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Significance of traditional fermented foods in the lower Mekong subregion: A focus on lactic acid bacteria. FOOD BIOSCI 2018. [DOI: 10.1016/j.fbio.2018.10.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Trček J, Barja F. Updates on quick identification of acetic acid bacteria with a focus on the 16S-23S rRNA gene internal transcribed spacer and the analysis of cell proteins by MALDI-TOF mass spectrometry. Int J Food Microbiol 2014; 196:137-44. [PMID: 25589227 DOI: 10.1016/j.ijfoodmicro.2014.12.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2014] [Revised: 11/13/2014] [Accepted: 12/05/2014] [Indexed: 10/24/2022]
Abstract
Acetic acid bacteria have attracted much attention over the past few years, due mainly to their metabolic traits that are of interest to the biotechnology industry. In addition, it turns out that their ecological habitats are almost unlimited since they have been found as symbionts in different insects and also as emerging opportunistic human pathogens. Very surprising is the finding that they colonize niches considered anaerobic, disproving the generalized statement that they are strict aerobes. Since they have taken on different biological roles in our environment, more and more people are charged with the task of identifying them. However, this turns out to be not always easy, especially if we are using phenotypic approaches for identification. A substantial step forward in making the identification of acetic acid bacteria easier was made possible using molecular biological methods, which have been extensively tested since 2000. However, some molecular methods require expensive machines and experienced staff, and moreover the level of their discrimination varies. All these factors must be considered when selecting the most appropriate approach for identifying acetic acid bacteria. With this objective in mind, this review article discusses the benefits and drawbacks of molecular biological methods for identification of acetic acid bacteria, with a focus on the 16S-23S rRNA gene ITS regions and the recently described alternative method for identification of acetic acid bacteria, MALDI-TOF MS.
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Affiliation(s)
- Janja Trček
- Department of Biology, Faculty of Natural Sciences and Mathematics, University of Maribor, Maribor, Slovenia; Faculty of Chemistry and Chemical Engineering, University of Maribor, Maribor, Slovenia.
| | - François Barja
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Jussy-Geneva, Switzerland
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Pitiwittayakul N, Yukphan P, Sintuprapa W, Yamada Y, Theeragool G. Identification of acetic acid bacteria isolated in Thailand and assigned to the genus Acetobacter by groEL gene sequence analysis. ANN MICROBIOL 2014. [DOI: 10.1007/s13213-014-0994-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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Huang CH, Chang MT, Huang L, Chua WS. Molecular discrimination and identification of Acetobacter genus based on the partial heat shock protein 60 gene (hsp60) sequences. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2014; 94:213-218. [PMID: 23681743 DOI: 10.1002/jsfa.6231] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Revised: 04/23/2013] [Accepted: 05/16/2013] [Indexed: 06/02/2023]
Abstract
BACKGROUND To identify the Acetobacter species using phenotypic and genotypic (16S rDNA sequence analysis) technique alone is inaccurate. The aim of this study was to use the hsp60 gene as a target for species discrimination in the genus Acetobacter, as well as to develop species-specific polymerase chain reaction and mini-sequencing methods for species identification and differentiation. RESULTS The average sequence similarity for the hsp60 gene (89.8%) among type strains was significantly less than that for the 16S rRNA gene (98.0%), and the most Acetobacter species could be clearly distinguished. In addition, a pair of species-specific primer was designed and used to specifically identify Acetobacter aceti, Acetobacter estunensis and Acetobacter oeni, but none of the other Acetobacter strains. Afterwards, two specific single-nucleotide polymorphism primers were designed and used to direct differentiate the strains belonging to the species A. aceti by mini-sequencing assay. CONCLUSION The phylogenetic relationships in the Acetobacter genus can be resolved by using hsp60 gene sequencing, and the species of A. aceti can be differentiated using novel species-specific PCR combined with the mini-sequencing technology.
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Affiliation(s)
- Chien-Hsun Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Road, Hsinchu, 30062, Taiwan, ROC
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Huang CH, Chang MT, Huang L, Chu WS. The gyrase B gene as a molecular marker to resolve interspecific relationships within the Acetobacter pasteurianus group and a novel target for species-specific PCR. Eur Food Res Technol 2014. [DOI: 10.1007/s00217-013-2076-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Huang CH, Chang MT, Huang L, Chu WS. Utilization of elongation factor Tu gene (tuf) sequencing and species-specific PCR (SS-PCR) for the molecular identification of Acetobacter species complex. Mol Cell Probes 2013; 28:31-3. [PMID: 23969032 DOI: 10.1016/j.mcp.2013.07.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 07/26/2013] [Accepted: 07/30/2013] [Indexed: 10/26/2022]
Abstract
The aim of this study was to use tuf gene as a molecular target for species discrimination in the Acetobacter genus, as well as to develop species-specific PCR method for direct species identification of Acetobacter aceti. The results showed that most Acetobacter species could be clearly distinguished, and the average sequence similarity for the tuf gene (89.5%) among type strains was significantly lower than that of the 16S rRNA gene sequence (98.0%). A pair of species-specific primers were designed and used to specifically identify A. aceti, but none of the other Acetobacter strains. Our data indicate that the phylogenetic relationships of most strains in the Acetobacter genus can be resolved using tuf gene sequencing, and the novel species-specific primer pair could be used to rapidly and accurately identify the species of A. aceti by the PCR based assay.
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Affiliation(s)
- Chien-Hsun Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Road, Hsinchu 30062, Taiwan, ROC
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Xu G, Wang X, Liu C, Li W, Wei S, Liu Y, Cheng X, Liu J. Authentication of official Da-huang by sequencing and multiplex allele-specific PCR of a short maturase K gene. Genome 2013; 56:109-13. [DOI: 10.1139/gen-2012-0182] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Rhubarb (official Da-huang) is an important medicinal herb in Asia. Many adulterants of official Da-huang have been discovered in Chinese markets in recent years, which has resulted in adverse effects in medicinal treatment. Here, novel molecular markers based on a short maturase K (matK) gene were developed for authenticating official Da-huang. This study showed that all the species from official Da-huang were clustered together in one clade in the polygenetic trees based on short matK. Two highly conserved single nucleotide polymorphisms of short matK were mined in the species from official Da-huang. Based on these polymophisms, four improved specific primers of official Da-huang were successfully developed that generated reproducible specific bands. These results suggest that the short matK sequence can be considered as a favorable candidate for distinguishing official Da-huang from its adulterants. The established multiplex allele-specific PCR was determined to be simple and accurate and may serve as a preferable tool for authentication of official Da-huang. In addition, we suggest that short-sized specific bands be developed to authenticate materials used in traditional Chinese medicine.
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Affiliation(s)
- Guojie Xu
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, No. 6, WangJing ZhongHuan South Street, Chao-Yang District, Beijing 100102, P.R. China
| | - Xueyong Wang
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, No. 6, WangJing ZhongHuan South Street, Chao-Yang District, Beijing 100102, P.R. China
| | - Chunsheng Liu
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, No. 6, WangJing ZhongHuan South Street, Chao-Yang District, Beijing 100102, P.R. China
| | - Weidong Li
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, No. 6, WangJing ZhongHuan South Street, Chao-Yang District, Beijing 100102, P.R. China
| | - Shengli Wei
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, No. 6, WangJing ZhongHuan South Street, Chao-Yang District, Beijing 100102, P.R. China
| | - Ying Liu
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, No. 6, WangJing ZhongHuan South Street, Chao-Yang District, Beijing 100102, P.R. China
| | - Xiaoli Cheng
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, No. 6, WangJing ZhongHuan South Street, Chao-Yang District, Beijing 100102, P.R. China
| | - Juan Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151, MaLianWa North Street, Hai-dian District, Beijing 100193, P.R. China
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