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Costa CFFA, Ferreira-Gomes J, Barbosa F, Sampaio-Maia B, Burnet PWJ. Importance of good hosting: reviewing the bi-directionality of the microbiome-gut-brain-axis. Front Neurosci 2024; 18:1386866. [PMID: 38812976 PMCID: PMC11133738 DOI: 10.3389/fnins.2024.1386866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 04/29/2024] [Indexed: 05/31/2024] Open
Abstract
Gut microorganisms have been shown to significantly impact on central function and studies that have associated brain disorders with specific bacterial genera have advocated an anomalous gut microbiome as the pathophysiological basis of several psychiatric and neurological conditions. Thus, our knowledge of brain-to-gut-to microbiome communication in this bidirectional axis seems to have been overlooked. This review examines the known mechanisms of the microbiome-to-gut-to-brain axis, highlighting how brain-to-gut-to-microbiome signaling may be key to understanding the cause of disrupted gut microbial communities. We show that brain disorders can alter the function of the brain-to-gut-to-microbiome axis, which will in turn contribute to disease progression, while the microbiome-to gut-to brain direction presents as a more versatile therapeutic axis, since current psychotropic/neurosurgical interventions may have unwanted side effects that further cause disruption to the gut microbiome. A consideration of the brain-to-gut-to-microbiome axis is imperative to better understand how the microbiome-gut-brain axis overall is involved in brain illnesses, and how it may be utilized as a preventive and therapeutic tool.
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Affiliation(s)
- Carolina F. F. A. Costa
- ICBAS-School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
- NanoBiomaterials for Targeted Therapies, INEB-Institute of Biomedical Engineering, i3S-Institute for Research and Innovation in Health, University of Porto, Porto, Portugal
| | - Joana Ferreira-Gomes
- Department of Biomedicine, Faculty of Medicine, University of Porto, Porto, Portugal
- IBMC-Institute for Molecular and Cell Biology, i3S-Institute for Research and Innovation in Health, University of Porto, Porto, Portugal
| | - Fernando Barbosa
- Laboratory of Neuropsychophysiology, Faculty of Psychology and Education Sciences, University of Porto, Porto, Portugal
| | - Benedita Sampaio-Maia
- NanoBiomaterials for Targeted Therapies, INEB-Institute of Biomedical Engineering, i3S-Institute for Research and Innovation in Health, University of Porto, Porto, Portugal
- Faculty of Dental Medicine, University of Porto, Porto, Portugal
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2
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Swedik SM, Madola A, Cruz MA, Llorens-Bonilla BJ, Levine AD. Th17-Derived Cytokines Synergistically Enhance IL-17C Production by the Colonic Epithelium. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 209:1768-1777. [PMID: 36130829 PMCID: PMC9588696 DOI: 10.4049/jimmunol.2200125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 08/29/2022] [Indexed: 11/06/2022]
Abstract
Tightly regulated communication between the gastrointestinal epithelium and immune cells in the underlying lamina propria is critical for immune homeostasis and inflammation. IL-17C, produced by epithelial cells after exposure to inflammatory stimuli, facilitates cell-to-cell communication by promoting inflammatory responses in Th17 cells. In this study, we demonstrate that Th17-derived cytokines TNF-α, IL-17A, and IL-22 synergistically enhance IL-17C expression in both human-transformed colonic epithelial cell lines and primary non-inflammatory bowel disease colonic epithelial spheroids. This synergistic expression requires activation of the transcription factor NF-κB downstream of the TNF-α stimulus, evidenced by the reduction of IL-17C expression in the presence of an IκBα inhibitor. IL-17A and IL-22 enhance IL-17C expression through the activation of the transcription factor AP-1 in a p38 MAPK-dependent manner. Colonic spheroids derived from uninvolved epithelial of ulcerative colitis patients stimulated with TNF-α, IL-17A, and IL-22 show muted responses compared with non-inflammatory bowel disease spheroids, and inflamed spheroids yielded more IL-17C expression in the presence of TNF-α, and no response to IL-22 stimulation. Altogether, a role for IL-17C in activating Th17 cells combined with our findings of Th17-derived cytokine-driven synergy in the expression of IL-17C identifies a novel inflammatory amplification loop in the gastrointestinal tract between epithelial cells and Th17 cells.
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Affiliation(s)
- Stephanie M Swedik
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH
| | - Abson Madola
- Department of Biology, Case Western Reserve University, Cleveland, OH
| | - Michelle A Cruz
- Department of Pathology, Case Western Reserve University, Cleveland, OH
| | | | - Alan D Levine
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH;
- Department of Pathology, Case Western Reserve University, Cleveland, OH
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH
- Department of Medicine, Case Western Reserve University, Cleveland, OH; and
- Department of Pediatrics, Case Western Reserve University, Cleveland, OH
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3
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Jiang Y, Luo J, Huang D, Liu Y, Li DD. Machine Learning Advances in Microbiology: A Review of Methods and Applications. Front Microbiol 2022; 13:925454. [PMID: 35711777 PMCID: PMC9196628 DOI: 10.3389/fmicb.2022.925454] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 05/09/2022] [Indexed: 12/18/2022] Open
Abstract
Microorganisms play an important role in natural material and elemental cycles. Many common and general biology research techniques rely on microorganisms. Machine learning has been gradually integrated with multiple fields of study. Machine learning, including deep learning, aims to use mathematical insights to optimize variational functions to aid microbiology using various types of available data to help humans organize and apply collective knowledge of various research objects in a systematic and scaled manner. Classification and prediction have become the main achievements in the development of microbial community research in the direction of computational biology. This review summarizes the application and development of machine learning and deep learning in the field of microbiology and shows and compares the advantages and disadvantages of different algorithm tools in four fields: microbiome and taxonomy, microbial ecology, pathogen and epidemiology, and drug discovery.
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4
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Zheng S, Wang L, Xiong J, Liang G, Xu Y, Lin F. Consensus Prediction of Human Gut Microbiota-Mediated Metabolism Susceptibility for Small Molecules by Machine Learning, Structural Alerts, and Dietary Compounds-Based Average Similarity Methods. J Chem Inf Model 2022; 62:1078-1099. [PMID: 35156807 DOI: 10.1021/acs.jcim.1c00948] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The human gut microbiota (HGM) colonizing human gastrointestinal tract (HGT) confers a repertoire of dynamic and unique metabolic capacities that are not possessed by the host and therefore is tentatively perceived as an alternative metabolic ″organ″ besides the liver in the host. Nevertheless, the significant contribution of HGM to the overall human metabolism is often overlooked in the modern drug discovery pipeline. Hence, a systematic evaluation of HGM-mediated drug metabolism is gradually important, and its computational prediction becomes increasingly necessary. In this work, a new data set containing both the HGM-mediated metabolism susceptible (HGMMS) and insusceptible (HGMMI) compounds (329 vs 320) was manually curated. Based on this data set, the first machine learning (ML) model, a new structural alerts (SA) model, and the K-nearest neighboring dietary compounds-based average similarity (AS) model were proposed to directly predict the HGM-mediated metabolism susceptibility for small molecules, and exhibit promising performance on three independent test sets. Finally, consensus prediction (ML/SA/AS) for DrugBank molecules revealed an intriguing phenomenon that a typical Michael acceptor ″α,β-unsaturated carbonyl group″ is a very common warhead for the design of covalent inhibitors and inclined to be metabolized by HGM in anaerobic HGT to generate the reduced metabolite without the reactive warhead, which could be a new concern to medicinal chemists. To the best of our knowledge, we gleaned the first HGMMS/HGMMI data set, developed the first HGMMS/HGMMI classification model, implemented a relatively comprehensive program based on ML/SA/AS approaches, and found a new phenomenon on the HGM-mediated deactivation of an extensively used warhead for covalent inhibitors.
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Affiliation(s)
- Suqing Zheng
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, P.R. China.,Chemical Biology Research Center, Wenzhou Medical University, Wenzhou, Zhejiang 325035, P.R. China
| | - Lei Wang
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, P.R. China
| | - Jun Xiong
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, P.R. China
| | - Guang Liang
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, P.R. China.,Chemical Biology Research Center, Wenzhou Medical University, Wenzhou, Zhejiang 325035, P.R. China
| | - Yong Xu
- Center of Chemical Biology, Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, P.R. China
| | - Fu Lin
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, P.R. China
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5
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Gallo A, Macerola N, Favuzzi AM, Nicolazzi MA, Gasbarrini A, Montalto M. The Gut in Heart Failure: Current Knowledge and Novel Frontiers. Med Princ Pract 2022; 31:203-214. [PMID: 35093952 PMCID: PMC9275003 DOI: 10.1159/000522284] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 01/23/2022] [Indexed: 11/22/2022] Open
Abstract
Heart failure (HF) represents a major health problem affecting millions of people worldwide. In the latest years, many efforts have been made to search for more effective strategies to prevent and modify the course of this disease, but results are still not satisfying. HF represents a complex clinical syndrome involving many other systems, including the gastrointestinal system. Although the relationship between the gut and HF is far from being fully understood, based on recent evidence highlighting the putative role of the gastrointestinal system in different cardiovascular diseases, it is conceivable that the gut-heart link may represent the basis for novel therapeutic approaches in the HF context as well. This intricate interplay involving typical hemodynamic changes and their consequences on gut morphology, permeability, and function, sets the stage for alterations in microbiota composition and is able to impact mechanisms of HF through different routes such as bacterial translocation and metabolic pathways. Thus, the modulation of the gut microbiota through diet, probiotics, and fecal transplantation has been suggested as a potential therapeutic approach. More interestingly, another effect of alteration in microbiota composition reflects in the upregulation of cotransporters (NHE3) with consequent salt and fluid overload and worsening visceral congestion. Therefore, the inhibitors of this cotransporter may also represent a novel therapeutic frontier. By review of recent data on this topic, we describe the current state of the complex interplay between the gastrointestinal and cardiac systems in HF, and the relevance of this knowledge in seeking new therapeutic strategies.
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Affiliation(s)
- Antonella Gallo
- Department of Medical Sciences, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
- *Antonella Gallo,
| | - Noemi Macerola
- Department of Medical Sciences, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Angela Maria Favuzzi
- Department of Medical Sciences, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Maria Anna Nicolazzi
- Department of Medical Sciences, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Antonio Gasbarrini
- Department of Medical Sciences, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
- Università Cattolica del Sacro Cuore, Rome, Italy
| | - Massimo Montalto
- Department of Medical Sciences, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
- Università Cattolica del Sacro Cuore, Rome, Italy
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6
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Nouri R, Hasani A, Shirazi KM, Aliand MR, Sepehri B, Sotoodeh S, Hemmati F, Rezaee MA. Escherichia coli and colorectal cancer: Unfolding the enigmatic relationship. Curr Pharm Biotechnol 2021; 23:1257-1268. [PMID: 34514986 DOI: 10.2174/1389201022666210910094827] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/21/2021] [Accepted: 06/07/2021] [Indexed: 11/22/2022]
Abstract
Colorectal cancer (CRC) is one of the deadliest cancers in the world. Specific strains of intestinal Escherichia coli (E. coli) may influence the initiation and development of CRC by exploiting virulence factors and inflammatory pathways. Mucosa-associated E. coli strains are more prevalent in CRC biopsies in comparison to healthy controls. Moreover, these strains can survive and replicate within macrophages and induce a pro-inflammatory response. Chronic exposure to inflammatory mediators can lead to increased cell proliferation and cancer. Production of colobactin toxin by the majority of mucosa-associated E. coli isolated from CRC patients is another notable finding. Colibactin-producing E. coli strains, in particular, induce double-strand DNA breaks, stop the cell cycle, involve in chromosomal rearrangements of mammalian cells and are implicated in carcinogenic effects in animal models. Moreover, some enteropathogenic E. coli (EPEC) strains are able to survive and replicate in colon cells as chronic intracellular pathogens and may promote susceptibility to CRC by downregulation of DNA Mismatch Repair (MMR) proteins. In this review, we discuss current evidence and focus on the mechanisms by which E. coli can influence the development of CRC.
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Affiliation(s)
- Rogayeh Nouri
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz. Iran
| | - Alka Hasani
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz. Iran
| | - Kourosh Masnadi Shirazi
- Liver and Gastrointestinal Diseases Research Center, Tabriz University of Medical Sciences, Tabriz. Iran
| | - Mohammad Reza Aliand
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz. Iran
| | - Bita Sepehri
- Liver and Gastrointestinal Diseases Research Center, Tabriz University of Medical Sciences, Tabriz. Iran
| | - Simin Sotoodeh
- Liver and Gastrointestinal Diseases Research Center, Tabriz University of Medical Sciences, Tabriz. Iran
| | - Fatemeh Hemmati
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz. Iran
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7
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Li J, Wang SP, Zong G, Kim E, Tsao CY, VanArsdale E, Wang LX, Bentley WE, Payne GF. Interactive Materials for Bidirectional Redox-Based Communication. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2007758. [PMID: 33788338 DOI: 10.1002/adma.202007758] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 02/09/2021] [Indexed: 06/12/2023]
Abstract
Emerging research indicates that biology routinely uses diffusible redox-active molecules to mediate communication that can span biological systems (e.g., nervous and immune) and even kingdoms (e.g., a microbiome and its plant/animal host). This redox modality also provides new opportunities to create interactive materials that can communicate with living systems. Here, it is reported that the fabrication of a redox-active hydrogel film can autonomously synthesize a H2 O2 signaling molecule for communication with a bacterial population. Specifically, a catechol-conjugated/crosslinked 4-armed thiolated poly(ethylene glycol) hydrogel film is electrochemically fabricated in which the added catechol moieties confer redox activity: the film can accept electrons from biological reductants (e.g., ascorbate) and donate electrons to O2 to generate H2 O2 . Electron-transfer from an Escherichia coli culture poises this film to generate the H2 O2 signaling molecule that can induce bacterial gene expression from a redox-responsive operon. Overall, this work demonstrates that catecholic materials can participate in redox-based interactions that elicit specific biological responses, and also suggests the possibility that natural phenolics may be a ubiquitous biological example of interactive materials.
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Affiliation(s)
- Jinyang Li
- Institute for Bioscience and Biotechnology Research, Fischell Department of Bioengineering, University of Maryland, College Park, MD, 20742, USA
| | - Sally P Wang
- Institute for Bioscience and Biotechnology Research, Fischell Department of Bioengineering, University of Maryland, College Park, MD, 20742, USA
| | - Guanghui Zong
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - Eunkyoung Kim
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD, 20742, USA
| | - Chen-Yu Tsao
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD, 20742, USA
| | - Eric VanArsdale
- Institute for Bioscience and Biotechnology Research, Fischell Department of Bioengineering, University of Maryland, College Park, MD, 20742, USA
| | - Lai-Xi Wang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - William E Bentley
- Institute for Bioscience and Biotechnology Research, Fischell Department of Bioengineering, University of Maryland, College Park, MD, 20742, USA
| | - Gregory F Payne
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD, 20742, USA
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8
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Zhou X, Zhang Z, Huang F, Yang C, Huang Q. In Vitro Digestion and Fermentation by Human Fecal Microbiota of Polysaccharides from Flaxseed. Molecules 2020; 25:E4354. [PMID: 32977374 PMCID: PMC7582239 DOI: 10.3390/molecules25194354] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 09/07/2020] [Accepted: 09/10/2020] [Indexed: 02/07/2023] Open
Abstract
The digestion of flaxseed polysaccharides (FSP) in simulated saliva, gastric and small intestine conditions was assessed, as well as in vitro fermentation of FSP by human gut microbiota. FSP was not degraded in the simulated digestive systems (there was no change in molecular weight or content of reducing sugars), indicating that ingested FSP would reach the large intestine intact. Changes in carbohydrate content, reducing sugars and culture pH suggested that FSP could be broken down and used by gut microbiota. FSP modulated the composition and structure of the gut microbiota by altering the Firmicutes/Bacteroidetes ratio and increasing the relative abundances of Prevotella, Phascolarctobacterium, Clostridium and Megamonas, which can degrade polysaccharides. Meanwhile, FSP fermentation increased the concentration of short-chain fatty acids, especially propionic and butyric acids. Our results indicate that FSP might be developed as a functional food that benefits gut health.
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Affiliation(s)
| | | | | | - Chen Yang
- Oil Crops and Lipids Process Technology National & Local Joint Engineering Laboratory, Hubei Key Laboratory of Lipid Chemistry and Nutrition, Key Laboratory of Oilseeds Processing, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural affairs, No. 2 Xudong 2nd Road, Wuhan 430062, China; (X.Z.); (Z.Z.); (F.H.); (Q.H.)
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9
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Rebuilding the Gut Microbiota Ecosystem. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2018; 15:ijerph15081679. [PMID: 30087270 PMCID: PMC6121872 DOI: 10.3390/ijerph15081679] [Citation(s) in RCA: 163] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 08/04/2018] [Indexed: 11/17/2022]
Abstract
A microbial ecosystem in which bacteria no longer live in a mutualistic association is called dysbiotic. Gut microbiota dysbiosis is a condition related with the pathogenesis of intestinal illnesses (irritable bowel syndrome, celiac disease, and inflammatory bowel disease) and extra-intestinal illnesses (obesity, metabolic disorder, cardiovascular syndrome, allergy, and asthma). Dysbiosis status has been related to various important pathologies, and many therapeutic strategies aimed at restoring the balance of the intestinal ecosystem have been implemented. These strategies include the administration of probiotics, prebiotics, and synbiotics; phage therapy; fecal transplantation; bacterial consortium transplantation; and a still poorly investigated approach based on predatory bacteria. This review discusses the various aspects of these strategies to counteract intestinal dysbiosis.
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10
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Bang SJ, Kim G, Lim MY, Song EJ, Jung DH, Kum JS, Nam YD, Park CS, Seo DH. The influence of in vitro pectin fermentation on the human fecal microbiome. AMB Express 2018; 8:98. [PMID: 29909506 PMCID: PMC6004267 DOI: 10.1186/s13568-018-0629-9] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 06/12/2018] [Indexed: 12/21/2022] Open
Abstract
Pectin is a complex dietary fiber and a prebiotic. To investigate pectin-induced changes in the gut microbiome and their effects on the short chain fatty acids (SCFAs) production, we performed in vitro pectin fermentation using the feces of three Korean donors. The pectin degradations in all three donors were observed. While the donors displayed differences in baseline gut microbiota composition, commonly increased bacteria after pectin fermentation included Lachnospira, Dorea, Clostridium, and Sutterella. Regarding SCFAs, acetate levels rapidly increased with incubation with pectin, and butyrate levels also increased after 6 h of incubation. The results suggest that pectin fermentation increases bacterial species belonging to Clostridium cluster XIV (Lachnospira, Dorea, and Clostridium), with Lachnospira displaying the greatest increase. The results also confirm that pectin fermentation leads to the production of acetate and butyrate.
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11
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Banerjee A, Dhar P. Amalgamation of polyphenols and probiotics induce health promotion. Crit Rev Food Sci Nutr 2018; 59:2903-2926. [PMID: 29787290 DOI: 10.1080/10408398.2018.1478795] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The residing microbiome with its vast repertoire of genes provide distinctive properties to the host by which they can degrade and utilise nutrients that otherwise pass the gastro-intestinal tract unchanged. The polyphenols in our diet have selective growth promoting effects which is of utmost importance as the state of good health has been linked to dominance of particular microbial genera. The polyphenols in native form might more skilfully exert anti-oxidative and anti-inflammatory properties but in a living system it is the microbial derivatives of polyphenol that play a key role in determining health outcome. This two way interaction has invoked great interest among researchers who have commenced several clinical surveys and numerous studies in in-vitro, simulated environment and living systems to find out in detail about the biomolecules involved in such interaction along with their subsequent physiological benefits. In this review, we have thoroughly discussed these studies to develop a fair idea on how the amalgamation of probiotics and polyphenol has an immense potential as an adjuvant therapeutic for disease prevention as well as treatment.
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Affiliation(s)
- Arpita Banerjee
- Laboratory of Food Science and Technology, Food and Nutrition Division, University of Calcutta , 20B Judges Court Road, Alipore, Kolkata , West Bengal , India
| | - Pubali Dhar
- Laboratory of Food Science and Technology, Food and Nutrition Division, University of Calcutta , 20B Judges Court Road, Alipore, Kolkata , West Bengal , India
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12
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New insight and metrics to understand the ontogeny and succession of Lactobacillus plantarum subsp. plantarum and Lactobacillus plantarum subsp. argentoratensis. Sci Rep 2018; 8:6029. [PMID: 29662105 PMCID: PMC5902611 DOI: 10.1038/s41598-018-24541-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 04/05/2018] [Indexed: 12/16/2022] Open
Abstract
Lactobacillus plantarum is one of the most extensively studied Lactobacillus species because of its presence in a variety of environmental niches, versatility, and metabolic capabilities, resulting in the use of this organism in many industrial applications. However, although extensive effort has been invested in screening this species from a variety of habitats, a reliable and accurate method for studying the succession and ontogeny of this organism in complex ecosystems is still required to confirm the activity of L. plantarum at the subspecies level. Therefore, in this study, novel subspecies-specific genes for the quantitative detection of two L. plantarum subspecies were identified by comparative genomic analysis. The specificity of primer sets for selected genes specific to each targeted microbe was confirmed in kimchi samples. Interestingly, in all the kimchi samples at 4 °C, the presence of L. plantarum subsp. argentoratensis was not observed. Hence, we found that low temperatures markedly affected the ontogeny of L. plantarum subsp. argentoratensis during kimchi fermentation. Subsequently, this touchstone method will offer new insight and metrics to understand the ontogeny and succession of L. plantarum subsp. plantarum and L. plantarum subsp. argentoratensis in various niches.
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Abstract
The developmental origin of health and disease highlights the importance of the period of the first 1000 days (from the conception to the 2 years of life). The process of the gut microbiota establishment is included in this time window. Various perinatal determinants, such as cesarean section delivery, type of feeding, antibiotics treatment, gestational age or environment, can affect the pattern of bacterial colonization and result in dysbiosis. The alteration of the early bacterial gut pattern can persist over several months and may have long-lasting functional effects with an impact on disease risk later in life. As for example, early gut dysbiosis has been involved in allergic diseases and obesity occurrence. Besides, while it was thought that the fetus developed under sterile conditions, recent data suggested the presence of a microbiota in utero, particularly in the placenta. Even if the origin of this microbiota and its eventual transfer to the infant are nowadays unknown, this placental microbiota could trigger immune responses in the fetus and would program the infant's immune development during fetal life, earlier than previously considered. Moreover, several studies demonstrated a link between the composition of placental microbiota and some pathological conditions of the pregnancy. All these data show the evidence of relationships between the neonatal gut establishment and future health outcomes. Hence, the use of pre- and/or probiotics to prevent or repair any early dysbiosis is increasingly attractive to avoid long-term health consequences.
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14
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Phelan JP, Reen FJ, Caparros-Martin JA, O'Connor R, O'Gara F. Rethinking the bile acid/gut microbiome axis in cancer. Oncotarget 2017; 8:115736-115747. [PMID: 29383197 PMCID: PMC5777809 DOI: 10.18632/oncotarget.22803] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 10/27/2017] [Indexed: 02/07/2023] Open
Abstract
Dietary factors, probiotic agents, aging and antibiotics/medicines impact on gut microbiome composition leading to disturbances in localised microbial populations. The impact can be profound and underlies a plethora of human disorders, including the focus of this review; cancer. Compromised microbiome populations can alter bile acid signalling and produce distinct pathophysiological bile acid profiles. These in turn have been associated with cancer development and progression. Exposure to high levels of bile acids, combined with localised molecular/genome instability leads to the acquisition of bile mediated neoplastic alterations, generating apoptotic resistant proliferation phenotypes. However, in recent years, several studies have emerged advocating the therapeutic benefits of bile acid signalling in suppressing molecular and phenotypic hallmarks of cancer progression. These studies suggest that in some instances, bile acids may reduce cancer phenotypic effects, thereby limiting metastatic potential. In this review, we contextualise the current state of the art to propose that the bile acid/gut microbiome axis can influence cancer progression to the extent that classical in vitro cancer hallmarks of malignancy (cell invasion, cell migration, clonogenicity, and cell adhesion) are significantly reduced. We readily acknowledge the existence of a bile acid/gut microbiome axis in cancer initiation, however, in light of recent advances, we focus exclusively on the role of bile acids as potentially beneficial molecules in suppressing cancer progression. Finally, we theorise that suppressing aggressive malignant phenotypes through bile acid/gut microbiome axis modulation could uncover new and innovative disease management strategies for managing cancers in vulnerable cohorts.
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Affiliation(s)
- John P Phelan
- BIOMERIT Research Centre, School of Microbiology, University College Cork - National University of Ireland, Cork, T12 YN60, Ireland
| | - F Jerry Reen
- BIOMERIT Research Centre, School of Microbiology, University College Cork - National University of Ireland, Cork, T12 YN60, Ireland
| | - Jose A Caparros-Martin
- Human Microbiome Programme, School of Biomedical Science, Curtin Health Innovation Research Institute, Curtin University, Perth, WA 6102, Australia
| | - Rosemary O'Connor
- School of Biochemistry and Cell Biology, University College Cork, National University of Ireland, Cork, T12 YN60, Ireland
| | - Fergal O'Gara
- BIOMERIT Research Centre, School of Microbiology, University College Cork - National University of Ireland, Cork, T12 YN60, Ireland.,Human Microbiome Programme, School of Biomedical Science, Curtin Health Innovation Research Institute, Curtin University, Perth, WA 6102, Australia
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15
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Abstract
Dysbiosis is a key term in human microbiome research, especially when microbiome patterns are associated with disease states. Although some questions have been raised about how this term is applied, its use continues undiminished in the literature. We investigate the ways in which microbiome researchers discuss dysbiosis and then assess the impact of different concepts of dysbiosis on microbiome research. After an overview of the term's historical roots, we conduct quantitative and qualitative analyses of a large selection of contemporary dysbiosis statements. We categorize both short definitions and longer conceptual statements about dysbiosis. Further analysis allows us to identify the problematic implications of how dysbiosis is used, particularly with regard to causal hypotheses and normal-abnormal distinctions. We suggest that researchers should reflect carefully on the ways in which they discuss dysbiosis, in order for the field to continue to develop greater predictive scope and explanatory depth.
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Affiliation(s)
- Katarzyna B Hooks
- Centre de Bioinformatique de Bordeaux, Centre de Génomique Fonctionnelle de Bordeaux, University of Bordeaux, Bordeaux, France
- Immunoconcept, CNRS UMR 5164, University of Bordeaux, Bordeaux, France
| | - Maureen A O'Malley
- Centre de Bioinformatique de Bordeaux, Centre de Génomique Fonctionnelle de Bordeaux, University of Bordeaux, Bordeaux, France
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Castro-Penalonga M, Roca-Saavedra P, Miranda JM, Porto-Arias JJ, Nebot C, Cardelle-Cobas A, Franco CM, Cepeda A. Influence of food consumption patterns and Galician lifestyle on human gut microbiota. J Physiol Biochem 2017. [PMID: 28624933 DOI: 10.1007/s13105-017-0570-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The proportion of different microbial populations in the human gut is an important factor that in recent years has been linked to obesity and numerous metabolic diseases. Because there are many factors that can affect the composition of human gut microbiota, it is of interest to have information about what is the composition of the gut microbiota in different populations in order to better understand the possibilities for improving nutritional management. A group of 31 volunteers were selected according to established inclusion and exclusion criteria and were asked about their diet history, lifestyle patterns, and adherence to the Southern European Atlantic Diet. Fecal samples were taken and subsequently analyzed by real-time PCR. The results indicated different dietary patterns for subjects who consumed a higher amount of fruits, vegetables, legumes, and fish and a lower amount of bakery foods and precooked foods and snacks compared to Spanish consumption data. Most participants showed intermediate or high adherence to Southern European Atlantic Diet, and an analysis of gut microbiota showed high numbers of total bacteria and Actinobacteria, as well as high amounts of bacteria belonging to the genera Lactobacillus spp. and Bifidobacterium spp. A subsequent statistical comparison also revealed differences in gut microbiota depending on the subject's body weight, age, or degree of adherence to the Southern European Atlantic Diet.
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Affiliation(s)
- María Castro-Penalonga
- Laboratorio de Higiene, Inspeccion y Control de Alimentos, Departamento de Quimica Analitica, Nutricion y Bromatologia, Universidade de Santiago de Compostela, 27002, Lugo, Spain
| | - Paula Roca-Saavedra
- Laboratorio de Higiene, Inspeccion y Control de Alimentos, Departamento de Quimica Analitica, Nutricion y Bromatologia, Universidade de Santiago de Compostela, 27002, Lugo, Spain
| | - Jose Manuel Miranda
- Laboratorio de Higiene, Inspeccion y Control de Alimentos, Departamento de Quimica Analitica, Nutricion y Bromatologia, Universidade de Santiago de Compostela, 27002, Lugo, Spain. .,Laboratorio de Higiene Inspeccion y Control de Alimentos, Facultad de Veterinaria pabellon 4 p.b. Campus Universitario, 27002, Lugo, Spain.
| | - Jose Julio Porto-Arias
- Laboratorio de Higiene, Inspeccion y Control de Alimentos, Departamento de Quimica Analitica, Nutricion y Bromatologia, Universidade de Santiago de Compostela, 27002, Lugo, Spain
| | - Carolina Nebot
- Laboratorio de Higiene, Inspeccion y Control de Alimentos, Departamento de Quimica Analitica, Nutricion y Bromatologia, Universidade de Santiago de Compostela, 27002, Lugo, Spain
| | - Alejandra Cardelle-Cobas
- Laboratorio de Higiene, Inspeccion y Control de Alimentos, Departamento de Quimica Analitica, Nutricion y Bromatologia, Universidade de Santiago de Compostela, 27002, Lugo, Spain
| | - Carlos Manuel Franco
- Laboratorio de Higiene, Inspeccion y Control de Alimentos, Departamento de Quimica Analitica, Nutricion y Bromatologia, Universidade de Santiago de Compostela, 27002, Lugo, Spain
| | - Alberto Cepeda
- Laboratorio de Higiene, Inspeccion y Control de Alimentos, Departamento de Quimica Analitica, Nutricion y Bromatologia, Universidade de Santiago de Compostela, 27002, Lugo, Spain
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17
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Roca-Saavedra P, Mendez-Vilabrille V, Miranda JM, Nebot C, Cardelle-Cobas A, Franco CM, Cepeda A. Food additives, contaminants and other minor components: effects on human gut microbiota-a review. J Physiol Biochem 2017; 74:69-83. [PMID: 28488210 DOI: 10.1007/s13105-017-0564-2] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 04/10/2017] [Indexed: 02/06/2023]
Abstract
Gut bacteria play an important role in several metabolic processes and human diseases, such as obesity and accompanying co-morbidities, such as fatty liver disease, insulin resistance/diabetes, and cardiovascular events. Among other factors, dietary patterns, probiotics, prebiotics, synbiotics, antibiotics, and non-dietary factors, such as stress, age, exercise, and climatic conditions, can dramatically impact the human gut microbiota equilibrium and diversity. However, the effect of minor food constituents, including food additives and trace contaminants, on human gut microbiota has received less attention. Consequently, the present review aimed to provide an objective perspective of the current knowledge regarding the impacts of minor food constituents on human gut microbiota and consequently, on human health.
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Affiliation(s)
- Paula Roca-Saavedra
- Laboratorio de Higiene Inspección y Control de Alimentos. Dpto. de Química Analítica, Nutrición y Bromatología, Universidade de Santiago de Compostela, 27002, Lugo, Spain
| | - Veronica Mendez-Vilabrille
- Laboratorio de Higiene Inspección y Control de Alimentos. Dpto. de Química Analítica, Nutrición y Bromatología, Universidade de Santiago de Compostela, 27002, Lugo, Spain
| | - Jose Manuel Miranda
- Laboratorio de Higiene Inspección y Control de Alimentos. Dpto. de Química Analítica, Nutrición y Bromatología, Universidade de Santiago de Compostela, 27002, Lugo, Spain.
| | - Carolina Nebot
- Laboratorio de Higiene Inspección y Control de Alimentos. Dpto. de Química Analítica, Nutrición y Bromatología, Universidade de Santiago de Compostela, 27002, Lugo, Spain
| | - Alejandra Cardelle-Cobas
- Laboratorio de Higiene Inspección y Control de Alimentos. Dpto. de Química Analítica, Nutrición y Bromatología, Universidade de Santiago de Compostela, 27002, Lugo, Spain
| | - Carlos M Franco
- Laboratorio de Higiene Inspección y Control de Alimentos. Dpto. de Química Analítica, Nutrición y Bromatología, Universidade de Santiago de Compostela, 27002, Lugo, Spain
| | - Alberto Cepeda
- Laboratorio de Higiene Inspección y Control de Alimentos. Dpto. de Química Analítica, Nutrición y Bromatología, Universidade de Santiago de Compostela, 27002, Lugo, Spain
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18
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Macedo D, Filho AJMC, Soares de Sousa CN, Quevedo J, Barichello T, Júnior HVN, Freitas de Lucena D. Antidepressants, antimicrobials or both? Gut microbiota dysbiosis in depression and possible implications of the antimicrobial effects of antidepressant drugs for antidepressant effectiveness. J Affect Disord 2017; 208:22-32. [PMID: 27744123 DOI: 10.1016/j.jad.2016.09.012] [Citation(s) in RCA: 156] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 09/13/2016] [Accepted: 09/18/2016] [Indexed: 02/07/2023]
Abstract
OBJECTIVES The first drug repurposed for the treatment of depression was the tuberculostatic iproniazid. At present, drugs belonging to new classes of antidepressants still have antimicrobial effects. Dysbiosis of gut microbiota was implicated in the development or exacerbation of mental disorders, such as major depressive disorder (MDD). Based on the current interest in the gut-brain axis, the focus of this narrative review is to compile the available studies regarding the influences of gut microbiota in behavior and depression and to show the antimicrobial effect of antidepressant drugs. A discussion regarding the possible contribution of the antimicrobial effect of antidepressant drugs to its effectiveness/resistance is included. METHODS The search included relevant articles from PubMed, SciELO, LILACS, PsycINFO, and ISI Web of Knowledge. RESULTS MDD is associated with changes in gut permeability and microbiota composition. In this respect, antidepressant drugs present antimicrobial effects that could also be related to the effectiveness of these drugs for MDD treatment. Conversely, some antimicrobials present antidepressant effects. CONCLUSION Both antidepressants and antimicrobials present neuroprotective/antidepressant and antimicrobial effects. Further studies are needed to evaluate the participation of antimicrobial mechanisms of antidepressants in MDD treatment as well as to determine the contribution of this effect to antidepressant resistance.
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Affiliation(s)
- Danielle Macedo
- Neuropharmacology Laboratory, Drug Research and Development Center, Department of Physiology and Pharmacology, Faculty of Medicine, Federal University of Ceará, Fortaleza, CE, Brazil.
| | - Adriano José Maia Chaves Filho
- Neuropharmacology Laboratory, Drug Research and Development Center, Department of Physiology and Pharmacology, Faculty of Medicine, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Caren Nádia Soares de Sousa
- Neuropharmacology Laboratory, Drug Research and Development Center, Department of Physiology and Pharmacology, Faculty of Medicine, Federal University of Ceará, Fortaleza, CE, Brazil
| | - João Quevedo
- Translational Psychiatry Program, Department of Psychiatry and Behavioral Sciences, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA; Center of Excellence on Mood Disorders, Department of Psychiatry and Behavioral Sciences, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA; Neuroscience Graduate Program, The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, TX, USA; Laboratory of Neurosciences, Graduate Program in Health Sciences, Health Sciences Unit, University of Southern Santa Catarina (UNESC), Criciúma, SC, Brazil
| | - Tatiana Barichello
- Translational Psychiatry Program, Department of Psychiatry and Behavioral Sciences, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA; Neuroscience Graduate Program, The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, TX, USA; Laboratory of Neurosciences, Graduate Program in Health Sciences, Health Sciences Unit, University of Southern Santa Catarina (UNESC), Criciúma, SC, Brazil; Laboratory of Experimental Microbiology, Graduate Program in Health Sciences, Health Sciences Unit, University of Southern Santa Catarina (UNESC), Criciúma, SC, Brazil
| | - Hélio Vitoriano Nobre Júnior
- Laboratory of Bioprospection and Experiments in Yeast (LABEL), Drug Research and Development Center, Federal University of Ceará, Fortaleza, CE, Brazil
| | - David Freitas de Lucena
- Neuropharmacology Laboratory, Drug Research and Development Center, Department of Physiology and Pharmacology, Faculty of Medicine, Federal University of Ceará, Fortaleza, CE, Brazil
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19
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Kawada-Matsuo M, Komatsuzawa H. Role of Streptococcus mutans two-component systems in antimicrobial peptide resistance in the oral cavity. JAPANESE DENTAL SCIENCE REVIEW 2017; 53:86-94. [PMID: 28725299 PMCID: PMC5501732 DOI: 10.1016/j.jdsr.2016.12.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 10/14/2016] [Accepted: 12/08/2016] [Indexed: 01/24/2023] Open
Abstract
Approximately 100 trillion microorganisms exist in the oral cavity. For the commensal bacteria of the oral cavity, it is important to adapt to environmental stimuli, including human- or bacteria-derived antimicrobial agents. Recently, bacterial-specific signal transduction regulatory systems, called two-component systems (TCSs), which appear to be focused on sensing and adapting to the environment, were discovered. Streptococcus mutans is an oral commensal bacteria and is also known as a cariogenic bacteria. Although the virulence factors of S. mutans have been well demonstrated, the mechanism underlying the adaptation of the species to the oral cavity is poorly understood. S. mutans UA159 has 15 sets of TCSs. Among them, several have been demonstrated to be involved in acid tolerance, competence and biofilm formation. Recently, together with our findings, it was demonstrated that 5 TCSs were involved in resistance to antimicrobial agents. Furthermore, another TCS was associated with the production of bacteriocin. Six of 15 TCSs are associated with antimicrobial agents, implying that S. mutans can survive in the oral cavity by resisting various antimicrobial peptides. In this review, we highlight the role of antimicrobial peptides in the oral cavity.
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Affiliation(s)
- Miki Kawada-Matsuo
- Department of Oral Microbiology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima 890-8544, Japan
| | - Hitoshi Komatsuzawa
- Department of Oral Microbiology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima 890-8544, Japan
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20
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Barbosa F. Toxicology of metals and metalloids: Promising issues for future studies in environmental health and toxicology. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART A 2017; 80:137-144. [PMID: 28277036 DOI: 10.1080/15287394.2016.1259475] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The function and behavior of chemical elements in ecosystems and in human health probably comprise one of the most studied issues and a theme of great interest and fascination in science. Hot topics are emerging on an annual basis in this field. Bearing this in mind, some promising themes to explore in the field of metals and metalloids in the environment and in toxicology are highlighted and briefly discussed herein.
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Affiliation(s)
- Fernando Barbosa
- a Laboratório de Toxicologia e Essencialidade de Metais, Faculdade de Ciências Farmacêuticas de Ribeirão Preto , Universidade de São Paulo , Ribeirão Preto , SP , Brazil
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21
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O'Donnell MM, Rea MC, O'Sullivan Ó, Flynn C, Jones B, McQuaid A, Shanahan F, Ross RP. Preparation of a standardised faecal slurry for ex-vivo microbiota studies which reduces inter-individual donor bias. J Microbiol Methods 2016; 129:109-116. [PMID: 27498348 DOI: 10.1016/j.mimet.2016.08.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 07/22/2016] [Accepted: 08/02/2016] [Indexed: 12/17/2022]
Abstract
BACKGROUND In-vitro gut fermentation systems provide suitable models for studying gut microbiota composition and functionality. However, such methods depend on the availability of donors and the assumption of reproducibility between microbial communities before experimental treatments commence. The aim of this study was to develop a frozen standardised inoculum (FSI) which minimizes inter-individual variation and to determine its stability over time using culture-dependent and culture-independent techniques. RESULTS A method for the preparation difference of a FSI is described which involves pooling the faecal samples, centrifugation and pelleting of the cell biomass and finally homogenising the cell pellets with phosphate buffer and glycerol. Using this approach, no significant difference in total anaerobe cell viability was observed between the fresh standardised inoculum (before freezing) and the 12days post freezing FSI. Moreover, Quantitative PCR revealed no significant alterations in the estimated bacterial numbers in the FSI preparations for any of the phyla. MiSeq sequencing revealed minute differences in the relative abundance at phylum, family and genus levels between the FSI preparations. Differences in the microbiota denoted as significant were limited between preparations in the majority of cases to changes in percentage relative abundance of ±0.5%. The independently prepared FSIs revealed a high degree of reproducibility in terms of microbial composition between the three preparations. CONCLUSIONS This study provides a method to produce a standardised human faecal inoculum suitable for freezing. Based on culture-dependent and independent analysis, the method ensures a degree of reproducibility between preparations by lessening the effect of inter-individual variation among the donors, thereby making the system more suitable for the accurate interpretation of the effects of experimental treatments.
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Affiliation(s)
- Michelle M O'Donnell
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland; APC Microbiome Institute, University College Cork, Ireland
| | - Mary C Rea
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland; APC Microbiome Institute, University College Cork, Ireland
| | - Órla O'Sullivan
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland; APC Microbiome Institute, University College Cork, Ireland
| | - Cal Flynn
- Kerry Ingredients, Tralee Road, Listowel, Co. Kerry, Ireland
| | - Beth Jones
- Kerry Ingredients & Flavours, Americas Regional Headquarters, 3330 Millington Road, Beloit, WI 53511, United States
| | - Albert McQuaid
- Kerry Ingredients, Tralee Road, Listowel, Co. Kerry, Ireland
| | | | - R Paul Ross
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland; APC Microbiome Institute, University College Cork, Ireland; School of Microbiology, University College Cork, Cork, Ireland.
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22
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23
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Larsen PE, Collart FR, Dai Y. Predicting Ecological Roles in the Rhizosphere Using Metabolome and Transportome Modeling. PLoS One 2015; 10:e0132837. [PMID: 26332409 PMCID: PMC4557938 DOI: 10.1371/journal.pone.0132837] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 06/18/2015] [Indexed: 12/17/2022] Open
Abstract
The ability to obtain complete genome sequences from bacteria in environmental samples, such as soil samples from the rhizosphere, has highlighted the microbial diversity and complexity of environmental communities. However, new algorithms to analyze genome sequence information in the context of community structure are needed to enhance our understanding of the specific ecological roles of these organisms in soil environments. We present a machine learning approach using sequenced Pseudomonad genomes coupled with outputs of metabolic and transportomic computational models for identifying the most predictive molecular mechanisms indicative of a Pseudomonad's ecological role in the rhizosphere: a biofilm, biocontrol agent, promoter of plant growth, or plant pathogen. Computational predictions of ecological niche were highly accurate overall with models trained on transportomic model output being the most accurate (Leave One Out Validation F-scores between 0.82 and 0.89). The strongest predictive molecular mechanism features for rhizosphere ecological niche overlap with many previously reported analyses of Pseudomonad interactions in the rhizosphere, suggesting that this approach successfully informs a system-scale level understanding of how Pseudomonads sense and interact with their environments. The observation that an organism's transportome is highly predictive of its ecological niche is a novel discovery and may have implications in our understanding microbial ecology. The framework developed here can be generalized to the analysis of any bacteria across a wide range of environments and ecological niches making this approach a powerful tool for providing insights into functional predictions from bacterial genomic data.
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Affiliation(s)
- Peter E. Larsen
- Argonne National Laboratory, Biosciences Division, Argonne, IL, United States of America
- University of Illinois at Chicago, Department of Bioengineering, Chicago, IL, United States of America
| | - Frank R. Collart
- Argonne National Laboratory, Biosciences Division, Argonne, IL, United States of America
| | - Yang Dai
- University of Illinois at Chicago, Department of Bioengineering, Chicago, IL, United States of America
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24
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Dore MP, Goni E, Di Mario F. Is There a Role for Probiotics in Helicobacter pylori Therapy? Gastroenterol Clin North Am 2015; 44:565-75. [PMID: 26314668 DOI: 10.1016/j.gtc.2015.05.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The role of probiotics in Helicobacter pylori therapy remains unclear. Lactobacilli can be shown to inhibit H pylori in vitro. Some strains of Lactobacilli may exert specific antimicrobial effects. There is no strong evidence of a benefit on eradication rate when probiotics are added to a regimen. Despite promising results obtained using compounds of L reuteri and S boulardii, high-quality trials are needed to define the role of probiotics as adjuvant therapy. Variables that remain to be studied with L reuteri, currently the most promising strain, include dosage, frequency of administration, administration in relation to meals, and duration of therapy.
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Affiliation(s)
- Maria P Dore
- Dipartimento di Medicina Clinica e Sperimentale, University of Sassari, Viale San Pietro n 8, Sassari 07100, Italy; Department of Medicine, Michael E. DeBakey VAMC, Baylor College of Medicine, 2002 Holcombe Boulevard, Houston, TX 77030, USA
| | - Elisabetta Goni
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke University, Magdeburg 39106, Germany
| | - Francesco Di Mario
- Department of Clinical and Experimental Medicine, University of Parma, School of Medicine, Via Gramsci 14, Parma 43125, Italy.
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25
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Schoster A, Mosing M, Jalali M, Staempfli HR, Weese JS. Effects of transport, fasting and anaesthesia on the faecal microbiota of healthy adult horses. Equine Vet J 2015; 48:595-602. [DOI: 10.1111/evj.12479] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 06/23/2015] [Indexed: 02/06/2023]
Affiliation(s)
- A. Schoster
- University of Zurich; Equine Department; Winterthurerstrasse; Zurich Switzerland
| | - M. Mosing
- University of Zurich; Equine Department; Winterthurerstrasse; Zurich Switzerland
| | - M. Jalali
- Department of Pathobiology; Ontario Veterinary College; University of Guelph; Canada
| | - H. R. Staempfli
- Department of Clinical Studies; Ontario Veterinary College; University of Guelph; Canada
| | - J. S. Weese
- Department of Pathobiology; Ontario Veterinary College; University of Guelph; Canada
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26
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Burns MB, Lynch J, Starr TK, Knights D, Blekhman R. Virulence genes are a signature of the microbiome in the colorectal tumor microenvironment. Genome Med 2015; 7:55. [PMID: 26170900 PMCID: PMC4499914 DOI: 10.1186/s13073-015-0177-8] [Citation(s) in RCA: 151] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Background The human gut microbiome is associated with the development of colon cancer, and recent studies have found changes in the microbiome in cancer patients compared to healthy controls. Studying the microbial communities in the tumor microenvironment may shed light on the role of host–bacteria interactions in colorectal cancer. Here, we highlight the major shifts in the colorectal tumor microbiome relative to that of matched normal colon tissue from the same individual, allowing us to survey the microbial communities in the tumor microenvironment and providing intrinsic control for environmental and host genetic effects on the microbiome. Methods We sequenced the microbiome in 44 primary tumor and 44 patient-matched normal colon tissue samples to determine differentially abundant microbial taxa These data were also used to functionally characterize the microbiome of the cancer and normal sample pairs and identify functional pathways enriched in the tumor-associated microbiota. Results We find that tumors harbor distinct microbial communities compared to nearby healthy tissue. Our results show increased microbial diversity in the tumor microenvironment, with changes in the abundances of commensal and pathogenic bacterial taxa, including Fusobacterium and Providencia. While Fusobacterium has previously been implicated in colorectal cancer, Providencia is a novel tumor-associated agent which has not been identified in previous studies. Additionally, we identified a clear, significant enrichment of predicted virulence-associated genes in the colorectal cancer microenvironment, likely dependent upon the genomes of Fusobacterium and Providencia. Conclusions This work identifies bacterial taxa significantly correlated with colorectal cancer, including a novel finding of an elevated abundance of Providencia in the tumor microenvironment. We also describe the predicted metabolic pathways and enzymes differentially present in the tumor-associated microbiome, and show an enrichment of virulence-associated bacterial genes in the tumor microenvironment. This predicted virulence enrichment supports the hypothesis that the microbiome plays an active role in colorectal cancer development and/or progression. Our results provide a starting point for future prognostic and therapeutic research with the potential to improve patient outcomes. Electronic supplementary material The online version of this article (doi:10.1186/s13073-015-0177-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Michael B Burns
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN USA ; Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN USA
| | - Joshua Lynch
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN USA ; Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN USA
| | - Timothy K Starr
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN USA ; Masonic Cancer Center, University of Minnesota, Minneapolis, MN USA ; Department of Obstetrics, Gynecology and Women's Health, University of Minnesota, Minneapolis, MN USA
| | - Dan Knights
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN USA ; Biotechnology Institute, University of Minnesota, Minneapolis, MN USA
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN USA ; Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN USA
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27
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Toh MC, Allen-Vercoe E. The human gut microbiota with reference to autism spectrum disorder: considering the whole as more than a sum of its parts. MICROBIAL ECOLOGY IN HEALTH AND DISEASE 2015; 26:26309. [PMID: 25634609 PMCID: PMC4310852 DOI: 10.3402/mehd.v26.26309] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 11/30/2014] [Accepted: 11/30/2014] [Indexed: 02/06/2023]
Abstract
The human gut microbiota is a complex microbial ecosystem that contributes an important component towards the health of its host. This highly complex ecosystem has been underestimated in its importance until recently, when a realization of the enormous scope of gut microbiota function has been (and continues to be) revealed. One of the more striking of these discoveries is the finding that the gut microbiota and the brain are connected, and thus there is potential for the microbiota in the gut to influence behavior and mental health. In this short review, we outline the link between brain and gut microbiota and urge the reader to consider the gut microbiota as an ecosystem ‘organ’ rather than just as a collection of microbes filling a niche, using the hypothesized role of the gut microbiota in autism spectrum disorder to illustrate the concept.
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Affiliation(s)
- Michael C Toh
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Canada
| | - Emma Allen-Vercoe
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Canada;
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28
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Ohland CL, Jobin C. Microbial activities and intestinal homeostasis: A delicate balance between health and disease. Cell Mol Gastroenterol Hepatol 2014; 1:28-40. [PMID: 25729763 PMCID: PMC4339954 DOI: 10.1016/j.jcmgh.2014.11.004] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The concept that the intestinal microbiota modulates numerous physiological processes including immune development and function, nutrition and metabolism as well as pathogen exclusion is relatively well established in the scientific community. The molecular mechanisms driving these various effects and the events leading to the establishment of a "healthy" microbiome are slowly emerging. The objective of this review is to bring into focus important aspects of microbial/host interactions in the intestine and to discuss key molecular mechanisms controlling health and disease states. We will discuss recent evidence on how microbes interact with the host and one another and their impact on intestinal homeostasis.
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Affiliation(s)
| | - Christian Jobin
- Department of Medicine, University of Florida, Gainesville, Florida
- Department of Infectious Diseases and Pathology, University of Florida, Gainesville, Florida
- Correspondence Address correspondence to: Christian Jobin, PhD, Department of Medicine, University of Florida, 2033 Mowry Road, Office 461, Gainesville, Florida 32610. fax: (352) 392-3944.
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