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Xu X, Nielsen LJD, Song L, Maróti G, Strube ML, Kovács ÁT. Enhanced specificity of Bacillus metataxonomics using a tuf-targeted amplicon sequencing approach. ISME COMMUNICATIONS 2023; 3:126. [PMID: 38012258 PMCID: PMC10682494 DOI: 10.1038/s43705-023-00330-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 11/01/2023] [Accepted: 11/08/2023] [Indexed: 11/29/2023]
Abstract
Bacillus species are ubiquitous in nature and have tremendous application potential in agriculture, medicine, and industry. However, the individual species of this genus vary widely in both ecological niches and functional phenotypes, which, hence, requires accurate classification of these bacteria when selecting them for specific purposes. Although analysis of the 16S rRNA gene has been widely used to disseminate the taxonomy of most bacterial species, this gene fails proper classification of Bacillus species. To circumvent this restriction, we designed novel primers and optimized them to allow exact species resolution of Bacillus species in both synthetic and natural communities using high-throughput amplicon sequencing. The primers designed for the tuf gene were not only specific for the Bacillus genus but also sufficiently discriminated species both in silico and in vitro in a mixture of 11 distinct Bacillus species. Investigating the primers using a natural soil sample, 13 dominant species were detected including Bacillus badius, Bacillus velezensis, and Bacillus mycoides as primary members, neither of which could be distinguished with 16S rRNA sequencing. In conclusion, a set of high-throughput primers were developed which allows unprecedented species-level identification of Bacillus species and aids the description of the ecological distribution of Bacilli in various natural environment.
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Affiliation(s)
- Xinming Xu
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, 2800, Lyngby, Denmark
- Institute of Biology Leiden, Leiden University, 2333 BE, Leiden, The Netherlands
| | - Lasse Johan Dyrbye Nielsen
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Lijie Song
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, 2800, Lyngby, Denmark
- BGI-Tianjin, BGI-Shenzhen, 300308, Tianjin, China
| | - Gergely Maróti
- Institute of Plant Biology, Biological Research Center, ELKH, 6726, Szeged, Hungary
| | - Mikael Lenz Strube
- Bacterial Ecophysiology and Biotechnology Group, DTU Bioengineering, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, 2800, Lyngby, Denmark.
- Institute of Biology Leiden, Leiden University, 2333 BE, Leiden, The Netherlands.
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Kiousi DE, Karadedos DM, Sykoudi A, Repanas P, Kamarinou CS, Argyri AA, Galanis A. Development of a Multiplex PCR Assay for Efficient Detection of Two Potential Probiotic Strains Using Whole Genome-Based Primers. Microorganisms 2023; 11:2553. [PMID: 37894211 PMCID: PMC10609308 DOI: 10.3390/microorganisms11102553] [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: 09/14/2023] [Revised: 10/02/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
Probiotics are microorganisms that exert strain-specific health-promoting effects on the host. Τhey are employed in the production of functional dairy or non-dairy food products; still, their detection in these complex matrices is a challenging task. Several culture-dependent and culture-independent methods have been developed in this direction; however, they present low discrimination at the strain level. Here, we developed a multiplex PCR assay for the detection of two potential probiotic lactic acid bacteria (LAB) strains, Lactiplantibacillus plantarum L125 and Lp. pentosus L33, in monocultures and yogurt samples. Unique genomic regions were identified via comparative genomic analysis and were used to produce strain-specific primers. Then, primer sets were selected that produced distinct electrophoretic DNA banding patterns in multiplex PCR for each target strain. This method was further implemented for the detection of the two strains in yogurt samples, highlighting its biotechnological applicability. Moreover, it can be applied with appropriate modifications to detect any bacterial strain with available WGS.
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Affiliation(s)
- Despoina E. Kiousi
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (D.E.K.); (D.M.K.); (A.S.); (P.R.); (C.S.K.)
| | - Dimitrios M. Karadedos
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (D.E.K.); (D.M.K.); (A.S.); (P.R.); (C.S.K.)
| | - Anastasia Sykoudi
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (D.E.K.); (D.M.K.); (A.S.); (P.R.); (C.S.K.)
| | - Panagiotis Repanas
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (D.E.K.); (D.M.K.); (A.S.); (P.R.); (C.S.K.)
| | - Christina S. Kamarinou
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (D.E.K.); (D.M.K.); (A.S.); (P.R.); (C.S.K.)
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organization—DIMITRA, 14123 Lycovrissi, Greece;
| | - Anthoula A. Argyri
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organization—DIMITRA, 14123 Lycovrissi, Greece;
| | - Alex Galanis
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (D.E.K.); (D.M.K.); (A.S.); (P.R.); (C.S.K.)
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Growth fitness, heme uptake and genomic variants in mutants of oxygen-tolerant Lacticaseibacillus casei and Lactiplantibacillus plantarum strains. Microbiol Res 2022; 262:127096. [DOI: 10.1016/j.micres.2022.127096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 06/04/2022] [Accepted: 06/14/2022] [Indexed: 11/18/2022]
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Di Biase M, Le Marc Y, Bavaro AR, De Bellis P, Lonigro SL, Lavermicocca P, Postollec F, Valerio F. A Predictive Growth Model for Pro-technological and Probiotic Lacticaseibacillus paracasei Strains Fermenting White Cabbage. Front Microbiol 2022; 13:907393. [PMID: 35733952 PMCID: PMC9207389 DOI: 10.3389/fmicb.2022.907393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 05/06/2022] [Indexed: 12/01/2022] Open
Abstract
Bacterial strains belonging to Lacticaseibacillus paracasei species are generally used as starters in food fermentations and/or as probiotics. In the current study, the growth cardinal parameters of four L. paracasei strains (IMPC2.1, IMPC4.1, P40 and P101), isolated from table olives or human source, were determined. Strains were grown in liquid medium and incubated at several temperatures (10 values from 5.5°C–40°C) and pH (15 values from 3.2 to 9.1) along the growth range. The cardinal temperature model was used to describe temperature effects on the maximum specific growth rate of L. paracasei whereas new equations were developed for the effect of pH. The estimated Tmin values ranged between −0.97°C and 1.95°C and were lower than 0°C for strains IMPC4.1 and P101. Strain P40 was able to grow in the most restricted range of temperature (from 1.95°C to 37.46°C), while strain IMPC4.1 was estimated to survive at extreme conditions showing the lowest pHmin. Maximum specific growth rates of L. paracasei IMPC2.1 in white cabbage (Brassica oleracea var. capitata) were used to calculate the correction factor (Cf) defined as the bias between the bacterial maximum specific growth rate in broth and in the food matrix. A simple bi-linear model was also developed for the effect of temperature on the maximum population density reached in white cabbage. This information was further used to simulate the growth of L. paracasei strains in cabbage and predict the time to reach the targeted probiotic level (7 log10 CFU/g) using in silico simulations. This study demonstrates the potential of the predictive microbiology to predict the growth of beneficial and pro-technological strains in foods in order to optimize the fermentative process.
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Affiliation(s)
- Mariaelena Di Biase
- Institute of Sciences of Food Production, National Research Council of Italy, Bari, Italy
| | - Yvan Le Marc
- ADRIA Food Technology Institute, UMT ACTIA 19.03 ALTER'iX, Creac'h Gwen, Quimper Cedex, France
| | - Anna Rita Bavaro
- Institute of Sciences of Food Production, National Research Council of Italy, Bari, Italy
| | - Palmira De Bellis
- Institute of Sciences of Food Production, National Research Council of Italy, Bari, Italy
| | - Stella Lisa Lonigro
- Institute of Sciences of Food Production, National Research Council of Italy, Bari, Italy
| | - Paola Lavermicocca
- Institute of Sciences of Food Production, National Research Council of Italy, Bari, Italy
| | - Florence Postollec
- ADRIA Food Technology Institute, UMT ACTIA 19.03 ALTER'iX, Creac'h Gwen, Quimper Cedex, France
| | - Francesca Valerio
- Institute of Sciences of Food Production, National Research Council of Italy, Bari, Italy
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Kamarinou CS, Papadopoulou OS, Doulgeraki AI, Tassou CC, Galanis A, Chorianopoulos NG, Argyri AA. Mapping the Key Technological and Functional Characteristics of Indigenous Lactic Acid Bacteria Isolated from Greek Traditional Dairy Products. Microorganisms 2022; 10:246. [PMID: 35208701 PMCID: PMC8875946 DOI: 10.3390/microorganisms10020246] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 11/25/2022] Open
Abstract
The aim of the current study was to isolate indigenous lactic acid bacteria (LAB) from traditional Greek cheeses and assess their biochemical, technological, and functional characteristics, so as to develop novel cultures with multi-functional properties. Hence, 109 LAB isolates were recovered from traditional fresh cheeses and were evaluated in vitro for their gas production; proteolytic, lipolytic, and haemolytic activity; exopolysaccharide production (EPS); enzymatic potential; and ability to grow at 6.5% NaCl and at different pH, temperature, and anaerobic conditions. Consequently, 48 selected isolates were further evaluated for their survival under simulated gastrointestinal tract conditions, partial bile salt hydrolase activity, antibiotic resistance, and antimicrobial activity against pathogens. These isolates were also incorporated as co-cultures in yogurt production to examine their sensory characteristics and their survival in the product. Some prominent isolates that showed favorable technological and functional characteristics (good survival rates at low pH and bile salts, ability to produce β-galactosidase, and EPS) and attributed desirable sensory characteristics to yogurt were Lactococcuslactis (SRX2, SRX3, SRX5, and SMX16), Lactobacillus paracasei SRX10, and Lactiplantibacillusplantarum (FRX7, FB1), while Leuconostoc mesenteroides FMX3 and L. lactis SMX2 showed an anti-listerial activity in vitro. The results of the present study are promising for the production of novel dairy functional products with an enhanced quality and safety.
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Affiliation(s)
- Christina S. Kamarinou
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organization—DIMITRA, 14123 Lycovrissi, Greece; (C.S.K.); (O.S.P.); (A.I.D.); (C.C.T.)
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece;
| | - Olga S. Papadopoulou
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organization—DIMITRA, 14123 Lycovrissi, Greece; (C.S.K.); (O.S.P.); (A.I.D.); (C.C.T.)
| | - Agapi I. Doulgeraki
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organization—DIMITRA, 14123 Lycovrissi, Greece; (C.S.K.); (O.S.P.); (A.I.D.); (C.C.T.)
| | - Chrysoula C. Tassou
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organization—DIMITRA, 14123 Lycovrissi, Greece; (C.S.K.); (O.S.P.); (A.I.D.); (C.C.T.)
| | - Alex Galanis
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece;
| | - Nikos G. Chorianopoulos
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organization—DIMITRA, 14123 Lycovrissi, Greece; (C.S.K.); (O.S.P.); (A.I.D.); (C.C.T.)
| | - Anthoula A. Argyri
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organization—DIMITRA, 14123 Lycovrissi, Greece; (C.S.K.); (O.S.P.); (A.I.D.); (C.C.T.)
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Farahmand N, Ouoba LII, Naghizadeh Raeisi S, Sutherland J, Ghoddusi HB. Probiotic Lactobacilli in Fermented Dairy Products: Selective Detection, Enumeration and Identification Scheme. Microorganisms 2021; 9:microorganisms9081600. [PMID: 34442679 PMCID: PMC8401870 DOI: 10.3390/microorganisms9081600] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 07/19/2021] [Accepted: 07/20/2021] [Indexed: 11/16/2022] Open
Abstract
A selection of 36 commercial probiotic fermented dairy products from UK and Europe markets were evaluated for the numbers, types, and viability of Lactobacillus strains against the stated information on their packages. A comparative study was carried out on selectivity of MRS-Clindamycin, MRS-Sorbitol, and MRS-IM Maltose, to select the right medium for enumeration of probiotic Lactobacillus. Based on selectivity of medium for recovery of the targeted lactobacilli, and also simplicity of preparation, MRS-Clindamycin was chosen as the best medium for enumeration of probiotic Lactobacillus in fermented milks. The results of enumeration of lactobacilli showed that 22 out of a total 36 tested products contained more than 106 colony-forming units/g at the end of their shelf life, which comply with the recommended minimum therapeutic level for probiotics. Rep-PCR using primer GTG-5 was applied for initial discrimination of isolated strains, and isolates, which presented different band profile, were placed in different groups. The isolated Lactobacillus spp. were identified mainly as Lactobacillus acidophilus, Lactobacillus casei, and Lactobacillus paracasei by analysis of partial sequences of the 16S ribosomal RNA and rpoA genes.
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7
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Lee JM, Park SH, Jin CZ, Kang MK, Park DJ, Kim CJ. The groESL ISR sequence-based species-specific identification of GRAS and non-GRAS Lactiplantibacillus as an alternative to 16S rRNA sequencing. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.111504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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8
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Metagenetic Analysis for Microbial Characterization of Focaccia Doughs Obtained by Using Two Different Starters: Traditional Baker's Yeast and a Selected Leuconostoc citreum Strain. Foods 2021; 10:foods10061189. [PMID: 34070312 PMCID: PMC8225195 DOI: 10.3390/foods10061189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/03/2021] [Accepted: 05/21/2021] [Indexed: 11/28/2022] Open
Abstract
Lactic acid bacteria (LAB) decisively influence the technological, nutritional, organoleptic and preservation properties of bakery products. Therefore, their use has long been considered an excellent strategy to improve the characteristics of those goods. The aim of this study was the evaluation of microbial diversity in different doughs used for the production of a typical Apulian flatbread, named focaccia. Leavening of the analyzed doughs was obtained with baker’s yeast or by applying an innovative “yeast-free” protocol based on a liquid sourdough obtained by using Leuconostoc citreum strain C2.27 as a starter. The microbial populations of the doughs were studied by both a culture-dependent approach and metagenetic analyses. The flours used for dough preparation were also subjected to the same analyses. The metagenetic analyses were performed by sequencing the V5–V6 hypervariable regions of the 16S rRNA gene and the V9 hypervariable region of the 18S rRNA gene. The results indicate that these hypervariable regions were suitable for studying the microbiota of doughs, highlighting a significant difference between the microbial community of focaccia dough with baker’s yeast and that of the dough inoculated with the bacterial starter. In particular, the dough made with baker’s yeast contained a microbiota with a high abundance of Proteobacteria (82% of the bacterial population), known to be negatively correlated with the biochemical properties of the doughs, while the Proteobacteria in dough produced with the L. citreum starter were about 43.5% lower than those in flour and dough prepared using baker’s yeast. Moreover, the results show that the L. citreum C2.27 starter was able to dominate the microbial environment and also reveal the absence of the genus Saccharomyces in the dough used for the production of the “yeast-free” focaccia. This result is particularly important because it highlights the suitability of the starter strain for obtaining an innovative “yeast-free” product.
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Scillato M, Spitale A, Mongelli G, Privitera GF, Mangano K, Cianci A, Stefani S, Santagati M. Antimicrobial properties of Lactobacillus cell-free supernatants against multidrug-resistant urogenital pathogens. Microbiologyopen 2021; 10:e1173. [PMID: 33970542 PMCID: PMC8483400 DOI: 10.1002/mbo3.1173] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 01/22/2021] [Accepted: 01/29/2021] [Indexed: 01/23/2023] Open
Abstract
The healthy vaginal microbiota is dominated by Lactobacillus spp., which provide an important critical line of defense against pathogens, as well as giving beneficial effects to the host. We characterized L. gasseri 1A‐TV, L. fermentum 18A‐TV, and L. crispatus 35A‐TV, from the vaginal microbiota of healthy premenopausal women, for their potential probiotic activities. The antimicrobial effects of the 3 strains and their combination against clinical urogenital bacteria were evaluated together with the activities of their metabolites produced by cell‐free supernatants (CFSs). Their beneficial properties in terms of ability to interfere with vaginal pathogens (co‐aggregation, adhesion to HeLa cells, biofilm formation) and antimicrobial activity mediated by CFSs were assessed against multidrug urogenital pathogens (S. agalactiae, E. coli, KPC‐producing K. pneumoniae, S. aureus, E. faecium VRE, E. faecalis, P. aeruginosa, P. mirabilis, P. vulgaris, C. albicans, C. glabrata). The Lactobacilli tested exhibited an extraordinary ability to interfere and co‐aggregate with urogenital pathogens, except for Candida spp., as well as to adhere to HeLa cells and to produce biofilm in the Lactobacillus combination. Lactobacillus CFSs and their combination revealed a strong bactericidal effect on the multidrug resistant indicator strains tested, except for E. faecium and E. faecalis. The antimicrobial activity was maintained after heat treatment but decreased after enzymatic treatment. All Lactobacilli showed lactic dehydrogenase activity and production of D‐ and L‐lactic acid isomers on Lactobacillus CFSs, while only 1A‐TV and 35A‐TV released hydrogen peroxide and carried helveticin J and acidocin A bacteriocins. These results suggest that they can be employed as a new vaginal probiotic formulation and bio‐therapeutic preparation against urogenital infections. Further, in vivo studies are needed to evaluate human health benefits in clinical situations.
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Affiliation(s)
- Marina Scillato
- Department of Biomedical and Biotechnological Sciences, Microbiology Section, University of Catania, Catania, Italy
| | - Ambra Spitale
- Department of Biomedical and Biotechnological Sciences, Microbiology Section, University of Catania, Catania, Italy
| | - Gino Mongelli
- Department of Biomedical and Biotechnological Sciences, Microbiology Section, University of Catania, Catania, Italy
| | - Grete Francesca Privitera
- Department of Biomedical and Biotechnological Sciences, Microbiology Section, University of Catania, Catania, Italy
| | - Katia Mangano
- Department of Biomedical and Biotechnological Sciences, Oncologic, Clinical, and General Pathology Section, University of Catania, Catania, Italy
| | - Antonio Cianci
- Department of General Surgery and Medical-Surgical Specialties, University of Catania, Catania, Italy
| | - Stefania Stefani
- Department of Biomedical and Biotechnological Sciences, Microbiology Section, University of Catania, Catania, Italy
| | - Maria Santagati
- Department of Biomedical and Biotechnological Sciences, Microbiology Section, University of Catania, Catania, Italy
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Plessas S, Kiousi DE, Rathosi M, Alexopoulos A, Kourkoutas Y, Mantzourani I, Galanis A, Bezirtzoglou E. Isolation of a Lactobacillus paracasei Strain with Probiotic Attributes from Kefir Grains. Biomedicines 2020; 8:biomedicines8120594. [PMID: 33322295 PMCID: PMC7764135 DOI: 10.3390/biomedicines8120594] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/06/2020] [Accepted: 12/09/2020] [Indexed: 02/06/2023] Open
Abstract
Κefir is a rich source of potentially probiotic bacteria. In the present study, firstly, in vitro screening for probiotic characteristics of ten lactic acid bacteria (LAB) isolated from kefir grains was performed. Strain AGR 4 was selected for further studies. Molecular characterization of strain AGR 4, confirmed that AGR 4 belongs to the Lactobacillus paracasei (reclassified to Lacticaseibacillus paracasei subsp. paracasei) species. Further testing revealed that L. paracasei AGR 4 displayed adhesion capacity on human adenocarcinoma cells, HT-29, similar to that of the reference strain, L. casei ATCC 393. In addition, the novel strain exerted significant time- and dose-dependent antiproliferative activity against HT-29 cells and human melanoma cell line, A375, as demonstrated by the sulforhodamine B cytotoxicity assay. Flow cytometry analysis was employed to investigate the mechanism of cellular death; however, it was found that AGR 4 did not act by inducing cell cycle arrest and/or apoptotic cell death. Taken together, these findings promote the probiotic character of the newly isolated strain L. paracasei AGR 4, while further studies are needed for the detailed description of its biological properties.
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Affiliation(s)
- Stavros Plessas
- Laboratory of Food Processing, Faculty of Agricultural Development, Democritus University of Thrace, 68200 Orestiada, Greece; (A.A.); (I.M.)
- Correspondence: ; Tel./Fax: +30-25520-41141
| | - Despoina Eugenia Kiousi
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (D.E.K.); (M.R.); (A.G.)
| | - Marina Rathosi
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (D.E.K.); (M.R.); (A.G.)
| | - Athanasios Alexopoulos
- Laboratory of Food Processing, Faculty of Agricultural Development, Democritus University of Thrace, 68200 Orestiada, Greece; (A.A.); (I.M.)
| | - Yiannis Kourkoutas
- Laboratory of Applied Microbiology and Biotechnology, Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece;
| | - Ioanna Mantzourani
- Laboratory of Food Processing, Faculty of Agricultural Development, Democritus University of Thrace, 68200 Orestiada, Greece; (A.A.); (I.M.)
| | - Alex Galanis
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (D.E.K.); (M.R.); (A.G.)
| | - Eugenia Bezirtzoglou
- Laboratory of Hygiene and Environmental Protection, Medical School, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece;
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Multi fragment melting analysis system (MFMAS) for one-step identification of lactobacilli. J Microbiol Methods 2020; 177:106045. [PMID: 32890569 DOI: 10.1016/j.mimet.2020.106045] [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: 09/02/2019] [Revised: 08/18/2020] [Accepted: 08/19/2020] [Indexed: 11/23/2022]
Abstract
The accurate identification of lactobacilli is essential for the effective management of industrial practices associated with lactobacilli strains, such as the production of fermented foods or probiotic supplements. For this reason, in this study, we proposed the Multi Fragment Melting Analysis System (MFMAS)-lactobacilli based on high resolution melting (HRM) analysis of multiple DNA regions that have high interspecies heterogeneity for fast and reliable identification and characterization of lactobacilli. The MFMAS-lactobacilli is a new and customized version of the MFMAS, which was developed by our research group. MFMAS-lactobacilli is a combined system that consists of i) a ready-to-use plate, which is designed for multiple HRM analysis, and ii) a data analysis software, which is used to characterize lactobacilli species via incorporating machine learning techniques. Simultaneous HRM analysis of multiple DNA fragments yields a fingerprint for each tested strain and the identification is performed by comparing the fingerprints of unknown strains with those of known lactobacilli species registered in the MFMAS. In this study, a total of 254 isolates, which were recovered from fermented foods and probiotic supplements, were subjected to MFMAS analysis, and the results were confirmed by a combination of different molecular techniques. All of the analyzed isolates were exactly differentiated and accurately identified by applying the single-step procedure of MFMAS, and it was determined that all of the tested isolates belonged to 18 different lactobacilli species. The individual analysis of each target DNA region provided identification with an accuracy range from 59% to 90% for all tested isolates. However, when each target DNA region was analyzed simultaneously, perfect discrimination and 100% accurate identification were obtained even in closely related species. As a result, it was concluded that MFMAS-lactobacilli is a multi-purpose method that can be used to differentiate, classify, and identify lactobacilli species. Hence, our proposed system could be a potential alternative to overcome the inconsistencies and difficulties of the current methods.
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Sánchez-Jiménez MM, de la Cuesta Zuluaga JJ, Garcia-Montoya GM, Dabral N, Alzate JF, Vemulapalli R, Olivera-Angel M. Diagnosis of human and canine Brucella canis infection: development and evaluation of indirect enzyme-linked immunosorbent assays using recombinant Brucella proteins. Heliyon 2020; 6:e04393. [PMID: 32685723 PMCID: PMC7358725 DOI: 10.1016/j.heliyon.2020.e04393] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/02/2020] [Accepted: 07/01/2020] [Indexed: 01/18/2023] Open
Abstract
Brucella canis, a Gram-negative coccobacilli belonging to the genus Brucellae, is a pathogenic bacterium that can produce infections in dogs and humans. Multiple studies have been carried out to develop diagnostic techniques to detect all zoonotic Brucellae. Diagnosis of Brucella canis infection is challenging due to the lack of highly specific and sensitive diagnostic assays. This work was divided in two phases: in the first one, were identified antigenic proteins in B. canis that could potentially be used for serological diagnosis of brucellosis. Human sera positive for canine brucellosis infection was used to recognize immunoreactive proteins that were then identified by performing 2D-GEL and immunoblot assays. These spots were analyzed using MALDI TOF MS and predicted proteins were identified. Of the 35 protein spots analyzed, 14 proteins were identified and subsequently characterized using bioinformatics, two of this were selected for the next phase. In the second phase, we developed and validated an indirect enzyme-linked immunosorbent assays using those recombinant proteins: inosine 5' phosphate dehydrogenase, pyruvate dehydrogenase E1 subunit beta (PdhB) and elongation factor Tu (Tuf). These genes were PCR-amplified from genomic DNA of B. canis strain Oliveri, cloned, and expressed in Escherichia coli. Recombinant proteins were purified by metal affinity chromatography, and used as antigens in indirect ELISA. Serum samples from healthy and B. canis-infected humans and dogs were used to evaluate the performance of indirect ELISAs. Our results suggest that PdhB and Tuf proteins could be used as antigens for serologic detection of B. canis infection in humans, but not in dogs. The use of recombinant antigens in iELISA assays to detect B. canis-specific antibodies in human serum could be a valuable tool to improve diagnosis of human brucellosis caused by B. canis.
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Affiliation(s)
- Miryan Margot Sánchez-Jiménez
- Vericel-Biogénesis Group, School of Veterinary Medicine, Faculty of Agricultural Sciences, Universidad of Antioquia, Medellín, Colombia
- Colombian Institute of Tropical Medicine, ICMT - CES University, Medellín, Colombia
| | - Juan Jacobo de la Cuesta Zuluaga
- Vericel-Biogénesis Group, School of Veterinary Medicine, Faculty of Agricultural Sciences, Universidad of Antioquia, Medellín, Colombia
| | - Gisela María Garcia-Montoya
- National Center for Genomic Sequencing -CNSG, University of Antioquia, Medellín, Colombia
- Parasitology Group, School of Medicine, University of Antioquia, Medellín, Colombia
| | - Neha Dabral
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, Indiana, United States
| | - Juan Fernando Alzate
- National Center for Genomic Sequencing -CNSG, University of Antioquia, Medellín, Colombia
- Parasitology Group, School of Medicine, University of Antioquia, Medellín, Colombia
| | - Ramesh Vemulapalli
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, Indiana, United States
| | - Martha Olivera-Angel
- Vericel-Biogénesis Group, School of Veterinary Medicine, Faculty of Agricultural Sciences, Universidad of Antioquia, Medellín, Colombia
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13
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Nel S, Davis SB, Endo A, Dicks LMT. Phylogenetic analysis of Leuconostoc and Lactobacillus species isolated from sugarcane processing streams. Microbiologyopen 2020; 9:e1065. [PMID: 32496663 PMCID: PMC7424246 DOI: 10.1002/mbo3.1065] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/17/2020] [Accepted: 05/11/2020] [Indexed: 11/17/2022] Open
Abstract
High levels of gums such as dextran, produced by Leuconostoc and Lactobacillus spp., have a severe impact on factory throughput and sugar quality. This study aimed to determine the phylogenetic relationships between gum‐producing Leuconostoc and Lactobacillus bacteria which were isolated from various locations in a sugarcane processing factory at times when low‐ and high‐dextran raw sugar, respectively, were produced. Phylogenetic analysis of 16S rRNA gene sequences grouped 81 isolates with the type strains of Leuconostoc mesenteroides (subspp. mesenteroides, dextranicum, and cremoris), Leuconostoc pseudomesenteroides, Leuconostoc lactis, and Leuconostoc citreum, respectively. Forty‐three isolates clustered with the type strain of Lactobacillus fermentum. The phylogenetic relatedness of the isolates was determined by sequencing and analysis of the housekeeping genes rpoA and dnaA for Leuconostoc spp. and the pheS and tuf genes for the Lactobacillus spp. The rpoA gene proved discriminatory for the phylogenetic resolution of all of the isolated Leuconostoc spp. and the dnaA housekeeping gene was shown to be effective for isolates clustering with the type strains of Leuc. mesenteroides and Leuc. citreum. None of the loci examined permitted differentiation at the subspecies level of Leuc. mesenteroides. Single‐locus analysis, as well as the concatenation of the pheS and tuf housekeeping gene sequences, yielded identical phylogenies for the Lactobacillus isolates corresponding to L. fermentum.
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Affiliation(s)
- Sanet Nel
- Sugar Milling Research Institute NPC, c/o University of KwaZulu-Natal, Durban, South Africa.,Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
| | - Stephen B Davis
- Sugar Milling Research Institute NPC, c/o University of KwaZulu-Natal, Durban, South Africa
| | - Akihito Endo
- Department of Food, Aroma and Cosmetic Chemistry, Tokyo University of Agriculture, Hokkaido, Japan
| | - Leon M T Dicks
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
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14
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Verruck S, Silva KJ, de Oliveira Santeli H, Scariot MC, Venturelli GL, Prudencio ES, Arisi ACM. Bifidobacterium animalis ssp. lactis BB-12 enumeration by quantitative PCR assay in microcapsules with full-fat goat milk and inulin-type fructans. Food Res Int 2020; 133:109131. [PMID: 32466908 DOI: 10.1016/j.foodres.2020.109131] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 02/25/2020] [Accepted: 02/26/2020] [Indexed: 12/16/2022]
Abstract
The current study was conducted to develop a quantitative polymerase chain reaction (qPCR) assay for Bifidobacterium animalis ssp. lactis BB-12 quantification in microcapsules matrix with full-fat goat milk and inulin-type fructans. DNA was isolated from milk, feed solutions (before spray drying) and microcapsules (after spray drying) using DNAzol. Two primer pairs targeting Bal-23S or Tuf sequences were evaluated by qPCR. The qPCR efficiency was higher (89.5%) using the Tuf primers than Bal-23S primers (84.8%). Tuf primer pair was able to selectively detect B. animalis ssp. lactis BB-12. After, quantification of bifidobacteria in the microcapsules matrix by Tuf qPCR assay was compared to conventional enumeration by plate counting. The analysis of probiotic feed solutions and microcapsules showed higher (P < 0.05) bacterial enumeration determined by Tuf qPCR assay compared to those obtained by plate counting. This qPCR assay was considered a rapid and sensitive alternative for the quantification of B. animalis ssp. lactis BB-12 in probiotic microcapsules compared to plate counting.
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Affiliation(s)
- Silvani Verruck
- Dairy Technology Laboratory, Food Science and Technology Department, Agrarian Science Center, Federal University of Santa Catarina, Rod. Admar Gonzaga, 1346, Itacorubi, 88034-001 Florianópolis, SC, Brazil
| | - Kelly Justin Silva
- Molecular Biology Laboratory, Food Science and Technology Department, Agrarian Science Center, Federal University of Santa Catarina, Rod. Admar Gonzaga, 1346, Itacorubi, 88034-001 Florianópolis, SC, Brazil
| | - Helena de Oliveira Santeli
- Molecular Biology Laboratory, Food Science and Technology Department, Agrarian Science Center, Federal University of Santa Catarina, Rod. Admar Gonzaga, 1346, Itacorubi, 88034-001 Florianópolis, SC, Brazil
| | - Mirella Christine Scariot
- Molecular Biology Laboratory, Food Science and Technology Department, Agrarian Science Center, Federal University of Santa Catarina, Rod. Admar Gonzaga, 1346, Itacorubi, 88034-001 Florianópolis, SC, Brazil
| | - Gustavo Luiz Venturelli
- Molecular Biology Laboratory, Food Science and Technology Department, Agrarian Science Center, Federal University of Santa Catarina, Rod. Admar Gonzaga, 1346, Itacorubi, 88034-001 Florianópolis, SC, Brazil
| | - Elane Schwinden Prudencio
- Dairy Technology Laboratory, Food Science and Technology Department, Agrarian Science Center, Federal University of Santa Catarina, Rod. Admar Gonzaga, 1346, Itacorubi, 88034-001 Florianópolis, SC, Brazil
| | - Ana Carolina Maisonnave Arisi
- Molecular Biology Laboratory, Food Science and Technology Department, Agrarian Science Center, Federal University of Santa Catarina, Rod. Admar Gonzaga, 1346, Itacorubi, 88034-001 Florianópolis, SC, Brazil.
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15
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Tagliazucchi D, Baldaccini A, Martini S, Bianchi A, Pizzamiglio V, Solieri L. Cultivable non-starter lactobacilli from ripened Parmigiano Reggiano cheeses with different salt content and their potential to release anti-hypertensive peptides. Int J Food Microbiol 2020; 330:108688. [PMID: 32497940 DOI: 10.1016/j.ijfoodmicro.2020.108688] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 04/15/2020] [Accepted: 05/24/2020] [Indexed: 01/19/2023]
Abstract
The impact of salt and fat intake on human health drives the consumer's attention towards dairy food with reduced salt and fat contents. How changes in salt and fat content modulate dairy LAB population and the associated proteolytic activities have been poorly studied. Here, non-starter LAB populations from 12 Parmigiano Reggiano (PR) cheeses (12-month ripened), clustered in low salt and fat content (LL-PR) and high salt and fat content (HH-PR) groups, were investigated and identified at specie-level with molecular assays. Lactobacillus rhamnosus was dominant in HH-PR samples, whereas Lactobacillus paracasei in LL-PR samples. (GTG)5 rep-PCR analysis discriminated 11 and 12 biotypes for L. rhamnosus and L. paracasei isolates, respectively. Screening for proteolytic activity identified L. rhamnosus strains more proteolytic than L. paracasei, and, within L. rhamnosus species, HH-PR strains were generally more proteolytic than LL-PR strains. Two L. rhamnosus representatives, namely strain 0503 from LL-PR and strain 2006 from HH-PR, were functionally characterized in cow milk fermentation assay. HH-PR strain 2006 overcame LL-PR strain 0503 in acidification performance, leading to a fermented milk with higher angiotensin I-converting enzyme inhibitory and antioxidant activities. L. rhamnosus 2006 was more prone to release VPP, while L. rhamnosus 0503 released higher amount of IPP. This study provides evidences that salt/fat content affects NSLAB cultivable fraction and the associated proteolytic ability resulting in a complex occurrence of bioactive peptides featuring health-promoting properties.
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Affiliation(s)
- Davide Tagliazucchi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, 42122 Reggio Emilia, Italy
| | - Andrea Baldaccini
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, 42122 Reggio Emilia, Italy
| | - Serena Martini
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, 42122 Reggio Emilia, Italy
| | - Aldo Bianchi
- Consorzio del Formaggio Parmigiano Reggiano, via J.F. Kennedy 18, 42124 Reggio Emilia, Italy
| | - Valentina Pizzamiglio
- Consorzio del Formaggio Parmigiano Reggiano, via J.F. Kennedy 18, 42124 Reggio Emilia, Italy
| | - Lisa Solieri
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, 42122 Reggio Emilia, Italy.
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16
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Blanco G, Ruiz L, Tamés H, Ruas-Madiedo P, Fdez-Riverola F, Sánchez B, Lourenço A, Margolles A. Revisiting the Metabolic Capabilities of Bifidobacterium longum susbp. longum and Bifidobacterium longum subsp. infantis from a Glycoside Hydrolase Perspective. Microorganisms 2020; 8:E723. [PMID: 32413974 PMCID: PMC7285499 DOI: 10.3390/microorganisms8050723] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 05/02/2020] [Accepted: 05/11/2020] [Indexed: 12/18/2022] Open
Abstract
Bifidobacteria are among the most abundant microorganisms inhabiting the intestine of humans and many animals. Within the genus Bifidobacterium, several beneficial effects have been attributed to strains belonging to the subspecies Bifidobacterium longum subsp. longum and Bifidobacterium longum subsp. infantis, which are often found in infants and adults. The increasing numbers of sequenced genomes belonging to these two subspecies, and the availability of novel computational tools focused on predicting glycolytic abilities, with the aim of understanding the capabilities of degrading specific carbohydrates, allowed us to depict the potential glycoside hydrolases (GH) of these bacteria, with a focus on those GH profiles that differ in the two subspecies. We performed an in silico examination of 188 sequenced B. longum genomes and depicted the commonly present and strain-specific GHs and GH families among representatives of this species. Additionally, GH profiling, genome-based and 16S rRNA-based clustering analyses showed that the subspecies assignment of some strains does not properly match with their genetic background. Furthermore, the analysis of the potential GH component allowed the distinction of clear GH patterns. Some of the GH activities, and their link with the two subspecies under study, are further discussed. Overall, our in silico analysis poses some questions about the suitability of considering the GH activities of B. longum subsp. longum and B. longum subsp. infantis to gain insight into the characterization and classification of these two subspecies with probiotic interest.
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Affiliation(s)
- Guillermo Blanco
- Escuela Superior de Ingeniería Informática, Edificio Politécnico, Campus Universitario As Lagoas s/n, University of Vigo, 32004 Ourense, Spain; (G.B.); (F.F.-R.)
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Paseo Río Linares S/N, Villaviciosa, 33300 Asturias, Spain; (H.T.); (P.R.-M.); (B.S.); (A.M.)
| | - Lorena Ruiz
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Paseo Río Linares S/N, Villaviciosa, 33300 Asturias, Spain; (H.T.); (P.R.-M.); (B.S.); (A.M.)
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, 33011 Asturias, Spain
| | - Hector Tamés
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Paseo Río Linares S/N, Villaviciosa, 33300 Asturias, Spain; (H.T.); (P.R.-M.); (B.S.); (A.M.)
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, 33011 Asturias, Spain
| | - Patricia Ruas-Madiedo
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Paseo Río Linares S/N, Villaviciosa, 33300 Asturias, Spain; (H.T.); (P.R.-M.); (B.S.); (A.M.)
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, 33011 Asturias, Spain
| | - Florentino Fdez-Riverola
- Escuela Superior de Ingeniería Informática, Edificio Politécnico, Campus Universitario As Lagoas s/n, University of Vigo, 32004 Ourense, Spain; (G.B.); (F.F.-R.)
- CINBIO-Centro de Investigaciones Biomédicas, University of Vigo, Campus Universitario Lagoas-Marcosende, 36310 Vigo, Spain
- SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Hospital Álvaro Cunqueiro, 36312 Vigo, Spain
| | - Borja Sánchez
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Paseo Río Linares S/N, Villaviciosa, 33300 Asturias, Spain; (H.T.); (P.R.-M.); (B.S.); (A.M.)
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, 33011 Asturias, Spain
| | - Anália Lourenço
- Escuela Superior de Ingeniería Informática, Edificio Politécnico, Campus Universitario As Lagoas s/n, University of Vigo, 32004 Ourense, Spain; (G.B.); (F.F.-R.)
- CINBIO-Centro de Investigaciones Biomédicas, University of Vigo, Campus Universitario Lagoas-Marcosende, 36310 Vigo, Spain
- SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Hospital Álvaro Cunqueiro, 36312 Vigo, Spain
- CEB-Centre of Biological Engineering, University of Minho, Campus de Campus de Gualtar, 4710-057 Braga, Portugal
| | - Abelardo Margolles
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Paseo Río Linares S/N, Villaviciosa, 33300 Asturias, Spain; (H.T.); (P.R.-M.); (B.S.); (A.M.)
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, 33011 Asturias, Spain
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17
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Jarocki P, Komoń-Janczara E, Glibowska A, Dworniczak M, Pytka M, Korzeniowska-Kowal A, Wzorek A, Kordowska-Wiater M. Molecular Routes to Specific Identification of the Lactobacillus Casei Group at the Species, Subspecies and Strain Level. Int J Mol Sci 2020; 21:ijms21082694. [PMID: 32294944 PMCID: PMC7216162 DOI: 10.3390/ijms21082694] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/05/2020] [Accepted: 04/10/2020] [Indexed: 12/12/2022] Open
Abstract
The genus Lactobacillus includes, among others, Lactobacillus casei, Lactobacillus paracasei and Lactobacillus rhamnosus, species that are collectively referred to as the Lactobacillus casei group. Many studies have shown that strains belonging to this group may decrease lactose intolerance, the effects of inflammatory bowel disease, diarrhea, constipation, food allergies and even colon cancer. Moreover, evidences exists of positive effects of these bacteria on mucosal immunity and blood cholesterol level. Because of their beneficial influence on human health, many of them are used as food additives and probiotic pharmaceuticals. It should be stressed that health-promoting properties are not attributed at the species level, but to specific strains. Therefore, procedures are necessary to allow specific identification at each phylogenetic level-genus, species and strain. In this paper we present a practical overview of molecular methods for the identification and differentiation of L. casei bacteria. The research included 30 bacterial strains belonging to three species: L.casei, L. paracasei and L. rhamnosus. Among the tested procedures were genus- and species-specific PCR, multiplex-PCR, Real-Time HRM analysis, RFLP-PCR, rep-PCR, RAPD-PCR, AFLP-PCR, and proteomic methods such as MALDI-TOF MS typing and SDS-PAGE fingerprinting. The obtained results showed that multiplex-PCR and MALDI-TOF MS turned out to be the most useful methods to identify the tested bacteria at the species level. At the strain level, the AFLP-PCR method showed the highest discriminatory power. We hope that the presented results will allow for the easy selection of an appropriate procedure, depending on the experiment conducted and the equipment capabilities of any given laboratory.
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Affiliation(s)
- Piotr Jarocki
- Department of Biotechnology, Microbiology and Human Nutrition, University of Life Sciences in Lublin, 8 Skromna St., 20-704 Lublin, Poland; (E.K.-J.); (A.G.); (M.D.); (M.P.)
- Correspondence: (P.J.); (M.K.-W.); Tel.: +48-81462-3351 (P.J.)
| | - Elwira Komoń-Janczara
- Department of Biotechnology, Microbiology and Human Nutrition, University of Life Sciences in Lublin, 8 Skromna St., 20-704 Lublin, Poland; (E.K.-J.); (A.G.); (M.D.); (M.P.)
| | - Agnieszka Glibowska
- Department of Biotechnology, Microbiology and Human Nutrition, University of Life Sciences in Lublin, 8 Skromna St., 20-704 Lublin, Poland; (E.K.-J.); (A.G.); (M.D.); (M.P.)
| | - Michał Dworniczak
- Department of Biotechnology, Microbiology and Human Nutrition, University of Life Sciences in Lublin, 8 Skromna St., 20-704 Lublin, Poland; (E.K.-J.); (A.G.); (M.D.); (M.P.)
| | - Monika Pytka
- Department of Biotechnology, Microbiology and Human Nutrition, University of Life Sciences in Lublin, 8 Skromna St., 20-704 Lublin, Poland; (E.K.-J.); (A.G.); (M.D.); (M.P.)
| | - Agnieszka Korzeniowska-Kowal
- Polish Collection of Microorganisms (PCM), Department of Immunology of Infectious Diseases, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla 12, 53-114 Wroclaw, Poland; (A.K.-K.); (A.W.)
| | - Anna Wzorek
- Polish Collection of Microorganisms (PCM), Department of Immunology of Infectious Diseases, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla 12, 53-114 Wroclaw, Poland; (A.K.-K.); (A.W.)
| | - Monika Kordowska-Wiater
- Department of Biotechnology, Microbiology and Human Nutrition, University of Life Sciences in Lublin, 8 Skromna St., 20-704 Lublin, Poland; (E.K.-J.); (A.G.); (M.D.); (M.P.)
- Correspondence: (P.J.); (M.K.-W.); Tel.: +48-81462-3351 (P.J.)
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18
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Ricciardi A, Storti LV, Zotta T, Felis GE, Parente E. Analysis of rpoB polymorphism and PCR-based approaches for the identification of Leuconostoc mesenteroides at the species and subspecies level. Int J Food Microbiol 2020; 318:108474. [PMID: 31841785 DOI: 10.1016/j.ijfoodmicro.2019.108474] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 11/21/2019] [Accepted: 12/07/2019] [Indexed: 10/25/2022]
Abstract
Leuconostoc mesenteroides includes the subsp. cremoris, subsp. dextranicum, subsp. mesenteroides and subsp. jonggajibkimchii, but the identification at the subspecies level using current phenotypic and/or genotypic methods is still difficult. In this study, a polyphasic approach based on the analysis of rpoB gene polymorphism, Multiplex-PCR and phenotypic tests was optimised and used to identify a collection of Leuc. mesenteroides strains at the species and subspecies levels. The annotation of published Leuc. mesenteroides genomes was also revised. A polymorphic region of rpoB gene was effective in separating Leuc. mesenteroides strains at the species (rpoB-species-specific-PCR) and subspecies (phylogenetic comparison) levels. Multiplex-PCR discriminated the subsp. mesenteroides from subsp. cremoris, but strains of uncertain attribution were found among subsp. dextranicum and subsp. jonggajibkimchii. Most of phenotypic features were not suitable for subspecies discrimination. Our assays may provide a rapid and reliable identification of subsp. mesenteroides and subsp. cremoris strains in fermented foods. The discrimination of subsp. dextranicum and subsp. jonggajibkimchii suffered from several limitations (e.g. low number of available strains and genomes, phenotypic profile close to subsp. mesenteroides, discrepancy between genotypic and phenotypic traits) and further investigations are needed to clarify their delineation and taxonomical position.
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Affiliation(s)
- Annamaria Ricciardi
- Scuola di Scienze Agrarie, Alimentari, Forestali ed Ambientali (SAFE), Università degli Studi della Basilicata, 85100 Potenza, Italy
| | - Livia V Storti
- Scuola di Scienze Agrarie, Alimentari, Forestali ed Ambientali (SAFE), Università degli Studi della Basilicata, 85100 Potenza, Italy
| | - Teresa Zotta
- Istituto di Scienze dell'Alimentazione-CNR, 83100 Avellino, Italy.
| | - Giovanna E Felis
- Dipartimento di Biotecnologie, Università degli Studi di Verona, 37100 Verona, Italy
| | - Eugenio Parente
- Dipartimento di Scienze, Università degli Studi della Basilicata, 85100 Potenza, Italy
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19
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Bartkiene E, Lele V, Ruzauskas M, Domig KJ, Starkute V, Zavistanaviciute P, Bartkevics V, Pugajeva I, Klupsaite D, Juodeikiene G, Mickiene R, Rocha JM. Lactic Acid Bacteria Isolation from Spontaneous Sourdough and Their Characterization Including Antimicrobial and Antifungal Properties Evaluation. Microorganisms 2019; 8:E64. [PMID: 31905993 PMCID: PMC7023352 DOI: 10.3390/microorganisms8010064] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 12/23/2019] [Accepted: 12/27/2019] [Indexed: 02/07/2023] Open
Abstract
This research effort aimed at isolating and phenotypically characterizing lactic acid bacteria (LAB) isolates from a spontaneous rye sourdough manufactured following traditional protocols, as well as at evaluating their antimicrobial and antifungal properties as key features for future industrial applications. Thirteen LAB strains of potential industrial interest were isolated and identified to species-level via PCR. Most of the sourdough isolates showed versatile carbohydrate metabolisms. The Leuconostoc mesenteroides No. 242 and Lactobacillus brevis No. 173 demonstrated to be gas producers; thus, revealing their heterofermenter or facultative homofermenter features. Viable counts higher than 7.0 log10 (CFU/mL) were observed for Lactobacillus paracasei No. 244, Lactobacillus casei No. 210, L. brevis No. 173, Lactobacillus farraginis No. 206, Pediococcus pentosaceus No. 183, Lactobacillus uvarum No. 245 and Lactobacillus plantarum No. 135 strains, after exposure at pH 2.5 for 2 h. Moreover, L. plantarum No. 122, L. casei No. 210, Lactobacillus curvatus No. 51, L. paracasei No. 244, and L. coryniformins No. 71 showed growth inhibition properties against all the tested fifteen pathogenic strains. Finally, all LAB isolates showed antifungal activities against Aspergillus nidulans, Penicillium funiculosum, and Fusarium poae. These results unveiled the exceptionality of spontaneous sourdough as a source of LAB with effective potential to be considered in the design of novel commercial microbial single/mixed starter cultures, intended for application in a wide range of agri-food industries, where the antimicrobial and antifungal properties are often sought and necessary. In addition, metabolites therefrom may also be considered as important functional and bioactive compounds with high potential to be employed in food and feed, as well as cosmetic and pharmaceutical applications.
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Affiliation(s)
- Elena Bartkiene
- Department of Food Safety and Quality, Veterinary Academy, Lithuanian University of Health Sciences, Mickeviciaus str. 9, LT–44307 Kaunas, Lithuania; (V.L.); (V.S.); (P.Z.); (R.M.)
- Institute of Animal Rearing Technologies, Veterinary Academy, Lithuanian University of Health Sciences, Mickeviciaus str. 9, LT–44307 Kaunas, Lithuania;
| | - Vita Lele
- Department of Food Safety and Quality, Veterinary Academy, Lithuanian University of Health Sciences, Mickeviciaus str. 9, LT–44307 Kaunas, Lithuania; (V.L.); (V.S.); (P.Z.); (R.M.)
- Institute of Animal Rearing Technologies, Veterinary Academy, Lithuanian University of Health Sciences, Mickeviciaus str. 9, LT–44307 Kaunas, Lithuania;
| | - Modestas Ruzauskas
- Microbiology and Virology Institute, Veterinary Academy, Lithuanian University of Health Sciences, Mickeviciaus str. 9, LT–44307 Kaunas, Lithuania;
- Department of Anatomy and Physiology, Veterinary Academy, Lithuanian University of Health Sciences, Mickeviciaus str. 9, LT–44307 Kaunas, Lithuania
| | - Konrad J. Domig
- Institute of Food Science, Department of Food Science and Technology, BOKU-University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190 Wien, Austria;
| | - Vytaute Starkute
- Department of Food Safety and Quality, Veterinary Academy, Lithuanian University of Health Sciences, Mickeviciaus str. 9, LT–44307 Kaunas, Lithuania; (V.L.); (V.S.); (P.Z.); (R.M.)
- Institute of Animal Rearing Technologies, Veterinary Academy, Lithuanian University of Health Sciences, Mickeviciaus str. 9, LT–44307 Kaunas, Lithuania;
| | - Paulina Zavistanaviciute
- Department of Food Safety and Quality, Veterinary Academy, Lithuanian University of Health Sciences, Mickeviciaus str. 9, LT–44307 Kaunas, Lithuania; (V.L.); (V.S.); (P.Z.); (R.M.)
- Institute of Animal Rearing Technologies, Veterinary Academy, Lithuanian University of Health Sciences, Mickeviciaus str. 9, LT–44307 Kaunas, Lithuania;
| | - Vadims Bartkevics
- Department of Chemistry, University of Latvia, Jelgavas iela 1, LV-1004 Riga, Latvia; (V.B.); (I.P.)
- Institute of Food Safety, Animal Health and Environment BIOR, Lejupesiela 3, LV-1076 Riga, Latvia
| | - Iveta Pugajeva
- Department of Chemistry, University of Latvia, Jelgavas iela 1, LV-1004 Riga, Latvia; (V.B.); (I.P.)
| | - Dovile Klupsaite
- Institute of Animal Rearing Technologies, Veterinary Academy, Lithuanian University of Health Sciences, Mickeviciaus str. 9, LT–44307 Kaunas, Lithuania;
| | - Grazina Juodeikiene
- Department of Food Science and Technology, Kaunas University of Technology, Radvilenu str. 19, LT-50254 Kaunas, Lithuania;
| | - Ruta Mickiene
- Department of Food Safety and Quality, Veterinary Academy, Lithuanian University of Health Sciences, Mickeviciaus str. 9, LT–44307 Kaunas, Lithuania; (V.L.); (V.S.); (P.Z.); (R.M.)
- Instrumental Analysis Open Access Centre, Faculty of Natural Sciences, Vytautas Magnus University, Vileikos 8, LT-44404 Kaunas, Lithuania
| | - João Miguel Rocha
- REQUIMTE–Rede de Química e Tecnologia, Laboratório de Química Verde (LAQV), Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto (FCUP), Rua do Campo Alegre, s/n. P-4169-007 Porto, Portugal;
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20
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Mekadim C, Bunešová V, Vlková E, Hroncová Z, Killer J. Genetic marker-based multi-locus sequence analysis for classification, genotyping, and phylogenetics of the family Bifidobacteriaceae as an alternative approach to phylogenomics. Antonie van Leeuwenhoek 2019; 112:1785-1800. [PMID: 31368048 DOI: 10.1007/s10482-019-01307-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 07/24/2019] [Indexed: 02/07/2023]
Abstract
Bifidobacteria are widely known for their probiotic potential; however, little is known regarding the ecological significance and potential probiotic effects of the phylogenetically related 'scardovial' genera (Aeriscardovia, Alloscardovia, Bombiscardovia, Galliscardovia, Neoscardovia, Parascardovia, Pseudoscardovia and Scardovia) and Gardnerella classified with bifidobacteria within the Bifidobacteriaceae family. Accurate classification and genotyping of bacteria using certain housekeeping genes is possible, whilst current phylogenomic analyses allow for extremely precise classification. Studies of applicable genetic markers may provide results comparable to those obtained from phylogenomic analyses of the family Bifidobacteriaceae. Segments of the glyS (624 nucleotides), pheS (555 nucleotides), rpsA (630 nucleotides), and rpsB (432 nucleotides) genes and their concatenated sequence were explored. The mean glyS, pheS, rpsB and rpsA gene sequence similarities calculated for Bifidobacterium taxa were 84.8, 85.2, 90.2 and 86.8%, respectively. Interestingly, the average value of the Average Nucleotide Identity among 67 type strains of the family Bifidobacteriaceae (84.70%) calculated based on values published recently was in agreement with the average pairwise similarity (84.6%) among 75 type strains of Bifidobacteriaceae family computed in this study using the concatenated sequences of four gene fragments. Similar to phylogenomic analyses, several gene sequence and phylogenetic analyses revealed that concatenated gene regions allow for classification of Bifidobacteriaceae strains into particular phylogenetic clusters and groups. Phylogeny reconstructed from the concatenated sequences assisted in defining two novel phylogenetic groups, the Bifidobacterium psychraerophilum group consisting of B. psychraerophilum, Bifidobacterium crudilactis and Bifidobacterium aquikefiri species and the Bifidobacterium bombi group consisting of B. bombi, Bifidobacterium bohemicum and Bifidobacterium commune.
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Affiliation(s)
- Chahrazed Mekadim
- Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Vídeňská 1083, Prague 4, 142 20, Krč, Czech Republic.,Department of Microbiology, Nutrition and Dietetics, Food and Natural Resources, Faculty of Agrobiology, Czech University of Life Sciences, Kamýcká 129, Prague 6, 165 00, Suchdol, Czech Republic
| | - Věra Bunešová
- Department of Microbiology, Nutrition and Dietetics, Food and Natural Resources, Faculty of Agrobiology, Czech University of Life Sciences, Kamýcká 129, Prague 6, 165 00, Suchdol, Czech Republic
| | - Eva Vlková
- Department of Microbiology, Nutrition and Dietetics, Food and Natural Resources, Faculty of Agrobiology, Czech University of Life Sciences, Kamýcká 129, Prague 6, 165 00, Suchdol, Czech Republic
| | - Zuzana Hroncová
- Department of Microbiology, Nutrition and Dietetics, Food and Natural Resources, Faculty of Agrobiology, Czech University of Life Sciences, Kamýcká 129, Prague 6, 165 00, Suchdol, Czech Republic
| | - Jiří Killer
- Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Vídeňská 1083, Prague 4, 142 20, Krč, Czech Republic. .,Department of Microbiology, Nutrition and Dietetics, Food and Natural Resources, Faculty of Agrobiology, Czech University of Life Sciences, Kamýcká 129, Prague 6, 165 00, Suchdol, Czech Republic.
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21
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Killer J, Mekadim C, Bunešová V, Mrázek J, Hroncová Z, Vlková E. Glutamine synthetase type I (glnAI) represents a rewarding molecular marker in the classification of bifidobacteria and related genera. Folia Microbiol (Praha) 2019; 65:143-151. [PMID: 31069634 DOI: 10.1007/s12223-019-00716-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 04/29/2019] [Indexed: 01/01/2023]
Abstract
The family Bifidobacteriaceae constitutes an important phylogenetic group that particularly includes bifidobacterial taxa demonstrating proven or debated positive effects on host health. The increasingly widespread application of probiotic cultures in the twenty-first century requires detailed classification to the level of particular strains. This study aimed to apply the glutamine synthetase class I (glnAI) gene region (717 bp representing approximately 50% of the entire gene sequence) using specific PCR primers for the classification, typing, and phylogenetic analysis of bifidobacteria and closely related scardovial genera. In the family Bifidobacteriaceae, this is the first report on the use of this gene for such purposes. To achieve high-value results, almost all valid Bifidobacteriaceae type strains (75) and 15 strains isolated from various environments were evaluated. The threshold value of the glnAI gene identity among Bifidobacterium species (86.9%) was comparable to that of other phylogenetic/identification markers proposed for bifidobacteria and was much lower compared to the 16S rRNA gene. Further statistical and phylogenetic analyses suggest that the glnAI gene can be applied as a novel genetic marker in the classification, genotyping, and phylogenetic analysis of isolates belonging to the family Bifidobacteriaceae.
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Affiliation(s)
- Jiří Killer
- Institute of Animal Physiology and Genetics, v.v.i., Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague 4, Krč, Czechia. .,Faculty of Agrobiology, Food and Natural Resources, Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Kamýcká 129, 165 00, Prague 6, Suchdol, Czechia.
| | - Chahrazed Mekadim
- Institute of Animal Physiology and Genetics, v.v.i., Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague 4, Krč, Czechia.,Faculty of Agrobiology, Food and Natural Resources, Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Kamýcká 129, 165 00, Prague 6, Suchdol, Czechia
| | - Věra Bunešová
- Faculty of Agrobiology, Food and Natural Resources, Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Kamýcká 129, 165 00, Prague 6, Suchdol, Czechia
| | - Jakub Mrázek
- Institute of Animal Physiology and Genetics, v.v.i., Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague 4, Krč, Czechia
| | - Zuzana Hroncová
- Faculty of Agrobiology, Food and Natural Resources, Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Kamýcká 129, 165 00, Prague 6, Suchdol, Czechia
| | - Eva Vlková
- Faculty of Agrobiology, Food and Natural Resources, Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Kamýcká 129, 165 00, Prague 6, Suchdol, Czechia
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22
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Assessment of the probiotic potential of lactic acid bacteria isolated from kefir grains: evaluation of adhesion and antiproliferative properties in in vitro experimental systems. ANN MICROBIOL 2019. [DOI: 10.1007/s13213-019-01467-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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23
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De Bellis P, Rizzello CG, Sisto A, Valerio F, Lonigro SL, Conte A, Lorusso V, Lavermicocca P. Use of a Selected Leuconostoc Citreum Strain as a Starter for Making a "Yeast-Free" Bread. Foods 2019; 8:foods8020070. [PMID: 30781845 PMCID: PMC6406974 DOI: 10.3390/foods8020070] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 01/30/2019] [Accepted: 02/08/2019] [Indexed: 02/06/2023] Open
Abstract
The aim of this study was the characterization and selection of bacterial strains suitable for the production of a “yeast-free” bread. The strains Leuconostoc citreum C2.27 and Weissella confusa C5.7 were selected for their leavening and acidification capabilities and individually used as starters in bread-making tests. Liquid type-II sourdoughs, singly inoculated with the two selected strains, were characterized and employed for bread-making, through the set-up of a biotechnological protocol without the use of baker’s yeast as a leavening agent. Aiming to verify the ability of the selected strains to dominate the fermentation process, bacteria and yeasts were isolated from liquid sourdoughs and doughs, genetically characterized and identified. Both the selected strains were suitable for the production of bread, even if L. citreum C2.27 showed the highest leavening capacity and was able to dominate the dough microbiota. The effects of different salt concentrations on the selected strain performances were also investigated. The applicability of the developed protocol, adapted for the production of the typical Apulian bread, “puccia”, and the suitability of the strain L. citreum C2.27 were confirmed at pilot scale in an industrial bakery. The puccia bread, which was produced with the liquid sourdough fermented with L. citreum C2.27, without baker’s yeast and salt, was similar in appearance to the conventional product containing baker’s yeast and was judged positively by a sensory analysis.
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Affiliation(s)
- Palmira De Bellis
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via G. Amendola 122/O, 70126 Bari, Italy.
| | - Carlo Giuseppe Rizzello
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Via G. Amendola 165/A, 70126 Bari, Italy.
| | - Angelo Sisto
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via G. Amendola 122/O, 70126 Bari, Italy.
| | - Francesca Valerio
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via G. Amendola 122/O, 70126 Bari, Italy.
| | - Stella Lisa Lonigro
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via G. Amendola 122/O, 70126 Bari, Italy.
| | - Amalia Conte
- Department of Agricultural Sciences, Food and Environment, University of Foggia, Via Napoli 25, 71122 Foggia, Italy.
| | - Valeria Lorusso
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via G. Amendola 122/O, 70126 Bari, Italy.
| | - Paola Lavermicocca
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via G. Amendola 122/O, 70126 Bari, Italy.
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24
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Pino A, Vaccalluzzo A, Solieri L, Romeo FV, Todaro A, Caggia C, Arroyo-López FN, Bautista-Gallego J, Randazzo CL. Effect of Sequential Inoculum of Beta-Glucosidase Positive and Probiotic Strains on Brine Fermentation to Obtain Low Salt Sicilian Table Olives. Front Microbiol 2019; 10:174. [PMID: 30800110 PMCID: PMC6376858 DOI: 10.3389/fmicb.2019.00174] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 01/22/2019] [Indexed: 11/13/2022] Open
Abstract
In the present study, the β-glucosidase positive strain Lactobacillus plantarum F3. 3 was used as starter during the fermentation of Sicilian table olives (Nocellara Etnea cultivar) at two different salt concentrations (5 and 8%), in order to accelerate the debittering process. The latter was monitored through the increase of hydroxytyrosol compound. In addition, the potential probiotic Lactobacillus paracasei N24 strain was added after 60 days of fermentation. Un-inoculated brine samples at 5 and 8% of salt were used as control. The fermentation was monitored till 120 days through physico-chemical and microbiological analyses. In addition, volatile organic compounds and sensorial analyses were performed during the process and at the end of the fermentation, respectively. Lactic acid bacteria and yeasts were, in depth, studied by molecular methods and the occurrence of the potential probiotic N24 strain in the final products was determined. Results highlighted that inoculated brines exhibited a higher acidification and debittering rate than control ones. In addition, inoculated brines at 5% of salt exhibited higher polyphenols (hydoxytyrosol, tyrosol, and verbascoside) content compared to samples at 8% of NaCl, suggesting a stronger oleuropeinolytic activity of the starter at low salt concentration. Lactobacilli and yeasts dominated during the fermentation process, with the highest occurrence of L. plantarum and Wickerhamomyces anomalus, respectively. Moreover, the potential probiotic L. paracasei N24 strain was able to survive in the final product. Hence, the sequential inoculum of beta-glucosidase positive and potential probiotic strains could be proposed as a suitable technology to produce low salt Sicilian table olives.
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Affiliation(s)
- Alessandra Pino
- Department of Agricultural, Food and Environment, University of Catania, Catania, Italy
| | - Amanda Vaccalluzzo
- Department of Agricultural, Food and Environment, University of Catania, Catania, Italy
| | - Lisa Solieri
- Department of Life Sciences, University of Modena and Reggio Emilia, Reggio Emilia, Italy
| | - Flora V Romeo
- Council for Agricultural Research and Economics, Research Centre for Olive, Citrus and Tree Fruit, Acireale, Italy
| | - Aldo Todaro
- Department of Agricultural, Food and Forest Science, University of Palermo, Palermo, Italy
| | - Cinzia Caggia
- Department of Agricultural, Food and Environment, University of Catania, Catania, Italy
| | - Francisco Noé Arroyo-López
- Food Biotechnology Department, Instituto de la Grasa, Consejo Superior de Investigaciones Científicas, Universidad Pablo de Olavide, Seville, Spain
| | - Joaquin Bautista-Gallego
- Food Biotechnology Department, Instituto de la Grasa, Consejo Superior de Investigaciones Científicas, Universidad Pablo de Olavide, Seville, Spain
| | - Cinzia L Randazzo
- Department of Agricultural, Food and Environment, University of Catania, Catania, Italy
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25
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Application of A Novel Potential Probiotic Lactobacillus paracasei Strain Isolated from Kefir Grains in the Production of Feta-Type Cheese. Microorganisms 2018; 6:microorganisms6040121. [PMID: 30501107 PMCID: PMC6313735 DOI: 10.3390/microorganisms6040121] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 11/17/2018] [Accepted: 11/28/2018] [Indexed: 02/04/2023] Open
Abstract
In the present study 38 lactic acid bacteria strains were isolated from kefir grains and were monitored regarding probiotic properties in a series of established in vitro tests, including resistance to low pH, resistance to pepsin and pancreatin, and tolerance to bile salts, as well as susceptibility against common antibiotics. Among them, the strain SP3 displayed potential probiotic properties. Multiplex PCR analysis indicated that the novel strain belongs to the paracasei species. Likewise, the novel strain (Lactobacillus paracasei SP3) was applied as a starter culture for Feta-type cheese production. Feta-type cheese production resulted in significantly higher acidity; lower pH; reduced counts of coliforms, yeasts and fungi; and improved quality characteristics compared with cheese samples produced with no starter culture. Finally, it is highlighted that the application of the novel strain led to Feta-type cheese production with improved overall quality and sensory characteristics.
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26
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Bottari B, Levante A, Neviani E, Gatti M. How the Fewest Become the Greatest. L. casei's Impact on Long Ripened Cheeses. Front Microbiol 2018; 9:2866. [PMID: 30524419 PMCID: PMC6262004 DOI: 10.3389/fmicb.2018.02866] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 11/07/2018] [Indexed: 12/23/2022] Open
Abstract
Members of the Lactobacillus casei group, including species classified currently as L. casei, L. paracasei, and L. rhamnosus, are among the most frequently found species in raw milk, hard cooked, long-ripened cheeses. Starting from very low numbers in raw milk, they become dominant in the cheese during ripening, selected by physical and chemical changes produced by cheese making and ripening. Their presence at different stages of cheese making and ripening is crucial in defining product features. For these reasons, the scientific community has been more and more interested in studying these “tiny but mighty microbes” and their implications during cheese making and ripening. The present paper reviews the current literature on the effect of L. casei in cheeses, with particular reference to the case of Parmigiano Reggiano and Grana Padano, two of the most famous PDO (Protected Designation of Origin) Italian cheeses. Recent advances regarding the selection of new wild strains able to persist until the end of ripening and carrying out slow but crucial activities resulting in specific aromatic features, are also presented.
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Affiliation(s)
| | - Alessia Levante
- Department of Food and Drug, University of Parma, Parma, Italy
| | - Erasmo Neviani
- Department of Food and Drug, University of Parma, Parma, Italy
| | - Monica Gatti
- Department of Food and Drug, University of Parma, Parma, Italy
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27
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Killer J, Mekadim C, Pechar R, Bunešová V, Vlková E. The threonine-tRNA ligase gene region is applicable in classification, typing, and phylogenetic analysis of bifidobacteria. J Microbiol 2018; 56:713-721. [DOI: 10.1007/s12275-018-8167-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 06/26/2018] [Accepted: 06/27/2018] [Indexed: 11/27/2022]
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28
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Strube ML, Hansen JE, Rasmussen S, Pedersen K. A detailed investigation of the porcine skin and nose microbiome using universal and Staphylococcus specific primers. Sci Rep 2018; 8:12751. [PMID: 30143677 PMCID: PMC6109091 DOI: 10.1038/s41598-018-30689-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 08/02/2018] [Indexed: 01/10/2023] Open
Abstract
MRSA is an increasing problem in humans as well as livestock. The bacterial co-colonization of the skin in MRSA carriers has been poorly investigated and moreover, there have been no methods for high resolution investigations of the Staphylococcus genus apart from tediously culturing or doing multiple PCRs. On 120 samples from pig ear, skin and nose, we generated amplicons from the V1-V2 region of the 16S rRNA gene to gather an overview of the genus-level microbiome, along with using MRSA specific plates to count MRSA. In parallel with this, amplicons of the tuf gene were generated, targeting only a region of the tuf gene found only in the Staphylococcus genus. Using these methods, we determined a core microbiota across the healthy pig and determined the Staphylococcus genus to be dominated by S. equorum. Moreover, we found Streptococcus to be inversely associated with Staphylococcus and MRSA, suggesting a role for this genus in combating MRSA. In this work, we have thoroughly investigated the skin and nose microbiome of the pig and developed a high throughput method for profiling the Staphylococcus genus which we believe will be useful for further investigations.
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Affiliation(s)
- Mikael Lenz Strube
- National Veterinary Institute, Technical University of Denmark, Kemitorvet, building 202, DK-2800, Kgs Lyngby, Denmark.
| | - Julie Elvekjær Hansen
- National Veterinary Institute, Technical University of Denmark, Kemitorvet, building 202, DK-2800, Kgs Lyngby, Denmark
| | - Sophia Rasmussen
- National Veterinary Institute, Technical University of Denmark, Kemitorvet, building 202, DK-2800, Kgs Lyngby, Denmark
| | - Karl Pedersen
- National Veterinary Institute, Technical University of Denmark, Kemitorvet, building 202, DK-2800, Kgs Lyngby, Denmark
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29
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Huang CH, Li SW, Huang L, Watanabe K. Identification and Classification for the Lactobacillus casei Group. Front Microbiol 2018; 9:1974. [PMID: 30186277 PMCID: PMC6113361 DOI: 10.3389/fmicb.2018.01974] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 08/06/2018] [Indexed: 12/14/2022] Open
Abstract
Lactobacillus casei, Lactobacillus paracasei, and Lactobacillus rhamnosus are phenotypically and genotypically closely related, and together comprise the L. casei group. Although the strains of this group are commercially valuable as probiotics, the taxonomic status and nomenclature of the L. casei group have long been contentious because of the difficulties in identifying these three species by using the most frequently used genotypic methodology of 16S rRNA gene sequencing. Long used as the gold standard for species classification, DNA–DNA hybridization is laborious, requires expert skills, and is difficult to use routinely in laboratories. Currently, genome-based comparisons, including average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH), are commonly applied to bacterial taxonomy as alternatives to the gold standard method for the demarcating phylogenetic relationships. To establish quick and accurate methods for identifying strains in the L. casei group at the species and subspecies levels, we developed species- and subspecies-specific identification methods based on housekeeping gene sequences and whole-cell matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) spectral pattern analysis. By phylogenetic analysis based on concatenated housekeeping gene sequences (dnaJ, dnaK, mutL, pheS, and yycH), 53 strains were separated into four clusters corresponding to the four species: L. casei, L. paracasei and L. rhamnosus, and Lactobacillus chiayiensis sp. nov. A multiplex minisequencing assay using single nucleotide polymorphism (SNP)-specific primers based on the dnaK gene sequences and species-specific primers based on the mutL gene sequences provided high resolution that enabled the strains at the species level to be identified as L. casei, L. paracasei, and L. rhamnosus. By MALDI-TOF MS analysis coupled with an internal database and ClinProTools software, species- and subspecies-level L. casei group strains were identified based on reliable scores and species- and subspecies-specific MS peaks. The L. paracasei strains were distinguished clearly at the subspecies level based on subspecies-specific MS peaks. This article describes the rapid and accurate methods used for identification and classification of strains in the L. casei group based on housekeeping gene sequences and MALDI-TOF MS analysis as well as the novel speciation of this group including L. chiayiensis sp. nov. and ‘Lactobacillus zeae’ by genome-based methods.
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Affiliation(s)
- Chien-Hsun Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan
| | - Shiao-Wen Li
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Lina Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan
| | - Koichi Watanabe
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan.,Department of Animal Science and Technology, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan
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30
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A Transposon Mutagenesis System for Bifidobacterium longum subsp. longum Based on an IS 3 Family Insertion Sequence, IS Blo11. Appl Environ Microbiol 2018; 84:AEM.00824-18. [PMID: 29934330 DOI: 10.1128/aem.00824-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Accepted: 06/16/2018] [Indexed: 12/29/2022] Open
Abstract
Bifidobacteria are a major component of the intestinal microbiota in humans, particularly breast-fed infants. Therefore, elucidation of the mechanisms by which these bacteria colonize the intestine is desired. One approach is transposon mutagenesis, a technique currently attracting much attention because, in combination with next-generation sequencing, it enables exhaustive identification of genes that contribute to microbial fitness. We now describe a transposon mutagenesis system for Bifidobacterium longum subsp. longum 105-A (JCM 31944) based on ISBlo11, a native IS3 family insertion sequence. To build this system, xylose-inducible or constitutive bifidobacterial promoters were tested to drive the expression of full-length or a truncated form at the N terminus of the ISBlo11 transposase. An artificial transposon plasmid, pBFS12, in which ISBlo11 terminal inverted repeats are separated by a 3-bp spacer, was also constructed to mimic the transposition intermediate of IS3 elements. The introduction of this plasmid into a strain expressing transposase resulted in the insertion of the plasmid with an efficiency of >103 CFU/μg DNA. The plasmid targets random 3- to 4-bp sequences, but with a preference for noncoding regions. This mutagenesis system also worked at least in B. longum NCC2705. Characterization of a transposon insertion mutant revealed that a putative α-glucosidase mediates palatinose and trehalose assimilation, demonstrating the suitability of transposon mutagenesis for loss-of-function analysis. We anticipate that this approach will accelerate functional genomic studies of B. longum subsp. longumIMPORTANCE Several hundred species of bacteria colonize the mammalian intestine. However, the genes that enable such bacteria to colonize and thrive in the intestine remain largely unexplored. Transposon mutagenesis, combined with next-generation sequencing, is a promising tool to comprehensively identify these genes but has so far been applied only to a small number of intestinal bacterial species. In this study, a transposon mutagenesis system was established for Bifidobacterium longum subsp. longum, a representative health-promoting Bifidobacterium species. The system enables the identification of genes that promote colonization and survival in the intestine and should help illuminate the physiology of this species.
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Evaluation of the infB and rpsB gene fragments as genetic markers intended for identification and phylogenetic analysis of particular representatives of the order Lactobacillales. Arch Microbiol 2018; 200:1427-1437. [PMID: 30039323 DOI: 10.1007/s00203-018-1554-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 06/28/2018] [Accepted: 07/17/2018] [Indexed: 10/28/2022]
Abstract
Detailed differentiation, classification, and phylogenetic analysis of the order Lactobacillales are performed using molecular techniques that involve the comparison of whole genomes, multilocus sequence analysis, DNA-DNA hybridisation, and 16S rRNA sequencing. Despite the wide application of the latter two techniques, issues associated with them are extensively discussed. Although complete genomic analyses are the most appropriate for phylogenetic studies, they are time-consuming and require high levels of expertise. Many phylogenetic/identification markers have been proposed for enterococci, lactobacilli, streptococci, and lactobacilli. However, none have been established for vagococci and some genera within the order Lactobacillales. The objective of the study was to find novel alternative housekeeping genes for classification, typing, and phylogenetic analysis of selected genera within the order Lactobacillales. We designed primers flanking variable regions of the infB (504 nt) and rpsB (333 nt) genes and amplified and sequenced them in 56 strains of different genera within the order Lactobacillales. Statistical analysis and characteristics of the gene regions suggested that they could be used for taxonomic purposes. Phylogenetic analyses, including assessment of (in)congruence between individual phylogenetic trees indicated the possibility of using the concatenation of the two genes as an alternative tool for the evaluation of phylogeny compared with the 16S rRNA gene representing the standard phylogenetic marker of prokaryotes. Moreover, infB, rpsB regions and their concatenate were phylogenetically consistent with two widely applied alternative genetic markers in taxonomy of particular Lactobacillales genera encoding the 60 kDa chaperonin protein (GroEL-hsp60) and phenylalanyl-tRNA synthetase, alpha subunit (pheS).
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Lactobacillus plantarum LUHS135 and paracasei LUHS244 as functional starter cultures for the food fermentation industry: Characterisation, mycotoxin-reducing properties, optimisation of biomass growth and sustainable encapsulation by using dairy by-products. Lebensm Wiss Technol 2018. [DOI: 10.1016/j.lwt.2018.04.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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tuf Gene Sequence Variation in Bifidobacterium longum subsp. infantis Detected in the Fecal Microbiota of Chinese Infants. Appl Environ Microbiol 2018; 84:AEM.00336-18. [PMID: 29703739 DOI: 10.1128/aem.00336-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 04/20/2018] [Indexed: 12/12/2022] Open
Abstract
Members of the bacterial genus Bifidobacterium generally dominate the fecal microbiota of infants. The species Bifidobacterium longum is prevalent, but the B. longum subsp. longum and B. longum subsp. infantis strains that are known to colonize the infant bowel are not usually differentiated in microbiota investigations. These subspecies differ in their capacities to metabolize human milk oligosaccharides (HMO) and may have different ecological and symbiotic roles in humans. Quantitative PCR provides a quick analytical method by which to accurately ascertain the abundances of target species in microbiotas and microcosms. However, amplification targets in DNA extracted from samples need to be dependably differential. We evaluated the tuf gene sequence as a molecular target for quantitative PCR measurements of the abundances of B. longum subsp. infantis and B. longum subsp. longum in fecal microbiotas. This approach resulted in the detection of a tuf gene variant (operational taxonomic unit 49 [OTU49]) in Chinese infants that has sequence similarities to both B. longum subsp. infantis and B. longum subsp. longum We compared the genome sequence and growth and transcriptional characteristics of an OTU49 isolate cultured in HMO medium to those of other B. longum subsp. infantis cultures. We concluded from these studies that OTU49 belongs to B. longum subsp. infantis, that dependable quantitative PCR (qPCR) differentiation between the B. longum subspecies cannot be achieved by targeting tuf gene sequences, and that functional genes involved in carbohydrate metabolism might be better targets because they delineate ecological functions.IMPORTANCE High-throughput DNA sequencing methods and advanced bioinformatics analysis have revealed the composition and biochemical capacities of microbial communities (microbiota and microbiome), including those that inhabit the gut of human infants. However, the microbiology and function of natural ecosystems have received little attention in recent decades, so an appreciation of the dynamics of gut microbiota interactions is lacking. With respect to infants, rapid methodologies, such as quantitative PCR, are needed to determine the prevalences and proportions of different bifidobacterial species in observational and microcosm studies in order to obtain a better understanding of the dynamics of bifidobacterial nutrition and syntrophy, knowledge that might be used to manipulate the microbiota and perhaps ensure the better health of infants.
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Thanissery R, Zeng D, Doyle RG, Theriot CM. A Small Molecule-Screening Pipeline to Evaluate the Therapeutic Potential of 2-Aminoimidazole Molecules Against Clostridium difficile. Front Microbiol 2018; 9:1206. [PMID: 29928268 PMCID: PMC5997789 DOI: 10.3389/fmicb.2018.01206] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 05/17/2018] [Indexed: 12/19/2022] Open
Abstract
Antibiotics are considered to be the first line of treatment for mild to moderately severe Clostridium difficile infection (CDI) in humans. However, antibiotics are also risk factors for CDI as they decrease colonization resistance against C. difficile by altering the gut microbiota and metabolome. Finding compounds that selectively inhibit different stages of the C. difficile life cycle, while sparing the indigenous gut microbiota is important for the development of alternatives to standard antibiotic treatment. 2-aminoimidazole (2-AI) molecules are known to disrupt bacterial protection mechanisms in antibiotic resistant bacteria such as Pseudomonas aeruginosa, Acinetobacter baumannii, and Staphylococcus aureus, but are yet to be evaluated against C. difficile. A comprehensive small molecule-screening pipeline was developed to investigate how novel small molecules affect different stages of the C. difficile life cycle (growth, toxin, and sporulation) in vitro, and a library of commensal bacteria that are associated with colonization resistance against C. difficile. The initial screening tested the efficacy of eleven 2-AI molecules (compound 1 through 11) against C. difficile R20291 compared to a vancomycin (2 μg/ml) control. Molecules were selected for their ability to inhibit C. difficile growth, toxin activity, and sporulation. Further testing included growth inhibition of other C. difficile strains (CD196, M68, CF5, 630, BI9, M120) belonging to distinct PCR ribotypes, and a commensal panel (Bacteroides fragilis, B. thetaiotaomicron, C. scindens, C. hylemonae, Lactobacillus acidophilus, L. gasseri, Escherichia coli, B. longum subsp. infantis). Three molecules compound 1 and 2, and 3 were microbicidal, whereas compounds 4, 7, 9, and 11 inhibited toxin activity without affecting the growth of C. difficile strains and the commensal microbiota. The antimicrobial and anti-toxin effects of 2-AI molecules need to be further characterized for mode of action and validated in a mouse model of CDI.
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Affiliation(s)
- Rajani Thanissery
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
| | - Daina Zeng
- Agile Sciences, Inc., Raleigh, NC, United States
| | - Raul G Doyle
- Agile Sciences, Inc., Raleigh, NC, United States
| | - Casey M Theriot
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
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Pino A, De Angelis M, Todaro A, Van Hoorde K, Randazzo CL, Caggia C. Fermentation of Nocellara Etnea Table Olives by Functional Starter Cultures at Different Low Salt Concentrations. Front Microbiol 2018; 9:1125. [PMID: 29922251 PMCID: PMC5996112 DOI: 10.3389/fmicb.2018.01125] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 05/14/2018] [Indexed: 11/13/2022] Open
Abstract
Nocellara Etnea is one of the main Sicilian cultivars traditionally used to produce both olive oil and naturally fermented table olives. In the present study, the effect of different salt concentrations on physico-chemical, microbiological, sensorial, and volatile organic compounds (VOCs) formation was evaluated in order to obtain functional Nocellara Etnea table olives. The experimental design consisted of 8 treatments as follow: fermentations at 4, 5, 6, and 8% of salt with (E1-E4 samples) and without (C1-C4 samples) the addition of starters. All the trials were carried out at room temperature (18 ± 2°C) and monitored for an overall period of 120 d. In addition, the persistence of the potential probiotic Lactobacillus paracasei N24 at the end of the process was investigated. Microbiological data revealed the dominance of lactic acid bacteria (LAB), starting from the 7th d of fermentation, and the reduction of yeasts and enterobacteria in the final product inoculated with starters. VOCs profile highlighted a high amount of aldehydes at the beginning of fermentation, which significantly decreased through the process and a concomitant increase of alcohols, acids, esters, and phenols. In particular, esters showed an occurrence percentage higher in experimental samples rather than in control ones, contributing to more pleasant flavors. Moreover, acetic acid, ethanol, and phenols, which often generate off-flavors, were negatively correlated with mesophilic bacteria and LAB. It is interesting to note that salt content did not affect the performances of starter cultures and slightly influenced the metabolome of table olives. Sensory data demonstrated significant differences among samples registering the highest overall acceptability in the experimental sample at 5% of NaCl. The persistence of the L. paracasei N24 strain in experimental samples, at the end of the process, revealed its promising perspectives as starter culture for the production of functional table olives with reduced salt content.
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Affiliation(s)
- Alessandra Pino
- Department of Agricultural, Food and Environment, University of Catania, Catania, Italy
| | - Maria De Angelis
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
| | - Aldo Todaro
- Department of Agricultural, Food and Forest Science, University of Palermo, Palermo, Italy
| | - Koenraad Van Hoorde
- Laboratory of Brewing and Biochemistry, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Cinzia L. Randazzo
- Department of Agricultural, Food and Environment, University of Catania, Catania, Italy
| | - Cinzia Caggia
- Department of Agricultural, Food and Environment, University of Catania, Catania, Italy
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Effects of selected bacterial cultures on safety and sensory traits of Nocellara Etnea olives produced at large factory scale. Food Chem Toxicol 2018; 115:491-498. [DOI: 10.1016/j.fct.2018.03.045] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 03/08/2018] [Accepted: 03/30/2018] [Indexed: 11/18/2022]
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Juvonen R, Partanen T, Koivula T. Evaluation of Reverse-Transcription PCR Detection of 16S rRNA andTufmRNA for Viable/Dead Discrimination of Beer-Spoilage Lactic Acid Bacteria. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2018. [DOI: 10.1094/asbcj-2010-0416-01] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
| | | | - Teija Koivula
- VTT Technical Research Centre of Finland, VTT, Finland
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Stachelska MA. Identification of Lactobacillus delbrueckii and Streptococcus thermophilus Strains Present in Artisanal Raw Cow Milk Cheese Using Real-time PCR and Classic Plate Count Methods. Pol J Microbiol 2017; 66:491-499. [DOI: 10.5604/01.3001.0010.7041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The aim of this paper was to detect Lactobacillus delbrueckii and Streptococcus thermophilus using real-time quantitative PCR assay in 7-day ripening cheese produced from unpasteurised milk. Real-time quantitative PCR assays were designed to identify and enumerate the chosen species of lactic acid bacteria (LAB) in ripened cheese. The results of molecular quantification and classic bacterial enumeration showed a high level of similarity proving that DNA extraction was carried out in a proper way and that genomic DNA solutions were free of PCR inhibitors. These methods revealed the presence of L. delbrueckii and S. thermophilus. The real-time PCR enabled quantification with a detection of 101–103 CFU/g of product. qPCR-standard curves were linear over seven log units down to 101 copies per reaction; efficiencies ranged from 77.9% to 93.6%. Cheese samples were analysed with plate count method and qPCR in parallel. Compared with the classic plate count method, the newly developed qPCR method provided faster and species specific identification of two dairy LAB and yielded comparable quantitative results.
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Affiliation(s)
- Milena A. Stachelska
- Institute of Food Technology and Gastronomy, Lomza State University of Applied Sciences, Lomza, Poland
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Assessment of Bifidobacterium Species Using groEL Gene on the Basis of Illumina MiSeq High-Throughput Sequencing. Genes (Basel) 2017; 8:genes8110336. [PMID: 29160815 PMCID: PMC5704249 DOI: 10.3390/genes8110336] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 11/15/2017] [Indexed: 11/17/2022] Open
Abstract
The next-generation high-throughput sequencing techniques have introduced a new way to assess the gut’s microbial diversity on the basis of 16S rRNA gene-based microbiota analysis. However, the precise appraisal of the biodiversity of Bifidobacterium species within the gut remains a challenging task because of the limited resolving power of the 16S rRNA gene in different species. The groEL gene, a protein-coding gene, evolves quickly and thus is useful for differentiating bifidobacteria. Here, we designed a Bifidobacterium-specific primer pair which targets a hypervariable sequence region within the groEL gene that is suitable for precise taxonomic identification and detection of all recognized species of the genus Bifidobacterium so far. The results showed that the novel designed primer set can specifically differentiate Bifidobacterium species from non-bifidobacteria, and as low as 104 cells of Bifidobacterium species can be detected using the novel designed primer set on the basis of Illumina Miseq high-throughput sequencing. We also developed a novel protocol to assess the diversity of Bifidobacterium species in both human and rat feces through high-throughput sequencing technologies using groEL gene as a discriminative marker.
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Killer J, Pechar R, Švec P, Salmonová H, Švejstil R, Geigerová M, Rada V, Vlková E, Mekadim C. Lactobacillus caviae sp. nov., an obligately heterofermentative bacterium isolated from the oral cavity of a guinea pig (Cavia aperea f. porcellus). Int J Syst Evol Microbiol 2017; 67:2903-2909. [DOI: 10.1099/ijsem.0.002044] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Jiri Killer
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, Prague 6 – Suchdol, 165 00, Czech Republic
- Institute of Animal Physiology and Genetics v.v.i., Czech Academy of Sciences, Vídeňská 1083, Prague 4 – Krč, 142 20, Czech Republic
| | - Radko Pechar
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, Prague 6 – Suchdol, 165 00, Czech Republic
- Food Research Institute Prague, Radiová 1285/7, Prague 10 – Hostivař, 102 00, Czech Republic
| | - Pavel Švec
- Department of Experimental Biology, Czech Collection of Microorganisms, Masaryk University, Faculty of Science, Kamenice 5, 625 00 Brno, Czech Republic
| | - Hana Salmonová
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, Prague 6 – Suchdol, 165 00, Czech Republic
| | - Roman Švejstil
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, Prague 6 – Suchdol, 165 00, Czech Republic
| | - Martina Geigerová
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, Prague 6 – Suchdol, 165 00, Czech Republic
| | - Vojtěch Rada
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, Prague 6 – Suchdol, 165 00, Czech Republic
| | - Eva Vlková
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, Prague 6 – Suchdol, 165 00, Czech Republic
| | - Chahrazed Mekadim
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, Prague 6 – Suchdol, 165 00, Czech Republic
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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.
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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
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Plessas S, Nouska C, Karapetsas A, Kazakos S, Alexopoulos A, Mantzourani I, Chondrou P, Fournomiti M, Galanis A, Bezirtzoglou E. Isolation, characterization and evaluation of the probiotic potential of a novel Lactobacillus strain isolated from Feta-type cheese. Food Chem 2017; 226:102-108. [DOI: 10.1016/j.foodchem.2017.01.052] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Revised: 12/07/2016] [Accepted: 01/11/2017] [Indexed: 01/15/2023]
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Janulaitiene M, Paliulyte V, Grinceviciene S, Zakareviciene J, Vladisauskiene A, Marcinkute A, Pleckaityte M. Prevalence and distribution of Gardnerella vaginalis subgroups in women with and without bacterial vaginosis. BMC Infect Dis 2017; 17:394. [PMID: 28583109 PMCID: PMC5460423 DOI: 10.1186/s12879-017-2501-y] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 05/28/2017] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Bacterial vaginosis (BV) is one of the leading causes of vaginal complaints among women of childbearing age. The role of Gardnerella vaginalis remains controversial due to its presence in healthy and BV-type vaginal microflora. The phenotypic and genotypic heterogeneity of G. vaginalis suggested the existence of strain variants linked with different health conditions. We sought to analyze prevalence and distribution of G. vaginalis subgroups (clades) in BV-positive (n = 29), partial BV (n = 27), and BV-negative (n = 53) vaginal samples from Lithuanian women. METHODS Vaginal samples were characterized by Amsel criteria and the Nugent method. Bacterial signatures characteristic of BV and concomitant infections were identified by culture and PCR. Using singleplex PCR assays, G. vaginalis subgroups were identified in 109 noncultured vaginal specimens by targeting clade-specific genes. Isolated G. vaginalis clinical strains were subtyped and the presence of the sialidase coding gene was detected by PCR. Data analysis was performed using GraphPad Prism statistical software. RESULTS G. vaginalis was found in 87% of women without BV. Clade 4 was most frequently detected (79.4%), followed by clade 1 (63.7%), clade 2 (42.2%), and clade 3 (15.7%). Multi-clade G. vaginalis communities showed a positive association with Nugent score (NS) ≥ 4 (OR 3.64; 95% CI 1.48-8.91; p = 0.005). Clade 1 and clade 2 were statistically significantly more common in samples with NS 7-10 (OR 4.69; 95% CI 1.38-15.88; p = 0.01 and OR 6.26; 95% CI 2.20-17.81; p ≤ 0.001, respectively). Clade 3 and clade 4 showed no association with high NS (OR 0.88; 95% CI 0.26-3.04; p = 1.00 and OR 1.31; 95% CI 0.39-4.41; p = 0.767, respectively). The gene coding for sialidase was detected in all isolates of clade 1 and clade 2, but not in clade 4 isolates. CONCLUSIONS We showed an association between the microbial state of vaginal microflora and specific subgroups of G. vaginalis, the distribution of which may determine the clinical manifestation of BV. The frequent detection of clade 4 in the BV-negative samples might be due its lack of the gene coding for sialidase.
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Affiliation(s)
- Migle Janulaitiene
- Institute of Biotechnology, Vilnius University, Sauletekio al. 7, 10257 Vilnius, Lithuania
- National Public Health Surveillance Laboratory, Zolyno g. 36, 10210 Vilnius, Lithuania
| | - Virginija Paliulyte
- Clinic of Obstetrics & Gynaecology, Faculty of Medicine, Vilnius University, Ciurlionio g. 21/27, 03101 Vilnius, Lithuania
- Centre of Obstetrics & Gynaecology, Vilnius University Hospital Santaros Klinikos, Santariskiu g. 2, 08661 Vilnius, Lithuania
- Antiaging Clinic, Sakalu g. 22, 08108 Vilnius, Lithuania
| | - Svitrigaile Grinceviciene
- Institute of Biotechnology, Vilnius University, Sauletekio al. 7, 10257 Vilnius, Lithuania
- Ona Gureviciene Family Clinic, Gedimino g. 17, 68307 Marijampole, Lithuania
| | - Jolita Zakareviciene
- Clinic of Obstetrics & Gynaecology, Faculty of Medicine, Vilnius University, Ciurlionio g. 21/27, 03101 Vilnius, Lithuania
- Centre of Obstetrics & Gynaecology, Vilnius University Hospital Santaros Klinikos, Santariskiu g. 2, 08661 Vilnius, Lithuania
- Antiaging Clinic, Sakalu g. 22, 08108 Vilnius, Lithuania
| | - Alma Vladisauskiene
- Centre of Obstetrics & Gynaecology, Vilnius University Hospital Santaros Klinikos, Santariskiu g. 2, 08661 Vilnius, Lithuania
- Antiaging Clinic, Sakalu g. 22, 08108 Vilnius, Lithuania
| | - Agne Marcinkute
- Antiaging Clinic, Sakalu g. 22, 08108 Vilnius, Lithuania
- Departament of Gynaecology, Vilnius City Clinical Hospital, Antakalnio g. 57, 10207 Vilnius, Lithuania
| | - Milda Pleckaityte
- Institute of Biotechnology, Vilnius University, Sauletekio al. 7, 10257 Vilnius, Lithuania
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Pino A, Van Hoorde K, Pitino I, Russo N, Carpino S, Caggia C, Randazzo CL. Survival of potential probiotic lactobacilli used as adjunct cultures on Pecorino Siciliano cheese ripening and passage through the gastrointestinal tract of healthy volunteers. Int J Food Microbiol 2017; 252:42-52. [PMID: 28458191 DOI: 10.1016/j.ijfoodmicro.2017.04.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 03/02/2017] [Accepted: 04/20/2017] [Indexed: 12/01/2022]
Abstract
In the present study, two lactobacilli strains, Lactobacillus rhamnosus H25 and Lactobacillus paracasei N24, used as adjunct cultures, were evaluated for their heat resistance both with and without prior heat adaptation and for their survival, at industrial scale, during the production and ripening of the Pecorino Siciliano cheese. In addition, the viability and persistence of the lactobacilli strains after passage through the gastrointestinal tract of healthy volunteers were evaluated by using rep-PCR analysis of viable cells. Both strains exhibited good heat resistance and survival throughout cheese production and ripening, and positively influenced the physico-chemical, the microbiological and the sensorial characteristics of the final product. In addition, the molecular typing of the lactobacilli isolates, retrieved from fecal samples of healthy volunteers during and after 15 days of the experimental cheese administration, revealed a high survival of the strains, highlighting their persistence during passage into the GI tract. In conclusion, this study proposes the two adjunct cultures as potential probiotic candidate deliverable by cheese.
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Affiliation(s)
- Alessandra Pino
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Santa Sofia 98, 95123 Catania, Italy
| | - Koenraad Van Hoorde
- Laboratory of Brewing and Biochemistry, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, 9000 Gent, Belgium
| | - Iole Pitino
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Santa Sofia 98, 95123 Catania, Italy
| | - Nunziatina Russo
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Santa Sofia 98, 95123 Catania, Italy
| | - Stefania Carpino
- CoRFiLaC, Regione Siciliana, S.P. 25 Km 5 Ragusa Mare, 97100 Ragusa, Italy
| | - Cinzia Caggia
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Santa Sofia 98, 95123 Catania, Italy.
| | - Cinzia L Randazzo
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Santa Sofia 98, 95123 Catania, Italy
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Mianzhi Y, Shah NP. Contemporary nucleic acid-based molecular techniques for detection, identification, and characterization of Bifidobacterium. Crit Rev Food Sci Nutr 2017; 57:987-1016. [PMID: 26565761 DOI: 10.1080/10408398.2015.1023761] [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] [Indexed: 12/31/2022]
Abstract
Bifidobacteria are one of the most important bacterial groups found in the gastrointestinal tract of humans. Medical and food industry researchers have focused on bifidobacteria because of their health-promoting properties. Researchers have historically relied on classic phenotypic approaches (culture and biochemical tests) for detection and identification of bifidobacteria. Those approaches still have values for the identification and detection of some bifidobacterial species, but they are often labor-intensive and time-consuming and can be problematic in differentiating closely related species. Rapid, accurate, and reliable methods for detection, identification, and characterization of bifidobacteria in a mixed bacterial population have become a major challenge. The advent of nucleic acid-based molecular techniques has significantly advanced isolation and detection of bifidobacteria. Diverse nucleic acid-based molecular techniques have been employed, including hybridization, target amplification, and fingerprinting. Certain techniques enable the detection, characterization, and identification at genus-, species-, and strains-levels, whereas others allow typing of species or strains of bifidobacteria. In this review, an overview of methodological principle, technique complexity, and application of various nucleic acid-based molecular techniques for detection, identification, and characterization of bifidobacteria is presented. Advantages and limitations of each technique are discussed, and significant findings based on particular techniques are also highlighted.
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Affiliation(s)
- Yao Mianzhi
- a Food and Nutritional Science , School of Biological Sciences, The University of Hong Kong , Hong Kong
| | - Nagendra P Shah
- a Food and Nutritional Science , School of Biological Sciences, The University of Hong Kong , Hong Kong
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Kwong WK, Medina LA, Koch H, Sing KW, Soh EJY, Ascher JS, Jaffé R, Moran NA. Dynamic microbiome evolution in social bees. SCIENCE ADVANCES 2017; 3:e1600513. [PMID: 28435856 PMCID: PMC5371421 DOI: 10.1126/sciadv.1600513] [Citation(s) in RCA: 254] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 02/10/2017] [Indexed: 05/18/2023]
Abstract
The highly social (eusocial) corbiculate bees, comprising the honey bees, bumble bees, and stingless bees, are ubiquitous insect pollinators that fulfill critical roles in ecosystem services and human agriculture. Here, we conduct wide sampling across the phylogeny of these corbiculate bees and reveal a dynamic evolutionary history behind their microbiota, marked by multiple gains and losses of gut associates, the presence of generalist as well as host-specific strains, and patterns of diversification driven, in part, by host ecology (for example, colony size). Across four continents, we found that different host species have distinct gut communities, largely independent of geography or sympatry. Nonetheless, their microbiota has a shared heritage: The emergence of the eusocial corbiculate bees from solitary ancestors appears to coincide with the acquisition of five core gut bacterial lineages, supporting the hypothesis that host sociality facilitates the development and maintenance of specialized microbiomes.
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Affiliation(s)
- Waldan K. Kwong
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA
- Department of Integrative Biology, University of Texas, Austin, Austin, TX 78712, USA
- Corresponding author. (W.K.K.); (N.A.M.)
| | - Luis A. Medina
- Department of Integrative Biology, University of Texas, Austin, Austin, TX 78712, USA
| | - Hauke Koch
- Department of Integrative Biology, University of Texas, Austin, Austin, TX 78712, USA
| | - Kong-Wah Sing
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Eunice Jia Yu Soh
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - John S. Ascher
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Rodolfo Jaffé
- Vale Institute of Technology, Sustainable Development, 66055-090 Belém PA, Brazil
- Department of Ecology, Universidade de São Paulo, Rua do Matão 321, 05508-090 São Paulo SP, Brazil
| | - Nancy A. Moran
- Department of Integrative Biology, University of Texas, Austin, Austin, TX 78712, USA
- Corresponding author. (W.K.K.); (N.A.M.)
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Demkin VV, Koshechkin SI, Slesarev A. A novel real-time PCR assay for highly specific detection and quantification of vaginal lactobacilli. Mol Cell Probes 2016; 32:33-39. [PMID: 27890610 DOI: 10.1016/j.mcp.2016.11.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 11/22/2016] [Accepted: 11/22/2016] [Indexed: 01/06/2023]
Abstract
PCR detection and quantification of vaginal lactobacilli remains problematic because of the high level of genetic heterogeneity and taxonomic complexity within the genus Lactobacillus. The aim of the present study was to identify conserved sequences among the genomes of major species of vaginal lactobacilli that could be used for the development of a PCR-based method for quantitative determination of vaginal microbiota-specific lactobacilli. Comparative analysis of the genomes of several species of vaginal lactobacilli allowed us to identify conserved regions in the rplK gene, which encodes ribosomal protein L11, and to design group-specific PCR primers and a probe for selected species from the L. acidophilus complex, including major vaginal lactobacilli Lactobacillus crispatus, L. gasseri, L. iners and L. jensenii as well as other species that are less common in vaginal microbiota. The applicability of the new assay in routine diagnostic testing was evaluated using a set of clinical samples. The assay was able to detect and quantify vagina-associated lactobacilli within a wide range of initial DNA template concentrations, indicating promising potential for clinical applications.
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Affiliation(s)
- Vladimir V Demkin
- Laboratory of Molecular Diagnostics, Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia.
| | - Stanislav I Koshechkin
- Laboratory of Molecular Diagnostics, Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Alexei Slesarev
- Zylacta Corporation, 7965 Cessna Avenue, Gaithersburg, MD 20879, USA; Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
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Górska S, Dylus E, Rudawska A, Brzozowska E, Srutkova D, Schwarzer M, Razim A, Kozakova H, Gamian A. Immunoreactive Proteins of Bifidobacterium longum ssp. longum CCM 7952 and Bifidobacterium longum ssp. longum CCDM 372 Identified by Gnotobiotic Mono-Colonized Mice Sera, Immune Rabbit Sera and Non-immune Human Sera. Front Microbiol 2016; 7:1537. [PMID: 27746766 PMCID: PMC5040718 DOI: 10.3389/fmicb.2016.01537] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 09/14/2016] [Indexed: 12/23/2022] Open
Abstract
The Bifidobacteria show great diversity in the cell surface architecture which may influence the physicochemical properties of the bacterial cell and strain specific properties. The immunomodulatory role of bifidobacteria has been extensively studied, however studies on the immunoreactivity of their protein molecules are very limited. Here, we compared six different methods of protein isolation and purification and we report identification of immunogenic and immunoreactive protein of two human Bifidobacterium longum ssp. longum strains. We evaluated potential immunoreactive properties of proteins employing polyclonal sera obtained from germ free mouse, rabbit and human. The protein yield was isolation method-dependent and the reactivity of proteins detected by SDS-PAGE and Western blotting was heterogeneous and varied between different serum samples. The proteins with the highest immunoreactivity were isolated, purified and have them sequenced. Among the immunoreactive proteins we identified enolase, aspartokinase, pyruvate kinase, DnaK (B. longum ssp. longum CCM 7952) and sugar ABC transporter ATP-binding protein, phosphoglycerate kinase, peptidoglycan synthethase penicillin-binding protein 3, transaldolase, ribosomal proteins and glyceraldehyde 3-phosphate dehydrogenase (B. longum ssp. longum CCDM 372).
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Affiliation(s)
- Sabina Górska
- Department of Medical Microbiology, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy of the Polish Academy of Sciences Wroclaw, Poland
| | - Ewa Dylus
- Department of Medical Microbiology, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy of the Polish Academy of Sciences Wroclaw, Poland
| | - Angelika Rudawska
- Department of Medical Microbiology, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy of the Polish Academy of Sciences Wroclaw, Poland
| | - Ewa Brzozowska
- Department of Medical Microbiology, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy of the Polish Academy of Sciences Wroclaw, Poland
| | - Dagmar Srutkova
- Laboratory of Gnotobiology, Institute of Microbiology, Academy of Sciences of the Czech Republic v. v. i., Novy Hradek, Czech Republic
| | - Martin Schwarzer
- Laboratory of Gnotobiology, Institute of Microbiology, Academy of Sciences of the Czech Republic v. v. i., Novy Hradek, Czech Republic
| | - Agnieszka Razim
- Department of Medical Microbiology, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy of the Polish Academy of Sciences Wroclaw, Poland
| | - Hana Kozakova
- Laboratory of Gnotobiology, Institute of Microbiology, Academy of Sciences of the Czech Republic v. v. i., Novy Hradek, Czech Republic
| | - Andrzej Gamian
- Department of Medical Microbiology, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy of the Polish Academy of Sciences Wroclaw, Poland
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Schlabritz-Loutsevitch N, Gygax SE, Dick E, Smith WL, Snider C, Hubbard G, Ventolini G. Vaginal Dysbiosis from an Evolutionary Perspective. Sci Rep 2016; 6:26817. [PMID: 27226349 PMCID: PMC4880931 DOI: 10.1038/srep26817] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 05/09/2016] [Indexed: 12/11/2022] Open
Abstract
Evolutionary approaches are powerful tools for understanding human disorders. The composition of vaginal microbiome is important for reproductive success and has not yet been characterized in the contexts of social structure and vaginal pathology in non-human primates (NHPs). We investigated vaginal size, vulvovaginal pathology and the presence of the main human subtypes of Lactobacillus spp./ BV-related species in the vaginal microflora of baboons (Papio spp.). We performed morphometric measurements of external and internal genitalia (group I, n = 47), analyzed pathology records of animals from 1999–2015 (group II, n = 64 from a total of 12,776), and evaluated vaginal swabs using polymerase chain reaction (PCR) (group III, n = 14). A total of 68 lesions were identified in 64 baboons. Lactobacillus iners, Gardnerella vaginalis, Atopobium vaginae, Megasphaera I, and Megasphaera II were not detected. L. jensenii, L. crispatus, and L. gasseri were detected in 2/14 (14.2%), 1/14 (7.1%), and 1/14 (7.1%) samples, respectively. BVAB2 was detected in 5/14 (35.7%) samples. The differences in the vaginal milieu between NHP and humans might be the factor associated with human-specific pattern of placental development and should be taken in consideration in NHP models of human pharmacology and microbiology.
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Affiliation(s)
| | - Scott E Gygax
- Femeris Women's Health Research Center, Genesis Biotechnology Group - Hamilton, New Jersey, USA
| | - Edward Dick
- Southwest National Primate Research Center, San Antonio, Texas, USA
| | - William L Smith
- Femeris Women's Health Research Center, Genesis Biotechnology Group - Hamilton, New Jersey, USA
| | - Cathy Snider
- Southwest National Primate Research Center, San Antonio, Texas, USA
| | - Gene Hubbard
- University of Texas Health Sciences Center, San Antonio, Texas, USA
| | - Gary Ventolini
- Texas Tech University Health Sciences Center at the Permian Basin, Odessa, Texas, USA
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Blandino G, Fazio D, Petronio GP, Inturri R, Tempera G, Furneri PM. Labeling quality and molecular characterization studies of products containing Lactobacillus spp. strains. Int J Immunopathol Pharmacol 2016; 29:121-8. [PMID: 26667227 PMCID: PMC5806746 DOI: 10.1177/0394632015600534] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 07/23/2015] [Indexed: 11/17/2022] Open
Abstract
The objective of the study was to characterize at species level by phenotypic and different molecular methods the strains of Lactobacillus spp. used as constituents of five oral and four vaginal products. Susceptibilities to representative antibiotics were evaluated. In addition, total viable counts at mid and 3 months to deadline of shelf life, in the different formulations and the presence of eventual contaminant microorganisms were investigated.In all oral products the molecular characterization at species level of the strains of Lactobacillus spp. confirmed the strains stated on the label, except for one strain cited on the label as Lactobacillus casei, that our study characterized as Lactobacillus paracasei. In oral products total viable cell content complied with content claimed on the label. In three out four vaginal products (one product claimed "bacillo di Döderlein"), molecular characterization complied with the bacterial name stated on the label. Two vaginal products reported viable counts on the label that were confirmed by our study. The other vaginal products, which did not report bacterial counts on the label, showed a similar decrease of viable counts at different dates to deadline compared to the others. From all the tested products, contaminant microorganisms and acquired resistance to representative antibiotics by the probiotic strains were not detected.
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Affiliation(s)
- Giovanna Blandino
- Dipartimento di Scienze Biomediche e Biotecnologiche, Sezione di Microbiologia, Università degli Studi di Catania, Catania, Italy
| | - Davide Fazio
- Dipartimento di Scienze Biomediche e Biotecnologiche, Sezione di Microbiologia, Università degli Studi di Catania, Catania, Italy
| | - Giulio Petronio Petronio
- Dipartimento di Scienze Biomediche e Biotecnologiche, Sezione di Microbiologia, Università degli Studi di Catania, Catania, Italy IRCCS San Raffaele Pisana, BioBIM - Multidisciplinary Interinstitutional BioBank, Rome, Italy
| | - Rosanna Inturri
- Dipartimento di Scienze Biomediche e Biotecnologiche, Sezione di Microbiologia, Università degli Studi di Catania, Catania, Italy
| | - Gianna Tempera
- Dipartimento di Scienze Biomediche e Biotecnologiche, Sezione di Microbiologia, Università degli Studi di Catania, Catania, Italy
| | - Pio Maria Furneri
- Dipartimento di Scienze Biomediche e Biotecnologiche, Sezione di Microbiologia, Università degli Studi di Catania, Catania, Italy
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