1
|
Hu YY, Lo IH, Hsiao JT, Sheu F. Real-time PCR-based quantitative microbiome profiling elucidates the microbial dynamic succession in backslopping fermentation of Taiwanese pickled cabbage. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024. [PMID: 38925544 DOI: 10.1002/jsfa.13688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 06/09/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024]
Abstract
BACKGROUND Microbiota succession determines the flavor and quality of fermented foods. Quantitative PCR-based quantitative microbiome profiling (QMP) has been applied broadly for microbial analysis from absolute abundance perspectives, transforming microbiota ratios into counts by normalizing 16S ribosomal RNA (16S rRNA) gene sequencing data with gene copies quantified by quantitative PCR. However, the application of QMP in fermented foods is still limited. RESULTS QMP elucidated microbial succession of Taiwanese pickled cabbage. In the spontaneous first-round fermentation (FR), the 16S rRNA gene copies of total bacteria increased from 6.1 to 10 log copies mL-1. The dominant lactic acid bacteria genera were successively Lactococcus, Leuconostoc and Lactiplantibacillus. Despite the decrease in the proportion of Lactococcus during the succession, the absolute abundance of Lactococcus still increased. In the backslopping second-round fermentation (SR), the total bacteria 16S rRNA gene copies increased from 7.6 to 9.9 log copies mL-1. The addition of backslopping starter and vinegar rapidly led to a homogenous microbial community dominated by Lactiplantibacillus. The proportion of Lactiplantibacillus remained consistently around 90% during SR, whereas its absolute abundance exhibited a continuous increase. In SR without vinegar, Leuconostoc consistently dominated the fermentation. CONCLUSION The present study highlights that compositional analysis would misinterpret microbial dynamics, whereas QMP reflected the real succession profiles and unveiled the essential role of vinegar in promoting Lactiplantibacillus dominance in backslopping fermentation of Taiwanese pickled cabbage. Quantitative microbiome profiling (QMP) was found to be a more promising approach for the detailed observation of microbiome succession in food fermentation compared to compositional analysis. © 2024 Society of Chemical Industry.
Collapse
Affiliation(s)
- You-Yun Hu
- Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei, Taiwan
| | - I-Hsuan Lo
- Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei, Taiwan
| | - Jhih-Ting Hsiao
- Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei, Taiwan
| | - Fuu Sheu
- Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei, Taiwan
- Center for Biotechnology, National Taiwan University, Taipei, Taiwan
| |
Collapse
|
2
|
Marole TA, Sibanda T, Buys EM. Assessing probiotic viability in mixed species yogurt using a novel propidium monoazide (PMAxx)-quantitative PCR method. Front Microbiol 2024; 15:1325268. [PMID: 38389538 PMCID: PMC10882272 DOI: 10.3389/fmicb.2024.1325268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/29/2024] [Indexed: 02/24/2024] Open
Abstract
Viability is a prerequisite for any therapeutic benefits associated with the ingestion of probiotic bacteria. Current culture-based techniques are inadequate for the enumeration of probiotics in mixed-species food products. This study utilized a quantitative PCR (qPCR) method coupled with propidium monoazide (PMAxx), and novel species-specific tuf gene primers to selectively enumerate Lacticaseibacillus rhamnosus, Bifidobacterium spp., and yogurt starter cultures in mixed-species probiotic yogurt. The method was optimized for PMAxx concentration and specificity and evaluated for efficiency and applicability. PMAxx-qPCR showed high specificity to the target organisms in mixed-species yogurt, quantifying only viable cells. The linear dynamic ranges were established over five to seven orders of magnitude. The assay was reliable with an efficiency of 91-99%, R2 values > 0.99, and a good correlation to the plate count method (r = 0.882). The results of this study demonstrate the high selectivity, improved lead time, and reliability of PMAxx-qPCR over the culture-dependent method, making it a valuable tool for inline viability verification during processing and improving probiotic quality assurance for processors and consumers.
Collapse
Affiliation(s)
- Tlaleo A Marole
- Department of Consumer and Food Sciences, University of Pretoria, Pretoria, South Africa
| | - Thulani Sibanda
- Department of Consumer and Food Sciences, University of Pretoria, Pretoria, South Africa
| | - Elna M Buys
- Department of Consumer and Food Sciences, University of Pretoria, Pretoria, South Africa
| |
Collapse
|
3
|
Gao Y, Wu M. Accounting for 16S rRNA copy number prediction uncertainty and its implications in bacterial diversity analyses. ISME COMMUNICATIONS 2023; 3:59. [PMID: 37301942 PMCID: PMC10257666 DOI: 10.1038/s43705-023-00266-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 05/10/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023]
Abstract
16S rRNA gene copy number (16S GCN) varies among bacterial species and this variation introduces potential biases to microbial diversity analyses using 16S rRNA read counts. To correct the biases, methods have been developed to predict 16S GCN. A recent study suggests that the prediction uncertainty can be so great that copy number correction is not justified in practice. Here we develop RasperGade16S, a novel method and software to better model and capture the inherent uncertainty in 16S GCN prediction. RasperGade16S implements a maximum likelihood framework of pulsed evolution model and explicitly accounts for intraspecific GCN variation and heterogeneous GCN evolution rates among species. Using cross-validation, we show that our method provides robust confidence estimates for the GCN predictions and outperforms other methods in both precision and recall. We have predicted GCN for 592605 OTUs in the SILVA database and tested 113842 bacterial communities that represent an exhaustive and diverse list of engineered and natural environments. We found that the prediction uncertainty is small enough for 99% of the communities that 16S GCN correction should improve their compositional and functional profiles estimated using 16S rRNA reads. On the other hand, we found that GCN variation has limited impacts on beta-diversity analyses such as PCoA, NMDS, PERMANOVA and random-forest test.
Collapse
Affiliation(s)
- Yingnan Gao
- Department of Biology, University of Virginia, 485 McCormick Road, Charlottesville, VA, 22904, USA
| | - Martin Wu
- Department of Biology, University of Virginia, 485 McCormick Road, Charlottesville, VA, 22904, USA.
| |
Collapse
|
4
|
Molecular Detection and Identification of Plant-Associated Lactiplantibacillus plantarum. Int J Mol Sci 2023; 24:ijms24054853. [PMID: 36902287 PMCID: PMC10003612 DOI: 10.3390/ijms24054853] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/27/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
Lactiplantibacillus plantarum is a lactic acid bacterium often isolated from a wide variety of niches. Its ubiquity can be explained by a large, flexible genome that helps it adapt to different habitats. The consequence of this is great strain diversity, which may make their identification difficult. Accordingly, this review provides an overview of molecular techniques, both culture-dependent, and culture-independent, currently used to detect and identify L. plantarum. Some of the techniques described can also be applied to the analysis of other lactic acid bacteria.
Collapse
|
5
|
Kong J, Fan C, Liao X, Chen A, Yang S, Zhao L, Li H. Accurate detection of Escherichia coli O157:H7 and Salmonella enterica serovar typhimurium based on the combination of next-generation sequencing and droplet digital PCR. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113913] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
6
|
Shi Z, Li X, Fan X, Xu J, Liu Q, Wu Z, Pan D. PMA-qPCR method for the selective quantitation of viable lactic acid bacteria in fermented milk. Front Microbiol 2022; 13:984506. [PMID: 36160254 PMCID: PMC9491339 DOI: 10.3389/fmicb.2022.984506] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 08/15/2022] [Indexed: 11/13/2022] Open
Abstract
The number of viable lactic acid bacteria (LAB) is a key indicator of the quality of fermented milk. Currently, the combination of propidium monoazide (PMA) and qPCR has been applied in the quantification of viable bacteria in various matrices. In this research, the PMA-qPCR method was used to detect the number of viable bacteria of each LAB species in fermented milk. By analyzing pheS gene and 16S rRNA gene sequence similarities in five species of LAB, namely Lactobacillus delbrueckii subsp. bulgaricus, Lactiplantibacillus plantarum, Streptococcus thermophilus, Lactobacillus helveticus, and Lactococcus lactis subsp. lactis, the pheS gene resolved species identities better and was thus selected to design specific primers and probes. The pheS gene was cloned into the pUC19 vector and used to construct a standard curve for absolute quantification. Standard curves for quantification were constructed for each LAB species for serial dilutions between 1011 and 106 CFU/mL, with R2 > 0.99. The number of viable bacteria in the fermented milk detected by PMA-qPCR was significantly lower than that of qPCR (P < 0.05), indicating that PMA inhibited the amplification of DNA from dead cells. This was corroborated by the results from bacterial staining and plate count experiments. The proposed PMA-qPCR method provided rapid qualitative and quantitative determination of the number of viable bacteria for each LAB species in fermented milk within 3 h.
Collapse
Affiliation(s)
- Zihang Shi
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, China
- Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, China
| | - Xiefei Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, China
- Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, China
| | - Xiankang Fan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, China
- Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, China
| | - Jue Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, China
- Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, China
| | - Qing Liu
- Nanjing Dairy Group, Nanjing, China
| | - Zhen Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, China
- Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, China
- *Correspondence: Zhen Wu,
| | - Daodong Pan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, China
- Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, China
- Daodong Pan,
| |
Collapse
|
7
|
Ji X, Li H, Zhang J, Saiyin H, Zheng Z. The collaborative effect of Chlorella vulgaris-Bacillus licheniformis consortia on the treatment of municipal water. JOURNAL OF HAZARDOUS MATERIALS 2019; 365:483-493. [PMID: 30458425 DOI: 10.1016/j.jhazmat.2018.11.039] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Revised: 10/28/2018] [Accepted: 11/10/2018] [Indexed: 06/09/2023]
Abstract
In this study, the effects of nutrient and dissolved organic matter removal, stress resistance (DNA methylation), and the algae-bacteria dynamic ratio of algal-bacterial consortia in actual municipal wastewater were investigated. Results indicate that the presence of a Chlorella vulgaris-Bacillus licheniformis consortium had profound effects. The removal rates of total nitrogen, ammonium, orthophosphate phosphorus and chemical oxygen demand were 88.82%, 84.98%, 84.87% and 82.25%, respectively. Protein-like substances, which are difficult to degrade in the natural water environment, were significantly degraded in actual municipal wastewater. Furthermore, the microbial diversity was measured. The algal-bacterial consortium did not disrupt the microbial in-situ diversity of the actual municipal wastewater under suitable conditions. The global nuclear DNA methylation level peaked at 7.80%. These results help to understand the effects of algal-bacterial consortia on nutrient and pollutant removal and adaptability in actual municipal wastewater.
Collapse
Affiliation(s)
- Xiyan Ji
- Department of Environmental Science and Engineering, Fudan University, Shanghai, 200433, PR China
| | - Huimin Li
- Department of Environmental Science and Engineering, Fudan University, Shanghai, 200433, PR China
| | - Jibiao Zhang
- Department of Environmental Science and Engineering, Fudan University, Shanghai, 200433, PR China.
| | - Hexige Saiyin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200433, PR China
| | - Zheng Zheng
- Department of Environmental Science and Engineering, Fudan University, Shanghai, 200433, PR China.
| |
Collapse
|
8
|
Srisukchayakul P, Charalampopoulos D, Karatzas KA. Study on the effect of citric acid adaptation toward the subsequent survival of Lactobacillus plantarum NCIMB 8826 in low pH fruit juices during refrigerated storage. Food Res Int 2018; 111:198-204. [PMID: 30007676 DOI: 10.1016/j.foodres.2018.05.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Revised: 05/05/2018] [Accepted: 05/08/2018] [Indexed: 01/16/2023]
Abstract
Pre-treatment of stationary phase cells of Lactobacillus plantarum NCMIB 8826 with citric acid (pH 3 to 6) for a short period of time significantly improved subsequent cell survival in several highly acidic fruit juices namely cranberry (pH 2.7), pomegranate (pH 3.5), and lemon & lime juices (pH 2.8). Although the mechanism for this adaptation is still unclear, the analysis of the cellular fatty acid content of acid adapted cells and the reverse transcription polymerase chain reaction (RT-PCR) showed a significant increase (by ~1.7 fold) of the cellular cyclopropane fatty acid, cis-11,12-methylene octadecanoic acid (C19:0cyclow7c) and a significant upregulation (~12 fold) of cyclopropane synthase (cfa) were observed, respectively, during acid adaptation. It is likely that these changes led to a decrease in membrane fluidity and to lower membrane permeability, which prevents the cells from proton influx during storage in these low pH fruit juices.
Collapse
Affiliation(s)
- Pornpoj Srisukchayakul
- Department of Food and Nutritional Sciences, University of Reading, PO Box 226, Whiteknights, Reading RG6 6AP, United Kingdom
| | - Dimitris Charalampopoulos
- Department of Food and Nutritional Sciences, University of Reading, PO Box 226, Whiteknights, Reading RG6 6AP, United Kingdom
| | - Kimon Andreas Karatzas
- Department of Food and Nutritional Sciences, University of Reading, PO Box 226, Whiteknights, Reading RG6 6AP, United Kingdom; CINN (Centre for Integrative Neuroscience and Neurodynamics), University of Reading, Whiteknights, Reading RG6 6BE, United Kingdom.
| |
Collapse
|
9
|
Yin X, Lee B, Zaragoza J, Marco ML. Dietary perturbations alter the ecological significance of ingested Lactobacillus plantarum in the digestive tract. Sci Rep 2017; 7:7267. [PMID: 28779118 PMCID: PMC5544775 DOI: 10.1038/s41598-017-07428-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 06/23/2017] [Indexed: 12/18/2022] Open
Abstract
Host diet is a major determinant of the composition and function of the intestinal microbiome. Less understood is the importance of diet on ingested strains with probiotic significance. We investigated the population dynamics of exogenous Lactobacillus plantarum and its interactions with intestinal bacteria in mice undergoing switches between high-fat, high-sugar (HFHSD) and low-fat, plant-polysaccharide rich (LFPPD) diets. The survival and persistence of ingested L. plantarum WCFS1 was significantly improved during mouse consumption of HFHSD and was negatively associated with the numbers of indigenous Lactobacillus species. Diet also rapidly changed the composition of the indigenous microbiota, but with some taxa differentially affected between HFHSD periods. L. plantarum was not integrated into indigenous bacterial community networks according to co-occurrence patterns but still conferred distinct effects on bacterial species diversity and microbiota stability largely in a diet-dependent manner. Metagenome predictions supported the premise that L. plantarum dampens the effects of diet on the microbiome. This strain also consistently altered the predicted genetic content in the distal gut by enriching for genes encoding glyosyltransferases and bile salt hydrolases. Our findings demonstrate the interactions between ingested, transient probiotic bacteria and intestinal bacterial communities and how they can differ depending on host diet.
Collapse
Affiliation(s)
- Xiaochen Yin
- Department of Food Science and Technology, University of California, Davis, USA.,Department of Plant Pathology, Univeristy of California, Davis, CA, USA
| | - Bokyung Lee
- Department of Food Science and Technology, University of California, Davis, USA.,Center for Comparative Medicine, Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Jose Zaragoza
- Department of Food Science and Technology, University of California, Davis, USA.,Bayer Crop Science, West Sacramento, CA, USA
| | - Maria L Marco
- Department of Food Science and Technology, University of California, Davis, USA.
| |
Collapse
|
10
|
Gaertig C, Niemann K, Berthold J, Giel L, Leitschuh N, Boehm C, Roussak L, Vetter K, Kuhlmeier D. Development of a point-of-care-device for fast detection of periodontal pathogens. BMC Oral Health 2015; 15:165. [PMID: 26702613 PMCID: PMC4690268 DOI: 10.1186/s12903-015-0155-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 12/17/2015] [Indexed: 11/24/2022] Open
Abstract
Background A number of pathogens can cause severe destruction of the periodontal apparatus during the course of periodontitis. The aim of this work was the development of a diagnostic device for the use at the point-of-need for the detection of periodontal pathogens to enable a personalized therapy for treatment of periodontitis. Methods This test system is based on the polymerase chain reaction of DNA isolated from periodontal pathogens and was examined to precisely detect species-specific sequences on a rotating chip with lyophilized reagents for polymerase chain reaction. The preservation of the reagents was optimized to ensure their stability during the storage. Results In the current work, we have developed a model point-of-care device and showed a proof of concept. It requires low sample volume, is timesaving and can therefore facilitate early diagnosis and treatment of periodontal diseases. Conclusions The developed device can provide fast diagnosis of the composition and amount of patients’ oral flora and might help to assess the stage of periodontitis infection. This can facilitate an optimization of therapeutic approaches in order to prevent some of the more serious consequences of the disease. Electronic supplementary material The online version of this article (doi:10.1186/s12903-015-0155-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Cornelia Gaertig
- Nanotechnology Unit, Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, 04103, Leipzig, Germany. .,Friedrich Schiller University, Jena, Germany.
| | - Katja Niemann
- Nanotechnology Unit, Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, 04103, Leipzig, Germany
| | - Jana Berthold
- Nanotechnology Unit, Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, 04103, Leipzig, Germany
| | - Lisa Giel
- Nanotechnology Unit, Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, 04103, Leipzig, Germany
| | - Nadine Leitschuh
- Nanotechnology Unit, Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, 04103, Leipzig, Germany
| | - Christoph Boehm
- Nanotechnology Unit, Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, 04103, Leipzig, Germany
| | - Liudmila Roussak
- Nanotechnology Unit, Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, 04103, Leipzig, Germany
| | | | - Dirk Kuhlmeier
- Nanotechnology Unit, Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, 04103, Leipzig, Germany
| |
Collapse
|
11
|
Dollive S, Chen YY, Grunberg S, Bittinger K, Hoffmann C, Vandivier L, Cuff C, Lewis JD, Wu GD, Bushman FD. Fungi of the murine gut: episodic variation and proliferation during antibiotic treatment. PLoS One 2013; 8:e71806. [PMID: 23977147 PMCID: PMC3747063 DOI: 10.1371/journal.pone.0071806] [Citation(s) in RCA: 166] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 07/03/2013] [Indexed: 01/01/2023] Open
Abstract
Antibiotic use in humans has been associated with outgrowth of fungi. Here we used a murine model to investigate the gut microbiome over 76 days of treatment with vancomycin, ampicillin, neomycin, and metronidazole and subsequent recovery. Mouse stool was studied as a surrogate for the microbiota of the lower gastrointestinal tract. The abundance of fungi and bacteria was measured using quantitative PCR, and the proportional composition of the communities quantified using 454/Roche pyrosequencing of rRNA gene tags. Prior to treatment, bacteria outnumbered fungi by >3 orders of magnitude. Upon antibiotic treatment, bacteria dropped in abundance >3 orders of magnitude, so that the predominant 16S sequences detected became transients derived from food. Upon cessation of treatment, bacterial communities mostly returned to their previous numbers and types after 8 weeks, though communities remained detectably different from untreated controls. Fungal communities varied substantially over time, even in the untreated controls. Separate cages within the same treatment group showed radical differences, but mice within a cage generally behaved similarly. Fungi increased ∼40-fold in abundance upon antibiotic treatment but declined back to their original abundance after cessation of treatment. At the last time point, Candida remained more abundant than prior to treatment. These data show that 1) gut fungal populations change radically during normal mouse husbandry, 2) fungi grow out in the gut upon suppression of bacterial communities with antibiotics, and 3) perturbations due to antibiotics persist long term in both the fungal and bacterial microbiota.
Collapse
Affiliation(s)
- Serena Dollive
- University of Pennsylvania School of Medicine, Department of Microbiology, Philadelphia, Pennsylvania, United States of America
| | - Ying-Yu Chen
- University of Pennsylvania School of Medicine, Department of Microbiology, Philadelphia, Pennsylvania, United States of America
| | - Stephanie Grunberg
- University of Pennsylvania School of Medicine, Department of Microbiology, Philadelphia, Pennsylvania, United States of America
| | - Kyle Bittinger
- University of Pennsylvania School of Medicine, Department of Microbiology, Philadelphia, Pennsylvania, United States of America
| | - Christian Hoffmann
- University of Pennsylvania School of Medicine, Department of Microbiology, Philadelphia, Pennsylvania, United States of America
| | - Lee Vandivier
- University of Pennsylvania School of Medicine, Department of Microbiology, Philadelphia, Pennsylvania, United States of America
| | - Christopher Cuff
- University of Pennsylvania School of Medicine, Department of Microbiology, Philadelphia, Pennsylvania, United States of America
| | - James D. Lewis
- University of Pennsylvania School of Medicine, Department of Microbiology, Philadelphia, Pennsylvania, United States of America
| | - Gary D. Wu
- University of Pennsylvania School of Medicine, Department of Microbiology, Philadelphia, Pennsylvania, United States of America
- * E-mail: (FDB); (GDW)
| | - Frederic D. Bushman
- University of Pennsylvania School of Medicine, Department of Microbiology, Philadelphia, Pennsylvania, United States of America
- * E-mail: (FDB); (GDW)
| |
Collapse
|
12
|
Větrovský T, Baldrian P. The variability of the 16S rRNA gene in bacterial genomes and its consequences for bacterial community analyses. PLoS One 2013; 8:e57923. [PMID: 23460914 PMCID: PMC3583900 DOI: 10.1371/journal.pone.0057923] [Citation(s) in RCA: 642] [Impact Index Per Article: 58.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Accepted: 01/28/2013] [Indexed: 11/19/2022] Open
Abstract
16S ribosomal RNA currently represents the most important target of study in bacterial ecology. Its use for the description of bacterial diversity is, however, limited by the presence of variable copy numbers in bacterial genomes and sequence variation within closely related taxa or within a genome. Here we use the information from sequenced bacterial genomes to explore the variability of 16S rRNA sequences and copy numbers at various taxonomic levels and apply it to estimate bacterial genome and DNA abundances. In total, 7,081 16S rRNA sequences were in silico extracted from 1,690 available bacterial genomes (1-15 per genome). While there are several phyla containing low 16S rRNA copy numbers, in certain taxa, e.g., the Firmicutes and Gammaproteobacteria, the variation is large. Genome sizes are more conserved at all tested taxonomic levels than 16S rRNA copy numbers. Only a minority of bacterial genomes harbors identical 16S rRNA gene copies, and sequence diversity increases with increasing copy numbers. While certain taxa harbor dissimilar 16S rRNA genes, others contain sequences common to multiple species. Sequence identity clusters (often termed operational taxonomic units) thus provide an imperfect representation of bacterial taxa of a certain phylogenetic rank. We have demonstrated that the information on 16S rRNA copy numbers and genome sizes of genome-sequenced bacteria may be used as an estimate for the closest related taxon in an environmental dataset to calculate alternative estimates of the relative abundance of individual bacterial taxa in environmental samples. Using an example from forest soil, this procedure would increase the abundance estimates of Acidobacteria and decrease these of Firmicutes. Using the currently available information, alternative estimates of bacterial community composition may be obtained in this way if the variation of 16S rRNA copy numbers among bacteria is considered.
Collapse
Affiliation(s)
- Tomáš Větrovský
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Academy of Sciences of the Czech Republic, Praha, Czech Republic
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Academy of Sciences of the Czech Republic, Praha, Czech Republic
- * E-mail:
| |
Collapse
|
13
|
Chen YT, Peng HL, Shia WC, Hsu FR, Ken CF, Tsao YM, Chen CH, Liu CE, Hsieh MF, Chen HC, Tang CY, Ku TH. Whole-genome sequencing and identification of Morganella morganii KT pathogenicity-related genes. BMC Genomics 2012; 13 Suppl 7:S4. [PMID: 23282187 PMCID: PMC3521468 DOI: 10.1186/1471-2164-13-s7-s4] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The opportunistic enterobacterium, Morganella morganii, which can cause bacteraemia, is the ninth most prevalent cause of clinical infections in patients at Changhua Christian Hospital, Taiwan. The KT strain of M. morganii was isolated during postoperative care of a cancer patient with a gallbladder stone who developed sepsis caused by bacteraemia. M. morganii is sometimes encountered in nosocomial settings and has been causally linked to catheter-associated bacteriuria, complex infections of the urinary and/or hepatobiliary tracts, wound infection, and septicaemia. M. morganii infection is associated with a high mortality rate, although most patients respond well to appropriate antibiotic therapy. To obtain insights into the genome biology of M. morganii and the mechanisms underlying its pathogenicity, we used Illumina technology to sequence the genome of the KT strain and compared its sequence with the genome sequences of related bacteria. RESULTS The 3,826,919-bp sequence contained in 58 contigs has a GC content of 51.15% and includes 3,565 protein-coding sequences, 72 tRNA genes, and 10 rRNA genes. The pathogenicity-related genes encode determinants of drug resistance, fimbrial adhesins, an IgA protease, haemolysins, ureases, and insecticidal and apoptotic toxins as well as proteins found in flagellae, the iron acquisition system, a type-3 secretion system (T3SS), and several two-component systems. Comparison with 14 genome sequences from other members of Enterobacteriaceae revealed different degrees of similarity to several systems found in M. morganii. The most striking similarities were found in the IS4 family of transposases, insecticidal toxins, T3SS components, and proteins required for ethanolamine use (eut operon) and cobalamin (vitamin B12) biosynthesis. The eut operon and the gene cluster for cobalamin biosynthesis are not present in the other Proteeae genomes analysed. Moreover, organisation of the 19 genes of the eut operon differs from that found in the other non-Proteeae enterobacterial genomes. CONCLUSIONS This is the first genome sequence of M. morganii, which is a clinically relevant pathogen. Comparative genome analysis revealed several pathogenicity-related genes and novel genes not found in the genomes of other members of Proteeae. Thus, the genome sequence of M. morganii provides important information concerning virulence and determinants of fitness in this pathogen.
Collapse
Affiliation(s)
- Yu-Tin Chen
- Department of Computer Science, National Tsing Hua University, 101, Section 2, Kuang-Fu Rd., Hsinchu, Taiwan
| | - Hwei-Ling Peng
- Department of Biological Science and Technology, National Chiao Tung University, 1001, University Road, Hsinchu, Taiwan
| | - Wei-Chung Shia
- Cancer Research Center, Changhua Christian Hospital, 135, Nanhsiao St., Changhua, Taiwan
| | - Fang-Rong Hsu
- Master's Program in Biomedical Informatics and Biomedical Engineering, Feng Chia University, 100 Wenhwa Rd., Taichung, Taiwan
- Department of Information Engineering and Computer Sciences, Feng Chia University, 100 Wenhwa Rd., Taichung, Taiwan
| | - Chuian-Fu Ken
- Institute of Biotechnology, National Changhua University of Education, 2 Shi-Da Rd., Changhua, Taiwan
| | - Yu-Ming Tsao
- Department of Anesthesiology, Changhua Christian Hospital, 135, Nanhsiao St., Changhua, Taiwan
| | - Chang-Hua Chen
- The Division of Infectious Diseases, Department of Internal Medicine, Changhua Christian Hospital, 135, Nanhsiao St., Changhua, Taiwan
| | - Chun-Eng Liu
- The Division of Infectious Diseases, Department of Internal Medicine, Changhua Christian Hospital, 135, Nanhsiao St., Changhua, Taiwan
| | - Ming-Feng Hsieh
- Department of Computer Science, National Tsing Hua University, 101, Section 2, Kuang-Fu Rd., Hsinchu, Taiwan
| | - Huang-Chi Chen
- Division of Critical Care Medicine, Department of Internal Medicine, Changhua Christian Hospital, 135, Nanhsiao St., Changhua, Taiwan
| | - Chuan-Yi Tang
- Department of Computer Science, National Tsing Hua University, 101, Section 2, Kuang-Fu Rd., Hsinchu, Taiwan
- Department of Computer Science, Providence University, 200, Chung-Chi Rd., Taichung, Taiwan
| | - Tien-Hsiung Ku
- Department of Anesthesiology, Changhua Christian Hospital, 135, Nanhsiao St., Changhua, Taiwan
| |
Collapse
|
14
|
Lee CM, Sieo CC, Cheah YK, Abdullah N, Ho YW. Discrimination of probiotic Lactobacillus strains for poultry by repetitive sequenced-based PCR fingerprinting. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2012; 92:660-666. [PMID: 21919004 DOI: 10.1002/jsfa.4627] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2011] [Revised: 04/30/2011] [Accepted: 07/14/2011] [Indexed: 05/31/2023]
Abstract
BACKGROUND Four repetitive element sequence-based polymerase chain reaction (rep-PCR) methods, namely repetitive extragenic palindromic PCR (REP-PCR), enterobacterial repetitive intergenic consensus PCR (ERIC-PCR), polytrinucleotide (GTG)₅ -PCR and BOX-PCR, were evaluated for the molecular differentiation of 12 probiotic Lactobacillus strains previously isolated from the gastrointestinal tract of chickens and used as a multistrain probiotic. This study represents the first analysis of the comparative efficacy of these four rep-PCR methods and their combination (composite rep-PCR) in the molecular typing of Lactobacillus strains based on a discriminatory index (D). RESULTS Species-specific and strain-specific profiles were observed from rep-PCR. From the numerical analysis of composite rep-PCR, BOX-PCR, (GTG)₅ -PCR, REP-PCR and ERIC-PCR, D values of 0.9118, 0.9044, 0.8897, 0.8750 and 0.8529 respectively were obtained. Composite rep-PCR analysis was the most discriminative method, with eight Lactobacillus strains, namely L. brevis ATCC 14869(T) , L. reuteri C 10, L. reuteri ATCC 23272(T) , L. gallinarum ATCC 33199(T) , L. salivarius ATCC 11741(T) , L. salivarius I 24, L. panis JCM 11053(T) and L. panis C 17, being differentiated at the strain level. CONCLUSION Composite rep-PCR analysis is potentially a useful fingerprinting method to discriminate probiotic Lactobacillus strains isolated from the gastrointestinal tract of chickens.
Collapse
Affiliation(s)
- Chin Mei Lee
- Laboratory of Industrial Biotechnology, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | | | | | | | | |
Collapse
|
15
|
Kang YJ, Cheng J, Mei LJ, Hu J, Piao Z, Yin SX. Multiple copies of 16S rRNA gene affect the restriction patterns and DGGE profile revealed by analysis of genome database. Microbiology (Reading) 2010. [DOI: 10.1134/s0026261710050103] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|
16
|
Inhibition of fungi and gram-negative bacteria by bacteriocin BacTN635 produced by Lactobacillus plantarum sp. TN635. Appl Biochem Biotechnol 2009; 162:1132-46. [PMID: 19888697 DOI: 10.1007/s12010-009-8821-7] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Accepted: 10/11/2009] [Indexed: 10/20/2022]
Abstract
The aim of this study was to evaluate 54 lactic acid bacteria (LAB) strains isolated from meat, fermented vegetables and dairy products for their capacity to produce antimicrobial activities against several bacteria and fungi. The strain designed TN635 has been selected for advanced studies. The supernatant culture of this strain inhibits the growth of all tested pathogenic including the four Gram-negative bacteria (Salmonella enterica ATCC43972, Pseudomonas aeruginosa ATCC 49189, Hafnia sp. and Serratia sp.) and the pathogenic fungus Candida tropicalis R2 CIP203. Based on the nucleotide sequence of the 16S rRNA gene of the strain TN635 (1,540 pb accession no FN252881) and the phylogenetic analysis, we propose the assignment of our new isolate bacterium as Lactobacillus plantarum sp. TN635 strain. Its antimicrobial compound was determined as a proteinaceous substance, stable to heat and to treatment with surfactants and organic solvents. Highest antimicrobial activity was found between pH 3 and 11 with an optimum at pH = 7. The BacTN635 was purified to homogeneity by a four-step protocol involving ammonium sulfate precipitation, centrifugal microconcentrators with a 10-kDa membrane cutoff, gel filtration Sephadex G-25, and C18 reverse-phase HPLC. SDS-PAGE analysis of the purified BacTN635, revealed a single band with an estimated molecular mass of approximately 4 kDa. The maximum bacteriocin production (5,000 AU/ml) was recorded after a 16-h incubation in Man, Rogosa, and Sharpe (MRS) medium at 30 degrees C. The mode of action of the partial purified BacTN635 was identified as bactericidal against Listeria ivanovii BUG 496 and as fungistatic against C. tropicalis R2 CIP203.
Collapse
|