prognosis and effective treatment.
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Affiliation(s)
- Se-Young Park
- Department of Applied Life Science, The Graduate School, Yonsei University, and BK21 FOUR Project, Yonsei University College of Dentistry, Seoul 03722, Korea; (S.-Y.P.); (B.-O.H.); (S.-H.O.)
| | - Byeong-Oh Hwang
- Department of Applied Life Science, The Graduate School, Yonsei University, and BK21 FOUR Project, Yonsei University College of Dentistry, Seoul 03722, Korea; (S.-Y.P.); (B.-O.H.); (S.-H.O.)
| | - Mihwa Lim
- Department of Oral Biology, Yonsei University College of Dentistry, Seoul 03722, Korea; (M.L.); (S.-K.L.); (K.-K.P.)
| | - Seung-Ho Ok
- Department of Applied Life Science, The Graduate School, Yonsei University, and BK21 FOUR Project, Yonsei University College of Dentistry, Seoul 03722, Korea; (S.-Y.P.); (B.-O.H.); (S.-H.O.)
| | - Sun-Kyoung Lee
- Department of Oral Biology, Yonsei University College of Dentistry, Seoul 03722, Korea; (M.L.); (S.-K.L.); (K.-K.P.)
| | - Kyung-Soo Chun
- College of Pharmacy, Keimyung University, Daegu 42601, Korea;
| | - Kwang-Kyun Park
- Department of Oral Biology, Yonsei University College of Dentistry, Seoul 03722, Korea; (M.L.); (S.-K.L.); (K.-K.P.)
| | - Yinling Hu
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA;
| | - Won-Yoon Chung
- Department of Oral Biology, Oral Cancer Research Institute, and BK21 FOUR Project, Yonsei University College of Dentistry, Seoul 03722, Korea;
| | - Na-Young Song
- Department of Oral Biology, Yonsei University College of Dentistry, Seoul 03722, Korea; (M.L.); (S.-K.L.); (K.-K.P.)
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34
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Oral–Gut Microbiome Axis in Gastrointestinal Disease and Cancer. Cancers (Basel) 2021. [DOI: 10.3390/cancers13071748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
It is well-known that microbiota dysbiosis is closely associated with numerous diseases in the human body. The oral cavity and gut are the two largest microbial habitats, playing a major role in microbiome-associated diseases. Even though the oral cavity and gut are continuous regions connected through the gastrointestinal tract, the oral and gut microbiome profiles are well-segregated due to the oral–gut barrier. However, the oral microbiota can translocate to the intestinal mucosa in conditions of the oral–gut barrier dysfunction. Inversely, the gut-to-oral microbial transmission occurs as well in inter- and intrapersonal manners. Recently, it has been reported that oral and gut microbiomes interdependently regulate physiological functions and pathological processes. Oral-to-gut and gut-to-oral microbial transmissions can shape and/or reshape the microbial ecosystem in both habitats, eventually modulating pathogenesis of disease. However, the oral–gut microbial interaction in pathogenesis has been underappreciated to date. Here, we will highlight the oral–gut microbiome crosstalk and its implications in the pathogenesis of the gastrointestinal disease and cancer. Better understanding the role of the oral–gut microbiome axis in pathogenesis will be advantageous for precise diagnosis/prognosis and effective treatment.
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35
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The Role of Enterobacteriaceae in Gut Microbiota Dysbiosis in Inflammatory Bowel Diseases. Microorganisms 2021; 9:microorganisms9040697. [PMID: 33801755 PMCID: PMC8066304 DOI: 10.3390/microorganisms9040697] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/19/2021] [Accepted: 03/23/2021] [Indexed: 12/12/2022] Open
Abstract
Inflammatory bowel diseases (IBDs) are a group of chronic gastrointestinal inflammatory diseases with unknown etiology. There is a combination of well documented factors in their pathogenesis, including intestinal microbiota dysbiosis. The symbiotic microbiota plays important functions in the host, and the loss of beneficial microbes could favor the expansion of microbial pathobionts. In particular, the bloom of potentially harmful Proteobacteria, especially Enterobacteriaceae, has been described as enhancing the inflammatory response, as observed in IBDs. Herein, we seek to investigate the contribution of Enterobacteriaceae to IBD pathogenesis whilst considering the continuous expansion of the literature and data. Despite the mechanism of their expansion still remaining unclear, their expansion could be correlated with the increase in nitrate and oxygen levels in the inflamed gut and with the bile acid dysmetabolism described in IBD patients. Furthermore, in several Enterobacteriaceae studies conducted at a species level, it has been suggested that some adherent-invasive Escherichia coli (AIEC) play an important role in IBD pathogenesis. Overall, this review highlights the pivotal role played by Enterobacteriaceae in gut dysbiosis associated with IBD pathogenesis and progression.
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36
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Wang H, Ong E, Kao JY, Sun D, He Y. Reverse Microbiomics: A New Reverse Dysbiosis Analysis Strategy and Its Usage in Prediction of Autoantigens and Virulent Factors in Dysbiotic Gut Microbiomes From Rheumatoid Arthritis Patients. Front Microbiol 2021; 12:633732. [PMID: 33717026 PMCID: PMC7947680 DOI: 10.3389/fmicb.2021.633732] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 02/08/2021] [Indexed: 11/13/2022] Open
Abstract
Alterations in the gut microbiome have been associated with various human diseases. Most existing gut microbiome studies stopped at the stage of identifying microbial alterations between diseased or healthy conditions. As inspired by reverse vaccinology (RV), we developed a new strategy called Reverse Microbiomics (RM) that turns this process around: based on the identified microbial alternations, reverse-predicting the molecular mechanisms underlying the disease and microbial alternations. Our RM methodology starts by identifying significantly altered microbiota profiles, performing bioinformatics analysis on the proteomes of the microbiota identified, and finally predicting potential virulence or protective factors relevant to a microbiome-associated disease. As a use case study, this reverse methodology was applied to study the molecular pathogenesis of rheumatoid arthritis (RA), a common autoimmune and inflammatory disease. Those bacteria differentially associated with RA were first identified and annotated from published data and then modeled and classified using the Ontology of Host-Microbiome Interactions (OHMI). Our study identified 14 species increased and 9 species depleted in the gut microbiota of RA patients. Vaxign was used to comparatively analyze 15 genome sequences of the two pairs of species: Gram-negative Prevotella copri (increased) and Prevotella histicola (depleted), as well as Gram-positive Bifidobacterium dentium (increased) and Bifidobacterium bifidum (depleted). In total, 21 auto-antigens were predicted to be related to RA, and five of them were previously reported to be associated with RA with experimental evidence. Furthermore, we identified 94 potential adhesive virulence factors including 24 microbial ABC transporters. While eukaryotic ABC transporters are key RA diagnosis markers and drug targets, we identified, for the first-time, RA-associated microbial ABC transporters and provided a novel hypothesis of RA pathogenesis. Our study showed that RM, by broadening the scope of RV, is a novel and effective strategy to study from bacterial level to molecular level factors and gain further insight into how these factors possibly contribute to the development of microbial alterations under specific diseases.
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Affiliation(s)
- Haihe Wang
- Department of Pathogen Biology, Harbin Medical University (Daqing), Daqing, China.,Unit for Laboratory Animal Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Edison Ong
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, United States
| | - John Y Kao
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Duxin Sun
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, MI, United States
| | - Yongqun He
- Unit for Laboratory Animal Medicine, University of Michigan, Ann Arbor, MI, United States.,Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, United States.,Center of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, United States
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