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Li D, Liu Z, Fan X, Zhao T, Wen D, Huang X, Li B. Lactic Acid Bacteria-Gut-Microbiota-Mediated Intervention towards Inflammatory Bowel Disease. Microorganisms 2024; 12:1864. [PMID: 39338538 PMCID: PMC11433943 DOI: 10.3390/microorganisms12091864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2024] [Revised: 09/01/2024] [Accepted: 09/02/2024] [Indexed: 09/30/2024] Open
Abstract
Inflammatory bowel disease (IBD), encompassing ulcerative colitis (UC) and Crohn's disease (CD), arises from intricate interactions involving genetics, environment, and pharmaceuticals with an ambiguous pathogenic mechanism. Recently, there has been an increasing utilization of lactic acid bacteria (LAB) in managing IBD, attributed to their ability to enhance intestinal barrier function, mitigate inflammatory responses, and modulate gut microbiota. This review initiates by elucidating the pathogenesis of IBD and its determinants, followed by an exploration of the mechanisms underlying LAB therapy in UC and CD. Special attention is directed towards their influence on intestinal barrier function and homeostasis regulated by gut microbiota. Furthermore, the review investigates the complex interplay among pivotal gut microbiota, metabolites, and pathways associated with inflammation. Moreover, it underscores the limitations of LAB in treating IBD, particularly in light of their varying roles in UC and CD. This comprehensive analysis endeavors to offer insights for the optimized application of LAB in IBD therapy.
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Affiliation(s)
- Diantong Li
- Institute of Animal Husbandry and Veterinary, Xizang Academy of Agricultural and Animal Husbandry Sciences, Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lhasa 850000, China; (D.L.); (Z.L.); (X.F.); (T.Z.); (D.W.)
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Zhenjiang Liu
- Institute of Animal Husbandry and Veterinary, Xizang Academy of Agricultural and Animal Husbandry Sciences, Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lhasa 850000, China; (D.L.); (Z.L.); (X.F.); (T.Z.); (D.W.)
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Xueni Fan
- Institute of Animal Husbandry and Veterinary, Xizang Academy of Agricultural and Animal Husbandry Sciences, Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lhasa 850000, China; (D.L.); (Z.L.); (X.F.); (T.Z.); (D.W.)
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Tingting Zhao
- Institute of Animal Husbandry and Veterinary, Xizang Academy of Agricultural and Animal Husbandry Sciences, Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lhasa 850000, China; (D.L.); (Z.L.); (X.F.); (T.Z.); (D.W.)
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Dongxu Wen
- Institute of Animal Husbandry and Veterinary, Xizang Academy of Agricultural and Animal Husbandry Sciences, Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lhasa 850000, China; (D.L.); (Z.L.); (X.F.); (T.Z.); (D.W.)
| | - Xiaodan Huang
- Institute of Animal Husbandry and Veterinary, Xizang Academy of Agricultural and Animal Husbandry Sciences, Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lhasa 850000, China; (D.L.); (Z.L.); (X.F.); (T.Z.); (D.W.)
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Bin Li
- Institute of Animal Husbandry and Veterinary, Xizang Academy of Agricultural and Animal Husbandry Sciences, Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lhasa 850000, China; (D.L.); (Z.L.); (X.F.); (T.Z.); (D.W.)
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Yang S, Qiao J, Zhang M, Kwok LY, Matijašić BB, Zhang H, Zhang W. Prevention and treatment of antibiotics-associated adverse effects through the use of probiotics: A review. J Adv Res 2024:S2090-1232(24)00230-3. [PMID: 38844120 DOI: 10.1016/j.jare.2024.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 05/18/2024] [Accepted: 06/03/2024] [Indexed: 06/29/2024] Open
Abstract
BACKGROUND The human gut hosts a diverse microbial community, essential for maintaining overall health. However, antibiotics, commonly prescribed for infections, can disrupt this delicate balance, leading to antibiotic-associated diarrhea, inflammatory bowel disease, obesity, and even neurological disorders. Recognizing this, probiotics have emerged as a promising strategy to counteract these adverse effects. AIM OF REVIEW This review aims to offer a comprehensive overview of the latest evidence concerning the utilization of probiotics in managing antibiotic-associated side effects. KEY SCIENTIFIC CONCEPTS OF REVIEW Probiotics play a crucial role in preserving gut homeostasis, regulating intestinal function and metabolism, and modulating the host immune system. These mechanisms serve to effectively alleviate antibiotic-associated adverse effects and enhance overall well-being.
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Affiliation(s)
- Shuwei Yang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Jiaqi Qiao
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Meng Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Lai-Yu Kwok
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Huhhot 010018, China
| | | | - Heping Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Wenyi Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Huhhot 010018, China.
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Sechovcová H, Mahayri TM, Mrázek J, Jarošíková R, Husáková J, Wosková V, Fejfarová V. Gut microbiota in relationship to diabetes mellitus and its late complications with a focus on diabetic foot syndrome: A review. Folia Microbiol (Praha) 2024; 69:259-282. [PMID: 38095802 DOI: 10.1007/s12223-023-01119-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 12/05/2023] [Indexed: 04/11/2024]
Abstract
Diabetes mellitus is a chronic disease affecting glucose metabolism. The pathophysiological reactions underpinning the disease can lead to the development of late diabetes complications. The gut microbiota plays important roles in weight regulation and the maintenance of a healthy digestive system. Obesity, diabetes mellitus, diabetic retinopathy, diabetic nephropathy and diabetic neuropathy are all associated with a microbial imbalance in the gut. Modern technical equipment and advanced diagnostic procedures, including xmolecular methods, are commonly used to detect both quantitative and qualitative changes in the gut microbiota. This review summarises collective knowledge on the role of the gut microbiota in both types of diabetes mellitus and their late complications, with a particular focus on diabetic foot syndrome.
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Affiliation(s)
- Hana Sechovcová
- Laboratory of Anaerobic Microbiology, Institute of Animal Physiology and Genetics, CAS, Vídeňská, 1083, 142 20, Prague, Czech Republic
- Faculty of Agrobiology, Food and Natural Resources, Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Prague, Czech Republic
| | - Tiziana Maria Mahayri
- Laboratory of Anaerobic Microbiology, Institute of Animal Physiology and Genetics, CAS, Vídeňská, 1083, 142 20, Prague, Czech Republic.
- Department of Veterinary Medicine, University of Sassari, 07100, Sassari, Italy.
| | - Jakub Mrázek
- Laboratory of Anaerobic Microbiology, Institute of Animal Physiology and Genetics, CAS, Vídeňská, 1083, 142 20, Prague, Czech Republic
| | - Radka Jarošíková
- Diabetes Centre, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
- Second Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Jitka Husáková
- Diabetes Centre, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Veronika Wosková
- Diabetes Centre, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Vladimíra Fejfarová
- Diabetes Centre, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
- Second Faculty of Medicine, Charles University, Prague, Czech Republic
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Singh AS, Pathak D, Devi MS, Anifowoshe AT, Nongthomba U. Antibiotic alters host's gut microbiota, fertility, and antimicrobial peptide gene expression vis-à-vis ampicillin treatment on model organism Drosophila melanogaster. Int Microbiol 2024:10.1007/s10123-024-00507-9. [PMID: 38502456 DOI: 10.1007/s10123-024-00507-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 02/20/2024] [Accepted: 03/10/2024] [Indexed: 03/21/2024]
Abstract
Antibiotics are commonly used to treat infectious diseases; however, persistence is often expressed by the pathogenic bacteria and their long-term relative effect on the host have been neglected. The present study investigated the impact of antibiotics in gut microbiota (GM) and metabolism of host. The effect of ampicillin antibiotics on GM of Drosophila melanogaster was analyzed through deep sequencing of 16S rRNA amplicon gene. The dominant phyla consisted of Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, Planctomycetes, Chloroflexi, Euryarchaeota, Acedobacteria, Verrucomicrobia, and Cyanobacteria. It was found that the composition of GM was significantly altered on administration of antibiotics. On antibiotic treatments, there were decline in relative abundance of Proteobacteria and Firmicutes, while there were increase in relative abundance of Chlorophyta and Bacteroidota. High abundance of 14 genera, viz., Wolbachia, Lactobacillus, Bacillus, Pseudomonas, Thiolamprovum, Pseudoalteromonas, Vibrio, Romboutsia, Staphylococcus, Alteromonas, Clostridium, Lysinibacillus, Litoricola, and Cellulophaga were significant (p ≤ 0.05) upon antibiotic treatment. Particularly, the abundance of Acetobacter was significantly (p ≤ 0.05) declined but increased for Wolbachia. Further, a significant (p ≤ 0.05) increase in Wolbachia endosymbiont of D. melanogaster, Wolbachia endosymbiont of Curculio okumai, and Wolbachia pipientis and a decrease in the Acinetobacter sp. were observed. We observed an increase in functional capacity for biosynthesis of certain nucleotides and the enzyme activities. Further, the decrease in antimicrobial peptide production in the treated group and potential effects on the host's defense mechanisms were observed. This study helps shed light on an often-overlooked dimension, namely the persistence of antibiotics' effects on the host.
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Affiliation(s)
- Asem Sanjit Singh
- Developmental and Biomedical Genetics Laboratory, Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru, India, 560012.
| | - Dhruv Pathak
- Developmental and Biomedical Genetics Laboratory, Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru, India, 560012
| | - Manoharmayum Shaya Devi
- ICAR-Central Inland Fisheries Research Institute, P.O. Monirampore, Barrackpore, Kolkata, India, 700 120
| | - Abass Toba Anifowoshe
- Developmental and Biomedical Genetics Laboratory, Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru, India, 560012
| | - Upendra Nongthomba
- Developmental and Biomedical Genetics Laboratory, Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru, India, 560012.
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5
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Di Vincenzo F, Nicoletti A, Negri M, Vitale F, Zileri Dal Verme L, Gasbarrini A, Ponziani FR, Cerrito L. Gut Microbiota and Antibiotic Treatments for the Main Non-Oncologic Hepato-Biliary-Pancreatic Disorders. Antibiotics (Basel) 2023; 12:1068. [PMID: 37370387 DOI: 10.3390/antibiotics12061068] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/10/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
The gut microbiota is a pivotal actor in the maintenance of the balance in the complex interconnections of hepato-biliary-pancreatic system. It has both metabolic and immunologic functions, with an influence on the homeostasis of the whole organism and on the pathogenesis of a wide range of diseases, from non-neoplastic ones to tumorigenesis. The continuous bidirectional metabolic communication between gut and hepato-pancreatic district, through bile ducts and portal vein, leads to a continuous interaction with translocated bacteria and their products. Chronic liver disease and pancreatic disorders can lead to reduced intestinal motility, decreased bile acid synthesis and intestinal immune dysfunction, determining a compositional and functional imbalance in gut microbiota (dysbiosis), with potentially harmful consequences on the host's health. The modulation of the gut microbiota by antibiotics represents a pioneering challenge with striking future therapeutic opportunities, even in non-infectious diseases. In this setting, antibiotics are aimed at harmonizing gut microbial function and, sometimes, composition. A more targeted and specific approach should be the goal to pursue in the future, tailoring the treatment according to the type of microbiota modulation to be achieved and using combined strategies.
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Affiliation(s)
- Federica Di Vincenzo
- Internal Medicine and Gastroenterology, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
| | - Alberto Nicoletti
- Internal Medicine and Gastroenterology, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
| | - Marcantonio Negri
- Internal Medicine and Gastroenterology, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
| | - Federica Vitale
- Internal Medicine and Gastroenterology, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
| | - Lorenzo Zileri Dal Verme
- Internal Medicine and Gastroenterology, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
| | - Antonio Gasbarrini
- Internal Medicine and Gastroenterology, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
- Dipartimento Universitario di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Francesca Romana Ponziani
- Internal Medicine and Gastroenterology, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
- Dipartimento Universitario di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Lucia Cerrito
- Internal Medicine and Gastroenterology, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
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6
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Nomura M. Association of the gut microbiome with cancer immunotherapy. Int J Clin Oncol 2023; 28:347-353. [PMID: 35568746 DOI: 10.1007/s10147-022-02180-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 04/24/2022] [Indexed: 11/26/2022]
Abstract
Immune checkpoint inhibitors, programmed cell death-1- and cytotoxic T-lymphocyte-associated protein 4-based immunotherapy have remarkably improved survival with durable response for patients with multiple cancer type. The accurate predictors of response and toxicity to immunotherapy are still unclear and have been focused on the gut microbiome. The gut microbiome, which refers to the microorganisms and their genes, affects the host immunity both locally and systemically. Modulation of the gut microbiota alters the immune systems and affects the efficacy of immune checkpoint inhibitor. In this review, we investigate the evidence on the role of the microbiome in cancer patients and discuss the impact of microbiome on the efficacy of immune checkpoint inhibitors in cancer.
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Affiliation(s)
- Motoo Nomura
- Department of Clinical Oncology, Kyoto University Hospital, 54 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan.
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7
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Olías-Molero AI, Botías P, Cuquerella M, García-Cantalejo J, Barcia E, Torrado S, Torrado JJ, Alunda JM. Effect of Clindamycin on Intestinal Microbiome and Miltefosine Pharmacology in Hamsters Infected with Leishmania infantum. Antibiotics (Basel) 2023; 12:362. [PMID: 36830274 PMCID: PMC9952363 DOI: 10.3390/antibiotics12020362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/02/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023] Open
Abstract
Visceral leishmaniasis (VL), a vector-borne parasitic disease caused by Leishmania donovani and L. infantum (Kinetoplastida), affects humans and dogs, being fatal unless treated. Miltefosine (MIL) is the only oral medication for VL and is considered a first choice drug when resistance to antimonials is present. Comorbidity and comedication are common in many affected patients but the relationship between microbiome composition, drugs administered and their pharmacology is still unknown. To explore the effect of clindamycin on the intestinal microbiome and the availability and distribution of MIL in target organs, Syrian hamsters (120-140 g) were inoculated with L. infantum (108 promastigotes/animal). Infection was maintained for 16 weeks, and the animals were treated with MIL (7 days, 5 mg/kg/day), clindamycin (1 mg/kg, single dose) + MIL (7 days, 5 mg/kg/day) or kept untreated. Infection was monitored by ELISA and fecal samples (16 wpi, 18 wpi, end point) were analyzed to determine the 16S metagenomic composition (OTUs) of the microbiome. MIL levels were determined by LC-MS/MS in plasma (24 h after the last treatment; end point) and target organs (spleen, liver) (end point). MIL did not significantly affect the composition of intestinal microbiome, but clindamycin provoked a transient albeit significant modification of the relative abundance of 45% of the genera, including Ruminococcaceae UCG-014, Ruminococcus 2; Bacteroides and (Eubacterium) ruminantium group, besides its effect on less abundant phyla and families. Intestinal dysbiosis in the antibiotic-treated animals was associated with significantly lower levels of MIL in plasma, though not in target organs at the end of the experiment. No clear relationship between microbiome composition (OTUs) and pharmacological parameters was found.
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Affiliation(s)
- Ana Isabel Olías-Molero
- ICPVet, Department of Animal Health, School of Veterinary Sciences, Complutense University of Madrid, 28040 Madrid, Spain
| | - Pedro Botías
- Genomics Unit, Research Assistance Center of Biological Techniques, Complutense University of Madrid, 28040 Madrid, Spain
| | - Montserrat Cuquerella
- ICPVet, Department of Animal Health, School of Veterinary Sciences, Complutense University of Madrid, 28040 Madrid, Spain
| | - Jesús García-Cantalejo
- Genomics Unit, Research Assistance Center of Biological Techniques, Complutense University of Madrid, 28040 Madrid, Spain
| | - Emilia Barcia
- Department of Pharmaceutics and Food Technology, School of Pharmacy, Complutense University of Madrid, 28040 Madrid, Spain
- Institute of Industrial Pharmacy UCM, School of Pharmacy, Complutense University of Madrid, 28040 Madrid, Spain
| | - Susana Torrado
- Department of Pharmaceutics and Food Technology, School of Pharmacy, Complutense University of Madrid, 28040 Madrid, Spain
- Institute of Industrial Pharmacy UCM, School of Pharmacy, Complutense University of Madrid, 28040 Madrid, Spain
| | - Juan José Torrado
- Department of Pharmaceutics and Food Technology, School of Pharmacy, Complutense University of Madrid, 28040 Madrid, Spain
- Institute of Industrial Pharmacy UCM, School of Pharmacy, Complutense University of Madrid, 28040 Madrid, Spain
| | - José María Alunda
- ICPVet, Department of Animal Health, School of Veterinary Sciences, Complutense University of Madrid, 28040 Madrid, Spain
- Institute of Industrial Pharmacy UCM, School of Pharmacy, Complutense University of Madrid, 28040 Madrid, Spain
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Leardini D, Venturelli F, Baccelli F, Cerasi S, Muratore E, Brigidi P, Pession A, Prete A, Masetti R. Pharmacomicrobiomics in Pediatric Oncology: The Complex Interplay between Commonly Used Drugs and Gut Microbiome. Int J Mol Sci 2022; 23:15387. [PMID: 36499714 PMCID: PMC9740824 DOI: 10.3390/ijms232315387] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 11/27/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
The gut microbiome (GM) has emerged in the last few years as a main character in several diseases. In pediatric oncological patients, GM has a role in promoting the disease, modulating the effectiveness of therapies, and determining the clinical outcomes. The therapeutic course for most pediatric cancer influences the GM due to dietary modifications and several administrated drugs, including chemotherapies, antibiotics and immunosuppressants. Interestingly, increasing evidence is uncovering a role of the GM on drug pharmacokinetics and pharmacodynamics, defining a bidirectional relationship. Indeed, the pediatric setting presents some contrasts with respect to the adult, since the GM undergoes a constant multifactorial evolution during childhood following external stimuli (such as diet modification during weaning). In this review, we aim to summarize the available evidence of pharmacomicrobiomics in pediatric oncology.
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Affiliation(s)
- Davide Leardini
- Pediatric Oncology and Hematology “Lalla Seràgnoli”, IRCCS Azienda Ospedaliero Universitaria di Bologna, 40138 Bologna, Italy
| | - Francesco Venturelli
- Pediatric Oncology and Hematology “Lalla Seràgnoli”, IRCCS Azienda Ospedaliero Universitaria di Bologna, 40138 Bologna, Italy
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, 40126 Bologna, Italy
| | - Francesco Baccelli
- Pediatric Oncology and Hematology “Lalla Seràgnoli”, IRCCS Azienda Ospedaliero Universitaria di Bologna, 40138 Bologna, Italy
| | - Sara Cerasi
- Pediatric Oncology and Hematology “Lalla Seràgnoli”, IRCCS Azienda Ospedaliero Universitaria di Bologna, 40138 Bologna, Italy
| | - Edoardo Muratore
- Pediatric Oncology and Hematology “Lalla Seràgnoli”, IRCCS Azienda Ospedaliero Universitaria di Bologna, 40138 Bologna, Italy
| | - Patrizia Brigidi
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Andrea Pession
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
- Pediatric Unit, IRCCS Azienda Ospedaliero Universitaria di Bologna, 40138 Bologna, Italy
| | - Arcangelo Prete
- Pediatric Oncology and Hematology “Lalla Seràgnoli”, IRCCS Azienda Ospedaliero Universitaria di Bologna, 40138 Bologna, Italy
| | - Riccardo Masetti
- Pediatric Oncology and Hematology “Lalla Seràgnoli”, IRCCS Azienda Ospedaliero Universitaria di Bologna, 40138 Bologna, Italy
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
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Moltzau Anderson J, Lachnit T, Lipinski S, Falk-Paulsen M, Rosenstiel P. Impact of antibiotic perturbation on fecal viral communities in mice. G3 (BETHESDA, MD.) 2022; 13:6839982. [PMID: 36413074 PMCID: PMC9836353 DOI: 10.1093/g3journal/jkac293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 10/27/2022] [Indexed: 11/23/2022]
Abstract
Viruses and bacteriophages have a strong impact on intestinal barrier function and the composition and functional properties of commensal bacterial communities. Shifts of the fecal virome might be involved in human diseases, including inflammatory bowel disease (IBD). Loss-of-function variants in the nucleotide-binding oligomerization domain-containing protein 2 (NOD2) gene are associated with an increased risk of developing Crohn's disease, a subtype of human chronic IBD, where specific changes in fecal viral communities have also been described. To improve our understanding of the dynamics of the enteric virome, we longitudinally characterized the virome in fecal samples from wild-type C57BL/6J and NOD2 knock-out mice in response to an antibiotic perturbation. Sequencing of virus-like particles demonstrated both a high diversity and high interindividual variation of the murine fecal virome composed of eukaryotic viruses and bacteriophages. Antibiotics had a significant impact on the fecal murine virome. Viral community composition only partially recovered in the observation period (10 weeks after cessation of antibiotics) irrespective of genotype. However, compositional shifts in the virome and bacteriome were highly correlated, suggesting that the loss of specific phages may contribute to prolonged dysregulation of the bacterial community composition. We suggest that therapeutic interference with the fecal virome may represent a novel approach in microbiota-targeted therapies.
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Affiliation(s)
- Jacqueline Moltzau Anderson
- Present address for Jacqueline Moltzau Anderson: Department of Medicine, University of California San Francisco, 94117 San Francisco, CA, USA
| | | | - Simone Lipinski
- Present address for Simone Lipinski: University Cancer Center Schleswig-Holstein, University Medical Center Campus Kiel, 24105 Kiel, Germany
| | - Maren Falk-Paulsen
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, 24098 Kiel, Germany
| | - Philip Rosenstiel
- Corresponding author: Institute of Clinical Molecular Biology (IKMB), Christian-Albrechts-University (CAU) Kiel, Rosalind-Franklin-Str. 12, Kiel 24105, Germany.
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Fernández-Alonso M, Aguirre Camorlinga A, Messiah SE, Marroquin E. Effect of adding probiotics to an antibiotic intervention on the human gut microbial diversity and composition: a systematic review. J Med Microbiol 2022; 71. [DOI: 10.1099/jmm.0.001625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Introduction. Millions of antibiotic prescriptions are written annually in the USA.
Gap Statement. Probiotics reduce antibiotic-induced gastrointestinal side effects; however, the effect of probiotics on preserving gut microbial composition in response to antibiotics is not well understood.
Aim. To evaluate whether the addition of probiotics is capable of reverting the changes in alpha diversity and gut microbial composition commonly observed in adult participants receiving antibiotics.
Methodology. A search was conducted by two researchers following the PRISMA guidelines using PubMed, Science Direct, Cochrane and Embase from January to December 2021 with the following inclusion criteria: (i) randomized clinical trials assessing the effect of antibiotics, probiotics or antibiotics+probiotics; (ii) 16S rRNA; (iii) adult participants; and (iv) in English. Once data was extracted in tables, a third researcher compared, evaluated and merged the collected data. The National Institutes of Health (NIH) rating system was utilized to analyse risk of bias.
Results. A total of 29 articles (n=11 antibiotics, n=11 probiotics and n=7 antibiotics+probiotics) met the inclusion criteria. The lack of standardization of protocols to analyse the gut microbial composition and the wide range of selected antibiotics/probiotics complicated data interpretation; however, despite these discrepancies, probiotic co-administration with antibiotics seemed to prevent some, but not all, of the gut microbial diversity and composition changes induced by antibiotics, including restoration of health-related bacteria such as
Faecalibacterium prausnitzii
.
Conclusion. Addition of probiotics to antibiotic interventions seems to preserve alpha diversity and ameliorate the changes to gut microbial composition caused by antibiotic interventions.
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Affiliation(s)
- Melissa Fernández-Alonso
- Escuela de Medicina y Ciencias de la Salud, Tecnológico de Monterrey, Monterrey, Nuevo León, Mexico
| | | | - Sarah E. Messiah
- Center for Pediatric Population Health, UTHealth School of Public Health and Children's Health System of Texas, Dallas, TX, USA
- School of Public Health, University of Texas Health Science Center at Houston, Dallas Campus, Dallas, TX, USA
| | - Elisa Marroquin
- Department of Nutritional Sciences, College of Science and Engineering, Texas Christian University, Fort Worth, TX, USA
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Zhong Z, Zhang Y, Li X, Li L, Zhang R, Zhang S. Differential Responses of Digesta- and Mucosa-Associated Jejunal Microbiota of Hu Sheep to Pelleted and Non-Pelleted High-Grain Diets. Animals (Basel) 2022; 12:ani12131695. [PMID: 35804593 PMCID: PMC9264909 DOI: 10.3390/ani12131695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 06/13/2022] [Accepted: 06/27/2022] [Indexed: 11/28/2022] Open
Abstract
In the present study, we utilized 16S rRNA sequencing to uncover the impacts of non-pelleted (HG) or high-grain pelleted (HP) diets on the microbial structure and potential functions of digesta- and mucosa-associated microbiota in the jejunum of Hu sheep. Here, we randomly assigned 15 healthy male Hu sheep into three groups and fed the control diets (CON), HG, and HP diets, respectively. The experiment period was 60 days. The HP diets had the same nutritional ingredients as the HG diets but in pelleted form. At the finish of the experiment, the jejunal digesta and mucosa were gathered for microbial sequencing. The results of PCoA and PERMANOVA showed that different dietary treatments had significant impact (p < 0.05) on digesta- and mucosa-associated microbiota in the jejunum of Hu sheep. For specific differences, HG diets significantly increased (p < 0.05) the abundance of some acid-producing bacteria in both jejunal digesta (Bifidobacterium, OTU151, and OTU16) and mucosa (Rikenellaceae RC9 gut group, and Bifidobacterium) of Hu sheep compared with the CON diets. Besides the similar effects of the HG diets (increased the acid-producing bacteria such as Olsenella, Pseudoramibacter, and Shuttleworthia), our results also showed that the HP diets significantly decreased (p < 0.05) the abundance of some pro-inflammatory bacteria in the jejunal digesta (Mogibacterium, and Marvinbryantia) and mucosa (Chitinophaga, and Candidatus Saccharimonas) of Hu sheep compared with the HG diets. Collectively, these findings contributed to enriching the knowledge about the effects of HG diets on the structure and function of intestinal microbiota in ruminants.
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12
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Shute A, Bihan DG, Lewis IA, Nasser Y. Metabolomics: The Key to Unraveling the Role of the Microbiome in Visceral Pain Neurotransmission. Front Neurosci 2022; 16:917197. [PMID: 35812241 PMCID: PMC9260117 DOI: 10.3389/fnins.2022.917197] [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] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 05/30/2022] [Indexed: 11/29/2022] Open
Abstract
Inflammatory bowel disease (IBD), comprising Crohn's disease and Ulcerative colitis, is a relapsing and remitting disease of the gastrointestinal tract, presenting with chronic inflammation, ulceration, gastrointestinal bleeding, and abdominal pain. Up to 80% of patients suffering from IBD experience acute pain, which dissipates when the underlying inflammation and tissue damage resolves. However, despite achieving endoscopic remission with no signs of ongoing intestinal inflammation or damage, 30-50% of IBD patients in remission experience chronic abdominal pain, suggesting altered sensory neuronal processing in this disorder. Furthermore, effective treatment for chronic pain is limited such that 5-25% of IBD outpatients are treated with narcotics, with associated morbidity and mortality. IBD patients commonly present with substantial alterations to the microbial community structure within the gastrointestinal tract, known as dysbiosis. The same is also true in irritable bowel syndrome (IBS), a chronic disorder characterized by altered bowel habits and abdominal pain, in the absence of inflammation. An emerging body of literature suggests that the gut microbiome plays an important role in visceral hypersensitivity. Specific microbial metabolites have an intimate relationship with host receptors that are highly expressed on host cell and neurons, suggesting that microbial metabolites play a key role in visceral hypersensitivity. In this review, we will discuss the techniques used to analysis the metabolome, current potential metabolite targets for visceral hypersensitivity, and discuss the current literature that evaluates the role of the post-inflammatory microbiota and metabolites in visceral hypersensitivity.
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Affiliation(s)
- Adam Shute
- Department of Medicine, Cumming School of Medicine, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada
| | - Dominique G. Bihan
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Ian A. Lewis
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Yasmin Nasser
- Department of Medicine, Cumming School of Medicine, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada
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Paromomycin Reduces Vairimorpha (Nosema) ceranae Infection in Honey Bees but Perturbs Microbiome Levels and Midgut Cell Function. Microorganisms 2022; 10:microorganisms10061107. [PMID: 35744625 PMCID: PMC9231153 DOI: 10.3390/microorganisms10061107] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 05/23/2022] [Accepted: 05/23/2022] [Indexed: 02/04/2023] Open
Abstract
Paromomycin is a naturally occurring aminoglycoside antibiotic that has effects on both prokaryotic and eukaryotic microbes. However, previous reports have indicated that it has little effect on microsporidia, including Vairimorpha (Nosema) ceranae, in cell culture models. V. ceranae is one of a number of microsporidia species that cause disease in honey bees and substantial efforts to find new treatment strategies for bees that are infected with these pathogens are ongoing. When testing compounds for potential activity against V. ceranae in whole organisms, we found that paromomycin reduces the infection intensity of this parasite. Critically, the necessary doses of paromomycin have high activity against the bacteria of the honey bee microbiome and cause evident stress in bees. Microsporidia have been shown to lack an essential binding site on the ribosome that is known to allow for maximal inhibition by paromomycin. Thus, it is possible that paromomycin impacts parasite levels through non-cell autonomous effects on microsporidia infection levels via effects on the microbiome or midgut cellular function. As paromomycin treatment could cause widespread honey bee health issues in agricultural settings, it does not represent an appropriate anti-microsporidia agent for use in the field.
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Haskey N, Ye J, Estaki M, Verdugo Meza AA, Barnett JA, Yousefi M, Birnie BW, Gruenheid S, Ghosh S, Gibson DL. A Mediterranean-like fat blend protects against the development of severe colitis in the mucin-2 deficient murine model. Gut Microbes 2022; 14:2055441. [PMID: 35471119 PMCID: PMC9045830 DOI: 10.1080/19490976.2022.2055441] [Citation(s) in RCA: 0] [Impact Index Per Article: 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
There is a growing appreciation that the interaction between diet, the gut microbiota and the immune system contribute to the development and progression of inflammatory bowel disease (IBD). A mounting body of scientific evidence suggests that high-fat diets exacerbate IBD; however, there is a lack of information on how specific types of fat impact colitis. The Mediterranean diet (MD) is considered a health-promoting diet containing approximately 40% total fat. It is not known if the blend of fats found in the MD contributes to its beneficial protective effects. Mice deficient in the mucin 2 gene (Muc 2-/-) were weaned to 40% fat, isocaloric, isonitrogenous diets. We compared the MD fat blend (high monounsaturated, 2:1 n-6:n-3 polyunsaturated and moderate saturated fat) to diets composed of corn oil (CO, n-6 polyunsaturated-rich), olive oil (monounsaturated-rich) or milk fat (MF, saturated-rich) on spontaneous colitis development in Muc2-/- mice. The MD resulted in lower clinical and histopathological scores and induced tolerogenic CD103+ CD11b+ dendritic, Th22 and IL-17+ IL-22+ cells necessary for intestinal barrier repair. The MD was associated with beneficial microbes and associated with higher cecal acetic acid levels negatively correlated with colitogenic microbes like Akkermansia muciniphila. In contrast, CO showed a higher prevalence of mucin-degraders including A. muciniphila and Enterobacteriaceae, which have been associated with colitis. A dietary blend of fats mimicking the MD, reduces disease activity, inflammation-related biomarkers and improves metabolic parameters in the Muc2-/- mouse model. Our findings suggest that the MD fat blend could be incorporated into a maintenance diet for colitis.
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Affiliation(s)
- Natasha Haskey
- Department of Biology, University of British Columbia - Okanagan Campus; Kelowna, British Columbia, Canada
| | - Jiayu Ye
- Department of Biology, University of British Columbia - Okanagan Campus; Kelowna, British Columbia, Canada
| | - Mehrbod Estaki
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
| | - Andrea A. Verdugo Meza
- Department of Biology, University of British Columbia - Okanagan Campus; Kelowna, British Columbia, Canada
| | - Jacqueline A. Barnett
- Department of Biology, University of British Columbia - Okanagan Campus; Kelowna, British Columbia, Canada
| | - Mitra Yousefi
- The Center for Phenogenomics Infection & McGill University Research Centre on Complex Traits; McGill University, Montreal, Quebec, Canada
| | - Blake W. Birnie
- Department of Medicine, University of British Columbia - Okanagan Campus, Kelowna, British Columbia, Canada
| | - Samantha Gruenheid
- Associate Professor - Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
| | - Sanjoy Ghosh
- Department of Biology, University of British Columbia - Okanagan Campus; Kelowna, British Columbia, Canada
| | - Deanna L. Gibson
- Department of Biology, University of British Columbia - Okanagan Campus; Kelowna, British Columbia, Canada,Department of Medicine, University of British Columbia - Okanagan Campus, Kelowna, British Columbia, Canada,CONTACT Deanna L. Gibson ASC 368, 3187University Way Kelowna, BCCanadaV1V 1V7250-807-8790; 250-807-8001
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15
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Association between pneumonia and chronic otitis media: A nested case-control study using a national health screening cohort. Int J Infect Dis 2022; 118:54-61. [DOI: 10.1016/j.ijid.2022.02.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 01/29/2022] [Accepted: 02/16/2022] [Indexed: 11/18/2022] Open
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Araji G, Maamari J, Ahmad FA, Zareef R, Chaftari P, Yeung SCJ. The Emerging Role of the Gut Microbiome in the Cancer Response to Immune Checkpoint Inhibitors: A Narrative Review. JOURNAL OF IMMUNOTHERAPY AND PRECISION ONCOLOGY 2022; 5:13-25. [PMID: 35663831 PMCID: PMC9138420 DOI: 10.36401/jipo-21-10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 08/10/2021] [Accepted: 09/16/2021] [Indexed: 12/02/2022]
Abstract
The discovery of immune checkpoint inhibitors (ICIs) has revolutionized the care of cancer patients. However, the response to ICI therapy exhibits substantial interindividual variability. Efforts have been directed to identify biomarkers that predict the clinical response to ICIs. In recent years, the gut microbiome has emerged as a critical player that influences the efficacy of immunotherapy. An increasing number of studies have suggested that the baseline composition of a patient's gut microbiota and its dysbiosis are correlated with the outcome of cancer immunotherapy. This review tackles the rapidly growing body of evidence evaluating the relationship between the gut microbiome and the response to ICI therapy. Additionally, this review highlights the impact of antibiotic-induced dysbiosis on ICI efficacy and discusses the possible therapeutic interventions to optimize the gut microbiota composition to augment immunotherapy efficacy.
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Affiliation(s)
- Ghada Araji
- LAU Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Byblos, Lebanon
| | - Julian Maamari
- LAU Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Byblos, Lebanon
| | - Fatima Ali Ahmad
- LAU Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Byblos, Lebanon
| | - Rana Zareef
- Faculty of Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Patrick Chaftari
- Department of Emergency Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sai-Ching Jim Yeung
- Department of Emergency Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Van Zyl KN, Matukane SR, Hamman BL, Whitelaw AC, Newton-Foot M. The effect of antibiotics on the human microbiome: a systematic review. Int J Antimicrob Agents 2021; 59:106502. [DOI: 10.1016/j.ijantimicag.2021.106502] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 12/01/2021] [Accepted: 12/11/2021] [Indexed: 12/01/2022]
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Liu J, Zhong Y, Luo XM, Ma Y, Liu J, Wang H. Intermittent Fasting Reshapes the Gut Microbiota and Metabolome and Reduces Weight Gain More Effectively Than Melatonin in Mice. Front Nutr 2021; 8:784681. [PMID: 34901130 PMCID: PMC8652062 DOI: 10.3389/fnut.2021.784681] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 11/05/2021] [Indexed: 12/19/2022] Open
Abstract
Background: Intermittent fasting (IF) can reduce energy intake and body weight (BW). Melatonin has many known functions, which include reducing appetite and preventing excessive weight gain. Objective: This study aimed to investigate the effects of IF on body fat and the gut microbiota and metabolome as well as a potential interaction with melatonin. Methods: Male C57BL/6J mice (23.0 ± 0.9 g, 6 wk old) were randomly assigned into four groups (12 mice/group): control (C), intermittent fasting (F), melatonin (M), and intermittent fasting plus melatonin (MF). The C and M groups mice were provided with ad libitum access to food and water, while the F and MF groups underwent alternative-day feed deprivation (15 cycles total). Melatonin was administered in the drinking water of the M and MF groups. Blood, epididymal fat, liver tissue, and intestinal tissue and contents were collected for lab measurements, histology, and microbiota and metabolome analysis. Main effects and interactions were tested by 2-factor ANOVA. Results: IF significantly reduced BW gain and serum glucose, total cholesterol (TC) and triglyceride (TG) levels. Adipocyte size significantly decreased with IF, then the number of adipocytes per square millimeter significantly increased (P < 0.05). Compared to the C group, the M and MF groups had significantly higher serum melatonin levels (17 and 21%, respectively), although melatonin monotherapy had no effect on serum parameters and adipocytes. There was no interaction between IF and melatonin on BW gain and serum parameters except for on adipocyte area and number per square millimeter, Bacteroidetes and Akkermansia bacterial abundance, and the levels of the intestinal metabolites alanine, valine and isoleucine. IF changed the intestinal microbiota structure, with the F and MF groups clearly separating from the C and M groups. Metabolomic analysis showed that there was obvious separation between all four groups. Conclusions: IF, but neither melatonin nor the interaction between IF and melatonin, could alter intestinal microbiota and metabolism and prevent obesity by reducing BW gain, serum glucose, TC, and TG, and adipocyte size in mice.
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Affiliation(s)
- Jingliang Liu
- College of Animal Science, Zhejiang University, The Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Hangzhou, China
| | - Yifan Zhong
- College of Animal Science, Zhejiang University, The Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Hangzhou, China
| | - Xin M. Luo
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, Blacksburg, VA, United States
| | - Yanfei Ma
- College of Animal Science, Zhejiang University, The Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Hangzhou, China
| | - Jianxin Liu
- College of Animal Science, Zhejiang University, The Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Hangzhou, China
| | - Haifeng Wang
- College of Animal Science, Zhejiang University, The Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Hangzhou, China
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Cuisiniere T, Calvé A, Fragoso G, Oliero M, Hajjar R, Gonzalez E, Santos MM. Oral iron supplementation after antibiotic exposure induces a deleterious recovery of the gut microbiota. BMC Microbiol 2021; 21:259. [PMID: 34583649 PMCID: PMC8480066 DOI: 10.1186/s12866-021-02320-0] [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: 04/22/2021] [Accepted: 09/16/2021] [Indexed: 02/08/2023] Open
Abstract
Background Oral iron supplementation is commonly prescribed for anemia and may play an important role in the gut microbiota recovery of anemic individuals who received antibiotic treatment. This study aims to investigate the effects of iron supplementation on gut microbiota recovery after antibiotics exposure. Results Mice were subjected to oral antibiotic treatment with neomycin and metronidazole and were fed diets with different concentrations of iron. The composition of the gut microbiota was followed throughout treatment by 16S rRNA sequencing of DNA extracted from fecal samples. Gut microbiota functions were inferred using PICRUSt2, and short-chain fatty acid concentration in fecal samples was assessed by liquid-chromatography mass spectrometry. Iron supplementation after antibiotic exposure shifted the gut microbiota composition towards a Bacteroidetes phylum-dominant composition. At the genus level, the iron-supplemented diet induced an increase in the abundance of Parasutterella and Bacteroides, and a decrease of Bilophila and Akkermansia. Parasutterella excrementihominis, Bacteroides vulgatus, and Alistipes finegoldii, were more abundant with the iron excess diet. Iron-induced shifts in microbiota composition were accompanied by functional modifications, including an enhancement of the biosynthesis of primary bile acids, nitrogen metabolism, cyanoamino acid metabolism and pentose phosphate pathways. Recovery after antibiotic treatment increased propionate levels independent of luminal iron levels, whereas butyrate levels were diminished by excess iron. Conclusions Oral iron supplementation after antibiotic therapy in mice may lead to deleterious changes in the recovery of the gut microbiota. Our results have implications on the use of oral iron supplementation after antibiotic exposure and justify further studies on alternative treatments for anemia in these settings. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02320-0.
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Affiliation(s)
- Thibault Cuisiniere
- Nutrition and Microbiome Laboratory, Institut du cancer de Montréal, Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM), CRCHUM - R10.426, 900 rue Saint-Denis, Montréal, Québec, H2X 0A9, Canada
| | - Annie Calvé
- Nutrition and Microbiome Laboratory, Institut du cancer de Montréal, Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM), CRCHUM - R10.426, 900 rue Saint-Denis, Montréal, Québec, H2X 0A9, Canada
| | - Gabriela Fragoso
- Nutrition and Microbiome Laboratory, Institut du cancer de Montréal, Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM), CRCHUM - R10.426, 900 rue Saint-Denis, Montréal, Québec, H2X 0A9, Canada
| | - Manon Oliero
- Nutrition and Microbiome Laboratory, Institut du cancer de Montréal, Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM), CRCHUM - R10.426, 900 rue Saint-Denis, Montréal, Québec, H2X 0A9, Canada
| | - Roy Hajjar
- Nutrition and Microbiome Laboratory, Institut du cancer de Montréal, Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM), CRCHUM - R10.426, 900 rue Saint-Denis, Montréal, Québec, H2X 0A9, Canada.,Digestive Surgery Service, Centre hospitalier de l'Université de Montréal, Montréal, Canada
| | - Emmanuel Gonzalez
- Canadian Centre for Computational Genomics, Department of Human Genetics; and Microbiome Platform Research, McGill Interdisciplinary Initiative in Infection and Immunity, McGill University, Montréal, Canada
| | - Manuela M Santos
- Nutrition and Microbiome Laboratory, Institut du cancer de Montréal, Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM), CRCHUM - R10.426, 900 rue Saint-Denis, Montréal, Québec, H2X 0A9, Canada. .,Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, Canada.
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20
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Pennycook JH, Scanlan PD. Ecological and Evolutionary responses to Antibiotic Treatment in the Human Gut Microbiota. FEMS Microbiol Rev 2021; 45:fuab018. [PMID: 33822937 PMCID: PMC8498795 DOI: 10.1093/femsre/fuab018] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/25/2021] [Indexed: 12/16/2022] Open
Abstract
The potential for antibiotics to affect the ecology and evolution of the human gut microbiota is well recognised and has wide-ranging implications for host health. Here, we review the findings of key studies that surveyed the human gut microbiota during antibiotic treatment. We find several broad patterns including the loss of diversity, disturbance of community composition, suppression of bacteria in the Actinobacteria phylum, amplification of bacteria in the Bacteroidetes phylum, and promotion of antibiotic resistance. Such changes to the microbiota were often, but not always, recovered following the end of treatment. However, many studies reported unique and/or contradictory results, which highlights our inability to meaningfully predict or explain the effects of antibiotic treatment on the human gut microbiome. This problem arises from variation between existing studies in three major categories: differences in dose, class and combinations of antibiotic treatments used; differences in demographics, lifestyles, and locations of subjects; and differences in measurements, analyses and reporting styles used by researchers. To overcome this, we suggest two integrated approaches: (i) a top-down approach focused on building predictive models through large sample sizes, deep metagenomic sequencing, and effective collaboration; and (ii) a bottom-up reductionist approach focused on testing hypotheses using model systems.
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Affiliation(s)
- Joseph Hugh Pennycook
- APC Microbiome Ireland, Biosciences Institute, University College Cork, College Road, Cork, T12 YT20, Ireland
- School of Mirobiology, Food Science & Technology Building, University College Cork, College Road, Cork, T12 K8AF, Ireland
| | - Pauline Deirdre Scanlan
- APC Microbiome Ireland, Biosciences Institute, University College Cork, College Road, Cork, T12 YT20, Ireland
- School of Mirobiology, Food Science & Technology Building, University College Cork, College Road, Cork, T12 K8AF, Ireland
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21
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Ghanem S, Kim CJ, Dutta D, Salifu M, Lim SH. Antimicrobial therapy during cancer treatment: Beyond antibacterial effects. J Intern Med 2021; 290:40-56. [PMID: 33372309 DOI: 10.1111/joim.13238] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/22/2020] [Accepted: 12/01/2020] [Indexed: 02/07/2023]
Abstract
Cancer treatment options have evolved to include immunotherapy and targeted therapy, in addition to traditional chemoradiation. Chemoradiation places the patient at a higher risk of infection through a myelosuppressive effect. High clinical suspicion and early use of antimicrobials play a major role in decreasing any associated morbidity and mortality. This has led to a widespread use of antimicrobials in cancer patients. Antimicrobial use, however, does not come without its perils. Dysbiosis caused by antimicrobial use affects responses to chemotherapeutic agents and is prognostic in the development and severity of certain cancer treatment-related complications such as graft-versus-host disease and Clostridioides difficile infections. Studies have also demonstrated that an intact gut microbiota is essential in the anticancer immune response. Antimicrobial use can therefore modulate responses and outcomes with immunotherapy targeting immune checkpoints. In this review, we highlight the perils associated with antimicrobial use during cancer therapy and the importance of a more judicious approach. We discuss the nature of the pathologic changes in the gut microbiota resulting from antimicrobial use. We explore the effect these changes have on responses and outcomes to different cancer treatment modalities including chemotherapy and immunotherapy, as well as potential adverse clinical consequences in the setting of stem cell transplant.
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Affiliation(s)
- S Ghanem
- From the, Division of Hematology and Oncology, Department of Medicine, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - C J Kim
- From the, Division of Hematology and Oncology, Department of Medicine, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - D Dutta
- From the, Division of Hematology and Oncology, Department of Medicine, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - M Salifu
- From the, Division of Hematology and Oncology, Department of Medicine, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - S H Lim
- From the, Division of Hematology and Oncology, Department of Medicine, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
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22
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The amphibian microbiome exhibits poor resilience following pathogen-induced disturbance. ISME JOURNAL 2021; 15:1628-1640. [PMID: 33564111 PMCID: PMC8163836 DOI: 10.1038/s41396-020-00875-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 11/24/2020] [Accepted: 12/07/2020] [Indexed: 12/29/2022]
Abstract
Infectious pathogens can disrupt the microbiome in addition to directly affecting the host. Impacts of disease may be dependent on the ability of the microbiome to recover from such disturbance, yet remarkably little is known about microbiome recovery after disease, particularly in nonhuman animals. We assessed the resilience of the amphibian skin microbial community after disturbance by the pathogen, Batrachochytrium dendrobatidis (Bd). Skin microbial communities of laboratory-reared mountain yellow-legged frogs were tracked through three experimental phases: prior to Bd infection, after Bd infection (disturbance), and after clearing Bd infection (recovery period). Bd infection disturbed microbiome composition and altered the relative abundances of several dominant bacterial taxa. After Bd infection, frogs were treated with an antifungal drug that cleared Bd infection, but this did not lead to recovery of microbiome composition (measured as Unifrac distance) or relative abundances of dominant bacterial groups. These results indicate that Bd infection can lead to an alternate stable state in the microbiome of sensitive amphibians, or that microbiome recovery is extremely slow—in either case resilience is low. Furthermore, antifungal treatment and clearance of Bd infection had the additional effect of reducing microbial community variability, which we hypothesize results from similarity across frogs in the taxa that colonize community vacancies resulting from the removal of Bd. Our results indicate that the skin microbiota of mountain yellow-legged frogs has low resilience following Bd-induced disturbance and is further altered by the process of clearing Bd infection, which may have implications for the conservation of this endangered amphibian.
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Wu J, Gan T, Zhang Y, Xia G, Deng S, Lv X, Zhang B, Lv B. The prophylactic effects of BIFICO on the antibiotic-induced gut dysbiosis and gut microbiota. Gut Pathog 2020; 12:41. [PMID: 32944084 PMCID: PMC7488247 DOI: 10.1186/s13099-020-00379-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 08/25/2020] [Indexed: 12/17/2022] Open
Abstract
Background The aim of this study is to evaluate the prophylactic effects of probiotic mixture BIFICO on antibiotic-induced gut dysbiosis (AIGD) and the influence on the change of the gut microbiota. Methods We conducted a prospective, randomized, controlled study and divided 196 patients who required intravenous beta-lactam antibiotics into three groups: a control group (no probiotics), a regular group (840 mg of BIFICO), and a double-dosage group (1680 mg of BIFICO). The symptoms of antibiotic-related diarrhea, bloating and abdominal pain and the incidence of AIGD were evaluated 7 days and 8–14 days after antibiotic use, with 10 patients in each group. 16S rDNA sequencing was performed to detect changes of the gut microbiota. Results Within 7 days of the initiation of antibiotic treatment, the incidences of AIGD in the control group, regular group (840 mg of BIFICO), and double-dosage group (1680 mg of BIFICO) were 21.88%, 14.93%, and 6.15% respectively. On days of 8–14th, the incidences of AIGD in the control group, regular group, and double-dosage group were 25%, 14.93%, and 4.62%, respectively. The incidence of AIGD in the double-dosage group within 7 days and 14 days were both significantly lower than that in relevant control group (P < 0.05). On day 14, the incidence of AIGD in the double-dosage group was lower than that in the regular group (P < 0.05). The number of operational taxonomic units (OTUs) in the control group after antibiotic treatment was significantly reduced compared to that prior to treatment, while those of the regular and double-dosage groups were stable. The species abundance, especially Parabacteroides, Phascolarctobacterium and Roseburia, of the double-dosage group was greater than that of the regular group and the control group. Conclusions BIFICO may reduce the occurrence of AIGD in a dose-dependent manner and can stabilize the gut microbiota balance.
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Affiliation(s)
- Jiannong Wu
- Department of Critical Care, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Tieer Gan
- Department of Infection Management, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Ying Zhang
- Center of Clinical Evaluation, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Guolian Xia
- Department of Critical Care, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Shu Deng
- Department of Hematology, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Xin Lv
- Department of Pneumology, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Bingxin Zhang
- Department of Pneumology, Fuyang District People's Hospital of Hangzhou, Hangzhou, China
| | - Bin Lv
- Department of Gastroenterology, The First Affiliated Hospital of Zhejiang Chinese Medical University, 54 Youdian RoadZhejiang Province, Hangzhou, 310009 China
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Bovine Lactoferrin Supplementation Does Not Disrupt Microbiota Development in Preterm Infants Receiving Probiotics. J Pediatr Gastroenterol Nutr 2020; 71:216-222. [PMID: 32404742 DOI: 10.1097/mpg.0000000000002734] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
OBJECTIVE The aim of the study was to assess whether bovine lactoferrin (bLf) supplementation disrupts intestinal microbiota development in preterm infants less than 31 weeks gestational age receiving prophylactic probiotic administration. METHODS Subjects were recruited from the LACUNA trial (ISRCTN66482337), designed to assess bLf safety. These subjects were randomized to daily receive either probiotic supplements or probiotics supplemented with 100 mg bLf mixed with their feeds (human milk or formula). Stools were collected weekly from enrolled infants for 1 month and the microbiota characterized using V6-16S rRNA gene amplicon profiling. RESULTS Infants' microbiomes did not increase in alpha diversity over time in both feeding interventions. Infants receiving bLf supplementation had overall higher species richness as compared with those not receiving these supplements and lactoferrin supplementation had differing effects on infant microbiota species richness depending on the infant's gestational age. Principal co-ordinate analysis revealed that the infant microbiotas did not separate by intervention group, gestational age bracket at birth or sampling time and the main factor dictating sample clustering was infant identity. There were very few detectable differences in taxa relative abundance or functional gene content between the microbiotas in the 2 study groups. CONCLUSIONS Bovine lactoferrin supplementation has minimal impact on microbiota composition/function in preterm infants receiving probiotics, and therefore, is unlikely to disrupt microbiota development.
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Tang Q, Jin G, Wang G, Liu T, Liu X, Wang B, Cao H. Current Sampling Methods for Gut Microbiota: A Call for More Precise Devices. Front Cell Infect Microbiol 2020; 10:151. [PMID: 32328469 PMCID: PMC7161087 DOI: 10.3389/fcimb.2020.00151] [Citation(s) in RCA: 221] [Impact Index Per Article: 55.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 03/23/2020] [Indexed: 12/14/2022] Open
Abstract
The development of next-generation sequencing technology has enabled researchers to explore and understand the gut microbiome from a broader and deeper perspective. However, the results of different studies on gut microbiota are highly variable even in the same disease, which makes it difficult to guide clinical diagnosis and treatment. The ideal sampling method should be non-invasive, involve little cross-contamination or bowel preparation, and collect gut microbiota at different sites. Currently, sequencing technologies are usually based on samples collected from feces, mucosal biopsy, intestinal fluid, etc. However, different parts of the gastrointestinal tract possess various physiological characteristics that are essential for particular species of living microbiota. Moreover, current sampling methods are somewhat defective. For example, fecal samples are just a proxy for intestinal microbiota, while biopsies are invasive for patients and not suitable for healthy controls. In this review, we summarize the current sampling methods and their advantages and shortcomings. New sampling technologies, such as the Brisbane Aseptic Biopsy Device and the intelligent capsule, are also mentioned to inspire the development of future precise description methods of the gut microbiome.
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Affiliation(s)
- Qiang Tang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin, China.,Tianjin Institute of Digestive Disease, General Hospital, Tianjin Medical University, Tianjin, China
| | - Ge Jin
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin, China.,Tianjin Institute of Digestive Disease, General Hospital, Tianjin Medical University, Tianjin, China
| | - Gang Wang
- Tianjin Institute of Digestive Disease, General Hospital, Tianjin Medical University, Tianjin, China
| | - Tianyu Liu
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin, China.,Tianjin Institute of Digestive Disease, General Hospital, Tianjin Medical University, Tianjin, China
| | - Xiang Liu
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin, China
| | - Bangmao Wang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin, China.,Tianjin Institute of Digestive Disease, General Hospital, Tianjin Medical University, Tianjin, China
| | - Hailong Cao
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin, China.,Tianjin Institute of Digestive Disease, General Hospital, Tianjin Medical University, Tianjin, China
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26
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Li X, Wu Y, Xu Z, Chen J, Li Y, Xing H, Zhang X, Yuan J. Effects of Hetiao Jianpi Decoction on Intestinal Injury and Repair in Rats with Antibiotic-Associated Diarrhea. Med Sci Monit 2020; 26:e921745. [PMID: 32062668 PMCID: PMC7043351 DOI: 10.12659/msm.921745] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Through observing the changes of indexes of the intestinal mucosal barrier and intestinal flora in rats, we explored the mechanism by which Hetiao Jianpi Decoction (HTJPD) treats antibiotic-associated diarrhea (AAD) by repairing intestinal mucosal injury and regulating intestinal flora. MATERIAL AND METHODS Samples of colon tissues were collected for HE staining. Enzyme-linked immunosorbent assay (ELISA) was used to assess levels of diamine oxidase (DAO) and D-lactic acid in rat plasma and the expression of secretory immunoglobulin A (SIgA) in colon tissue. We assessed the abundance of intestinal contents by high-throughput sequencing of the 16S rRNA gene. RESULTS Compared with the Model group, the muscle layer and intestinal mucosal edema were improved, and the continuity was restored; the levels of DAO and D-lactic acid in plasma decreased, and the SIgA level were increased in the HTJPD group. The structure of the intestinal flora changed, as indicated by increased levels of certain beneficial bacteria (Verrucomicrobia, Actinobacteria, CF231, and Akkermansia), decreased levels of pathogenic bacteria (Spirochaetes and Treponema), and increased species diversity. CONCLUSIONS By improving the permeability and immune function of the intestinal mucosa, Hetiao Jianpi decoction prevented the occurrence of AAD by repairing the intestinal mucosal damage and regulating the structure and diversity of intestinal flora.
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Affiliation(s)
- Xiaoya Li
- College of Basic Medical Science, Yunnan University of Chinese Medicine, Kunming, Yunnan, China (mainland)
| | - Yueying Wu
- College of First Clinical Medical Science, Yunnan University of Chinese Medicine, Kunming, Yunnan, China (mainland)
| | - Zhenyuan Xu
- College of Basic Medical Science, Yunnan University of Chinese Medicine, Kunming, Yunnan, China (mainland)
| | - Jing Chen
- College of Basic Medical Science, Yunnan University of Chinese Medicine, Kunming, Yunnan, China (mainland).,Provincial Innovation Team of Yunnan University of Chinese Medicine for Traditional Chinese Medicine to Regulate Human Microecology, Kunming, Yunnan, China (mainland)
| | - Yuqing Li
- College of Basic Medical Science, Yunnan University of Chinese Medicine, Kunming, Yunnan, China (mainland).,Provincial Innovation Team of Yunnan University of Chinese Medicine for Traditional Chinese Medicine to Regulate Human Microecology, Kunming, Yunnan, China (mainland)
| | - Haijing Xing
- College of Basic Medical Science, Yunnan University of Chinese Medicine, Kunming, Yunnan, China (mainland).,Provincial Innovation Team of Yunnan University of Chinese Medicine for Traditional Chinese Medicine to Regulate Human Microecology, Kunming, Yunnan, China (mainland)
| | - Xiaomei Zhang
- College of Basic Medical Science, Yunnan University of Chinese Medicine, Kunming, Yunnan, China (mainland).,Provincial Innovation Team of Yunnan University of Chinese Medicine for Traditional Chinese Medicine to Regulate Human Microecology, Kunming, Yunnan, China (mainland)
| | - Jiali Yuan
- Provincial Innovation Team of Yunnan University of Chinese Medicine for Traditional Chinese Medicine to Regulate Human Microecology, Kunming, Yunnan, China (mainland)
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Hu Y, Wang L, Shao D, Wang Q, Wu Y, Han Y, Shi S. Selectived and Reshaped Early Dominant Microbial Community in the Cecum With Similar Proportions and Better Homogenization and Species Diversity Due to Organic Acids as AGP Alternatives Mediate Their Effects on Broilers Growth. Front Microbiol 2020; 10:2948. [PMID: 31993028 PMCID: PMC6971172 DOI: 10.3389/fmicb.2019.02948] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 12/06/2019] [Indexed: 01/16/2023] Open
Abstract
Understanding the differences in microbial communities shaped by different food selective forces, especially during early post-hatch period, is critical to gain insight into how to select, evaluate, and improve antibiotic growth promoters (AGPs) alternatives in food animals. As a model system, commercial diet-administered OAs (DOAs) and water-administered OAs (WOAs) were used separately or in combination as Virginiamycin alternatives for broiler feeding during two growth phases: 1–21 days and 22–42 days. Among these three OA-treated groups, the DOA group was most similar to the AGP group in the composition and the proportion of these dominant bacterial communities at the level of phylum, family, and genus in cecal chyme of broilers. Sub-therapeutic Virginiamycin decreased the richness, homogenization, and species diversity of gut microbiota, especially in the early growth stage from days 1 to 21. Among these three OA supplementation schemes, it was clear that DOA supplementation was more likely to increase or maintain the richness, homogenization, species diversity, and predicted gene functions of cecal microbiota in treated broilers than either no supplementation or AGP supplementation during two experimental stages. The interference of DOA treatment with early colonization of probiotics and pathogens in broiler cecum was the most similar to AGP treatment, and OAs did not cause the occurrence of Virginiamycin-resistant strains of Enterococcus at the end of this trial. In terms of the predicted gene functions of the microbiota, AGP and DOA treatments provided a similar selective force for microbial metabolism functions in the cecum of broiler chickens, especially in the early growth stage. Noticeably, the relative abundance of some microbiome that was modified by Virginiamycin or DOA supplementation was significantly correlated with body weight gain and KEGG pathway analysis-annotated gene functions such as replication and repair, translation, nucleotide metabolism, and so on. With the comprehensive analysis of these results and practical application, shortened DOA supplementation, after optimization of the amount of addition, would be a suitable alternative to sub-therapeutic Virginiamycin. It was suggested that the programed intestinal microecology under such early selection forces and the effective addition time may be the key elements to focus on the designed alternate strategies of AGPs in food animals.
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Affiliation(s)
- Yan Hu
- Poultry Institute, Chinese Academy of Agriculture Sciences, Yangzhou, China.,Center of Effective Evaluation of Feed and Feed Additive, Poultry Institute, Ministry of Agriculture, Yangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Laidi Wang
- Poultry Institute, Chinese Academy of Agriculture Sciences, Yangzhou, China.,Center of Effective Evaluation of Feed and Feed Additive, Poultry Institute, Ministry of Agriculture, Yangzhou, China
| | - Dan Shao
- Poultry Institute, Chinese Academy of Agriculture Sciences, Yangzhou, China.,Center of Effective Evaluation of Feed and Feed Additive, Poultry Institute, Ministry of Agriculture, Yangzhou, China
| | - Qiang Wang
- Poultry Institute, Chinese Academy of Agriculture Sciences, Yangzhou, China.,Center of Effective Evaluation of Feed and Feed Additive, Poultry Institute, Ministry of Agriculture, Yangzhou, China
| | - Yuanyuan Wu
- Trouw Nutrition R&D, Amersfoort, Netherlands
| | - Yanming Han
- Trouw Nutrition R&D, Amersfoort, Netherlands
| | - Shourong Shi
- Poultry Institute, Chinese Academy of Agriculture Sciences, Yangzhou, China.,Center of Effective Evaluation of Feed and Feed Additive, Poultry Institute, Ministry of Agriculture, Yangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
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Zimmermann P, Curtis N. The effect of antibiotics on the composition of the intestinal microbiota - a systematic review. J Infect 2019; 79:471-489. [PMID: 31629863 DOI: 10.1016/j.jinf.2019.10.008] [Citation(s) in RCA: 187] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 10/13/2019] [Indexed: 02/06/2023]
Abstract
OBJECTIVE Antibiotics change the composition of the intestinal microbiota. The magnitude of the effect of antibiotics on the microbiota and whether the effects are short-term or persist long-term remain uncertain. In this review, we summarise studies that have investigated the effect of antibiotics on the composition of the human intestinal microbiota. METHODS A systematic search was done to identify original studies that have investigated the effect of systemic antibiotics on the intestinal microbiota in humans. RESULTS We identified 129 studies investigating 2076 participants and 301 controls. Many studies reported a decrease in bacterial diversity with antibiotic treatment. Penicillin only had minor effects on the intestinal microbiota. Amoxicillin, amoxcillin/clavulanate, cephalosporins, lipopolyglycopeptides, macrolides, ketolides, clindamycin, tigecycline, quinolones and fosfomycin all increased abundance of Enterobacteriaea other than E. coli (mainly Citrobacter spp., Enterobacter spp. and Klebsiella spp.). Amoxcillin, cephalosporins, macrolides, clindamycin, quinolones and sulphonamides decreased abundance of E. coli, while amoxcillin/clavulante, in contrast to other penicillins, increased abundance of E. coli. Amoxicllin, piperacillin and ticarcillin, cephalosporins (except fifth generation cephalosporins), carbapenems and lipoglycopeptides were associated with increased abundance of Enterococcus spp., while macrolides and doxycycline decreased its abundance. Piperacillin and ticarcillin, carbapenems, macrolides, clindamycin and quinolones strongly decreased the abundance of anaerobic bacteria. In the studies that investigated persistence, the longest duration of changes was reported after treatment with ciprofloxacin (one year), clindamycin (two years) and clarithromycin plus metronidazole (four years). Many antibiotics were associated with a decrease in butyrate or butryrate-producing bacteria. CONCLUSION Antibiotics have profound and sometimes persisting effects on the intestinal microbiota, characterised by diminished abundance of beneficial commensals and increased abundance of potentially detrimental microorganisms. Understanding these effects will help tailor antibiotic treatment and the use of probiotics to minimise this 'collateral damage'.
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Affiliation(s)
- Petra Zimmermann
- Department of Paediatrics, Fribourg Hospital HFR and Faculty of Science and Medicine, University of Fribourg, Switzerland; Department of Paediatrics, The University of Melbourne, Parkville, Australia; Infectious Diseases Research Group, Murdoch Children's Research Institute, Parkville, Australia; Infectious Diseases Unit, The Royal Children's Hospital Melbourne, Parkville, Australia.
| | - Nigel Curtis
- Department of Paediatrics, The University of Melbourne, Parkville, Australia; Infectious Diseases Research Group, Murdoch Children's Research Institute, Parkville, Australia; Infectious Diseases Unit, The Royal Children's Hospital Melbourne, Parkville, Australia
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29
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Baindara P, Mandal SM. Antimicrobial Peptides and Vaccine Development to Control Multi-drug Resistant Bacteria. Protein Pept Lett 2019; 26:324-331. [PMID: 31237198 DOI: 10.2174/0929866526666190228162751] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/10/2019] [Accepted: 02/12/2019] [Indexed: 12/20/2022]
Abstract
Antimicrobial resistance (AMR) reported to increase globally at alarming levels in the recent past. A number of potential alternative solutions discussed and implemented to control AMR in bacterial pathogens. Stringent control over the clinical application of antibiotics for a reduction in uses is a special consideration along with alternative solutions to fight against AMR. Although alternatives to conventional antibiotics like antimicrobial peptides (AMP) might warrant serious consideration to fight against AMR, there is a thriving recognition for vaccines in encountering the problem of AMR. Vaccines can reduce the prevalence of AMR by reducing the number of specific pathogens, which result in cutting down the antimicrobial need and uses. However, conventional vaccines produced using live or attenuated microorganisms while the presence of immunologically redundant biological components or impurities might cause major side effects and health related problems. Here we discussed AMPs based vaccination strategies as an emerging concept to overcome the disadvantages of traditional vaccines while boosting the AMPs to control multidrug resistant bacteria or AMR. Nevertheless, the poor immune response is a major challenge in the case of peptide vaccines as minimal antigenic epitopes used for immunization in peptide vaccines.
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Affiliation(s)
- Piyush Baindara
- Department of Microbiology and Immunology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, United States
| | - Santi M Mandal
- Central Research Facility, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, WB, India
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30
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Janket SJ, Ackerson LK, Diamandis EP. Gut microbiotas and immune checkpoint inhibitor therapy response: a causal or coincidental relationship? ACTA ACUST UNITED AC 2019; 58:18-24. [DOI: 10.1515/cclm-2019-0605] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 08/06/2019] [Indexed: 01/20/2023]
Abstract
Abstract
As the largest immune organ, human gut microbiome could influence the efficacy of immune checkpoint inhibitor therapy (ICI). However, identifying contributory microbes from over 35,000 species is virtually impossible and the identified microbes are not consistent among studies. The reason for the disparity may be that the microbes found in feces are markers of other factors that link immune response and microbiotas. Notably, gut microbiome is influenced by stool consistency, diet and other lifestyle factors. Therefore, the ICI and microbiotas relationship must be adjusted for potential confounders and analyzed longitudinally. Moreover, a recent study where 11 low-abundance commensal bacteria induced interferon-γ-producing CD8 T cells, challenges the validity of the abundance-oriented microbiotas investigations. This study also confirmed the hierarchy in immunogenic roles among microbiotas. Fecal transplantation trials in germ-free mice provided “the proof of principle” that germ-free mice reproduce the donor’s microbiome and corresponding ICI efficacy. However, species-specific biological differences prevent direct extrapolation between the results in murine and human models. Fecal transplantation or supplementation with microbes found in ICI responders requires caution due to potential adverse events.
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Affiliation(s)
- Sok-Ja Janket
- Translational Oral Medicine Section, Forsyth Institute , Cambridge , MA , USA
| | - Leland K. Ackerson
- Department of Public Health , University of Massachusetts at Lowell , Lowell , MA , USA
| | - Eleftherios P. Diamandis
- Department of Pathology and Laboratory Medicine , Mount Sinai Hospital , Toronto , ON , Canada
- Department of Laboratory Medicine and Pathobiology , University of Toronto , Toronto , ON , Canada
- Department of Clinical Biochemistry , University Health Network , Toronto , ON , Canada
- Head of Clinical Biochemistry , Mount Sinai Hospital and University Health Network , Toronto , Canada
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31
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The mucosal-luminal interface: an ideal sample to study the mucosa-associated microbiota and the intestinal microbial biogeography. Pediatr Res 2019; 85:895-903. [PMID: 30758325 DOI: 10.1038/s41390-019-0326-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 12/22/2018] [Accepted: 01/28/2019] [Indexed: 01/02/2023]
Abstract
BACKGROUND Alterations in gastrointestinal microbial communities have been linked to human disease. Most studies use fecal samples as a proxy for the intestinal microbiota; however, the fecal microbiome is not fully representative of the mucosa-associated microbiota at the site of disease. While mucosal biopsies can be used instead, they often contain a high proportion of host DNA that can confound 16S ribosomal RNA (rRNA) gene sequencing studies. METHODS To overcome these limitations, we sampled the mucosal-luminal interface (MLI) to study the mucosa-associated microbiota. We also employed a simple bioinformatics workflow to remove contaminants from 16S rRNA gene profiling results. RESULTS Our results indicate that the microbial differences between individuals are greater than those between different microenvironments within the same individual. Moreover, biopsy samples frequently contained contaminants that could significantly impact biopsy profiling results. CONCLUSIONS Our findings highlight the utility of collecting MLI aspirates to complement biopsies and stools for characterizing human microbial communities.
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Grzywacz K, Butcher J, Romain G, Li J, Stintzi A. The impact of probiotics and lactoferrin supplementation on piglet gastrointestinal microbial communities. Biometals 2019; 32:533-543. [PMID: 31041632 DOI: 10.1007/s10534-019-00195-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 04/09/2019] [Indexed: 11/26/2022]
Abstract
Probiotics and lactoferrin are currently being used in neonatal intensive care units in the hopes of reducing rates of sepsis and necrotizing enterocolitis (NEC). While studies have shown that these measures can be clinically beneficial to premature babies, and there are ongoing trials to measure their impact on NEC and sepsis rates, little is known about how they may impact microbiota development. We thus employed a newborn piglet model to assess the impact of feeding probiotics or a combination of probiotics and lactoferrin on development of the gastrointestinal microbiota. Healthy full-term piglets were fed either probiotics alone or probiotics and a bovine lactoferrin supplement over the first weeks of life, and their microbiota profiles were compared with unsupplemented controls. We found that both probiotic and probiotic plus lactoferrin treatments impacted the microbial composition within the gastrointestinal tract, with differing impacts on various regions within the gut. In addition, the impact of probiotics was often reversed by the presence of lactoferrin and both feeding interventions altered the microbiota's genetic propensity to use ferric versus ferrous ions. These results suggest that iron availability may be a key factor to consider when designing feeding interventions that target the microbiome.
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Affiliation(s)
- Kelly Grzywacz
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, K1H 8M5, Canada
- Department of Pediatric Gastroenterology, Hepatology and Nutrition, CHU Sainte Justine, Montreal, QC, Canada
| | - James Butcher
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, K1H 8M5, Canada
| | - Guillaume Romain
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, K1H 8M5, Canada
| | - Jennifer Li
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, K1H 8M5, Canada
| | - Alain Stintzi
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, K1H 8M5, Canada.
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McConnell MJ. Where are we with monoclonal antibodies for multidrug-resistant infections? Drug Discov Today 2019; 24:1132-1138. [PMID: 30853568 DOI: 10.1016/j.drudis.2019.03.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 01/21/2019] [Accepted: 03/01/2019] [Indexed: 01/17/2023]
Abstract
Widespread antibiotic resistance threatens the continued efficacy of antimicrobial therapy based on small-molecule antibiotics. Infections caused by multidrug-resistant Gram-negative bacteria are particularly worrisome owing to the lack of antimicrobials retaining sufficient activity against these microorganisms. Despite the explosion in monoclonal antibody therapies that have been developed for oncologic and rheumatic indications, only three antibacterial monoclonal antibodies have been approved for clinical use. In the present review, the therapeutic potential of this drug class for treating multidrug-resistant infections is discussed, and considerations for the development of antibacterial monoclonal antibodies are presented. Finally, the state of development of monoclonal antibody therapies for some of the most problematic multidrug-resistant Gram-negative infections is summarized.
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Affiliation(s)
- Michael J McConnell
- Antimicrobial Resistance and Hospital Acquired Infections Reference Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Majadahonda, Spain.
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Chronic Inflammatory Diseases: Are We Ready for Microbiota-based Dietary Intervention? Cell Mol Gastroenterol Hepatol 2019; 8:61-71. [PMID: 30836147 PMCID: PMC6517864 DOI: 10.1016/j.jcmgh.2019.02.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 02/22/2019] [Accepted: 02/22/2019] [Indexed: 12/12/2022]
Abstract
The last 15 years have witnessed the emergence of a new field of research that focuses on the roles played by the intestinal microbiota in health and disease. This research field has produced accumulating evidence indicating that dysregulation of host-microbiota interactions contributes to a range of chronic inflammatory diseases, including inflammatory bowel diseases, colorectal cancer, and metabolic syndrome. Although dysregulation of the microbiota can take complex forms, in some cases, specific bacterial species that can drive specific clinical outcomes have been identified. Among the numerous factors influencing the intestinal microbiota composition, diet is a central actor, wherein numerous dietary factors can beneficially or detrimentally impact the host/microbiota relationship. This review will highlight recent literature that has advanced understanding of microbiota-diet-disease interplay, with a central focus on the following question: Are we ready to use intestinal microbiota composition-based personalized dietary interventions to treat chronic inflammatory diseases?
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Skelton F, Suda K, Evans C, Trautner B. Effective antibiotic stewardship in spinal cord injury: Challenges and a way forward. J Spinal Cord Med 2019; 42:251-254. [PMID: 29324181 PMCID: PMC6419644 DOI: 10.1080/10790268.2017.1396183] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
CONTEXT Antibiotic stewardship, defined as a multidisciplinary program to reduce the misuse of antibiotics, and in turn, antibiotic resistance, is a high priority. Persons with spinal cord injury/disorder (SCI/D) are vulnerable to receiving multiple courses of antibiotics over their lifetime given frequent healthcare exposure, and have high rates of bacterial infection with multi-drug resistant organisms. Additional challenges to evaluating appropriate use of antibiotics in this population include bacterial colonization in the urine and the differences in the presenting signs and symptoms of infection. Therefore, Veterans Health Administration (VHA) facilities with SCI/D centers need effective antibiotic stewardship programs. RESULTS We analyzed the results of a 2012 VHA-wide survey evaluating available antibiotic stewardship resources, and compared the resources present at facilities with SCI/D (n=23) versus non-SCI/D facilities (n=107). VHA facilities with SCI/D centers are more likely to have components of an antibiotic stewardship program that have led to reduced antibiotic use in previous studies. They are also more likely to have personnel with infectious diseases training. CONCLUSION VHA facilities with SCI/D centers have the resources needed for antibiotic stewardship. The next step will be to determine how to implement effective antibiotic stewardship tailored for this patient care setting.
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Affiliation(s)
- Felicia Skelton
- Center for Innovations in Quality, Effectiveness and Safety (IQuESt), Michael E. DeBakey VA Medical Center, Houston, Texas,Department of Physical Medicine and Rehabilitation, Baylor College of Medicine, Houston, Texas,Correspondence to: Felicia Skelton, MD, BS, Michael E. DeBakey VA Medical Center, Houston Center for Innovations in Quality, Effectiveness & Safety (IQuESt), 2002 Holcombe Blvd. (152), Houston, TX77030.
| | - Katie Suda
- Center for Innovation for Complex Chronic Care (CINCCH), Edward Hines Jr. VA Hospital, Hines, Illinois,University of Illinois at Chicago, Chicago, Illinois
| | - Charlesnika Evans
- Center for Innovation for Complex Chronic Care (CINCCH), Edward Hines Jr. VA Hospital, Hines, Illinois,Northwestern University, Department of Preventive Medicine and Center for Health Care Studies, Institute for Public Health and Medicine, Feinberg School of Medicine, Chicago, Illinois
| | - Barbara Trautner
- Center for Innovations in Quality, Effectiveness and Safety (IQuESt), Michael E. DeBakey VA Medical Center, Houston, Texas,Department of Medicine, Baylor College of Medicine, Houston, Texas
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36
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Moen AEF, Lindstrøm JC, Tannæs TM, Vatn S, Ricanek P, Vatn MH, Jahnsen J. The prevalence and transcriptional activity of the mucosal microbiota of ulcerative colitis patients. Sci Rep 2018; 8:17278. [PMID: 30467421 PMCID: PMC6250705 DOI: 10.1038/s41598-018-35243-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 11/01/2018] [Indexed: 12/16/2022] Open
Abstract
Active microbes likely have larger impact on gut health status compared to inactive or dormant microbes. We investigate the composition of active and total mucosal microbiota of treatment-naïve ulcerative colitis (UC) patients to determine the microbial picture at the start-up phase of disease, using both a 16S rRNA transcript and gene amplicon sequencing. DNA and RNA were isolated from the same mucosal colonic biopsies. Our aim was to identify active microbial members of the microbiota in early stages of disease and reveal which members are present, but do not act as major players. We demonstrated differences in active and total microbiota of UC patients when comparing inflamed to non-inflamed tissue. Several taxa, among them the Proteobacteria phyla and families therein, revealed lower transcriptional activity despite a high presence. The Bifidobacteriaceae family of the Actinobacteria phylum showed lower abundance in the active microbiota, although no difference in presence was detected. The most abundant microbiota members of the inflamed tissue in UC patients were not the most active. Knowledge of active members of microbiota in UC patients could enhance our understanding of disease etiology. The active microbial community composition did not deviate from the total when comparing UC patients to non-IBD controls.
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Affiliation(s)
- Aina E Fossum Moen
- Department of Clinical Molecular Biology (EpiGen), Division of Medicine, Akershus University Hospital, Lørenskog, and University of Oslo, Oslo, Norway
| | - Jonas Christoffer Lindstrøm
- Health Services Research Unit, Akershus University Hospital, Lørenskog, Norway
- Institute of Clinical Medicine, Campus Ahus, University of Oslo, Oslo, Norway
| | - Tone Møller Tannæs
- Department of Clinical Molecular Biology (EpiGen), Division of Medicine, Akershus University Hospital, Lørenskog, and University of Oslo, Oslo, Norway.
| | - Simen Vatn
- Department of Gastroenterology, Division of Medicine, Akershus University Hospital, Lørenskog, and University of Oslo, Oslo, Norway
| | - Petr Ricanek
- Department of Gastroenterology, Division of Medicine, Akershus University Hospital, Lørenskog, and University of Oslo, Oslo, Norway
| | - Morten H Vatn
- Institute of Clinical Medicine, Campus Ahus, University of Oslo, Oslo, Norway
| | - Jørgen Jahnsen
- Institute of Clinical Medicine, Campus Ahus, University of Oslo, Oslo, Norway
- Department of Gastroenterology, Division of Medicine, Akershus University Hospital, Lørenskog, and University of Oslo, Oslo, Norway
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Borgo F, Garbossa S, Riva A, Severgnini M, Luigiano C, Benetti A, Pontiroli AE, Morace G, Borghi E. Body Mass Index and Sex Affect Diverse Microbial Niches within the Gut. Front Microbiol 2018; 9:213. [PMID: 29491857 PMCID: PMC5817072 DOI: 10.3389/fmicb.2018.00213] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 01/30/2018] [Indexed: 12/12/2022] Open
Abstract
Gut microbiota is considered a separate organ with endocrine capabilities, actively contributing to tissue homeostasis. It consists of at least two separate microbial populations, the lumen-associated (LAM) and the mucosa-associated microbiota (MAM). In the present study, we compared LAM and MAM, by collecting stools and sigmoid brush samples of forty adults without large-bowel symptoms, and through a 16S rRNA gene next-generation sequencing (NGS) approach. MAM sample analysis revealed enrichment in aerotolerant Proteobacteria, probably selected by a gradient of oxygen that decreases from tissue to lumen, and in Streptococcus and Clostridium spp., highly fermenting bacteria. On the other hand, LAM microbiota showed an increased abundance in Bacteroides, Prevotella, and Oscillospira, genera able to digest and to degrade biopolymers in the large intestine. Predicted metagenomic analysis showed LAM to be enriched in genes encoding enzymes mostly involved in energy extraction from carbohydrates and lipids, whereas MAM in amino acid and vitamin metabolism. Moreover, LAM and MAM communities seemed to be influenced by different host factors, such as diet and sex. LAM is affected by body mass index (BMI) status. Indeed, BMI negatively correlates with Faecalibacterium prausnitzii and Flavonifractor plautii abundance, putative biomarkers of healthy status. In contrast, MAM microbial population showed a significant grouping according to sex. Female MAM was enriched in Actinobacteria (with an increased trend of the genus Bifidobacterium), and a significant depletion in Veillonellaceae. Interestingly, we found the species Gemmiger formicilis to be associated with male and Bifidobacterium adolescentis, with female MAM samples. In conclusion, our results suggest that gut harbors microbial niches that differ in both composition and host factor susceptibility, and their richness and diversity may be overlooked evaluating only fecal samples.
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Affiliation(s)
- Francesca Borgo
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | | | - Alessandra Riva
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy.,Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network "Chemistry meets Microbiology", University of Vienna, Vienna, Austria
| | - Marco Severgnini
- Institute of Biomedical Technologies, National Research Council, Segrate, Italy
| | | | | | - Antonio E Pontiroli
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy.,ASST Santi Paolo e Carlo Hospital, Milan, Italy
| | - Giulia Morace
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Elisa Borghi
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
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Zhang L, Wu W, Lee YK, Xie J, Zhang H. Spatial Heterogeneity and Co-occurrence of Mucosal and Luminal Microbiome across Swine Intestinal Tract. Front Microbiol 2018; 9:48. [PMID: 29472900 PMCID: PMC5810300 DOI: 10.3389/fmicb.2018.00048] [Citation(s) in RCA: 128] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 01/10/2018] [Indexed: 01/17/2023] Open
Abstract
Pigs are one of the most important economic livestock. Gut microbiota is not only critical to the health but also the production efficiency of pigs. Manipulating gut microbiota relies on the full view of gut microbiome and the understanding of drive forces shaping microbial communities. 16s rDNA sequencing was used to profile microbiota along the longitudinal and radical axes to obtain the topographical map of microbiome in different intestinal compartments in young pigs. Alpha and beta-diversities revealed distinct differences in microbial compositions between the distal ileum and cecum and colon, as well as between the lumen and mucosa. Firmicutes and Proteobacteria dominated in the ileum, constituting 95 and 80% of the luminal and mucosa-attached microbiome. Transitioning from the small intestine to the large intestine, luminal Bacteroidetes increased from 1.69 to 45.98% in the cecum and 40.09% in the colon, while mucosal Bacteroidetes raised from 9 to 35.36% and 27.96%. Concurrently, luminal Firmicutes and Proteobacteria and mucosal-attached Proteobacteria remarkably decreased. By co-occurrence network analyses, Prevotellaceae, Ruminococcaceae, Lachnospiraceae and Veillonellaceae were recognized as the central nodes of luminal microbial network, and Prevotellaceae and Enterobacteriaceae, Caulobacteraceae, Enterococcaceae, Xanthomonadaceae, Pseudomonadaceae were identified as mucosal central nodes. Co-abundance was uncovered among Prevotellaceae, Lachnospiraceae, and Veillonellaceae in the luminal and mucosal microbiome, while opportunistic pathogens from γ-Proteobacteria in the mucosa. Strong co-exclusion was shown between Enterobacteriaceae with Prevotellaceae-centered microbial groups in the lumen. Redundancy analysis found bile acids and short chain fatty acids explained 37.1 and 41% of variations in the luminal microbial composition, respectively. Primary bile acid, taurine- and glycine- conjugated bile acids were positively correlated with Lactobacillaceae, Enterobacteriaceae, Clostridiaceae_1, Peptostreptococcaceae, whereas secondary bile acids, acetate, propionate, butyrate, and valerate were positively correlated with Prevotellaceae, Acidaminococcaceae, Ruminococcaceae, Lachnospiraceae, Desulfovibronaceae, Veillonellaceae. Functional analyses demonstrated that Prevotella, Veillonellaceae, Lachnospiraceae, and Ruminococcaceae were positively correlated with gene functions related to amino acids, energy, cofactors and vitamins metabolism, which are indispensable for the hosts. These results suggested site specific colonization and co-occurrence of swine gut microbiome closely relate to the microenvironment in each niche. Interactions of core gut microbiome greatly contributed to metabolism and/or immunity in the swine intestine.
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Affiliation(s)
- Li Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Weida Wu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuan-Kun Lee
- Department of Microbiology and Immunology, National University of Singapore, Singapore, Singapore
| | - Jingjing Xie
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongfu Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Abstract
PURPOSE OF REVIEW Crohn's disease and ulcerative colitis, the two major forms of inflammatory bowel disease (IBD), represent chronic diseases of unknown cause, and they are regarded as prototypical complex diseases. Despite all the recent advances, a complete appreciation of the pathogenesis of IBD is still limited. In this review, we present recent information contributing to a better understanding of mechanisms underlying IBD. RECENT FINDINGS Here, we attempt to highlight novel environmental triggers, data on the gut microbiota, its interaction with the host, and the potential influence of diet and food components. We discuss recent findings on defective signaling pathways and the potential effects on the immune response, and we present new data on epigenetic changes, inflammasome, and damage-associated molecular patterns associated with IBD. SUMMARY The continuing identification of several epigenetic, transcriptomic, proteomic, and metabolomic alterations in patients with IBD reflects the complex nature of the disease and suggests the need for innovative approaches such as systems biology for identifying novel relevant targets in IBD.
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Sommer F, Anderson JM, Bharti R, Raes J, Rosenstiel P. The resilience of the intestinal microbiota influences health and disease. Nat Rev Microbiol 2017. [DOI: 10.1038/nrmicro.2017.58] [Citation(s) in RCA: 460] [Impact Index Per Article: 65.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Ferrer M, Méndez-García C, Rojo D, Barbas C, Moya A. Antibiotic use and microbiome function. Biochem Pharmacol 2017; 134:114-126. [PMID: 27641814 DOI: 10.1016/j.bcp.2016.09.007] [Citation(s) in RCA: 191] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 09/12/2016] [Indexed: 02/06/2023]
Abstract
Our microbiome should be understood as one of the most complex components of the human body. The use of β-lactam antibiotics is one of the microbiome covariates that influence its composition. The extent to which our microbiota changes after an antibiotic intervention depends not only on the chemical nature of the antibiotic or cocktail of antibiotics used to treat specific infections, but also on the type of administration, duration and dose, as well as the level of resistance that each microbiota develops. We have begun to appreciate that not all bacteria within our microbiota are vulnerable or reactive to different antibiotic interventions, and that their influence on both microbial composition and metabolism may differ. Antibiotics are being used worldwide on a huge scale and the prescription of antibiotics is continuing to rise; however, their effects on our microbiota have been reported for only a limited number of them. This article presents a critical review of the antibiotics or antibiotic cocktails whose use in humans has been linked to changes in the composition of our microbial communities, with a particular focus on the gut, oral, respiratory, skin and vaginal microbiota, and on their molecular agents (genes, proteins and metabolites). We review the state of the art as of June 2016, and cover a total of circa 68 different antibiotics. The data herein are the first to compile information about the bacteria, fungi, archaea and viruses most influenced by the main antibiotic treatments prescribed nowadays.
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Affiliation(s)
- Manuel Ferrer
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain.
| | | | - David Rojo
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Madrid, Spain
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Madrid, Spain
| | - Andrés Moya
- Foundation for the Promotion of Health and Biomedical Research in the Valencian Community Public Health (FISABIO), Valencia, Spain; Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain; Instituto Cavanilles de Biodiversidad y Biología Evolutiva (Universidad de Valencia), Valencia, Spain.
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Khan I, Azhar EI, Abbas AT, Kumosani T, Barbour EK, Raoult D, Yasir M. Metagenomic Analysis of Antibiotic-Induced Changes in Gut Microbiota in a Pregnant Rat Model. Front Pharmacol 2016; 7:104. [PMID: 27199748 PMCID: PMC4849429 DOI: 10.3389/fphar.2016.00104] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 04/07/2016] [Indexed: 12/28/2022] Open
Abstract
Food and Drug Administration (FDA, USA)-approved category B antibiotics are commonly prescribed to treat infections during pregnancy. The aim of this study was to investigate antibiotic-induced changes in gut microbiota (GM) that occur during pregnancy. The 16S rRNA amplicon deep-sequencing method was used to analyze the effect of category B antibiotics (azithromycin, amoxicillin and cefaclor) on GM during pregnancy using a rat model. The GM composition was substantially modulated by pregnancy and antibiotics administration. Firmicutes, Bacteroidetes, Proteobacteria, Chlamydiae, Actinobacteria, and Cyanobacteria were the dominant phyla. Antibiotic treatment during pregnancy increased the relative abundance of Proteobacteria and reduced Firmicutes. The genera Shigella, Streptococcus, Candidatus Arthromitus, and Helicobacter were significantly (p < 0.05) more abundant during pregnancy. Antibiotics significantly (p < 0.05) reduced the relative abundance of Lactobacillus but increased that of Enterobacter. There was a significant (p < 0.05) decrease in Lactobacillus sp., Lactobacillus gallinarum and Lactobacillus crispatus during pregnancy. Antibiotic treatment reduced bacterial diversity; the lowest number of operational taxonomic units (OTUs) were detected in the cefaclor-treated groups. Antibiotics significantly (p < 0.05) promoted weight gain during pregnancy, and increased relative abundance of Shigella sonnei, Enterococcus hormaechei, and Acinetobacter sp. GM perturbations were accompanied by increases in Proteobacteria abundance and weight gain in pregnancy following antibiotic treatment.
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Affiliation(s)
- Imran Khan
- Biochemistry Department, Faculty of Science, King Abdulaziz UniversityJeddah, Saudi Arabia; Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz UniversityJeddah, Saudi Arabia
| | - Esam I Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz UniversityJeddah, Saudi Arabia; Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz UniversityJeddah, Saudi Arabia
| | - Aymn T Abbas
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz UniversityJeddah, Saudi Arabia; Biotechnology Research Laboratories, Gastroenterology Surgery Center, Mansoura UniversityMansoura, Egypt
| | - Taha Kumosani
- Biochemistry Department, Faculty of Science, King Abdulaziz UniversityJeddah, Saudi Arabia; Biochemistry Department, Faculty of Science - Production of Bioproducts for Industrial Applications Research Group - Experimental Biochemistry Unit, King Fahd Medical Research Center King Abdulaziz UniversityJeddah, Saudi Arabia
| | - Elie K Barbour
- Faculty of Agricultural and Food Sciences, American University of BeirutBeirut, Lebanon; Adjunct to Biochemistry Department, Faculty of Science - Production of Bioproducts for Industrial Applications Research Group, King Abdulaziz UniversityJeddah, Saudi Arabia
| | - Didier Raoult
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz UniversityJeddah, Saudi Arabia; URMITE CNRS-IRD 198 UMR 6236, Faculté de Médecine et de Pharmacie, Université de la MéditerranéeMarseille, France
| | - Muhammad Yasir
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University Jeddah, Saudi Arabia
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Abstract
The gut microbiota influences essential human functions including digestion, energy metabolism, and inflammation by modulating multiple endocrine, neural, and immune pathways of the host. Its composition and complexity varies markedly across individuals and across different sites of the gut, but provides a certain level of resilience against external perturbation. Short-term antibiotic treatment is able to shift the gut microbiota to long-term alternative dysbiotic states, which may promote the development and aggravation of disease. Common features of post-antibiotic dysbiosis include a loss of taxonomic and functional diversity combined with reduced colonization resistance against invading pathogens, which harbors the danger of antimicrobial resistance. This review summarizes the antibiotic-related changes of the gut microbiota and potential consequences in health and disease.
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Affiliation(s)
- Kathleen Lange
- Department of Internal Medicine IV (Gastroenterology, Hepatology, and Infectious Diseases), Jena University Hospital, Jena, Germany
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Vaccines for Antibiotic-Resistant Bacteria: Possibility or Pipe Dream? Trends Pharmacol Sci 2016; 37:143-152. [DOI: 10.1016/j.tips.2015.10.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Revised: 10/13/2015] [Accepted: 10/16/2015] [Indexed: 11/19/2022]
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