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Li X, Yang J, Shi S, Lan H, Zhao W, Hung W, He J, Wang R. The Genome of Bifidobacterium longum subsp. infantis YLGB-1496 Provides Insights into Its Carbohydrate Utilization and Genetic Stability. Genes (Basel) 2024; 15:466. [PMID: 38674400 PMCID: PMC11154571 DOI: 10.3390/genes15040466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/02/2024] [Accepted: 04/03/2024] [Indexed: 04/28/2024] Open
Abstract
Bifidobacterium longum subsp. infantis YLGB-1496 (YLGB-1496) is a probiotic strain isolated from human breast milk. The application of YLGB-1496 is influenced by carbohydrate utilization and genetic stability. This study used genome sequencing and morphology during continuous subculture to determine the carbohydrate utilization characteristics and genetic stability of YLGB-1496. The complete genome sequence of YLGB-1496 consists of 2,758,242 base pairs, 2442 coding sequences, and a GC content of 59.87%. A comparison of carbohydrate transport and metabolism genes of Bifidobacterium longum subsp. infantis (B. infantis) showed that YLGB-1496 was rich in glycosyl hydrolase 13, 20, 25, and 109 gene families. During continuous subculture, the growth characteristics and fermentation activity of the strain were highly stable. The bacterial cell surface and edges of the 1000th-generation strains were progressively smoother and well-defined, with no perforations or breaks in the cell wall. There were 20 SNP loci at the 1000th generation, fulfilling the requirement of belonging to the same strain. The presence of genes associated with cell adhesion and the absence of resistance genes supported the probiotic characteristics of the strain. The data obtained in this study provide insights into broad-spectrum carbohydrate utilization, genomic stability, and probiotic properties of YLGB-1496, which provide theoretical support to promote the use of YLGB-1496.
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Affiliation(s)
- Xiaoxia Li
- Research Center for Probiotics, Department of Nutrition and Health, China Agricultural University, Beijing 100190, China; (X.L.); (J.Y.); (S.S.); (W.Z.)
| | - Jianjun Yang
- Research Center for Probiotics, Department of Nutrition and Health, China Agricultural University, Beijing 100190, China; (X.L.); (J.Y.); (S.S.); (W.Z.)
| | - Shaoqi Shi
- Research Center for Probiotics, Department of Nutrition and Health, China Agricultural University, Beijing 100190, China; (X.L.); (J.Y.); (S.S.); (W.Z.)
| | - Hanglian Lan
- National Center of Technology Innovation for Dairy, Hohhot 010110, China; (H.L.); (W.H.); (J.H.)
| | - Wen Zhao
- Research Center for Probiotics, Department of Nutrition and Health, China Agricultural University, Beijing 100190, China; (X.L.); (J.Y.); (S.S.); (W.Z.)
| | - Weilian Hung
- National Center of Technology Innovation for Dairy, Hohhot 010110, China; (H.L.); (W.H.); (J.H.)
| | - Jian He
- National Center of Technology Innovation for Dairy, Hohhot 010110, China; (H.L.); (W.H.); (J.H.)
| | - Ran Wang
- Research Center for Probiotics, Department of Nutrition and Health, China Agricultural University, Beijing 100190, China; (X.L.); (J.Y.); (S.S.); (W.Z.)
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Duboux S, Ngom-Bru C, De Bruyn F, Bogicevic B. Phylogenetic, Functional and Safety Features of 1950s B. infantis Strains. Microorganisms 2022; 10:microorganisms10020203. [PMID: 35208658 PMCID: PMC8879182 DOI: 10.3390/microorganisms10020203] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 01/04/2022] [Accepted: 01/06/2022] [Indexed: 02/05/2023] Open
Abstract
Strains of Bifidobacterium longum subsp. infantis (B. infantis) are amongst the first to colonize the infant gut, partly due to their capacity to metabolize complex human milk oligosaccharides (HMO), and are proposed to play a key role in the development of the infant gut. Since early life, B. infantis supplementation is of high interest, and detailed phylogenetic, functional and safety characterization of the selected strains should be pursued. Using a combination of long and short-read sequencing technologies, we first decipher the genetic distance between different isolates of the same B. infantis strain. Using the same approach, we show that several publicly available genomes recapitulate this strain-level distance as compared to two of the first strains obtained in the 1950s. Furthermore, we demonstrate that the two 1950s B. infantis strains display different functional and safety attributes, as ATCC 15697 is resistant to streptomycin and shows a preference towards lacto-N-tetraose LNT and sialylated HMOs, while LMG 11588 is sensitive to all tested antibiotics and shows a preference towards fucosylated HMOs. Overall, our work highlights that the current diversity observed in B. infantis is likely underestimated and that strain selection within this subspecies must be the subject of scientific pursuit and associated evaluation.
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Affiliation(s)
- Stéphane Duboux
- Société des Produits Nestlé SA, Nestlé Research, Route du Jorat 57, CH-1000 Lausanne 26, Switzerland; (C.N.-B.); (B.B.)
- Correspondence:
| | - Catherine Ngom-Bru
- Société des Produits Nestlé SA, Nestlé Research, Route du Jorat 57, CH-1000 Lausanne 26, Switzerland; (C.N.-B.); (B.B.)
| | - Florac De Bruyn
- Société des Produits Nestlé SA, Nestlé Research & Development, Nestléstrasse 3, CH-3510 Konolfingen, Switzerland;
| | - Biljana Bogicevic
- Société des Produits Nestlé SA, Nestlé Research, Route du Jorat 57, CH-1000 Lausanne 26, Switzerland; (C.N.-B.); (B.B.)
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Fu X, Lyu L, Wang Y, Zhang Y, Guo X, Chen Q, Liu C. Safety assessment and probiotic characteristics of Enterococcus lactis JDM1. Microb Pathog 2022; 163:105380. [PMID: 34979271 DOI: 10.1016/j.micpath.2021.105380] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 12/22/2021] [Accepted: 12/28/2021] [Indexed: 01/05/2023]
Abstract
OBJECTIVE The aims of this study were to evaluate the safety and probiotic characteristics of the newly isolated Enterococcus lactis strain JDM1. METHODS Safety assessment of E. lactis JDM1 was accomplished by the combination of whole genome sequence information analysis and phenotypic assays, including antimicrobial susceptibility test, haemolysis assay, biogenic amine production assay, cytotoxicity assay. The bacteriostatic experiment and gastrointestinal tolerance experiment were also conducted to evaluate its applicability. RESULTS E. lactis JDM1 possesses good gastrointestinal tolerance and can inhibit the growth of the pathogenic bacteria Clostridioides difficile and Listeria monocytogenes. The chromosome size of JDM1 was 2,570,998 bp with a GC content of 38.46%, which contained a plasmid. One intact prophage, 13 genomic islands and 19 IS elements were predicted in the JDM1 chromosome. Five resistance-related genes and seven virulence-related genes were predicted in the genome. Most resistance genes were conserved, and virulence factors were not related to functional pathogenicity. Antimicrobial susceptibility tests showed that JDM1 was sensitive to tedizolid, ciprofloxacin, levofloxacin, penicillin, ampicillin, vancomycin, linezolid, tetracycline, high-level gentamicin and high-level streptomycin. Genes encoding putative enzymes responsible for adverse metabolites were not found and JDM1 was unable to produce the six main biogenic amines. Cytotoxicity test showed that the JDM1 supernatant had no toxic effect. CONCLUSION E. lactis JDM1 is expected to be developed as a probiotic, and its probiotic properties are worthy of further exploration.
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Affiliation(s)
- Xiaomei Fu
- Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Lin Lyu
- Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yue Wang
- Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yan Zhang
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xiaokui Guo
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Qian Chen
- Institute of Intestinal Diseases, Shanghai Tenth People's Hospital Affiliated to Tongji University, Shanghai, 200072, China.
| | - Chang Liu
- Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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Literature-Based Phenotype Survey and In Silico Genotype Investigation of Antibiotic Resistance in the Genus Bifidobacterium. Curr Microbiol 2020; 77:4104-4113. [PMID: 33057753 DOI: 10.1007/s00284-020-02230-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 09/29/2020] [Indexed: 01/05/2023]
Abstract
Bifidobacteria are typical commensals inhabiting the human intestine and are beneficial to the host because of their probiotic properties. One of the risks concerning probiotics is the potential of introducing antibiotic resistance genes (ARGs) to the host gut pathogens. This study was aimed to depict the general antibiotic resistance characteristics of the genus Bifidobacterium by combining the reported phenotype dataset and in silico genotype prediction. Bifidobacteria were mostly reported to be sensitive to beta-lactams, glycopeptides, chloramphenicol, and rifampicin, but resistant to aminoglycosides, polypeptides, quinolones, and mupirocin. Generally, the resistance phenotypes to erythromycin, tetracycline, fusidic acid, metronidazole, clindamycin, and trimethoprim were variable. Besides cmX and tetQ, characterized in bifidobacterial resident plasmids, 3520 putative ARGs were identified from 831 bifidobacterial genomes through BLASTP search. The identified ARGs matched thirty-eight reference ARGs, four of which seemed to be mutant housekeeping genes. The two high-abundant ARGs, tetW and ermX, were found to have different distribution traits. The predicted ARGs reasonably explained most of the corresponding resistant phenotypes in the published literature.
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Liu D, Zeng L, Yan Z, Jia J, Gao J, Wei Y. The mechanisms and safety of probiotics against toxigenic clostridium difficile. Expert Rev Anti Infect Ther 2020; 18:967-975. [PMID: 32520637 DOI: 10.1080/14787210.2020.1778464] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
INTRODUCTION Toxigenic Clostridium difficile (C. difficile) is the main cause of antibiotic-associated diarrhea and can induce pseudomembranous colitis and infrequent toxic megacolon, which are potentially fatal. The standard antibiotic therapy for C. difficile infection (CDI) is limited by antibiotics' broad spectrum and further disruptive effects on indigenous microbiota. Probiotics may offer a prospective and alternative strategy for the prevention and treatment of CDI. AREAS COVERED In this article, the mechanisms implying the probiotic effect against C. difficile and the safety profile highlighting the patient groups with inappropriate application of probiotics were reviewed from 2015 to 2020. EXPERT OPINION Although many strains with ability against C. difficile have been reported, the usage of probiotics for CDI prevention and/or treatment is scarce since the number of clinical trials is not sufficient to prove probiotics' efficacy and safety in CDI treatment, especially for premature infant and immunocompromised patient. Especially, there are few well-defined clinical studies supporting safety of probiotics for CDI. A few strains from Lactobacillus and Saccharomyces genus have been studied more extensively than other probiotic strains through clinical trials for CDI. Thus, more clinical intervention studies regarding the benefit and the comprehensive safety assessments of probiotics for CDI are needed.
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Affiliation(s)
- Dianbin Liu
- School of Stomatology/Department of Pathogenic Biology and Immunology, Jiangsu Key Laboratory of Immunity and Metabolism, Xuzhou Medical University , Xuzhou, Jiangsu Province, China
| | - Lingbing Zeng
- Department of clinical microbiology, The First Affiliated Hospital of Nanchang University , Nanchang, Jiangxi Province, China
| | - Zhihan Yan
- School of Stomatology/Department of Pathogenic Biology and Immunology, Jiangsu Key Laboratory of Immunity and Metabolism, Xuzhou Medical University , Xuzhou, Jiangsu Province, China
| | - Junqi Jia
- School of Stomatology/Department of Pathogenic Biology and Immunology, Jiangsu Key Laboratory of Immunity and Metabolism, Xuzhou Medical University , Xuzhou, Jiangsu Province, China
| | - Jing Gao
- School of Stomatology/Department of Pathogenic Biology and Immunology, Jiangsu Key Laboratory of Immunity and Metabolism, Xuzhou Medical University , Xuzhou, Jiangsu Province, China
| | - Yanxia Wei
- School of Stomatology/Department of Pathogenic Biology and Immunology, Jiangsu Key Laboratory of Immunity and Metabolism, Xuzhou Medical University , Xuzhou, Jiangsu Province, China
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Li T, Yang J, Zhang H, Xie Y, Jin J. Bifidobacterium from breastfed infant faeces prevent high-fat-diet-induced glucose tolerance impairment, mediated by the modulation of glucose intake and the incretin hormone secretion axis. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2020; 100:3308-3318. [PMID: 32108348 DOI: 10.1002/jsfa.10360] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 02/16/2020] [Accepted: 02/27/2020] [Indexed: 06/10/2023]
Abstract
BACKGROUND Probiotics are defined as microorganisms that can exert health benefits for the host. Among the recognized probiotics, Bifidobacterium are the most frequently used probiotics in humans. The aim of this study was to evaluate the antidiabetic activity of Bifidobacterium strains isolated from breastfed infant faeces, both in vitro, using the Caco-2 monolayer transwell model, and in vivo, using a mice model of impaired glucose tolerance induced by a high-fat diet (HFD). RESULTS The cell-free supernatant of Bifidobacterium lactis A12 showed better inhibitory activity of α-glucosidase and inhibited the glucose absorption and transport than B. lactis BB12, which is a typical probiotic with antidiabetic capabilities. B. lactis A12 improved the impaired glucose intolerance, restored islet function and morphology with insulin resistance induced by the HFD in C57BL/6J mice. Furthermore, in small intestine tissues, the cell-free supernatant of B. lactis A12 decreased the messenger RNA expressions of sucrase-isomaltase, live B. lactis A12 cells decreased glucose transporters 2. B. lactis A12 significantly stimulated the glucagon like peptide-1 (GLP-1) secretion and upregulated proglucagon messenger RNA levels. CONCLUSION B. lactis A12 protect against the deleterious effects of HFD-induced diabetes by inhibiting the utilization, absorption, and transport of glucose by intestinal epithelial cells and promoting the expression and secretion of GLP-1. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Tong Li
- Food Science and Engineering College, Beijing University of Agriculture, Beijing Laboratory of Food Quality and Safety, Beijing Key Laboratory of Detection and Control of Spoilage Organisms and Pesticide Residues in Agricultural Products, Beijing, China
| | - Jianjun Yang
- Food Science and Engineering College, Beijing University of Agriculture, Beijing Laboratory of Food Quality and Safety, Beijing Key Laboratory of Detection and Control of Spoilage Organisms and Pesticide Residues in Agricultural Products, Beijing, China
| | - Hongxing Zhang
- Food Science and Engineering College, Beijing University of Agriculture, Beijing Laboratory of Food Quality and Safety, Beijing Key Laboratory of Detection and Control of Spoilage Organisms and Pesticide Residues in Agricultural Products, Beijing, China
| | - Yuanhong Xie
- Food Science and Engineering College, Beijing University of Agriculture, Beijing Laboratory of Food Quality and Safety, Beijing Key Laboratory of Detection and Control of Spoilage Organisms and Pesticide Residues in Agricultural Products, Beijing, China
| | - Junhua Jin
- Food Science and Engineering College, Beijing University of Agriculture, Beijing Laboratory of Food Quality and Safety, Beijing Key Laboratory of Detection and Control of Spoilage Organisms and Pesticide Residues in Agricultural Products, Beijing, China
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7
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Probiotics and Preterm Infants: A Position Paper by the European Society for Paediatric Gastroenterology Hepatology and Nutrition Committee on Nutrition and the European Society for Paediatric Gastroenterology Hepatology and Nutrition Working Group for Probiotics and Prebiotics. J Pediatr Gastroenterol Nutr 2020; 70:664-680. [PMID: 32332478 DOI: 10.1097/mpg.0000000000002655] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
More than 10,000 preterm infants have participated in randomised controlled trials on probiotics worldwide, suggesting that probiotics in general could reduce rates of necrotising enterocolitis (NEC), sepsis, and mortality. Answers to relevant clinical questions as to which strain to use, at what dosage, and how long to supplement are, however, not available. On the other hand, an increasing number of commercial products containing probiotics are available from sometimes suboptimal quality. Also, a large number of units around the world are routinely offering probiotic supplementation as the standard of care despite lacking solid evidence. Our recent network meta-analysis identified probiotic strains with greatest efficacy regarding relevant clinical outcomes for preterm neonates. Efficacy in reducing mortality and morbidity was found for only a minority of the studied strains or combinations. In the present position paper, we aim to provide advice, which specific strains might potentially be used and which strains should not be used. In addition, we aim to address safety issues of probiotic supplementation to preterm infants, who have reduced immunological capacities and occasional indwelling catheters. For example, quality reassurance of the probiotic product is essential, probiotic strains should be devoid of transferable antibiotic resistance genes, and local microbiologists should be able to routinely detect probiotic sepsis. Provided all safety issues are met, there is currently a conditional recommendation (with low certainty of evidence) to provide either Lactobacillus rhamnosus GG ATCC53103 or the combination of Bifidobacterium infantis Bb-02, Bifidobacterium lactis Bb-12, and Streptococcus thermophilus TH-4 in order to reduce NEC rates.
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8
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Dlamini ZC, Langa RLS, Aiyegoro OA, Okoh AI. Safety Evaluation and Colonisation Abilities of Four Lactic Acid Bacteria as Future Probiotics. Probiotics Antimicrob Proteins 2020; 11:397-402. [PMID: 29881953 DOI: 10.1007/s12602-018-9430-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The study evaluated the safety and colonisation properties of four lactic acid bacteria (LAB), by determining their cell hydrophobicity and aggregation abilities. In addition, the presence of virulence and resistance genes was assayed in these probiotic candidates. Lactobacillus reuteri ZJ625, Lactobacillus reuteri VB4, Lactobacillus salivarius ZJ614 and Streptococcus salivarius NBRC13956 were tested for cell surface hydrophobicity abilities against xylene, chloroform and ethyl acetate. The isolates were also tested for auto-aggregation and co-aggregation abilities; the optical densities of cell growth were measured after 1, 2, 3 and 4 h of experimental set-up. DNA was extracted from all the four isolates and amplified using PCR with specific primers to detect virulence genes of adhesion collagen protein (ace) and aggregation substances (agg and asa); also, resistance genes of Vancomycin vanA, Vancomycin vanC1 and Vancomycin vanC2/3 were assayed in the four isolates. The isolates showed high hydrophobicity to all solvents: xylene (78-84%), chloroform (68-75%) and ethyl acetate (52-60%). High auto- and co-aggregations ranging from 60 to 70% and from 45 to 56% respectively were observed in the isolates after 4 h of incubation at 37 °C. Some of the tested isolates showed the presence of virulence and resistance genes; however, this does not indicate that these genes are unsafe because their transmission and expression abilities are unknown. Therefore, in this study, the isolates studied are considered safe for use as future probiotics, as revealed from results presented, which generally represents the scanned safety evaluations of the isolates as promising probiotics.
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Affiliation(s)
- Ziyanda C Dlamini
- Agricultural Research Council - Animal Production Institute, Gastrointestinal Microbiology and Biotechnology Division, Irene, 0062, South Africa.,SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, 5700, South Africa
| | - Rashwahla L S Langa
- Agricultural Research Council - Animal Production Institute, Gastrointestinal Microbiology and Biotechnology Division, Irene, 0062, South Africa
| | - Olayinka A Aiyegoro
- Agricultural Research Council - Animal Production Institute, Gastrointestinal Microbiology and Biotechnology Division, Irene, 0062, South Africa. .,SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, 5700, South Africa.
| | - Anthony I Okoh
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, 5700, South Africa
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Huang G, Pan H, Zhu Z, Li Q. The complete genome sequence of Bifidobacterium longum LTBL16, a potential probiotic strain from healthy centenarians with strong antioxidant activity. Genomics 2019; 112:769-773. [PMID: 31226482 DOI: 10.1016/j.ygeno.2019.05.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 05/15/2019] [Accepted: 05/17/2019] [Indexed: 12/24/2022]
Abstract
B. longum LTBL16 is a potential probiotic strain that was isolated from healthy centenarians in Bama, China. In vitro experiments show that B. longum LTBL16 has a strong antioxidant activity and the complete genome of B. longum LTBL16 was sequenced in this work. The genome consists of one 2,430,682 bp circular chromosome that is plasmid free. The circular chromosome has a GC content of 61.23% and contains 2071 coding sequences (CDSs), 4 rRNA manipulators and 55 tRNA coding genes. Genetic analysis showed that at least five protein-coding genes were associated with antioxidant activity, and the abundance of these genes may be related to free radical scavenging rates and oxygen tolerance. In addition, the safety of B. longum LTBL16 was evaluated using a virulence factor database and antibiotic resistance gene database. The results indicate that B. longum LTBL16 has the good potential for the development and utilization as a probiotic.
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Affiliation(s)
- Guohong Huang
- College of Light Industry and Food Engineering, Guangxi University, 100 Daxue Road, Nanning 530004, People's Republic of China; College of Food and Biological Technology, Guangxi Vocational and Technical College, Ming Yang Industrial Park Jiangnan District, Nanning 530226, People's Republic of China
| | - Haibo Pan
- College of Light Industry and Food Engineering, Guangxi University, 100 Daxue Road, Nanning 530004, People's Republic of China
| | - Zhenjun Zhu
- College of Light Industry and Food Engineering, Guangxi University, 100 Daxue Road, Nanning 530004, People's Republic of China
| | - Quanyang Li
- College of Light Industry and Food Engineering, Guangxi University, 100 Daxue Road, Nanning 530004, People's Republic of China.
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10
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Lokesh D, Parkesh R, Kammara R. Bifidobacterium adolescentis is intrinsically resistant to antitubercular drugs. Sci Rep 2018; 8:11897. [PMID: 30093677 PMCID: PMC6085307 DOI: 10.1038/s41598-018-30429-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 07/31/2018] [Indexed: 12/15/2022] Open
Abstract
Multiple mutations in the β subunit of the RNA polymerase (rpoβ) of Mycobacterium tuberculosis (Mtb) are the primary cause of resistance to rifamycin (RIF). In the present study, bifidobacterial rpoβ sequences were analyzed to characterize the mutations that contribute to the development of intrinsic resistance to RIF, isoniazid, streptomycin and pyrazinamide. Sequence variations, which mapped to cassettes 1 and 2 of the rpoβ pocket, are also found in multidrug-resistant Mtb (MDR Mtb). Growth curves in the presence of osmolytes and different concentrations of RIF showed that the bacteria adapted rapidly by shortening the growth curve lag time. Insight into the adapted rpoβ DNA sequences revealed that B. adolescentis harbored mutations both in the RIF pocket and in regions outside the pocket. The minimum inhibitory concentrations (MICs) and mutant prevention concentrations (MPCs) indicated that B. longum, B. adolescentis and B. animalis are resistant to antitubercular drugs. 3D-homology modeling and binding interaction studies using computational docking suggested that mutants had reduced binding affinity towards RIF. RIF-exposed/resistant bacteria exhibited variant protein profiles along with morphological differences, such as elongated and branched cells, surface conversion from rough to smooth, and formation of a concentrating ring.
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Affiliation(s)
- Dhanashree Lokesh
- Senior Research Fellow, Department of Protein Chemistry and Technology, CSIR-CFTRI, Mysore, 20, India
| | - Raman Parkesh
- Principal Scientist, Protein Science Center, Institute of Microbial Technology, Sector-39A, Chandigarh, India
| | - Rajagopal Kammara
- Senior Research Fellow, Department of Protein Chemistry and Technology, CSIR-CFTRI, Mysore, 20, India.
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Safety Assessment of Lactobacillus helveticus KLDS1.8701 Based on Whole Genome Sequencing and Oral Toxicity Studies. Toxins (Basel) 2017; 9:toxins9100301. [PMID: 28946645 PMCID: PMC5666348 DOI: 10.3390/toxins9100301] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 09/04/2017] [Accepted: 09/20/2017] [Indexed: 01/19/2023] Open
Abstract
Lactobacillus helveticus KLDS1.8701 isolated from Chinese traditional fermented dairy product has been shown earlier to possess probiotic potentials but it is important to evaluate its safety in view of its possible use as a probiotic. The aim of the present study is to critically assess the safety of L. helveticus KLDS1.8701 through multiple perspectives. The complete genome of L. helveticus KLDS1.8701 was sequenced to mine for safety-associated genes. The minimum inhibitory concentrations of 15 antimicrobials and the adverse metabolites were determined. Standard acute oral and subacute toxicity studies were conducted in rats. The results in silico disclosed that the genome of L. helveticus KLDS1.8701 carries no transferable antibiotic resistance genes, no virulence factors and only 3 genes related to adverse metabolites. In vitro results showed that L. helveticus KLDS1.8701 was resistant against 6 antimicrobials and did not raise safety concerns about biogenic amine, D-lactic acid and nitroreductase. The results in vivo revealed that no adverse effects on experimental rats were observed in the oral toxicity tests. Overall, findings from this study suggest that L. helveticus KLDS1.8701 is safe and can be used as a potential probiotic for human consumption.
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12
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Walsh AM, Crispie F, Claesson MJ, Cotter PD. Translating Omics to Food Microbiology. Annu Rev Food Sci Technol 2017; 8:113-134. [DOI: 10.1146/annurev-food-030216-025729] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Aaron M. Walsh
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Fiona Crispie
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Marcus J. Claesson
- APC Microbiome Institute, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Paul D. Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, Ireland
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13
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Klein RS, Garber C, Howard N. Infectious immunity in the central nervous system and brain function. Nat Immunol 2017; 18:132-141. [PMID: 28092376 DOI: 10.1038/ni.3656] [Citation(s) in RCA: 141] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 12/02/2016] [Indexed: 11/09/2022]
Abstract
Inflammation is emerging as a critical mechanism underlying neurological disorders of various etiologies, yet its role in altering brain function as a consequence of neuroinfectious disease remains unclear. Although acute alterations in mental status due to inflammation are a hallmark of central nervous system (CNS) infections with neurotropic pathogens, post-infectious neurologic dysfunction has traditionally been attributed to irreversible damage caused by the pathogens themselves. More recently, studies indicate that pathogen eradication within the CNS may require immune responses that interfere with neural cell function and communication without affecting their survival. In this Review we explore inflammatory processes underlying neurological impairments caused by CNS infection and discuss their potential links to established mechanisms of psychiatric and neurodegenerative diseases.
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Affiliation(s)
- Robyn S Klein
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA.,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA.,Department of Neuroscience, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Charise Garber
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Nicole Howard
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA.,Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
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Imperial ICVJ, Ibana JA. Addressing the Antibiotic Resistance Problem with Probiotics: Reducing the Risk of Its Double-Edged Sword Effect. Front Microbiol 2016; 7:1983. [PMID: 28018315 PMCID: PMC5156686 DOI: 10.3389/fmicb.2016.01983] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Accepted: 11/28/2016] [Indexed: 12/27/2022] Open
Abstract
Antibiotic resistance is a global public health problem that requires our attention. Indiscriminate antibiotic use is a major contributor in the introduction of selective pressures in our natural environments that have significantly contributed in the rapid emergence of antibiotic-resistant microbial strains. The use of probiotics in lieu of antibiotic therapy to address certain health conditions in both animals and humans may alleviate these antibiotic-mediated selective pressures. Probiotic use is defined as the actual application of live beneficial microbes to obtain a desired outcome by preventing diseased state or improving general health. Multiple studies have confirmed the beneficial effects of probiotic use in the health of both livestock and humans. As such, probiotics consumption is gaining popularity worldwide. However, concerns have been raised in the use of some probiotics strains that carry antibiotic resistance genes themselves, as they have the potential to pass the antibiotic resistance genes to pathogenic bacteria through horizontal gene transfer. Therefore, with the current public health concern on antibiotic resistance globally, in this review, we underscore the need to screen probiotic strains that are used in both livestock and human applications to assure their safety and mitigate their potential in significantly contributing to the spread of antibiotic resistance genes in our natural environments.
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Affiliation(s)
- Ivan C V J Imperial
- Immunopharmacology Research Laboratory, Institute of Biology, College of Science, University of the Philippines Diliman Quezon City, Philippines
| | - Joyce A Ibana
- Immunopharmacology Research Laboratory, Institute of Biology, College of Science, University of the Philippines Diliman Quezon City, Philippines
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15
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Feasibility of Genome-Wide Screening for Biosafety Assessment of Probiotics: A Case Study of Lactobacillus helveticus MTCC 5463. Probiotics Antimicrob Proteins 2016. [PMID: 26223907 DOI: 10.1007/s12602-015-9199-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Recent years have witnessed an explosion in genome sequencing of probiotic strains for accurate identification and characterization. Regulatory bodies are emphasizing on the need for performing phase I safety studies for probiotics. The main hypothesis of this study was to explore the feasibility of using genome databases for safety screening of strains. In this study, we attempted to develop a framework for the safety assessment of a potential probiotic strain, Lactobacillus helveticus MTCC 5463 based on genome mining for genes associated with antibiotic resistance, production of harmful metabolites, and virulence. The sequencing of MTCC 5463 was performed using GS-FLX Titanium reagents. Genes coding for antibiotic resistance and virulence were identified using Antibiotic Resistance Genes Database and Virulence Factors Database. Results indicated that MTCC 5463 carried antibiotic resistance genes associated with beta-lactam and fluoroquinolone. There is no threat of transfer of these genes to host gut commensals because the genes are not plasmid encoded. The presence of genes for adhesion, biofilm, surface proteins, and stress-related proteins provides robustness to the strain. The presence of hemolysin gene in the genome revealed a theoretical risk of virulence. The results of in silico analysis complemented the in vitro studies and human clinical trials, confirming the safety of the probiotic strain. We propose that the safety assessment of probiotic strains administered live at high doses using a genome-wide screening could be an effective and time-saving tool for identifying prognostic biomarkers of biosafety.
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16
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Kwak MJ, Kwon SK, Yoon JK, Song JY, Seo JG, Chung MJ, Kim JF. Evolutionary architecture of the infant-adapted group of Bifidobacterium species associated with the probiotic function. Syst Appl Microbiol 2016; 39:429-439. [PMID: 27524178 DOI: 10.1016/j.syapm.2016.07.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 07/19/2016] [Accepted: 07/22/2016] [Indexed: 01/11/2023]
Abstract
Bifidobacteria, often associated with the gastrointestinal tract of animals, are well known for their roles as probiotics. Among the dozens of Bifidobacterium species, Bifidobacterium bifidum, B. breve, and B. longum are the ones most frequently isolated from the feces of infants and known to help the digestion of human milk oligosaccharides. To investigate the correlation between the metabolic properties of bifidobacteria and their phylogeny, we performed a phylogenomic analysis based on 452 core genes of forty-four completely sequenced Bifidobacterium species. Results show that a major evolutionary event leading to the clade of the infant-adapted species is linked to carbohydrate metabolism, but it is not the only factor responsible for the adaptation of bifidobacteria to the gut. The genome of B. longum subsp. infantis, a typical bifidobacterium in the gut of breast-fed infants, encodes proteins associated with several kinds of species-specific metabolic pathways, including urea metabolism and biosynthesis of riboflavin and lantibiotics. Our results demonstrate that these metabolic features, which are associated with the probiotic function of bifidobacteria, are species-specific and highly correlate with their phylogeny.
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Affiliation(s)
- Min-Jung Kwak
- Department of Systems Biology and Division of Life Sciences, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Soon-Kyeong Kwon
- Department of Systems Biology and Division of Life Sciences, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Jae-Kyung Yoon
- Department of Systems Biology and Division of Life Sciences, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Ju Yeon Song
- Department of Systems Biology and Division of Life Sciences, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Jae-Gu Seo
- R&D Center, Cell Biotech Co., Ltd., 50, Aegibong-ro 409 beon-gil, Wolgot-myeon, Gimpo-si, Gyeonggi-do 10003, Republic of Korea
| | - Myung Jun Chung
- R&D Center, Cell Biotech Co., Ltd., 50, Aegibong-ro 409 beon-gil, Wolgot-myeon, Gimpo-si, Gyeonggi-do 10003, Republic of Korea
| | - Jihyun F Kim
- Department of Systems Biology and Division of Life Sciences, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea; Strategic Initiative for Microbiomes in Agriculture and Food, Yonsei University, Seoul 03722, Republic of Korea.
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17
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Babot JD, Argañaraz-Martínez E, Lorenzo-Pisarello MJ, Apella MC, Perez Chaia A. Cytotoxic damage of soybean agglutinin on intestinal epithelial cells of broiler chicks:in vitroprotection byBifidobacterium infantisCRL1395. FEMS Microbiol Lett 2016; 363:fnw114. [DOI: 10.1093/femsle/fnw114] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2016] [Indexed: 12/28/2022] Open
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18
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Salvetti E, Orrù L, Capozzi V, Martina A, Lamontanara A, Keller D, Cash H, Felis GE, Cattivelli L, Torriani S, Spano G. Integrate genome-based assessment of safety for probiotic strains: Bacillus coagulans GBI-30, 6086 as a case study. Appl Microbiol Biotechnol 2016; 100:4595-605. [PMID: 26952108 DOI: 10.1007/s00253-016-7416-9] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Revised: 02/18/2016] [Accepted: 02/22/2016] [Indexed: 12/17/2022]
Abstract
Probiotics are microorganisms that confer beneficial effects on the host; nevertheless, before being allowed for human consumption, their safety must be verified with accurate protocols. In the genomic era, such procedures should take into account the genomic-based approaches. This study aims at assessing the safety traits of Bacillus coagulans GBI-30, 6086 integrating the most updated genomics-based procedures and conventional phenotypic assays. Special attention was paid to putative virulence factors (VF), antibiotic resistance (AR) genes and genes encoding enzymes responsible for harmful metabolites (i.e. biogenic amines, BAs). This probiotic strain was phenotypically resistant to streptomycin and kanamycin, although the genome analysis suggested that the AR-related genes were not easily transferrable to other bacteria, and no other genes with potential safety risks, such as those related to VF or BA production, were retrieved. Furthermore, no unstable elements that could potentially lead to genomic rearrangements were detected. Moreover, a workflow is proposed to allow the proper taxonomic identification of a microbial strain and the accurate evaluation of risk-related gene traits, combining whole genome sequencing analysis with updated bioinformatics tools and standard phenotypic assays. The workflow presented can be generalized as a guideline for the safety investigation of novel probiotic strains to help stakeholders (from scientists to manufacturers and consumers) to meet regulatory requirements and avoid misleading information.
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Affiliation(s)
- Elisa Salvetti
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy.,APC Microbiome Institute, University College Cork, Western Road, Cork, T12 Y337, Ireland
| | - Luigi Orrù
- Consiglio per la Ricerca in Agricoltura e l'analisi dell'economia Agraria, Genomics Research Centre, Via S. Protaso 302 Fiorenzuola d'Arda, 29017, Piacenza, Italy
| | - Vittorio Capozzi
- Department of Agriculture, Food and Environment Sciences, University of Foggia, Via Napoli 25, 71122, Foggia, Italy
| | - Alessia Martina
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Antonella Lamontanara
- Consiglio per la Ricerca in Agricoltura e l'analisi dell'economia Agraria, Genomics Research Centre, Via S. Protaso 302 Fiorenzuola d'Arda, 29017, Piacenza, Italy
| | - David Keller
- Ganeden Biotech Inc., 5800 Landerbrook Drive Suite 300, Mayfield Heights, OH, 44124, USA
| | - Howard Cash
- Ganeden Biotech Inc., 5800 Landerbrook Drive Suite 300, Mayfield Heights, OH, 44124, USA
| | - Giovanna E Felis
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Luigi Cattivelli
- Consiglio per la Ricerca in Agricoltura e l'analisi dell'economia Agraria, Genomics Research Centre, Via S. Protaso 302 Fiorenzuola d'Arda, 29017, Piacenza, Italy
| | - Sandra Torriani
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy.
| | - Giuseppe Spano
- Department of Agriculture, Food and Environment Sciences, University of Foggia, Via Napoli 25, 71122, Foggia, Italy
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19
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Characterization and in vitro properties of potential probiotic Bifidobacterium strains isolated from breast-fed infant feces. ANN MICROBIOL 2015. [DOI: 10.1007/s13213-015-1187-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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20
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Varankovich NV, Nickerson MT, Korber DR. Probiotic-based strategies for therapeutic and prophylactic use against multiple gastrointestinal diseases. Front Microbiol 2015; 6:685. [PMID: 26236287 PMCID: PMC4500982 DOI: 10.3389/fmicb.2015.00685] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 06/22/2015] [Indexed: 12/18/2022] Open
Abstract
Probiotic bacteria offer a number of potential health benefits when administered in sufficient amounts that in part include reducing the number of harmful organisms in the intestine, producing antimicrobial substances and stimulating the body's immune response. However, precisely elucidating the probiotic effect of a specific bacterium has been challenging due to the complexity of the gut's microbial ecosystem and a lack of definitive means for its characterization. This review provides an overview of widely used and recently described probiotics, their impact on the human's gut microflora as a preventative treatment of disease, human/animal models being used to help show efficacy, and discusses the potential use of probiotics in gastrointestinal diseases associated with antibiotic administration.
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Affiliation(s)
| | | | - Darren R. Korber
- Department of Food and Bioproduct Sciences, University of Saskatchewan, SaskatoonSK, Canada
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21
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Roy A, Mukhopadhyay S, Sarkar I, Sen A. Comparative investigation of the various determinants that influence the codon and amino acid usage patterns in the genus Bifidobacterium. World J Microbiol Biotechnol 2015; 31:959-81. [DOI: 10.1007/s11274-015-1850-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Accepted: 03/31/2015] [Indexed: 12/31/2022]
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22
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Fedorova IA, Danilenko VN. Immunogenic properties of a probiotic component of the human gastrointestinal tract microbiota. ACTA ACUST UNITED AC 2015. [DOI: 10.1134/s2079086414060036] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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23
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Shu XL, Yu TT, Kang K, Xu H, Lei T. Protective effects of bifidobacterial adhesin on intestinal mucosa of stressed male rats via modulation of inflammation. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2014; 7:3324-31. [PMID: 25031756 PMCID: PMC4097288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 04/19/2014] [Accepted: 05/28/2014] [Indexed: 06/03/2023]
Abstract
This study aimed to assess BA impact on inflammation markers and repair of intestinal mucosa. Forty-eight rats were randomly divided into stress (n = 24) and BA (n = 24) groups. Stress was induced by fettering in all animals, fed enterally with 125.4 kJ/kg/d and 0.2 g/kg/d nitrogen. Then, rats were treated for 8 days with 5 mg/kg/d BA (BA group) or 5 mg/kg/d saline (Stress group). Levels of NF-κB, IL-10, TNF-α, and IFN-γ were measured at different time points, in plasma and intestinal mucosa samples. Changes in intestinal mucosa morphology were observed by electron microscopy. Plasma and/or mucosal levels of NF-κB, TNF-α, and IFN-γ were significantly higher in both groups after stress induction (P < 0.05). These high levels persisted in control animals throughout the experiment, and were significantly reduced in the BA group, 3 and 8 days after stress induction (P < 0.05). Interestingly, IL-10 levels were increased after BA treatment (P < 0.05). At day 8, ileal mucosal villi and crypt structure were significantly restored in the BA group. Bifidobacterial adhesin plays a role in repairing intestinal mucosa injury after stress by regulating the release of inflammatory mediators in the intestinal mucosa.
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Affiliation(s)
- Xiao-Liang Shu
- Department of Nutrition, East Hospital, Tong Ji University School of MedicineShanghai, 200000, China
| | - Tin-Tin Yu
- Department of Nutrition, East Hospital, Tong Ji University School of MedicineShanghai, 200000, China
| | - Kai Kang
- Department of Nutrition, East Hospital, Tong Ji University School of MedicineShanghai, 200000, China
| | - Han Xu
- Department of Nutrition, East Hospital, Tong Ji University School of MedicineShanghai, 200000, China
| | - Tao Lei
- Department of Endorine, Tong Ji Hospital, Tong Ji University School of MedicineShanghai, 200000, China
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24
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-Biao Guo F, Lin Y, -Ling Chen L. Recognition of Protein-coding Genes Based on Z-curve Algorithms. Curr Genomics 2014; 15:95-103. [PMID: 24822027 PMCID: PMC4009845 DOI: 10.2174/1389202915999140328162724] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2013] [Revised: 11/19/2013] [Accepted: 11/20/2013] [Indexed: 01/18/2023] Open
Abstract
Recognition of protein-coding genes, a classical bioinformatics issue, is an absolutely needed step for annotating newly sequenced genomes. The Z-curve algorithm, as one of the most effective methods on this issue, has been successfully applied in annotating or re-annotating many genomes, including those of bacteria, archaea and viruses. Two Z-curve based ab initio gene-finding programs have been developed: ZCURVE (for bacteria and archaea) and ZCURVE_V (for viruses and phages). ZCURVE_C (for 57 bacteria) and Zfisher (for any bacterium) are web servers for re-annotation of bacterial and archaeal genomes. The above four tools can be used for genome annotation or re-annotation, either independently or combined with the other gene-finding programs. In addition to recognizing protein-coding genes and exons, Z-curve algorithms are also effective in recognizing promoters and translation start sites. Here, we summarize the applications of Z-curve algorithms in gene finding and genome annotation.
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Affiliation(s)
- Feng -Biao Guo
- Center of Bioinformatics and Key Laboratory for NeuroInformation of the Ministry of Education, University of Elec-tronic Science and Technology of China, Chengdu, 610054, China
| | - Yan Lin
- Department of Physics, Tianjin University, Tianjin 300072, China
| | - Ling -Ling Chen
- cCollege of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
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25
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Sharma P, Tomar SK, Goswami P, Sangwan V, Singh R. Antibiotic resistance among commercially available probiotics. Food Res Int 2014. [DOI: 10.1016/j.foodres.2014.01.025] [Citation(s) in RCA: 141] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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26
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Moore AM, Patel S, Forsberg KJ, Wang B, Bentley G, Razia Y, Qin X, Tarr PI, Dantas G. Pediatric fecal microbiota harbor diverse and novel antibiotic resistance genes. PLoS One 2013; 8:e78822. [PMID: 24236055 PMCID: PMC3827270 DOI: 10.1371/journal.pone.0078822] [Citation(s) in RCA: 125] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 09/10/2013] [Indexed: 12/13/2022] Open
Abstract
Emerging antibiotic resistance threatens human health. Gut microbes are an epidemiologically important reservoir of resistance genes (resistome), yet prior studies indicate that the true diversity of gut-associated resistomes has been underestimated. To deeply characterize the pediatric gut-associated resistome, we created metagenomic recombinant libraries in an Escherichia coli host using fecal DNA from 22 healthy infants and children (most without recent antibiotic exposure), and performed functional selections for resistance to 18 antibiotics from eight drug classes. Resistance-conferring DNA fragments were sequenced (Illumina HiSeq 2000), and reads assembled and annotated with the PARFuMS computational pipeline. Resistance to 14 of the 18 antibiotics was found in stools of infants and children. Recovered genes included chloramphenicol acetyltransferases, drug-resistant dihydrofolate reductases, rRNA methyltransferases, transcriptional regulators, multidrug efflux pumps, and every major class of beta-lactamase, aminoglycoside-modifying enzyme, and tetracycline resistance protein. Many resistance-conferring sequences were mobilizable; some had low identity to any known organism, emphasizing cryptic organisms as potentially important resistance reservoirs. We functionally confirmed three novel resistance genes, including a 16S rRNA methylase conferring aminoglycoside resistance, and two tetracycline-resistance proteins nearly identical to a bifidobacterial MFS transporter (B. longum s. longum JDM301). We provide the first report to our knowledge of resistance to folate-synthesis inhibitors conferred by a predicted Nudix hydrolase (part of the folate synthesis pathway). This functional metagenomic survey of gut-associated resistomes, the largest of its kind to date, demonstrates that fecal resistomes of healthy children are far more diverse than previously suspected, that clinically relevant resistance genes are present even without recent selective antibiotic pressure in the human host, and that cryptic gut microbes are an important resistance reservoir. The observed transferability of gut-associated resistance genes to a gram-negative (E. coli) host also suggests that the potential for gut-associated resistomes to threaten human health by mediating antibiotic resistance in pathogens warrants further investigation.
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Affiliation(s)
- Aimée M. Moore
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Sanket Patel
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Kevin J. Forsberg
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Bin Wang
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Gayle Bentley
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Yasmin Razia
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Division of Gastroenterology, Department of Pediatrics, Children’s Hospital and Regional Medical Center, Seattle, Washington, United States of America
| | - Xuan Qin
- Department of Microbiology, Seattle Children’s Hospital, Seattle, Washington, United States of America
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
| | - Phillip I. Tarr
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Gautam Dantas
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- * E-mail:
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27
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Abstract
After a short overview of the history of probiotics, the author presents the development of human intestinal microflora based on the newest genetic data and the microbiological features of main probiotics. The indications of probiotic administration have been defined and extended in recent years. The author reviews significant results of probiotic treatment in some gastrointestinal diseases based on meta-analytical data. Probiotics are useful in preventing and treating diarrhoea caused by antibiotics and Clostridium difficile caused diarrhoea. In the treatment of Helicobacter pylori infection, preparations containing certain Lactobacillus,Bifidobacterium strains or Saccaromyces boulardii could enhance by 5-10% the rate of successful eradication and reduce the incidence and severity of the side effects. Some symptoms of irritable bowel syndrome and thus the quality of life can be improved by probiotics. Their beneficial effect in ulcerative colitis was proven, while in Crohn's disease has not yet been defined. The use of probiotics is not included in guidelines, with the exception of the Maastricht IV/Florence consensus. For each disease it is advisable to use probiotics containing strains only with proven beneficial effect. The efficiency of preparations containing mixed strains has not yet been properly investigated. The author reviews the rare but potentially serious side effects of probiotics. In Hungary, there are many probiotic preparations available which can be purchased in pharmacies without prescription: their use is more empirical than evidence-based. The European Food Safety Authority has recently rejected claims for probiotics to be classed as medicines given the lack of convincing evidence on the effects of probiotics on human health and well-being. Clearly, further research is needed to collect evidence which could be incorporated into the international guidelines.
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Affiliation(s)
- György Miklós Buzás
- Ferencvárosi Egészségügyi Szolgáltató Kiemelkedően Közhasznú Nonprofit Kft. Gasztroenterológiai szakrendelés Budapest.
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28
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Yin X, Yu B, Tang Z, He B, Ren J, Xiao X, Tang W. Bifidobacterium infantis-mediated HSV-TK/GCV suicide gene therapy induces both extrinsic and intrinsic apoptosis in a rat model of bladder cancer. Cancer Gene Ther 2012; 20:77-81. [PMID: 23258087 DOI: 10.1038/cgt.2012.86] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Bladder cancer is the most common cancer in the urological tract. Here, we investigated the molecular pathways involved in the apoptosis of rodent bladder cancer, which was treated with Bifidobacterium infantis (BI)-mediated herpes simplex virus thymidine kinase (HSV-TK)/ganciclovir (GCV) suicide gene therapy. We engineered the BI-TK system, which consists of BI with the recombinant plasmid PGEX-1λT carrying HSV-TK (that is, TK) gene. Tumor-bearing rats were randomly divided into three groups and tail vein injected with normal saline (group A), BI/PGEX-1λT (group B) or BI-TK (group C), followed by intraperitoneal injection of GCV. The BI-TK/GCV system (group C) was shown to inhibit tumor growth and caused the apoptosis of tumor cells as assessed by in situ terminal transferase dUTP nick-end labeling assay. While varied extents of apoptosis were detected in tumor cells from all groups, tumor cells treated with BI-TK/GCV system (group C) exhibited the highest level of apoptosis (P < 0.05), consistent with our previous studies. Furthermore, we found that the expression levels of Fas, FasL, Cyt-C and caspase-9 in tumor tissues derived from group C were significantly higher than the other two groups (P < 0.001). Therefore, our results have demonstrated that the BI-TK/GCV therapy system exhibits a sustainable antitumor growth activity in the rodent model of bladder cancer. Mechanistically, both extrinsic and intrinsic apoptosis pathways are involved in the BI-TK/GCV antitumor functionality.
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Affiliation(s)
- X Yin
- Department of Urology, The First Affiliated Hospital, Chongqing Medical University, Chongqing, China
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