1
|
Characterization of Lactic Acid Bacteria Isolated from Spontaneously Fermented Sausages: Bioprotective, Technological and Functional Properties. Foods 2023; 12:foods12040727. [PMID: 36832801 PMCID: PMC9955731 DOI: 10.3390/foods12040727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 01/24/2023] [Accepted: 01/31/2023] [Indexed: 02/10/2023] Open
Abstract
Fermentation is one of the most ancient strategies to improve safety and extend shelf-life of the products. Starter cultures are mainly represented by lactic acid bacteria (LAB), which may also be bioprotective agents controlling the fermentation process, the native microbiota and pathogen outgrowth. This work aimed to select new LAB strains from spontaneously fermented sausages produced in different areas of Italy, which can be effective as starter cultures and bioprotective agents in fermented salami. The strains, mainly belonging to the Latilactobacillus sakei species, were characterized for their ability to inhibit major meat pathogens, the presence of antibiotic resistances and amine production. Moreover, technological performances, such as growth and acidification kinetics at increasing NaCl concentrations, were studied. As a result, new autochthonous Lat. sakei strains were obtained, lacking antibiotic resistance, possessing antimicrobial activity against Clostridium sporogenes, Listeria monocytogenes, Salmonella and Escherichia coli and with high growth performance under osmotic pressure. These strains have the potential for future application to improve the safety of fermented meats, even under conditions in which chemical preservatives are reduced or eliminated. Moreover, studies on autochthonous cultures are pivotal for guaranteeing specific characteristics of traditional products that represent an important cultural heritage.
Collapse
|
2
|
Yu L, Chen Y, Duan H, Qiao N, Wang G, Zhao J, Zhai Q, Tian F, Chen W. Latilactobacillus sakei: a candidate probiotic with a key role in food fermentations and health promotion. Crit Rev Food Sci Nutr 2022; 64:978-995. [PMID: 35997270 DOI: 10.1080/10408398.2022.2111402] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Latilactobacillus sakei is used extensively in industrial production and food fermentations. The species is primarily derived from fermented meat and vegetable products and is also found in human feces. Genomics and metabolomics have revealed unique metabolic pathways in L. sakei and molecular mechanisms underlying its competitive advantages in different habitats, which are mostly attributed to its flexible carbohydrate metabolism, cold tolerance, acid and salt tolerance, ability to cope with oxygen changes, and heme uptake. In recent years, probiotic effects of L. sakei and its metabolites have been identified, including the ability to effectively alleviate metabolic syndrome, inflammatory bowel disease, and atopic dermatitis. This review summarizes the genomic and metabolic characteristics of L. sakei and its metabolites and describes their applications, laying a foundation for their expanded use across the food and healthcare industries.
Collapse
Affiliation(s)
- Leilei Yu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi, Jiangsu, China
| | - Ying Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Hui Duan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu, China
| | - Nanzhen Qiao
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Gang Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi, Jiangsu, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu, China
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi, Jiangsu, China
| | - Fengwei Tian
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi, Jiangsu, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi, Jiangsu, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu, China
| |
Collapse
|
3
|
Ferrocino I, Rantsiou K, Cocolin L. Microbiome and -omics application in food industry. Int J Food Microbiol 2022; 377:109781. [DOI: 10.1016/j.ijfoodmicro.2022.109781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 05/31/2022] [Accepted: 06/03/2022] [Indexed: 11/30/2022]
|
4
|
Integrated Phenotypic-Genotypic Analysis of Latilactobacillus sakei from Different Niches. Foods 2021; 10:foods10081717. [PMID: 34441495 PMCID: PMC8393274 DOI: 10.3390/foods10081717] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 11/16/2022] Open
Abstract
Increasing attention has been paid to the potential probiotic effects of Latilactobacillus sakei. To explore the genetic diversity of L. sakei, 14 strains isolated from different niches (feces, fermented kimchi, and meat products) and 54 published strains were compared and analyzed. The results showed that the average genome size and GC content of L. sakei were 1.98 Mb and 41.22%, respectively. Its core genome mainly encodes translation and transcription, amino acid synthesis, glucose metabolism, and defense functions. L. sakei has open pan-genomic characteristics, and its pan-gene curve shows an upward trend. The genetic diversity of L. sakei is mainly reflected in carbohydrate utilization, antibiotic tolerance, and immune/competition-related factors, such as clustering regular interval short palindromic repeat sequence (CRISPR)-Cas. The CRISPR system is mainly IIA type, and a few are IIC types. This work provides a basis for the study of this species.
Collapse
|
5
|
Assessment of the spoilage microbiota in minced free-range chicken meat during storage at 4 C in retail modified atmosphere packages. Food Microbiol 2021; 99:103822. [PMID: 34119107 DOI: 10.1016/j.fm.2021.103822] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 03/18/2021] [Accepted: 04/23/2021] [Indexed: 11/21/2022]
Abstract
This study assessed the evolution of spoilage microbiota in association with the changes in pH and concentrations of lactic and acetic acids in retail oxygen-free modified atmosphere (30:70 CO2/N2) packages (MAP) of minced free-range chicken meat during storage at 4 °C for 10 days. MAP retarded growth of spoilage lactic acid bacteria (LAB) below 6.5 log cfu/g and fully suppressed growth of pseudomonads, enterobacteria, enterococci, staphylococci and yeasts. Two distinct Latilactobacillus sakei strain biotypes were predominant and Leuconostoc carnosum, Carnobacterium divergens, Latilactobacillus fuchuensis and Weissella koreensis were subdominant at spoilage. The chicken meat pH ranged from 5.8 to 6.1. l-lactate (832 mg/100 g on day-0) decreased slightly on day-7. d-lactate remained constantly below 20 mg/100 g, whereas acetate (0-59 mg/100 g) increased 5-fold on day-7. All MAP samples developed off-odors on day-7 and a strong 'blown-pack' sulfur-type of spoilage on day-10. However, neither the predominant Lb. sakei nor other LAB or gram-negative isolates formed H2S in vitro, except for C. divergens.
Collapse
|
6
|
Schuster JA, Vogel RF, Ehrmann MA. Biodiversity of Lactobacillus helveticus isolates from dairy and cereal fermentations reveals habitat-adapted biotypes. FEMS Microbiol Lett 2021; 367:5817842. [PMID: 32267927 DOI: 10.1093/femsle/fnaa058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 03/30/2020] [Indexed: 12/31/2022] Open
Abstract
For the present study, we collected 22 Lactobacillus helveticus strains from different dairy (n = 10) and cereal (n = 12) fermentations to investigate their biodiversity and to uncover habitat-specific traits. Biodiversity was assessed by comparison of genetic fingerprints, low-molecular-weight subproteomes, metabolic and enzymatic activities, growth characteristics and acidification kinetics in food matrices. A clear distinction between the dairy and cereal strains was observed in almost all examined features suggesting that the different habitats are domiciled by different L. helveticus biotypes that are adapted to the specific environmental conditions. Analysis of the low-molecular-weight subproteome divided the cereal isolates into two clusters, while the dairy isolates formed a separate homogeneous cluster. Differences regarding carbohydrate utilization were observed for lactose, galactose, sucrose and cellobiose as well as for plant-derived glucosides. Enzymatic differences were observed mainly for ß-galactosidase and ß-glucosidase activities. Further, growth temperature was optimal in the range from 33 to 37°C for the cereal strains, whereas the dairy strains showed optimal growth at 40°C. Taken together, adaptation of the various biotypes results in a growth benefit in the particular environment. Acidification and growth tests using either sterile skim milk or a wheat flour extract confirmed these results. Differentiation of these biotypes and their physiological characteristics enables knowledge-based starter culture development for cereal versus dairy products within one species.
Collapse
Affiliation(s)
- Julian A Schuster
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Gregor-Mendel-Straße 4, 85354 Freising, Germany
| | - Rudi F Vogel
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Gregor-Mendel-Straße 4, 85354 Freising, Germany
| | - Matthias A Ehrmann
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Gregor-Mendel-Straße 4, 85354 Freising, Germany
| |
Collapse
|
7
|
Samelis J, Kakouri A. Growth Inhibitory and Selective Pressure Effects of Sodium Diacetate on the Spoilage Microbiota of Frankfurters Stored at 4 °C and 12 °C in Vacuum. Foods 2021; 10:E74. [PMID: 33401509 PMCID: PMC7824339 DOI: 10.3390/foods10010074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/21/2020] [Accepted: 12/25/2020] [Indexed: 01/01/2023] Open
Abstract
This study evaluated microbial growth in commercial frankfurters formulated with 1.8% sodium lactate (SL) singly or combined with 0.25% sodium diacetate (SDA), vacuum-packaged (VP) and stored at 4 °C and 12 °C. Standard frankfurters without SDA, containing 0.15% SL, served as controls (CN). Lactic acid bacteria (LAB) were the exclusive spoilers in all treatments at both storage temperatures. However, compared to the CN and SL treatments, SL + SDA delayed growth of LAB by an average of 5.1 and 3.1 log units, and 3.0 and 2.0 log units, respectively, after 30 and 60 days at 4 °C. On day 90, the SL + SDA frankfurters were unspoiled whereas the SL and CN frankfurters had spoiled on day 60 and day 30 to 60, respectively. At 12 °C, LAB growth was similar in all treatments after day 15, but strong defects developed in the CN and SL frankfurters only. Differential spoilage patterns were associated with a major reversal of the LAB biota from gas- and slime-producing Leuconostoc mesenteroides and Leuconostoc carnosum in the CN and SL frankfurters to Lactobacillus sakei/curvatus in the SL + SDA frankfurters. Thus, SL + SDA extends the retail shelf life of VP frankfurters by delaying total LAB growth and selecting for lactobacilli with a milder cured meat spoilage potential than leuconostocs, particularly under refrigeration.
Collapse
Affiliation(s)
- John Samelis
- Hellenic Agricultural Organization ‘DIMITRA’, Dairy Research Department, 45221 Katsikas, Ioannina, Greece;
| | | |
Collapse
|
8
|
Huang CH, Chen CC, Chiu SH, Liou JS, Lin YC, Lin JS, Huang L, Watanabe K. Development of a High-Resolution Single-Nucleotide Polymorphism Strain-Typing Assay Using Whole Genome-Based Analyses for the Lactobacillus acidophilus Probiotic Strain. Microorganisms 2020; 8:E1445. [PMID: 32967209 PMCID: PMC7564606 DOI: 10.3390/microorganisms8091445] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/02/2020] [Accepted: 09/16/2020] [Indexed: 11/24/2022] Open
Abstract
Lactobacillus acidophilus is one of the most commonly used industrial products worldwide. Since its probiotic efficacy is strain-specific, the identification of probiotics at both the species and strain levels is necessary. However, neither phenotypic nor conventional genotypic methods have enabled the effective differentiation of L. acidophilus strains. In this study, a whole-genome sequence-based analysis was carried out to establish high-resolution strain typing of 41 L. acidophilus strains (including commercial isolates and reference strains) using the cano-wgMLST_BacCompare analytics platform; consequently, a strain-specific discrimination method for the probiotic strain LA1063 was developed. Using a core-genome multilocus sequence-typing (cgMLST) scheme based on 1390 highly conserved genes, 41 strains could be assigned to 34 sequence types. Subsequently, we screened a set of 92 loci with a discriminatory power equal to that of the 1390 loci cgMLST scheme. A strain-specific polymerase chain reaction combined with a multiplex minisequencing method was developed based on four (phoU, secY, tilS, and uvrA_1) out of 21 loci, which could be discriminated between LA1063 and other L. acidophilus strains using the cgMLST data. We confirmed that the strain-specific single-nucleotide polymorphisms method could be used to quickly and accurately identify the L. acidophilus probiotic strain LA1063 in commercial products.
Collapse
Affiliation(s)
- Chien-Hsun Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan; (C.-H.H.); (S.-H.C.); (J.-S.L.); (L.H.)
| | - Chih-Chieh Chen
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 80424, Taiwan;
- Rapid Screening Research Center for Toxicology and Biomedicine, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - Shih-Hau Chiu
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan; (C.-H.H.); (S.-H.C.); (J.-S.L.); (L.H.)
| | - Jong-Shian Liou
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan; (C.-H.H.); (S.-H.C.); (J.-S.L.); (L.H.)
| | - Yu-Chun Lin
- Livestock Research Institute, Council of Agriculture, Executive Yuan, Tainan 71246, Taiwan;
| | - Jin-Seng Lin
- Culture Collection & Research Institute, Synbio Tech Inc., Kaohsiung 82151, Taiwan;
| | - Lina Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan; (C.-H.H.); (S.-H.C.); (J.-S.L.); (L.H.)
| | - Koichi Watanabe
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan; (C.-H.H.); (S.-H.C.); (J.-S.L.); (L.H.)
- Culture Collection & Research Institute, Synbio Tech Inc., Kaohsiung 82151, Taiwan;
- Department of Animal Science and Technology, College of Bioresources and Agriculture, National Taiwan University, No. 50, Ln. 155, Sec. 3, Keelung Rd., Taipei 10673, Taiwan
| |
Collapse
|
9
|
Metabolism of Lactobacillus sakei Chr82 in the Presence of Different Amounts of Fermentable Sugars. Foods 2020; 9:foods9060720. [PMID: 32498333 PMCID: PMC7353496 DOI: 10.3390/foods9060720] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 04/30/2020] [Accepted: 05/27/2020] [Indexed: 12/15/2022] Open
Abstract
Lactobacillus sakei is widely used as a starter culture in fermented sausages since it is well adapted to meat environments and able to maintain high viability thanks to secondary pathways activated when hexoses are depleted (i.e., metabolism of pentoses and amino acids). In this study, a commercial strain of L. sakei was inoculated in a defined medium with ribose or glucose as the carbon source, at optimal or reduced concentrations, to evaluate its different physiological and metabolic responses in relation to different growth conditions. The results obtained with different approaches (HPLC, 1H-NMR, flow cytometry) evidenced different growth performances, amino acid consumptions and physiological states of cells in relation to the carbon source as an active response to harsh conditions. As expected, higher concentrations of sugars induced higher growth performances and the accumulation of organic acids. The low sugars amount induced the presence of dead cells, while injured cells increased with ribose. Arginine was the main amino acid depleted, especially in the presence of higher ribose, and resulted in the production of ornithine. Moreover, the 1H-NMR analysis evidenced a higher consumption of serine at the optimal sugars concentration (pyruvate production). This information can be helpful to optimize the use of these species in the industrial production of fermented sausages.
Collapse
|
10
|
Zheng J, Wittouck S, Salvetti E, Franz CMAP, Harris HMB, Mattarelli P, O'Toole PW, Pot B, Vandamme P, Walter J, Watanabe K, Wuyts S, Felis GE, Gänzle MG, Lebeer S. A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae. Int J Syst Evol Microbiol 2020; 70:2782-2858. [PMID: 32293557 DOI: 10.1099/ijsem.0.004107] [Citation(s) in RCA: 1498] [Impact Index Per Article: 374.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The genus Lactobacillus comprises 261 species (at March 2020) that are extremely diverse at phenotypic, ecological and genotypic levels. This study evaluated the taxonomy of Lactobacillaceae and Leuconostocaceae on the basis of whole genome sequences. Parameters that were evaluated included core genome phylogeny, (conserved) pairwise average amino acid identity, clade-specific signature genes, physiological criteria and the ecology of the organisms. Based on this polyphasic approach, we propose reclassification of the genus Lactobacillus into 25 genera including the emended genus Lactobacillus, which includes host-adapted organisms that have been referred to as the Lactobacillus delbrueckii group, Paralactobacillus and 23 novel genera for which the names Holzapfelia, Amylolactobacillus, Bombilactobacillus, Companilactobacillus, Lapidilactobacillus, Agrilactobacillus, Schleiferilactobacillus, Loigolactobacilus, Lacticaseibacillus, Latilactobacillus, Dellaglioa, Liquorilactobacillus, Ligilactobacillus, Lactiplantibacillus, Furfurilactobacillus, Paucilactobacillus, Limosilactobacillus, Fructilactobacillus, Acetilactobacillus, Apilactobacillus, Levilactobacillus, Secundilactobacillus and Lentilactobacillus are proposed. We also propose to emend the description of the family Lactobacillaceae to include all genera that were previously included in families Lactobacillaceae and Leuconostocaceae. The generic term 'lactobacilli' will remain useful to designate all organisms that were classified as Lactobacillaceae until 2020. This reclassification reflects the phylogenetic position of the micro-organisms, and groups lactobacilli into robust clades with shared ecological and metabolic properties, as exemplified for the emended genus Lactobacillus encompassing species adapted to vertebrates (such as Lactobacillus delbrueckii, Lactobacillus iners, Lactobacillus crispatus, Lactobacillus jensensii, Lactobacillus johnsonii and Lactobacillus acidophilus) or invertebrates (such as Lactobacillus apis and Lactobacillus bombicola).
Collapse
Affiliation(s)
- Jinshui Zheng
- Huazhong Agricultural University, State Key Laboratory of Agricultural Microbiology, Hubei Key Laboratory of Agricultural Bioinformatics, Wuhan, Hubei, PR China
| | - Stijn Wittouck
- Research Group Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Elisa Salvetti
- Dept. of Biotechnology, University of Verona, Verona, Italy
| | - Charles M A P Franz
- Max Rubner-Institut, Department of Microbiology and Biotechnology, Kiel, Germany
| | - Hugh M B Harris
- School of Microbiology & APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
| | - Paola Mattarelli
- University of Bologna, Dept. of Agricultural and Food Sciences, Bologna, Italy
| | - Paul W O'Toole
- School of Microbiology & APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
| | - Bruno Pot
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Vrije Universiteit Brussel, Brussels, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Jens Walter
- Department of Biological Sciences, University of Alberta, Edmonton, Canada.,Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, Canada
| | - Koichi Watanabe
- Food Industry Research and Development Institute, Bioresource Collection and Research Center, Hsinchu, Taiwan, ROC.,National Taiwan University, Dept. of Animal Science and Technology, Taipei, Taiwan, ROC
| | - Sander Wuyts
- Research Group Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | | | - Michael G Gänzle
- Hubei University of Technology, College of Bioengineering and Food Science, Wuhan, Hubei, PR China.,Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, Canada
| | - Sarah Lebeer
- Research Group Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| |
Collapse
|
11
|
Genomic and metabolic features of Lactobacillus sakei as revealed by its pan-genome and the metatranscriptome of kimchi fermentation. Food Microbiol 2019; 86:103341. [PMID: 31703875 DOI: 10.1016/j.fm.2019.103341] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 09/08/2019] [Accepted: 09/20/2019] [Indexed: 12/20/2022]
Abstract
The genomic and metabolic features of Lactobacillus sakei were investigated using its pan-genome and by analyzing the metatranscriptome of kimchi fermentation. In the genome-based relatedness analysis, the strains were divided into the Lb. sakei ssp. sakei and Lb. sakei ssp. carnosus lineage groups. Genomic and metabolic pathway analysis revealed that all Lb. sakei strains have the capability of producing d/l-lactate, ethanol, acetate, CO2, formate, l-malate, diacetyl, acetoin, and 2,3-butanediol from d-glucose, d-fructose, d-galactose, sucrose, d-lactose, l-arabinose, cellobiose, d-mannose, d-gluconate, and d-ribose through homolactic and heterolactic fermentation, whereas their capability of d-maltose, d-xylose, l-xylulose, d-galacturonate, and d-glucuronate metabolism is strain-specific. All strains carry genes for the biosynthesis of folate and thiamine, whereas genes for biogenic amine and toxin production, hemolysis, and antibiotic resistance were not identified. The metatranscriptomic analysis showed that the expression of Lb. sakei transcripts involved in carbohydrate metabolism increased as kimchi fermentation progressed, suggesting that Lb. sakei is more competitive during late fermentation stage. Homolactic fermentation pathway was highly expressed and generally constant during kimchi fermentation, whereas expression of heterolactic fermentation pathway increased gradually as fermentation progressed. l-Lactate dehydrogenase was more highly expressed than d-lactate dehydrogenase, suggesting that l-lactate is the major lactate metabolized by Lb. sakei.
Collapse
|
12
|
Steensels J, Gallone B, Voordeckers K, Verstrepen KJ. Domestication of Industrial Microbes. Curr Biol 2019; 29:R381-R393. [DOI: 10.1016/j.cub.2019.04.025] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
13
|
Comparative genomics of Lactobacillus sakei supports the development of starter strain combinations. Microbiol Res 2019; 221:1-9. [DOI: 10.1016/j.micres.2019.01.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/07/2019] [Accepted: 01/10/2019] [Indexed: 11/19/2022]
|
14
|
Douillard FP, de Vos WM. Biotechnology of health-promoting bacteria. Biotechnol Adv 2019; 37:107369. [PMID: 30876799 DOI: 10.1016/j.biotechadv.2019.03.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 02/15/2019] [Accepted: 03/11/2019] [Indexed: 12/20/2022]
Abstract
Over the last decade, there has been an increasing scientific and public interest in bacteria that may positively contribute to human gut health and well-being. This interest is reflected by the ever-increasing number of developed functional food products containing health-promoting bacteria and reaching the market place as well as by the growing revenue and profits of notably bacterial supplements worldwide. Traditionally, the origin of probiotic-marketed bacteria was limited to a rather small number of bacterial species that mostly belong to lactic acid bacteria and bifidobacteria. Intensifying research efforts on the human gut microbiome offered novel insights into the role of human gut microbiota in health and disease, while also providing a deep and increasingly comprehensive understanding of the bacterial communities present in this complex ecosystem and their interactions with the gut-liver-brain axis. This resulted in rational and systematic approaches to select novel health-promoting bacteria or to engineer existing bacteria with enhanced probiotic properties. In parallel, the field of gut microbiomics developed into a fertile framework for the identification, isolation and characterization of a phylogenetically diverse array of health-promoting bacterial species, also called next-generation therapeutic bacteria. The present review will address these developments with specific attention for the selection and improvement of a selected number of health-promoting bacterial species and strains that are extensively studied or hold promise for future food or pharma product development.
Collapse
Affiliation(s)
- François P Douillard
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Willem M de Vos
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands.
| |
Collapse
|
15
|
Schuster JA, Vogel RF, Ehrmann MA. Characterization and distribution of CRISPR–Cas systems in Lactobacillus sakei. Arch Microbiol 2019; 201:337-347. [DOI: 10.1007/s00203-019-01619-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 01/04/2019] [Accepted: 01/08/2019] [Indexed: 01/01/2023]
|
16
|
Janßen D, Eisenbach L, Ehrmann MA, Vogel RF. Assertiveness of Lactobacillus sakei and Lactobacillus curvatus in a fermented sausage model. Int J Food Microbiol 2018; 285:188-197. [DOI: 10.1016/j.ijfoodmicro.2018.04.030] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 04/11/2018] [Accepted: 04/16/2018] [Indexed: 11/15/2022]
|
17
|
Terán LC, Coeuret G, Raya R, Zagorec M, Champomier-Vergès MC, Chaillou S. Phylogenomic Analysis of Lactobacillus curvatus Reveals Two Lineages Distinguished by Genes for Fermenting Plant-Derived Carbohydrates. Genome Biol Evol 2018; 10:1516-1525. [PMID: 29850855 PMCID: PMC6007345 DOI: 10.1093/gbe/evy106] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2018] [Indexed: 12/20/2022] Open
Abstract
Lactobacillus curvatus is a lactic acid bacterium encountered in many different types of fermented food (meat, seafood, vegetables, and cereals). Although this species plays an important role in the preservation of these foods, few attempts have been made to assess its genomic diversity. This study uses comparative analyses of 13 published genomes (complete or draft) to better understand the evolutionary processes acting on the genome of this species. Phylogenomic analysis, based on a coalescent model of evolution, revealed that the 6,742 sites of single nucleotide polymorphism within the L. curvatus core genome delineate two major groups, with lineage 1 represented by the newly sequenced strain FLEC03, and lineage 2 represented by the type-strain DSM20019. The two lineages could also be distinguished by the content of their accessory genome, which sheds light on a long-term evolutionary process of lineage-dependent genetic acquisition and the possibility of population structure. Interestingly, one clade from lineage 2 shared more accessory genes with strains of lineage 1 than with other strains of lineage 2, indicating recent convergence in carbohydrate catabolism. Both lineages had a wide repertoire of accessory genes involved in the fermentation of plant-derived carbohydrates that are released from polymers of α/β-glucans, α/β-fructans, and N-acetylglucosan. Other gene clusters were distributed among strains according to the type of food from which the strains were isolated. These results give new insight into the ecological niches in which L. curvatus may naturally thrive (such as silage or compost heaps) in addition to fermented food.
Collapse
Affiliation(s)
- Lucrecia C Terán
- CERELA-CONICET, Centro de Referencia para Lactobacilos, San Miguel de Tucumán, Argentina
| | - Gwendoline Coeuret
- MICALIS Institute, INRA, AgroParisTech, Université Paris-Saclay, Domaine de Vilvert, Jouy-en-Josas, France
| | - Raúl Raya
- CERELA-CONICET, Centro de Referencia para Lactobacilos, San Miguel de Tucumán, Argentina
| | - Monique Zagorec
- SECALIM, INRA, Oniris, Université Bretagne Loire, Nantes, France
| | | | - Stéphane Chaillou
- MICALIS Institute, INRA, AgroParisTech, Université Paris-Saclay, Domaine de Vilvert, Jouy-en-Josas, France
| |
Collapse
|
18
|
Poirier S, Rué O, Peguilhan R, Coeuret G, Zagorec M, Champomier-Vergès MC, Loux V, Chaillou S. Deciphering intra-species bacterial diversity of meat and seafood spoilage microbiota using gyrB amplicon sequencing: A comparative analysis with 16S rDNA V3-V4 amplicon sequencing. PLoS One 2018; 13:e0204629. [PMID: 30252901 PMCID: PMC6155546 DOI: 10.1371/journal.pone.0204629] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 09/11/2018] [Indexed: 12/21/2022] Open
Abstract
Meat and seafood spoilage ecosystems harbor extensive bacterial genomic diversity that is mainly found within a small number of species but within a large number of strains with different spoilage metabolic potential. To decipher the intraspecies diversity of such microbiota, traditional metagenetic analysis using the 16S rRNA gene is inadequate. We therefore assessed the potential benefit of an alternative genetic marker, gyrB, which encodes the subunit B of DNA gyrase, a type II DNA topoisomerase. A comparison between 16S rDNA-based (V3-V4) amplicon sequencing and gyrB-based amplicon sequencing was carried out in five types of meat and seafood products, with five mock communities serving as quality controls. Our results revealed that bacterial richness in these mock communities and food samples was estimated with higher accuracy using gyrB than using16S rDNA. However, for Firmicutes species, 35% of putative gyrB reads were actually identified as sequences of a gyrB paralog, parE, which encodes subunit B of topoisomerase IV; we therefore constructed a reference database of published sequences of both gyrB and pare for use in all subsequent analyses. Despite this co-amplification, the deviation between relative sequencing quantification and absolute qPCR quantification was comparable to that observed for 16S rDNA for all the tested species. This confirms that gyrB can be used successfully alongside 16S rDNA to determine the species composition (richness and evenness) of food microbiota. The major benefit of gyrB sequencing is its potential for improving taxonomic assignment and for further investigating OTU richness at the subspecies level, thus allowing more accurate discrimination of samples. Indeed, 80% of the reads of the 16S rDNA dataset were represented by thirteen 16S rDNA-based OTUs that could not be assigned at the species-level. Instead, these same clades corresponded to 44 gyrB-based OTUs, which differentiated various lineages down to the subspecies level. The increased ability of gyrB-based analyses to track and trace phylogenetically different groups of strains will generate improved resolution and more reliable results for studies of the strains implicated in food processes.
Collapse
Affiliation(s)
- Simon Poirier
- MICALIS, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Olivier Rué
- MaIAGE, INRA, Université Paris-Saclay, Jouy-en-Josas, France
| | - Raphaëlle Peguilhan
- MICALIS, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Gwendoline Coeuret
- MICALIS, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | | | | | - Valentin Loux
- MaIAGE, INRA, Université Paris-Saclay, Jouy-en-Josas, France
| | - Stéphane Chaillou
- MICALIS, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| |
Collapse
|
19
|
Montanari C, Barbieri F, Magnani M, Grazia L, Gardini F, Tabanelli G. Phenotypic Diversity of Lactobacillus sakei Strains. Front Microbiol 2018; 9:2003. [PMID: 30210476 PMCID: PMC6121134 DOI: 10.3389/fmicb.2018.02003] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Accepted: 08/08/2018] [Indexed: 11/13/2022] Open
Abstract
Lactobacillus sakei is a lactic acid bacteria (LAB) species highly adapted to the meat environment. For this reason, selected strains are often used as starter culture in the production of fermented sausages, especially in Mediterranean countries. It often represents the dominant species in these products and can maintain its viability during all the ripening period, which can take also some months. This ability is guaranteed by the possibility of the species to obtain energy through pathways active even when hexoses are depleted. This species is characterized by a relevant genetic and phenotypic diversity and its metabolism can be further affected by the growth condition applied. In this work we investigate the metabolic responses of six different L. sakei in a synthetic medium (DM) containing defined amounts of amino acids in relation to temperature and NaCl concentration. In addition, the activities of cells pre-grown in presence of glucose o ribose were tested. Arginine was efficiently up-taken with the exception of the type strain DSMZ 20017t. Other amino acids (i.e., serine, asparagine, cysteine, and methionine) were metabolized through potentially energetic pathways which start from pyruvate accumulation, as demonstrated by the organic acid accumulation trend in the condition tested, especially in DM without sugar added. The presence of excesses of pyruvate deriving from amino acids lead to the accumulation of diacetyl and acetoin by all the strains when sugars were added. This approach allowed a deeper insight into the phenotypic variability of the species and improved the comprehension of the metabolic pathways adopted by L. sakei to survive and grow in restrictive conditions such as those found in fermented sausages during fermentations. Thus, the results obtained are useful information for improving and optimizing the use of such strains as starter culture for these products.
Collapse
Affiliation(s)
- Chiara Montanari
- Interdepartmental Center for Industrial Agri-Food Research, University of Bologna, Cesena, Italy
| | - Federica Barbieri
- Interdepartmental Center for Industrial Agri-Food Research, University of Bologna, Cesena, Italy
| | - Michael Magnani
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Luigi Grazia
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Fausto Gardini
- Interdepartmental Center for Industrial Agri-Food Research, University of Bologna, Cesena, Italy.,Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Giulia Tabanelli
- Interdepartmental Center for Industrial Agri-Food Research, University of Bologna, Cesena, Italy
| |
Collapse
|
20
|
Diversity and evolution of Lactobacillus casei group isolated from fermented dairy products in Tibet. Arch Microbiol 2018; 200:1111-1121. [DOI: 10.1007/s00203-018-1528-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 11/30/2017] [Accepted: 05/18/2018] [Indexed: 12/16/2022]
|
21
|
Complete and Draft Genome Sequences of Nine Lactobacillus sakei Strains Selected from the Three Known Phylogenetic Lineages and Their Main Clonal Complexes. GENOME ANNOUNCEMENTS 2018; 6:6/16/e00082-18. [PMID: 29674528 PMCID: PMC5908949 DOI: 10.1128/genomea.00082-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We present here the complete and draft genome sequences of nine Lactobacillus sakei strains, selected from the entire range of clonal complexes from the three known lineages of the species. The strains were chosen to provide a wide view of pangenomic and plasmidic diversity for this important foodborne species.
Collapse
|
22
|
Genetic diversity analysis of Leuconostoc mesenteroides from Korean vegetables and food products by multilocus sequence typing. Appl Microbiol Biotechnol 2018; 102:4853-4861. [PMID: 29619504 DOI: 10.1007/s00253-018-8942-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 03/07/2018] [Accepted: 03/14/2018] [Indexed: 10/17/2022]
Abstract
In the present study, 35 Leuconostoc mesenteroides strains isolated from vegetables and food products from South Korea were studied by multilocus sequence typing (MLST) of seven housekeeping genes (atpA, groEL, gyrB, pheS, pyrG, rpoA, and uvrC). The fragment sizes of the seven amplified housekeeping genes ranged in length from 366 to 1414 bp. Sequence analysis indicated 27 different sequence types (STs) with 25 of them being represented by a single strain indicating high genetic diversity, whereas the remaining 2 were characterized by five strains each. In total, 220 polymorphic nucleotide sites were detected among seven housekeeping genes. The phylogenetic analysis based on the STs of the seven loci indicated that the 35 strains belonged to two major groups, A (28 strains) and B (7 strains). Split decomposition analysis showed that intraspecies recombination played a role in generating diversity among strains. The minimum spanning tree showed that the evolution of the STs was not correlated with food source. This study signifies that the multilocus sequence typing is a valuable tool to access the genetic diversity among L. mesenteroides strains from South Korea and can be used further to monitor the evolutionary changes.
Collapse
|
23
|
Ojha KS, Burgess CM, Duffy G, Kerry JP, Tiwari BK. Integrated phenotypic-genotypic approach to understand the influence of ultrasound on metabolic response of Lactobacillus sakei. PLoS One 2018; 13:e0191053. [PMID: 29370210 PMCID: PMC5784923 DOI: 10.1371/journal.pone.0191053] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 12/27/2017] [Indexed: 11/18/2022] Open
Abstract
The lethal effects of soundwaves on a range of microorganisms have been known for almost a century whereas, the use of ultrasound to promote or control their activity is much more recent. Moreover, the fundamental molecular mechanism influencing the behaviour of microorganisms subjected to ultrasonic waves is not well established. In this study, we investigated the influence of ultrasonic frequencies of 20, 45, 130 and 950 kHz on growth kinetics of Lactobacillus sakei. A significant increase in the growth rate of L. sakei was observed following ultrasound treatment at 20 kHz despite the treatment yielding a significant reduction of ca. 3 log cfu/mL in cells count. Scanning electron microscopy showed that ultrasound caused significant changes on the cell surface of L. sakei culture with the formation of pores "sonoporation". Phenotypic microarrays showed that all ultrasound treated L. sakei after exposure to various carbon, nitrogen, phosphorus and sulphur sources had significant variations in nutrient utilisation. Integration of this phenotypic data with the genome of L. sakei revealed that various metabolic pathways were being influenced by the ultrasound treatments. Results presented in this study showed that the physiological response of L. sakei in response to US is frequency dependent and that it can influence metabolic pathways. Hence, ultrasound treatments can be employed to modulate microbial activity for specialised applications.
Collapse
Affiliation(s)
- K Shikha Ojha
- Food Chemistry and Technology, Teagasc Food Research Centre, Dublin, Ireland
| | | | | | - Joseph P Kerry
- Food Packaging Group, University College Cork, Cork, Ireland
| | - Brijesh K Tiwari
- Food Chemistry and Technology, Teagasc Food Research Centre, Dublin, Ireland
| |
Collapse
|
24
|
Molecular discrimination of Lactobacillus brevis strains isolated from food products in South Korea using multilocus sequence typing. Lebensm Wiss Technol 2017. [DOI: 10.1016/j.lwt.2017.08.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
25
|
Papizadeh M, Rohani M, Nahrevanian H, Javadi A, Pourshafie MR. Probiotic characters of Bifidobacterium and Lactobacillus are a result of the ongoing gene acquisition and genome minimization evolutionary trends. Microb Pathog 2017; 111:118-131. [DOI: 10.1016/j.micpath.2017.08.021] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 08/12/2017] [Accepted: 08/16/2017] [Indexed: 02/07/2023]
|
26
|
Zagorec M, Champomier-Vergès MC. Lactobacillus sakei: A Starter for Sausage Fermentation, a Protective Culture for Meat Products. Microorganisms 2017; 5:microorganisms5030056. [PMID: 28878171 PMCID: PMC5620647 DOI: 10.3390/microorganisms5030056] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 08/29/2017] [Accepted: 09/05/2017] [Indexed: 12/28/2022] Open
Abstract
Among lactic acid bacteria of meat products, Lactobacillus sakei is certainly the most studied species due to its role in the fermentation of sausage and its prevalence during cold storage of raw meat products. Consequently, the physiology of this bacterium regarding functions involved in growth, survival, and metabolism during meat storage and processing are well known. This species exhibits a wide genomic diversity that can be observed when studying different strains and on which probably rely its multiple facets in meat products: starter, spoiler, or protective culture. The emerging exploration of the microbial ecology of meat products also revealed the multiplicity of bacterial interactions L. sakei has to face and their various consequences on microbial quality and safety at the end of storage.
Collapse
|
27
|
Bottari B, Felis GE, Salvetti E, Castioni A, Campedelli I, Torriani S, Bernini V, Gatti M. Effective identification of Lactobacillus casei group species: genome-based selection of the gene mutL as the target of a novel multiplex PCR assay. MICROBIOLOGY-SGM 2017; 163:950-960. [PMID: 28721852 DOI: 10.1099/mic.0.000497] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Lactobacillus casei,Lactobacillus paracasei and Lactobacillusrhamnosus form a closely related taxonomic group (the L. casei group) within the facultatively heterofermentative lactobacilli. Strains of these species have been used for a long time as probiotics in a wide range of products, and they represent the dominant species of nonstarter lactic acid bacteria in ripened cheeses, where they contribute to flavour development. The close genetic relationship among those species, as well as the similarity of biochemical properties of the strains, hinders the development of an adequate selective method to identify these bacteria. Despite this being a hot topic, as demonstrated by the large amount of literature about it, the results of different proposed identification methods are often ambiguous and unsatisfactory. The aim of this study was to develop a more robust species-specific identification assay for differentiating the species of the L. casei group. A taxonomy-driven comparative genomic analysis was carried out to select the potential target genes whose similarity could better reflect genome-wide diversity. The gene mutL appeared to be the most promising one and, therefore, a novel species-specific multiplex PCR assay was developed to rapidly and effectively distinguish L. casei, L. paracasei and L. rhamnosus strains. The analysis of a collection of 76 wild dairy isolates, previously identified as members of the L. casei group combining the results of multiple approaches, revealed that the novel designed primers, especially in combination with already existing ones, were able to improve the discrimination power at the species level and reveal previously undiscovered intraspecific biodiversity.
Collapse
Affiliation(s)
- Benedetta Bottari
- Department of Food and Drug Science, University of Parma, Viale delle Scienze 49/A, 43124 Parma, Italy.,Multidisciplinary Interdepartmental Dairy Center - MILC, University of Parma, Parma, Italy
| | - Giovanna E Felis
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Elisa Salvetti
- School of Microbiology and APC Microbiome Institute, University College Cork, Western Road, Cork, Ireland
| | - Anna Castioni
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy.,Present address: Panificio Zorzi S.r.l., Loc. Brà 1, 37020 Brentino Belluno, Verona, Italy
| | - Ilenia Campedelli
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Sandra Torriani
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Valentina Bernini
- Department of Food and Drug Science, University of Parma, Viale delle Scienze 49/A, 43124 Parma, Italy
| | - Monica Gatti
- Department of Food and Drug Science, University of Parma, Viale delle Scienze 49/A, 43124 Parma, Italy.,Multidisciplinary Interdepartmental Dairy Center - MILC, University of Parma, Parma, Italy
| |
Collapse
|
28
|
Duar RM, Lin XB, Zheng J, Martino ME, Grenier T, Pérez-Muñoz ME, Leulier F, Gänzle M, Walter J. Lifestyles in transition: evolution and natural history of the genus Lactobacillus. FEMS Microbiol Rev 2017; 41:S27-S48. [DOI: 10.1093/femsre/fux030] [Citation(s) in RCA: 255] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 06/06/2017] [Indexed: 02/07/2023] Open
|
29
|
Sulaiman IM, Jacobs E, Simpson S, Kerdahi K. Multilocus Genetic Characterization of Lactobacillus fermentum Isolated from Ready-to-Eat Canned Food. J Food Prot 2017; 80:963-968. [PMID: 28467184 DOI: 10.4315/0362-028x.jfp-16-546] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The primary mission of the U.S. Food and Drug Administration is to enforce the Food, Drug, and Cosmetic Act and regulate food, drug, and cosmetic products. Thus, this agency monitors the presence of pathogenic microorganisms in these products, including canned foods, as one of the regulatory action criteria and also ensures that these products are safe for human consumption. This study was carried out to investigate the effectiveness of pathogen control and integrity of ready-to-eat canned food containing Black Bean Corn Poblano Salsa. A total of nine unopened and recalled canned glass jars from the same lot were examined initially by conventional microbiologic protocols that involved a two-step enrichment, followed by streaking on selective agar plates, for the presence of gram-positive and gram-negative bacteria. Of the eight subsamples examined for each sample, all subsamples of one of the containers were found positive for the presence of slow-growing rod-shaped, gram-positive, facultative anaerobic bacteria. The recovered isolates were subsequently sequenced at rRNA and gyrB loci. Afterward, multilocus sequence typing (MLST) was performed characterizing 11 additional known MLST loci (clpX, dnaA, dnaK, groEL, murC, murE, pepX, pyrG, recA, rpoB, and uvrC). Analyses of the nucleotide sequences of rRNA, gyrB, and 11 MLST loci confirmed these gram-positive bacteria recovered from canned food to be Lactobacillus fermentum . Thus, the DNA sequencing of housekeeping MLST genes can provide species identification of L. fermentum and can be used in the canned food monitoring program of public health importance.
Collapse
Affiliation(s)
- Irshad M Sulaiman
- Southeast Regional Laboratory, U.S. Food and Drug Administration, 60 Eighth Street N.E., Atlanta, Georgia 30309, USA
| | - Emily Jacobs
- Southeast Regional Laboratory, U.S. Food and Drug Administration, 60 Eighth Street N.E., Atlanta, Georgia 30309, USA
| | - Steven Simpson
- Southeast Regional Laboratory, U.S. Food and Drug Administration, 60 Eighth Street N.E., Atlanta, Georgia 30309, USA
| | - Khalil Kerdahi
- Southeast Regional Laboratory, U.S. Food and Drug Administration, 60 Eighth Street N.E., Atlanta, Georgia 30309, USA
| |
Collapse
|
30
|
Talagrand-Reboul E, Roger F, Kimper JL, Colston SM, Graf J, Latif-Eugenín F, Figueras MJ, Petit F, Marchandin H, Jumas-Bilak E, Lamy B. Delineation of Taxonomic Species within Complex of Species: Aeromonas media and Related Species as a Test Case. Front Microbiol 2017; 8:621. [PMID: 28458658 PMCID: PMC5394120 DOI: 10.3389/fmicb.2017.00621] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Accepted: 03/27/2017] [Indexed: 11/13/2022] Open
Abstract
Aeromonas media is an opportunistic pathogen for human and animals mainly found in aquatic habitats and which has been noted for significant genomic and phenotypic heterogeneities. We aimed to better understand the population structure and diversity of strains currently affiliated to A. media and the related species A. rivipollensis. Forty-one strains were included in a population study integrating, multilocus genetics, phylogenetics, comparative genomics, as well as phenotypics, lifestyle, and evolutionary features. Sixteen gene-based multilocus phylogeny delineated three clades. Clades corresponded to different genomic groups or genomospecies defined by phylogenomic metrics ANI (average nucleotide identity) and isDDH (in silico DNA-DNA hybridization) on 14 whole genome sequences. DL-lactate utilization, cefoxitin susceptibility, nucleotide signatures, ribosomal multi-operon diversity, and differences in relative effect of recombination and mutation (i.e., in evolution mode) distinguished the two species Aeromonas media and Aeromonas rivipollensis. The description of these two species was emended accordingly. The genome metrics and comparative genomics suggested that a third clade is a distinct genomospecies. Beside the species delineation, genetic and genomic data analysis provided a more comprehensive knowledge of the cladogenesis determinants at the root and inside A. media species complex among aeromonads. Particular lifestyles and phenotypes as well as major differences in evolution modes may represent putative factors associated with lineage emergence and speciation within the A. media complex. Finally, the integrative and populational approach presented in this study is considered broadly in order to conciliate the delineation of taxonomic species and the population structure in bacterial genera organized in species complexes.
Collapse
Affiliation(s)
- Emilie Talagrand-Reboul
- Équipe Pathogènes Hydriques Santé Environnements, UMR 5569 HSM, Université de MontpellierMontpellier, France.,Département d'Hygiène Hospitalière, CHRU de MontpellierMontpellier, France
| | - Frédéric Roger
- Équipe Pathogènes Hydriques Santé Environnements, UMR 5569 HSM, Université de MontpellierMontpellier, France
| | - Jean-Luc Kimper
- Équipe Pathogènes Hydriques Santé Environnements, UMR 5569 HSM, Université de MontpellierMontpellier, France
| | - Sophie M Colston
- Department of Molecular and Cell Biology, University of ConnecticutStorrs, CT, USA
| | - Joerg Graf
- Department of Molecular and Cell Biology, University of ConnecticutStorrs, CT, USA
| | - Fadua Latif-Eugenín
- Unidad de Microbiologia, Facultad de Medicina y Ciencias de la Salud, IISPV, Universidad Rovira i VirgiliReus, Spain
| | - Maria José Figueras
- Unidad de Microbiologia, Facultad de Medicina y Ciencias de la Salud, IISPV, Universidad Rovira i VirgiliReus, Spain
| | - Fabienne Petit
- Normandie Univ, UNIROUEN, UNICAEN, Centre National de la Recherche Scientifique, M2CRouen, France.,Sorbonne Universités, UPMC, Centre National de la Recherche Scientifique, EPHE, UMR 7619 METISParis, France
| | - Hélène Marchandin
- Équipe Pathogènes Hydriques Santé Environnements, UMR 5569 HSM, Université de MontpellierMontpellier, France.,Département de Bactériologie, CHRU de MontpellierMontpellier, France
| | - Estelle Jumas-Bilak
- Équipe Pathogènes Hydriques Santé Environnements, UMR 5569 HSM, Université de MontpellierMontpellier, France.,Département d'Hygiène Hospitalière, CHRU de MontpellierMontpellier, France
| | - Brigitte Lamy
- Équipe Pathogènes Hydriques Santé Environnements, UMR 5569 HSM, Université de MontpellierMontpellier, France.,Département de Bactériologie, CHU de NiceNice, France
| |
Collapse
|
31
|
Poluektova EU, Yunes RA, Epiphanova MV, Orlova VS, Danilenko VN. The Lactobacillus rhamnosus and Lactobacillus fermentum strains from human biotopes characterized with MLST and toxin-antitoxin gene polymorphism. Arch Microbiol 2017; 199:683-690. [PMID: 28213763 DOI: 10.1007/s00203-017-1346-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Revised: 01/17/2017] [Accepted: 01/20/2017] [Indexed: 11/29/2022]
Abstract
The diversity of Lb. rhamnosus and Lb. fermentum strains isolated from feces, saliva, and the vaginal cavity of 18-22-year-old healthy women residing in central regions of the Russian Federation has been characterized. The results obtained using multilocus sequence typing were identical to those obtained with the analysis of genetic and genomic polymorphism in TA systems. Different as well as identical Lb. rhamnosus and Lb. fermentum sequence types (ST) were isolated from various parts of the body of the same person. Identical ST were also isolated from different women, suggesting that such strains belong to a common pool of strains circulating among the population members. Our results demonstrate that TAs are suitable for characterizing intra-specific diversity of Lb. rhamnosus and Lb. fermentum strains. The advantage of using polymorphisms in TA systems for genotyping is based on the weak number of genes used, and consequently, less time is required for the analysis.
Collapse
Affiliation(s)
- E U Poluektova
- Laboratory of Genetics of Microorganisms, Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkin Street, GSP-1, Moscow, 119333, Russian Federation
| | - R A Yunes
- Laboratory of Genetics of Microorganisms, Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkin Street, GSP-1, Moscow, 119333, Russian Federation. .,Peoples' Friendship University of Russia (RUDN), 6 Miklukho-Maklai Street, Moscow, 117198, Russian Federation.
| | - M V Epiphanova
- Laboratory of Genetics of Microorganisms, Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkin Street, GSP-1, Moscow, 119333, Russian Federation
| | - V S Orlova
- Peoples' Friendship University of Russia (RUDN), 6 Miklukho-Maklai Street, Moscow, 117198, Russian Federation
| | - V N Danilenko
- Laboratory of Genetics of Microorganisms, Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkin Street, GSP-1, Moscow, 119333, Russian Federation
| |
Collapse
|
32
|
Park S, Ji Y, Park H, Lee K, Park H, Beck BR, Shin H, Holzapfel WH. Evaluation of functional properties of lactobacilli isolated from Korean white kimchi. Food Control 2016. [DOI: 10.1016/j.foodcont.2016.04.037] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
|
33
|
Bao Q, Song Y, Xu H, Yu J, Zhang W, Menghe B, Zhang H, Sun Z. Multilocus sequence typing of Lactobacillus casei isolates from naturally fermented foods in China and Mongolia. J Dairy Sci 2016; 99:5202-5213. [PMID: 27179867 DOI: 10.3168/jds.2016-10857] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 03/28/2016] [Indexed: 11/19/2022]
Abstract
Lactobacillus casei is a lactic acid bacterium used in manufacturing of many fermented food products. To investigate the genetic diversity and population biology of this food-related bacterium, 224 Lb. casei isolates and 5 reference isolates were examined by multilocus sequence typing (MLST). Among them, 224 Lb. casei isolates were isolated from homemade fermented foods, including naturally fermented dairy products, acidic gruel, and Sichuan pickles from 38 different regions in China and Mongolia. The MLST scheme was developed based on the analysis of 10 selected housekeeping genes (carB, clpX, dnaA, groEL, murE, pyrG, pheS, recA, rpoC, and uvrC). All 229 isolates could be allocated to 171 unique sequence types, including 25 clonal complexes and 71 singletons. The high index of association value (1.3524) and standardized index of association value (0.1503) indicate the formation of an underlying clonal population by all the isolates. However, split-decomposition, relative frequency of occurrence of recombination and mutation, and relative effect of recombination and mutation in the diversification values confirm that recombination may have occurred, and were more frequent than mutation during the evolution of Lb. casei. Results from Structure analyses (version 2.3; http://pritch.bsd.uchicago.edu/structure.html) demonstrated that there were 5 lineages in the Lb. casei isolates, and the overall relatedness built by minimum spanning tree showed no clear relationship between the clonal complexes with either the isolation sources or sampling locations of the isolates. Our newly developed MLST scheme of Lb. casei was an easy and valuable tool that, together with the construction of an MLST database, will contribute to further detailed studies on the evolution and population genetics of Lb. casei from various niches.
Collapse
Affiliation(s)
- Qiuhua Bao
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, School of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Yuqin Song
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, School of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Haiyan Xu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, School of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Jie Yu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, School of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Wenyi Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, School of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Bilige Menghe
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, School of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Heping Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, School of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Zhihong Sun
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, School of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot 010018, China.
| |
Collapse
|
34
|
|
35
|
Lhomme E, Urien C, Legrand J, Dousset X, Onno B, Sicard D. Sourdough microbial community dynamics: An analysis during French organic bread-making processes. Food Microbiol 2016; 53:41-50. [DOI: 10.1016/j.fm.2014.11.014] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 11/20/2014] [Accepted: 11/28/2014] [Indexed: 10/24/2022]
|
36
|
Lactic acid bacterium and yeast microbiotas of sixteen French traditional sourdoughs. Int J Food Microbiol 2015; 215:161-70. [DOI: 10.1016/j.ijfoodmicro.2015.09.015] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 09/11/2015] [Accepted: 09/22/2015] [Indexed: 11/21/2022]
|
37
|
Yu J, Sun Z, Liu W, Xi X, Song Y, Xu H, Lv Q, Bao Q, Menghe B, Sun T. Multilocus sequence typing of Streptococcus thermophilus from naturally fermented dairy foods in China and Mongolia. BMC Microbiol 2015; 15:236. [PMID: 26497818 PMCID: PMC4620635 DOI: 10.1186/s12866-015-0551-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 10/07/2015] [Indexed: 12/04/2022] Open
Abstract
Background Streptococcus thermophilus is a major dairy starter used for manufacturing of dairy products. In the present study, we developed a multilocus sequence typing (MLST) scheme for this important food bacterium. Sequences of 10 housekeeping genes (carB, clpX, dnaA, murC, murE, pepN, pepX, pyrG, recA, and rpoB) were obtained for 239 S. thermophilus strains, which were isolated from home-made fermented dairy foods in 18 different regions of Mongolia and China. Methods All 10 genes of S. thermophilus were sequenced, aligned, and defined sequence types (STs) using the BioNumerics Software. The nucleotide diversity was calculated by START v2.0. The population structure, phylogenetic relationships and the role of recombination were inferred using ClonalFrame v1.2, SplitsTree 4.0 and Structure v2.3. Results The 239 S. thermophilus isolates and 18 reference strains could be assigned into 119 different STs, which could be further separated into 16 clonal complexes (CCs) and 38 singletons. Among the 10 loci, a total of 132 polymorphic sites were detected. The standardized index of association (IAS = 0.0916), split-decomposition and ρ/θ (relative frequency of occurrence of recombination and mutation) and r/m value (relative impact of recombination and mutation in the diversification) confirms that recombination may have occurred, but it occurred at a low frequency in these 10 loci. Phylogenetic trees indicated that there were five lineages in the S. thermophilus isolates used in our study. MSTree and ClonalFrame tree analyses suggest that the evolution of S. thermophilus isolates have little relationship with geographic locality, but revealed no association with the types of fermented dairy product. Phylogenetic analysis of 36 whole genome strains (18 S. thermophilus, 2 S. vestibularis and 16 S. salivarius strains) indicated that our MLST scheme could clearly separate three closely related species within the salivarius group and is suitable for analyzing the population structure of the other two species in the salivarius group. Conclusions Our newly developed MLST scheme improved the understanding on the genetic diversity and population structure of the S. thermophilus, as well as provided useful information for further studies on the genotyping and evolutionary research for S. thermophilus strains with global diversity. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0551-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Jie Yu
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, P. R. China.
| | - Zhihong Sun
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, P. R. China.
| | - Wenjun Liu
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, P. R. China.
| | - Xiaoxia Xi
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, P. R. China.
| | - Yuqin Song
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, P. R. China.
| | - Haiyan Xu
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, P. R. China.
| | - Qiang Lv
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, P. R. China.
| | - Qiuhua Bao
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, P. R. China.
| | - Bilige Menghe
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, P. R. China.
| | - Tiansong Sun
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, P. R. China.
| |
Collapse
|
38
|
Amadoro C, Rossi F, Piccirilli M, Colavita G. Features of Lactobacillus Sakei Isolated from Italian Sausages: Focus on Strains from Ventricina del Vastese. Ital J Food Saf 2015; 4:5449. [PMID: 27802352 PMCID: PMC5076685 DOI: 10.4081/ijfs.2015.5449] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2015] [Revised: 09/23/2015] [Accepted: 10/09/2015] [Indexed: 01/24/2023] Open
Abstract
In this study bacterial isolates from Ventricina del Vastese sausage, previously identified as Lactobacillus (L.) sakei, were characterised genotypically, physiologically and on the basis of some technologically relevant traits. A total of 70 L. sakei isolates from sausages manufactured with spontaneous fermentation in the same producing plant were taken into account. Six genotypic groups were distinguished on the basis of Rep-polymerase chain reaction with the GTG5 primer, some of which were found only in the sausages ripened at temperatures lower than 10°C for the first two months and lower than 16°C for the remaining three months, according to the traditional ripening process. Six strains were selected as representative of the genotypic profiles and further characterised. A high diversity in their fermentation profiles was observed, and different groups were separated on the basis of growth and acidifying capacity in meat extract. None of the strains produced histamine or tyramine in vitro. One strain was able to slightly inhibit Listeria (L.) monocytogenes and L. innocua and all six strains were able to slightly inhibit Enterobacteriaceae isolated from Ventricina del Vastese sausages in vitro. Results showed that most L. sakei strains can have a role in improving the safety of low acidity fermented sausages, even though a limited acidifying capacity was observed in a meat-like substrate, and that L. sakei strains able to produce biogenic amines are unlikely to occur in spontaneously fermented meat products.
Collapse
Affiliation(s)
- Carmela Amadoro
- Department of Medicine and Health Sciences, University of Molise , Campobasso, Italy
| | - Franca Rossi
- Department of Medicine and Health Sciences, University of Molise , Campobasso, Italy
| | - Michele Piccirilli
- Department of Medicine and Health Sciences, University of Molise , Campobasso, Italy
| | - Giampaolo Colavita
- Department of Medicine and Health Sciences, University of Molise , Campobasso, Italy
| |
Collapse
|
39
|
Dan T, Liu W, Song Y, Xu H, Menghe B, Zhang H, Sun Z. The evolution and population structure of Lactobacillus fermentum from different naturally fermented products as determined by multilocus sequence typing (MLST). BMC Microbiol 2015; 15:107. [PMID: 25990318 PMCID: PMC4437502 DOI: 10.1186/s12866-015-0447-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 05/14/2015] [Indexed: 11/11/2022] Open
Abstract
Background Lactobacillus fermentum is economically important in the production and preservation of fermented foods. A repeatable and discriminative typing method was devised to characterize L. fermentum at the molecular level. The multilocus sequence typing (MLST) scheme developed was based on analysis of the internal sequence of 11 housekeeping gene fragments (clpX, dnaA, dnaK, groEL, murC, murE, pepX, pyrG, recA, rpoB, and uvrC). Results MLST analysis of 203 isolates of L. fermentum from Mongolia and seven provinces/ autonomous regions in China identified 57 sequence types (ST), 27 of which were represented by only a single isolate, indicating high genetic diversity. Phylogenetic analyses based on the sequence of the 11 housekeeping gene fragments indicated that the L. fermentum isolates analyzed belonged to two major groups. A standardized index of association (IAS) indicated a weak clonal population structure in L. fermentum. Split decomposition analysis indicated that recombination played an important role in generating the genetic diversity observed in L. fermentum. The results from the minimum spanning tree strongly suggested that evolution of L. fermentum STs was not correlated with geography or food-type. Conclusions The MLST scheme developed will be valuable for further studies on the evolution and population structure of L. fermentum isolates used in food products. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0447-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Tong Dan
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Department of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, P. R. China.
| | - Wenjun Liu
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Department of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, P. R. China.
| | - Yuqin Song
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Department of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, P. R. China.
| | - Haiyan Xu
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Department of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, P. R. China.
| | - Bilige Menghe
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Department of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, P. R. China.
| | - Heping Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Department of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, P. R. China.
| | - Zhihong Sun
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Department of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, P. R. China.
| |
Collapse
|
40
|
Sun Z, Liu W, Song Y, Xu H, Yu J, Bilige M, Zhang H, Chen Y. Population structure of Lactobacillus helveticus isolates from naturally fermented dairy products based on multilocus sequence typing. J Dairy Sci 2015; 98:2962-72. [DOI: 10.3168/jds.2014-9133] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 01/23/2015] [Indexed: 01/14/2023]
|
41
|
Ellegaard KM, Tamarit D, Javelind E, Olofsson TC, Andersson SGE, Vásquez A. Extensive intra-phylotype diversity in lactobacilli and bifidobacteria from the honeybee gut. BMC Genomics 2015; 16:284. [PMID: 25880915 PMCID: PMC4449606 DOI: 10.1186/s12864-015-1476-6] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 03/23/2015] [Indexed: 01/09/2023] Open
Abstract
Background In the honeybee Apis mellifera, the bacterial gut community is consistently colonized by eight distinct phylotypes of bacteria. Managed bee colonies are of considerable economic interest and it is therefore important to elucidate the diversity and role of this microbiota in the honeybee. In this study, we have sequenced the genomes of eleven strains of lactobacilli and bifidobacteria isolated from the honey crop of the honeybee A. mellifera. Results Single gene phylogenies confirmed that the isolated strains represent the diversity of lactobacilli and bifidobacteria in the gut, as previously identified by 16S rRNA gene sequencing. Core genome phylogenies of the lactobacilli and bifidobacteria further indicated extensive divergence between strains classified as the same phylotype. Phylotype-specific protein families included unique surface proteins. Within phylotypes, we found a remarkably high level of gene content diversity. Carbohydrate metabolism and transport functions contributed up to 45% of the accessory genes, with some genomes having a higher content of genes encoding phosphotransferase systems for the uptake of carbohydrates than any previously sequenced genome. These genes were often located in highly variable genomic segments that also contained genes for enzymes involved in the degradation and modification of sugar residues. Strain-specific gene clusters for the biosynthesis of exopolysaccharides were identified in two phylotypes. The dynamics of these segments contrasted with low recombination frequencies and conserved gene order structures for the core genes. Hits for CRISPR spacers were almost exclusively found within phylotypes, suggesting that the phylotypes are associated with distinct phage populations. Conclusions The honeybee gut microbiota has been described as consisting of a modest number of phylotypes; however, the genomes sequenced in the current study demonstrated a very high level of gene content diversity within all three described phylotypes of lactobacilli and bifidobacteria, particularly in terms of metabolic functions and surface structures, where many features were strain-specific. Together, these results indicate niche differentiation within phylotypes, suggesting that the honeybee gut microbiota is more complex than previously thought. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1476-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Kirsten M Ellegaard
- Department of Molecular Evolution, Cell and Molecular Biology, Science for Life Laboratory, Biomedical Centre, Uppsala University, Husargatan 3, SE-751 24, Uppsala, Sweden.
| | - Daniel Tamarit
- Department of Molecular Evolution, Cell and Molecular Biology, Science for Life Laboratory, Biomedical Centre, Uppsala University, Husargatan 3, SE-751 24, Uppsala, Sweden.
| | - Emelie Javelind
- Department of Molecular Evolution, Cell and Molecular Biology, Science for Life Laboratory, Biomedical Centre, Uppsala University, Husargatan 3, SE-751 24, Uppsala, Sweden.
| | - Tobias C Olofsson
- Department of Laboratory Medicine, Medical Microbiology, Lund University, Medicon Village, Scheelevägen 2, SE-223 62, Lund, Sweden.
| | - Siv G E Andersson
- Department of Molecular Evolution, Cell and Molecular Biology, Science for Life Laboratory, Biomedical Centre, Uppsala University, Husargatan 3, SE-751 24, Uppsala, Sweden.
| | - Alejandra Vásquez
- Department of Laboratory Medicine, Medical Microbiology, Lund University, Medicon Village, Scheelevägen 2, SE-223 62, Lund, Sweden.
| |
Collapse
|
42
|
Zhang W, Liu W, Song Y, Xu H, Menghe B, Zhang H, Sun Z. Multilocus sequence typing of a dairy-associated Leuconostoc mesenteroides population reveals clonal structure with intragenic homologous recombination. J Dairy Sci 2015; 98:2284-93. [DOI: 10.3168/jds.2014-9227] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 12/31/2014] [Indexed: 11/19/2022]
|
43
|
Rahkila R, Johansson P, Säde E, Paulin L, Auvinen P, Björkroth J. Multilocus sequence typing of Leuconostoc gelidum subsp. gasicomitatum, a Psychrotrophic lactic acid bacterium causing spoilage of packaged perishable foods. Appl Environ Microbiol 2015; 81:2474-80. [PMID: 25616799 PMCID: PMC4357932 DOI: 10.1128/aem.04013-14] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 01/20/2015] [Indexed: 11/20/2022] Open
Abstract
Leuconostoc gelidum subsp. gasicomitatum is a psychrotrophic lactic acid bacterium (LAB) that causes spoilage of a variety of modified-atmosphere-packaged (MAP) cold-stored food products. During the past 10 years, this spoilage organism has been increasingly reported in MAP meat and vegetable products in northern Europe. In the present study, the population structure within 252 L. gelidum subsp. gasicomitatum strains was determined based on a novel multilocus sequence-typing (MLST) scheme employing seven housekeeping genes. These strains had been isolated from meat and vegetable sources over a time span of 15 years, and all 68 previously detected pulsed-field gel electrophoresis (PFGE) genotypes were represented. A total of 46 sequence types (STs) were identified, with a majority of the strains (>60%) belonging to three major STs, which were grouped into three clonal complexes (CCs) and 17 singletons by Global Optimal eBURST (goeBURST). The results by Bayesian analysis of population structure (BAPS) mostly correlated with the grouping by goeBURST. Admixture analysis by BAPS indicated a very low level of exchange of genetic material between the subpopulations. Niche specificity was observed within the subpopulations: CC1 and BAPS cluster 1 consisted mostly of strains from a variety of MAP meats, whereas vegetable strains grouped together with strains from MAP poultry within CC2 and BAPS cluster 2. The MLST scheme presented in this study provides a shareable and continuously growing sequence database enabling global comparison of strains associated with spoilage cases. This will further advance our understanding of the microbial ecology of this industrially important LAB.
Collapse
Affiliation(s)
- Riitta Rahkila
- Department of Food Hygiene and Environmental Health, University of Helsinki, Helsinki, Finland
| | - Per Johansson
- Department of Food Hygiene and Environmental Health, University of Helsinki, Helsinki, Finland
| | - Elina Säde
- Department of Food Hygiene and Environmental Health, University of Helsinki, Helsinki, Finland
| | - Lars Paulin
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Petri Auvinen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Johanna Björkroth
- Department of Food Hygiene and Environmental Health, University of Helsinki, Helsinki, Finland
| |
Collapse
|
44
|
Draft Genome Sequence of Lactobacillus sakei Strain wikim 22, Isolated from Kimchi in Chungcheong Province, South Korea. GENOME ANNOUNCEMENTS 2014; 2:2/6/e01296-14. [PMID: 25502679 PMCID: PMC4263841 DOI: 10.1128/genomea.01296-14] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report the draft genome sequence of Lactobacillus sakei strain wikim 22, a Lactobacillus species isolated from kimchi in North Chungcheong Province, South Korea, having 155 contigs with 2,447 genes and an average G+C content of 40.61%.
Collapse
|
45
|
Pothakos V, Nyambi C, Zhang BY, Papastergiadis A, De Meulenaer B, Devlieghere F. Spoilage potential of psychrotrophic lactic acid bacteria (LAB) species: Leuconostoc gelidum subsp. gasicomitatum and Lactococcus piscium, on sweet bell pepper (SBP) simulation medium under different gas compositions. Int J Food Microbiol 2014; 178:120-9. [DOI: 10.1016/j.ijfoodmicro.2014.03.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 03/07/2014] [Accepted: 03/10/2014] [Indexed: 11/27/2022]
|
46
|
High genetic diversity among strains of the unindustrialized lactic acid bacterium Carnobacterium maltaromaticum in dairy products as revealed by multilocus sequence typing. Appl Environ Microbiol 2014; 80:3920-9. [PMID: 24747901 DOI: 10.1128/aem.00681-14] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Dairy products are colonized with three main classes of lactic acid bacteria (LAB): opportunistic bacteria, traditional starters, and industrial starters. Most of the population structure studies were previously performed with LAB species belonging to these three classes and give interesting knowledge about the population structure of LAB at the stage where they are already industrialized. However, these studies give little information about the population structure of LAB prior their use as an industrial starter. Carnobacterium maltaromaticum is a LAB colonizing diverse environments, including dairy products. Since this bacterium was discovered relatively recently, it is not yet commercialized as an industrial starter, which makes C. maltaromaticum an interesting model for the study of unindustrialized LAB population structure in dairy products. A multilocus sequence typing scheme based on an analysis of fragments of the genes dapE, ddlA, glpQ, ilvE, pyc, pyrE, and leuS was applied to a collection of 47 strains, including 28 strains isolated from dairy products. The scheme allowed detecting 36 sequence types with a discriminatory index of 0.98. The whole population was clustered in four deeply branched lineages, in which the dairy strains were spread. Moreover, the dairy strains could exhibit a high diversity within these lineages, leading to an overall dairy population with a diversity level as high as that of the nondairy population. These results are in agreement with the hypothesis according to which the industrialization of LAB leads to a diversity reduction in dairy products.
Collapse
|