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Li B, Chen D, Lin F, Wu C, Cao L, Chen H, Hu Y, Yin Y. Genomic Island-Mediated Horizontal Transfer of the Erythromycin Resistance Gene erm(X) among Bifidobacteria. Appl Environ Microbiol 2022; 88:e0041022. [PMID: 35477272 PMCID: PMC9128502 DOI: 10.1128/aem.00410-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 04/02/2022] [Indexed: 01/20/2023] Open
Abstract
Antibiotic resistance is a serious medical issue driven by antibiotic misuse. Bifidobacteria may serve as a reservoir for antibiotic resistance genes (ARGs) that have the potential risk of transfer to pathogens. The erythromycin resistance gene erm(X) is an ARG with high abundance in bifidobacteria, especially in Bifidobacterium longum species. However, the characteristics of the spread and integration of the gene erm(X) into the bifidobacteria genome are poorly understood. In this study, 10 tetW-positive bifidobacterial strains and 1 erm(X)-positive bifidobacterial strain were used to investigate the transfer of ARGs. Conjugation assays found that the erm(X) gene could transfer to five other bifidobacterial strains. Dimethyl sulfoxide (DMSO) and vorinostat significantly promoted the transfer of the erm(X) from strain Bifidobacterium catenulatum subsp. kashiwanohense DSM 21854 to Bifidobacterium longum subsp. suis DSM 20211. Whole-genome sequencing and comparative genomic analysis revealed that the erm(X) gene was located on the genomic island BKGI1 and that BKGI1 was conjugally mobile and transferable. To our knowledge, this is the first report that a genomic island-mediated gene erm(X) transfer in bifidobacteria. Additionally, BKGI1 is very unstable in B. catenulatum subsp. kashiwanohense DSM 21854 and transconjugant D2TC and is highly excisable and has an intermediate circular formation. In silico analysis showed that the BKGI1 homologs were also present in other bifidobacterial strains and were especially abundant in B. longum strains. Thus, our results confirmed that genomic island BKGI1 was one of the vehicles for erm(X) spread. These findings suggest that genomic islands play an important role in the dissemination of the gene erm(X) among Bifidobacterium species. IMPORTANCE Bifidobacteria are a very important group of gut microbiota, and the presence of these bacteria has many beneficial effects for the host. Thus, bifidobacteria have attracted growing interest owing to their potential probiotic properties. Bifidobacteria have been widely exploited by the food industry as probiotic microorganisms, and some species have a long history of safe use in food and feed production. However, the presence of antibiotic resistance raises the risk of its application. In this study, we analyzed the transfer of the erythromycin resistance gene erm(X) and revealed that the molecular mechanism behind the spread of the gene erm(X) was mediated by genomic island BKGI1. To the best of our knowledge this is the first report to describe the transfer of the gene erm(X) via genomic islands among bifidobacteria. This may be an important way to disseminate the gene erm(X) among bifidobacteria.
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Affiliation(s)
- Baiyuan Li
- Key Laboratory of Comprehensive Utilization of Advantage Plant Resources in Hunan South, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou, Hunan, China
| | - Dan Chen
- Key Laboratory of Comprehensive Utilization of Advantage Plant Resources in Hunan South, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou, Hunan, China
| | - Fan Lin
- Key Laboratory of Comprehensive Utilization of Advantage Plant Resources in Hunan South, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou, Hunan, China
| | - Chuanyu Wu
- Key Laboratory of Comprehensive Utilization of Advantage Plant Resources in Hunan South, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou, Hunan, China
| | - Linyan Cao
- Key Laboratory of Comprehensive Utilization of Advantage Plant Resources in Hunan South, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou, Hunan, China
| | - Huahai Chen
- Key Laboratory of Comprehensive Utilization of Advantage Plant Resources in Hunan South, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou, Hunan, China
| | - Yunfei Hu
- Key Laboratory of Comprehensive Utilization of Advantage Plant Resources in Hunan South, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou, Hunan, China
| | - Yeshi Yin
- Key Laboratory of Comprehensive Utilization of Advantage Plant Resources in Hunan South, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou, Hunan, China
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2
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Tarracchini C, Viglioli M, Lugli GA, Mancabelli L, Fontana F, Alessandri G, Turroni F, Ventura M, Milani C. The Integrated Probiotic Database: a genomic compendium of bifidobacterial health-promoting strains. MICROBIOME RESEARCH REPORTS 2022; 1:9. [PMID: 38045645 PMCID: PMC10688828 DOI: 10.20517/mrr.2021.13] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/14/2022] [Accepted: 02/07/2022] [Indexed: 12/05/2023]
Abstract
Background: The World Health Organization defines probiotics as "live microorganisms, which when administered in adequate amounts confer a health benefit on the host". In this framework, probiotic strains should be regarded as safe for human and animal consumption, i.e., they should possess the GRAS (generally recognized as safe) status, notified by the local authorities. Consistently, strains of selected Bifidobacterium species are extensively used as probiotic agents to prevent and ameliorate a broad spectrum of human and/or animal gastrointestinal disorders. Even though probiotic properties are often genus- or species-associated, strain-level differences in the genetic features conferring individual probiotic properties to commercialized bifidobacterial strains have not been investigated in detail. Methods: In this study, we built a genomic database named Integrated Probiotic DataBase (IPDB), whose first iteration consists of common bifidobacterial strains used in probiotic products for which public genome sequences were available, such as members of B. longum subsp. longum, B. longum subsp. infantis, B. bifidum, B. breve, and B. animalis subsp. lactis taxa. Furthermore, the IPDB was exploited to perform comparative genome analyses focused on genetic factors conferring structural, functional, and chemical features predicted to be involved in microbe-host and microbe-microbe interactions. Results and conclusion: Our analyses revealed strain-level genetic differences, underlining the importance of inspecting the strain-specific and outcome-specific efficacy of probiotics. In this context, IPDB represents a valuable resource for obtaining genetic information of well-established bifidobacterial probiotic strains.
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Affiliation(s)
- Chiara Tarracchini
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, Parma 43124, Italy
| | - Martina Viglioli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, Parma 43124, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, Parma 43124, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, Parma 43124, Italy
| | - Federico Fontana
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, Parma 43124, Italy
- GenProbio Srl, Via delle Scienze, 11/A, Parma 43100, Italy
| | - Giulia Alessandri
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, Parma 43124, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, Parma 43124, Italy
- Microbiome Research Hub, University of Parma, Parco Area delle Scienze 11a, Parma 43124, Italy
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, Parma 43124, Italy
- Microbiome Research Hub, University of Parma, Parco Area delle Scienze 11a, Parma 43124, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, Parma 43124, Italy
- Microbiome Research Hub, University of Parma, Parco Area delle Scienze 11a, Parma 43124, Italy
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3
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Daniali M, Nikfar S, Abdollahi M. Antibiotic resistance propagation through probiotics. Expert Opin Drug Metab Toxicol 2020; 16:1207-1215. [PMID: 32938241 DOI: 10.1080/17425255.2020.1825682] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION The widespread use of probiotics globally has established an argument against their safety profile. Recent studies investigated the gastrointestinal tract (GIT) as a reservoir for antibiotic resistance genes and horizontal gene transfer (HGT) amongst opportunistic pathogens, probiotics, and the normal microbiota which might cause severe clinical implications. AREAS COVERED In this review, we aimed to discuss the potential role of probiotics in spreading antibiotic resistance. All relevant data were found through online/updated databases such as PubMed, Google Scholar, and Clinicaltrials.gov. This review is based on the studies undertaken over the past two decades (2000-2020). EXPERT OPINION Microorganisms are capable of transferring resistance genes to survive against antimicrobial medications. Transference of resistance genes among pathogens, probiotics, and gut microbiota in the GIT through HGT endow probiotics as a possible source for antimicrobial resistance genes, which is responsible for the development of the antibiotic resistance crisis. According to the expression of genes in mechanisms of antibiotics resistance and probiotics HGT, the hypothesis of the role of these microorganisms in personalized medicine and gene therapy could also be considered.
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Affiliation(s)
- Marzieh Daniali
- Toxicology and Diseases Group (TDG), Pharmaceutical Sciences Research Center (PSRC), the Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences , Tehran, Iran.,Department of Toxicology and Pharmacology, School of Pharmacy, Tehran University of Medical Sciences , Tehran, Iran
| | - Shekoufeh Nikfar
- Personalized Medicine Research Center (PMRC), the Endocrinology and Metabolism Research Institute (EMRI), Tehran University of Medical Sciences , Tehran, Iran.,Evidence-Based Evaluation of Cost-Effectiveness and Clinical Outcomes Group, Pharmaceutical Sciences Research Center (PSRC), and the Pharmaceutical Management and Economics Research Center (PMERC), the Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences , Tehran, Iran.,Department of Pharmacoeconomics and Pharmaceutical Administration, School of Pharmacy, Tehran University of Medical Sciences , Tehran, Iran
| | - Mohammad Abdollahi
- Toxicology and Diseases Group (TDG), Pharmaceutical Sciences Research Center (PSRC), the Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences , Tehran, Iran.,Department of Toxicology and Pharmacology, School of Pharmacy, Tehran University of Medical Sciences , Tehran, Iran.,Personalized Medicine Research Center (PMRC), the Endocrinology and Metabolism Research Institute (EMRI), Tehran University of Medical Sciences , Tehran, Iran
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Abstract
The probiotic properties of Bifidobacterium breve CECT7263, as well as its safety, have been the focus of in several studies since 2008, including the sequencing of its genome in 2012. This study aims to complete the available genomic data to deepen the knowledge of some phenotypic characteristics of this strain.
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Lescat M, Launay A, Ghalayini M, Magnan M, Glodt J, Pintard C, Dion S, Denamur E, Tenaillon O. Using long-term experimental evolution to uncover the patterns and determinants of molecular evolution of an Escherichia coli natural isolate in the streptomycin-treated mouse gut. Mol Ecol 2016; 26:1802-1817. [PMID: 27661780 DOI: 10.1111/mec.13851] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 08/31/2016] [Accepted: 09/01/2016] [Indexed: 01/10/2023]
Abstract
Although microbial ecology of the gut is now a major focus of interest, little is known about the molecular determinants of microbial adaptation in the gut. Experimental evolution coupled with whole-genome sequencing can provide insights of the adaptive process. In vitro experiments have revealed some conserved patterns: intermediate convergence, and epistatic interactions between beneficial mutations and mutations in global regulators. To test the relevance of these patterns and to identify the selective pressures acting in vivo, we have performed a long-term adaptation of an E. coli natural isolate, the streptomycin-resistant strain 536, in the digestive tract of streptomycin-treated mice. After a year of evolution, a clone from 15 replicates was sequenced. Consistently with in vitro observations, the identified mutations revealed a strong pattern of convergence at the mutation, gene, operon and functional levels. Yet, the rate of molecular evolution was lower than in in vitro, and no mutations in global regulators were recovered. More specific targets were observed: the dgo operon, involved in the galactonate pathway that improved growth on D-galactonate, and rluD and gidB, implicated in the maturation of the ribosomes, which mutations improved growth only in the presence of streptomycin. As in vitro, the nonrandom associations of mutations within the same pathways suggested a role of epistasis in shaping the adaptive landscape. Overall, we show that 'evolve and sequence' approach coupled with an analysis of convergence, when applied to a natural isolate, can be used to study adaptation in vivo and uncover the specific selective pressures of that environment.
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Affiliation(s)
- Mathilde Lescat
- INSERM, IAME, UMR 1137, Paris, France.,Université Paris Nord, Sorbonne Paris Cité, Paris, France.,APHP, Hôpitaux Universitaires Paris Seine Saint-Denis, Paris, France
| | - Adrien Launay
- INSERM, IAME, UMR 1137, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Mohamed Ghalayini
- INSERM, IAME, UMR 1137, Paris, France.,Université Paris Nord, Sorbonne Paris Cité, Paris, France
| | - Mélanie Magnan
- INSERM, IAME, UMR 1137, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Jérémy Glodt
- INSERM, IAME, UMR 1137, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Coralie Pintard
- INSERM, IAME, UMR 1137, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Sara Dion
- INSERM, IAME, UMR 1137, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Erick Denamur
- INSERM, IAME, UMR 1137, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France.,APHP, Hôpitaux Universitaires Paris Nord Val de Seine, Paris, France
| | - Olivier Tenaillon
- INSERM, IAME, UMR 1137, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
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Nagyzbekky E, Abitayeva G, Anuarbekov S, Shaikhina D, Li K, Shaikhin S, Almagambet K, Abzhalelov A, Saduakhass S, Kushugulov A, Marotta F. Investigation of Acid and Bile Tolerance, Antimicrobial Activity and Antibiotic Resistance of Lactobacillus Strains Isolated from Kazakh Dairy Foods. ACTA ACUST UNITED AC 2016. [DOI: 10.3923/ajaps.2016.143.158] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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7
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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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8
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9
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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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10
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Fouhy F, O’Connell Motherway M, Fitzgerald GF, Ross RP, Stanton C, van Sinderen D, Cotter PD. In silico assigned resistance genes confer Bifidobacterium with partial resistance to aminoglycosides but not to β-lactams. PLoS One 2013; 8:e82653. [PMID: 24324818 PMCID: PMC3855789 DOI: 10.1371/journal.pone.0082653] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 11/05/2013] [Indexed: 12/25/2022] Open
Abstract
Bifidobacteria have received significant attention due to their contribution to human gut health and the use of specific strains as probiotics. It is thus not surprising that there has also been significant interest with respect to their antibiotic resistance profile. Numerous culture-based studies have demonstrated that bifidobacteria are resistant to the majority of aminoglycosides, but are sensitive to β-lactams. However, limited research exists with respect to the genetic basis for the resistance of bifidobacteria to aminoglycosides. Here we performed an in-depth in silico analysis of putative Bifidobacterium-encoded aminoglycoside resistance proteins and β-lactamases and assess the contribution of these proteins to antibiotic resistance. The in silico-based screen detected putative aminoglycoside and β-lactam resistance proteins across the Bifidobacterium genus. Laboratory-based investigations of a number of representative bifidobacteria strains confirmed that despite containing putative β-lactamases, these strains were sensitive to β-lactams. In contrast, all strains were resistant to the aminoglycosides tested. To assess the contribution of genes encoding putative aminoglycoside resistance proteins in Bifidobacterium sp. two genes, namely Bbr_0651 and Bbr_1586, were targeted for insertional inactivation in B. breve UCC2003. As compared to the wild-type, the UCC2003 insertion mutant strains exhibited decreased resistance to gentamycin, kanamycin and streptomycin. This study highlights the associated risks of relying on the in silico assignment of gene function. Although several putative β-lactam resistance proteins are located in bifidobacteria, their presence does not coincide with resistance to these antibiotics. In contrast however, this approach has resulted in the identification of two loci that contribute to the aminoglycoside resistance of B. breve UCC2003 and, potentially, many other bifidobacteria.
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Affiliation(s)
- Fiona Fouhy
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
- Microbiology Department, University College Cork, Cork, Ireland
| | - Mary O’Connell Motherway
- Microbiology Department, University College Cork, Cork, Ireland
- Alimentary Pharmabiotic Centre, Cork, Ireland
| | - Gerald F. Fitzgerald
- Microbiology Department, University College Cork, Cork, Ireland
- Alimentary Pharmabiotic Centre, Cork, Ireland
| | - R. Paul Ross
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
- Alimentary Pharmabiotic Centre, Cork, Ireland
| | - Catherine Stanton
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
- Alimentary Pharmabiotic Centre, Cork, Ireland
| | - Douwe van Sinderen
- Microbiology Department, University College Cork, Cork, Ireland
- Alimentary Pharmabiotic Centre, Cork, Ireland
| | - Paul D. Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
- Alimentary Pharmabiotic Centre, Cork, Ireland
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Gueimonde M, Sánchez B, G. de los Reyes-Gavilán C, Margolles A. Antibiotic resistance in probiotic bacteria. Front Microbiol 2013; 4:202. [PMID: 23882264 PMCID: PMC3714544 DOI: 10.3389/fmicb.2013.00202] [Citation(s) in RCA: 320] [Impact Index Per Article: 29.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 06/28/2013] [Indexed: 11/17/2022] Open
Abstract
Probiotics are live microorganisms which when administered in adequate amounts confer a health benefit on the host. The main probiotic bacteria are strains belonging to the genera Lactobacillus and Bifidobacterium, although other representatives, such as Bacillus or Escherichia coli strains, have also been used. Lactobacillus and Bifidobacterium are two common inhabitants of the human intestinal microbiota. Also, some species are used in food fermentation processes as starters, or as adjunct cultures in the food industry. With some exceptions, antibiotic resistance in these beneficial microbes does not constitute a safety concern in itself, when mutations or intrinsic resistance mechanisms are responsible for the resistance phenotype. In fact, some probiotic strains with intrinsic antibiotic resistance could be useful for restoring the gut microbiota after antibiotic treatment. However, specific antibiotic resistance determinants carried on mobile genetic elements, such as tetracycline resistance genes, are often detected in the typical probiotic genera, and constitute a reservoir of resistance for potential food or gut pathogens, thus representing a serious safety issue.
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Affiliation(s)
| | | | | | - Abelardo Margolles
- Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones CientíficasVillaviciosa, Spain
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Quantitative detection of viable Bifidobacterium bifidum BF-1 cells in human feces by using propidium monoazide and strain-specific primers. Appl Environ Microbiol 2013; 79:2182-8. [PMID: 23354719 DOI: 10.1128/aem.03294-12] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
We developed a PCR-based method to detect and quantify viable Bifidobacterium bifidum BF-1 cells in human feces. This method (PMA-qPCR) uses propidium monoazide (PMA) to distinguish viable from dead cells and quantitative PCR using a BF-1-specific primer set designed from the results of randomly amplified polymorphic DNA analysis. During long-term culture (10 days), the number of viable BF-1 cells detected by counting the number of CFU on modified MRS agar, by measuring the ATP contents converted to CFU, and by using PMA-qPCR decreased from about 10(10) to 10(6) cells/ml; in contrast, the total number of (viable and dead) BF-1 cells detected by counting 4',6-diamidino-2-phenylindolee (DAPI)-stained cells and by using qPCR without PMA and reverse transcription-qPCR remained constant. The number of viable BF-1 cells in fecal samples detected by using PMA-qPCR was highly and significantly correlated with the number of viable BF-1 cells added to the fecal samples, within the range of 10(5.3) to 10(10.3) cells/g feces (wet weight) (r > 0.99, P < 0.001). After 12 healthy subjects ingested 10(10.3) to 10(11.0) CFU of BF-1 in a fermented milk product daily for 28 days, 10(4.5 ± 1.5) (mean ± standard deviation [SD]) BF-1 CFU/g was detected in fecal samples by using strain-specific selective agar; in contrast, 10(6.2 ± 0.4) viable BF-1 cells/g were detected by using PMA-qPCR, and a total of 10(7.6 ± 0.7) BF-1 cells/g were detected by using qPCR without PMA. Thus, the number of viable BF-1 cells detected by PMA-qPCR was about 50 times higher (P < 0.01) than that detected by the culture-dependent method. We conclude that strain-specific PMA-qPCR can be used to quickly and accurately evaluate viable BF-1 in feces.
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O'Connor M, Gregory ST. Inactivation of the RluD pseudouridine synthase has minimal effects on growth and ribosome function in wild-type Escherichia coli and Salmonella enterica. J Bacteriol 2011; 193:154-62. [PMID: 21037010 PMCID: PMC3019933 DOI: 10.1128/jb.00970-10] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Accepted: 10/18/2010] [Indexed: 11/20/2022] Open
Abstract
The Escherichia coli rluD gene encodes a pseudouridine synthase responsible for the pseudouridine (Ψ) modifications at positions 1911, 1915, and 1917 in helix 69 of 23S rRNA. It has been reported that deletion of rluD in K-12 strains of E. coli is associated with extremely slow growth, increased readthrough of stop codons, and defects in 50S ribosomal subunit assembly and 30S-50S subunit association. Suppressor mutations in the prfB and prfC genes encoding release factor 2 (RF2) and RF3 that restore the wild type-growth rate and also correct the ribosomal defects have now been isolated. These suppressors link helix 69 Ψ residues with the termination phase of protein synthesis. However, further genetic analysis reported here also reveals that the slow growth and other defects associated with inactivation of rluD in E. coli K-12 strains are due to a defective RF2 protein, with a threonine at position 246, which is present in all K-12 strains. This is in contrast to the more typical alanine found at this position in most bacterial RF2s, including those of other E. coli strains. Inactivation of rluD in E. coli strains containing the prfB allele from E. coli B or in Salmonella enterica, both carrying an RF2 with Ala246, has negligible effects on growth, termination, or ribosome function. The results indicate that, in contrast to those in wild bacteria, termination functions in E. coli K-12 strains carrying a partially defective RF2 protein are especially susceptible to perturbation of ribosome-RF interactions, such as that caused by loss of h69 Ψ modifications.
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Affiliation(s)
- Michael O'Connor
- School of Biological Sciences, University of Missouri-Kansas City, 5007 Rockhill Rd, Kansas City, Missouri 64110, USA.
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