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Jiang CS, Gu CT. Proposal to Reclassify Companilactobacillus futsaii subsp. chongqingensis as a Later Heterotypic Synonym of Companilactobacillus futsaii subsp. futsaii. Curr Microbiol 2023; 81:17. [PMID: 38006417 DOI: 10.1007/s00284-023-03541-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 10/26/2023] [Indexed: 11/27/2023]
Abstract
Previous studies have shown that Lactobacillus futsaii (now Companilactobacillus futsaii) can be subdivided at the subspecies level. The main purpose of this study is to explore whether this is correct by using a polyphasic taxonomic approach. Lactobacillus futsaii subsp. chongqingii was proposed and effectively published in 2019. The names L. futsaii subsp. chongqingensis corrig. and Lactobacillus futsaii subsp. futsaii were not validated until March 2023. However, in the reclassification of the genus Lactobacillus by Zheng et al. in April 2020, L. futsaii was transferred to Companilactobacillus as Companilactobacillus futsaii. So Lactobacillus futsaii subsp. chongqingensis and Lactobacillus futsaii subsp. futsaii should be transferred to Companilactobacillus futsaii now. In the present study, the relationship between L. futsaii subsp. chongqingensis and L. futsaii subsp. futsaii was re-evaluated. The type strains of L. futsaii subsp. chongqingensis and L. futsaii subsp. futsaii shared identical pheS and rpoA sequences, high dDDH value, similar phenotypic characteristics and fatty acid compositions, indicating that they belonged to the same subspecies. Here, we propose to reclassify Lactobacillus futsaii subsp. chongqingensis and Lactobacillus futsaii subsp. futsaii as Companilactobacillus futsaii subsp. chongqingensis comb. nov. and Companilactobacillus futsaii subsp. futsaii comb. nov., respectively, and Companilactobacillus futsaii subsp. chongqingensis as a later heterotypic synonym of Companilactobacillus futsaii subsp. futsaii.
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Affiliation(s)
- Cheng-Shan Jiang
- College of Life Sciences, Northeast Agricultural University, Harbin, 150030, People's Republic of China
| | - Chun Tao Gu
- College of Life Sciences, Northeast Agricultural University, Harbin, 150030, People's Republic of China.
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Oren A, Göker M. Validation List no. 210. Valid publication of new names and new combinations effectively published outside the IJSEM. Int J Syst Evol Microbiol 2023; 73. [PMID: 37000643 DOI: 10.1099/ijsem.0.005812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/01/2023] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, 38124 Braunschweig, Germany
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Xin Z, Wei X, Jiao Q, Gou Q, Zhang Y, Peng C, Pan Q. Whole genome sequence analysis of two subspecies of Companilactobacillus Futsaii and experimental verification of drug resistance and effect on the exploratory behavior of mice based on unique gene. PLoS One 2022; 17:e0274244. [PMID: 36084068 PMCID: PMC9462788 DOI: 10.1371/journal.pone.0274244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 08/24/2022] [Indexed: 11/18/2022] Open
Abstract
This study characterized the whole genome of Companilactobacillus futsaii subsp. chongqingii CQ16Z1 isolated from Chongqing of China, performed genome sequence analysis with Companilactobacillus futsaii subsp. futsaii YM0097 isolated from Taiwan of China, and experimentally verified drug resistance and effect on the exploratory behavior of male C57BL/6 mice and analysis of gut microbiota and metabolomic studies. The genome of CQ16Z1 is 2.6 Mb. Sequence analysis between genomes showed that the two strains are Companilactobacillus futsaii. The unique genes of CQ16Z1 and YM0097 are 217 and 267, which account for 9% and 11% of the whole genomes, respectively. According to unique gene annotation, the results showed that genes associated with carbohydrate metabolism, environmental information processing, metabolism of cofactors and vitamins, cell wall/membrane/envelope biogenesis, phage and drug resistance are significantly different. The results of the drug resistance experiment showed that YM0097 had different degrees of resistance to 13 antibiotics, while CQ16Z1 was sensitive to more than half of them. YM0097 contains 9 prophage regions and CQ16Z1 contains 3 prophage regions. The results of the open field test showed that the time (P = 0.005; P = 0.047) and distance (P < 0.010; P = 0.046) of the central area of Y97 group and CQ group are significantly different from the control group. The results of the elevated plus maze test showed that compared with the control group, Y97 group had significant differences in the number of entries to the open arms and the percentage of open arms entry times (P = 0.004; P = 0.025), while the difference between the CQ group and the control group was not significant. YM0097 has a more obvious effect on the exploratory behavior of mice. The effects of YM0097 and CQ16Z1 on the intestinal flora of mice are also different. YM0097 may be more beneficial to the intestinal flora of the host. And LC/MS also showed that the metabolic effects of the two strains on the host are different. Finally, we believe that YM0097 is more suitable for application research as a psychobiotics.
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Affiliation(s)
- Zhao Xin
- Department of Pathogenic Biology, Chengdu Medical College, Chengdu, China
| | - Xing Wei
- Department of Clinical Laboratory, Pidu District People’s Hospital, Chengdu, China
| | - Qiuxia Jiao
- Department of Pathogenic Biology, Chengdu Medical College, Chengdu, China
| | - Qiufeng Gou
- Department of Pathogenic Biology, Chengdu Medical College, Chengdu, China
| | - Yumeng Zhang
- Department of Pathogenic Biology, Chengdu Medical College, Chengdu, China
| | - Chaoming Peng
- First Affiliated Hospital, Chengdu Medical College, Chengdu, China
- * E-mail: (CP); (QP)
| | - Qu Pan
- Department of Pathogenic Biology, Chengdu Medical College, Chengdu, China
- * E-mail: (CP); (QP)
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Zhang Z, Tsapekos P, Alvarado-Morales M, Zhu X, Zervas A, Jacobsen CS, Angelidaki I. Enhanced fermentative lactic acid production from source-sorted organic household waste: Focusing on low-pH microbial adaptation and bio-augmentation strategy. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 808:152129. [PMID: 34863737 DOI: 10.1016/j.scitotenv.2021.152129] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 11/20/2021] [Accepted: 11/28/2021] [Indexed: 06/13/2023]
Abstract
Lactic acid (LA) production at low pH could significantly reduce the need for neutralizing agents, leading to reduction of operational costs. In the present study, LA production at acidic conditions was investigated using source-sorted organic household waste (SSOHW). Controlling the pH at low value (i.e. 5.0) and bio-augmenting with Pediococcus acidilactici led to a concentration of 39.3 ± 0.5 g-LA/L with a yield of 0.75 ± 0.02 g-LA/g-sugar. In contrast, secondary fermentation at higher pH level (i.e. 5.5 and 6.0) resulted in complete LA degradation. Subsequently, consecutive batch fermentations were conducted to adapt P. acidilactici to SSOHW and improve the LA production. Results showed that P. acidilactici could successively adapt in the SSOHW reaching a relative abundance above 2.8% at adaptation process. The added P. acidilactici ensured a high concentration of LA at three consecutive generations, achieving an increment above 18% compared to control test (abiotic augmentation). Moreover, adaptation processes (i.e. maintaining pH at 4.0 or stepwise decreasing the pH from 5.0 to 4.0) significantly improved LA concentration and productivity at the pH of 4.0. Overall, the results provide a promising method to reduce the LA production costs using residual resources.
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Affiliation(s)
- Zengshuai Zhang
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark
| | - Panagiotis Tsapekos
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark.
| | - Merlin Alvarado-Morales
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark
| | - Xinyu Zhu
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark
| | - Athanasios Zervas
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, DK-4000 Roskilde, Denmark
| | - Carsten S Jacobsen
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, DK-4000 Roskilde, Denmark
| | - Irini Angelidaki
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark
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Forouhandeh H, Vahed SZ, Ahangari H, Tarhriz V, Hejazi MS. Phenotypic and phylogenetic characterization of Lactobacillus species isolated from traditional Lighvan cheese. FOOD PRODUCTION, PROCESSING AND NUTRITION 2021. [DOI: 10.1186/s43014-021-00065-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Abstract
Lighvan cheese (Lighvan panir) is among the most famous traditional cheese in Iran for its desired aroma and flavor. Undoubtedly, the lactic acid bacteria especially the genus Lactobacillus are the critical factors in developing the aroma, flavor, and texture in Lighvan cheese. In this study, the Lactobacillus population of the main Lighvan cheese was investigated. The Lactobacillus of the main Lighvan cheese was isolated using specific culture methods according to previously published Guidelines. Then, the phylogenetic features were investigated and the phenotypic characteristics were examined using specific culture methods. Twenty-eight Gram-positive bacterial species were identified belonged to the genus Lactobacillus. According to the same sequences as each other, three groups (A, B, and C) of isolates were categorized with a high degree of similarity to L. fermentum (100%) and L. casei group (L. casei, L. paracasei, and L. rhamnosus) (99.0 to 100%). Random amplified polymorphic DNA (RAPD) fingerprint analysis manifested the presence of three clusters that were dominant in traditional Lighvan cheese. Cluster І was divided into 4 sub-clusters. By the result of carbohydrate fermentation pattern and 16S rRNA sequencing, isolates were identified as L. rhamnosus. The isolates in clusters II and III represented L. paracasei and L. fermentum, respectively as they were identified by 16S rRNA sequencing and fermented carbohydrate patterns. Our result indicated that the specific aroma and flavor of traditional Lighvan cheese can be related to its Lactobacillus population including L. fermentum, L. casei, L. paracasei, and L. rhamnosus.
Graphical abstract
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Yang X, Xiang R, Iqbal NM, Duan YH, Zhang XA, Wang L, Yu LZ, Li JZ, Sun MF, Yang Q, Zheng CT, Liao SQ. Marinobacter shengliensis subsp. alexandrii Subsp. Nov., Isolated from Cultivable Phycosphere Microbiota of Highly Toxic Dinoflagellate Alexandrium catenella LZT09 and Description of Marinobacter shengliensis Subsp. shengliensis Subsp. Nov. Curr Microbiol 2021; 78:1648-1655. [PMID: 33651189 DOI: 10.1007/s00284-021-02431-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 02/12/2021] [Indexed: 02/03/2023]
Abstract
Phycosphere hosts the boundary of unique holobionts harboring dynamic algae-bacteria interactions. During our investigating the microbial consortia composition of phycosphere microbiota (PM) derived from diverse harmful algal blooms (HAB) dinoflagellates, a novel rod-shaped, motile and faint yellow-pigmented bacterium, designated as strain LZ-6 T, was isolated from HAB Alexandrium catenella LZT09 which produces high levels paralytic shellfish poisoning toxins. Phylogenetic analysis based on 16S rRNA gene and two housekeeping genes, rpoA and pheS sequences showed that the novel isolate shared the highest gene similarity with Marinobacter shengliensis CGMCC 1.12758 T (99.6%) with the similarity values of 99.6%, 99.9% and 98.5%, respectively. Further phylogenomic calculations of average nucleotide identity (ANI), average amino acid identity (AAI) and digital DNA-DNA hybridization (dDDH) values between strains LZ-6 T and the type strain of M. shengliensis were 95.9%, 96.4% and 68.5%, respectively. However, combined phenotypic and chemotaxonomic characterizations revealed that the new isolate was obviously different from the type strain of M. shengliensis. The obtained taxonomic evidences supported that strain LZ-6 T represents a novel subspecies of M. shengliensis, for which the name is proposed, Marinobacter shengliensis subsp. alexandrii subsp. nov. with the type strain LZ-6 T (= CCTCC AB 2018388TT = KCTC 72197 T). This proposal automatically creates Marinobacter shengliensis subsp. shengliensis for which the type strain is SL013A34A2T (= LMG 27740 T = CGMCC 1.12758 T).
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Affiliation(s)
- Xi Yang
- Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Livestock and Poultry Breeding, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Maoming Branch of Guangdong Laboratory for Lingnan Modern Agriculture, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.,Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Rong Xiang
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Maoming Branch of Guangdong Laboratory for Lingnan Modern Agriculture, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Nurhezreen Md Iqbal
- Malaysia Genome Institute, National Institute of Biotechnology, 43000, Kajang, Malaysia
| | - Yu-Han Duan
- Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Livestock and Poultry Breeding, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Maoming Branch of Guangdong Laboratory for Lingnan Modern Agriculture, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.,ABI Group, GPM Project, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Xiao-Ai Zhang
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Lei Wang
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Lin-Zeng Yu
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Maoming Branch of Guangdong Laboratory for Lingnan Modern Agriculture, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Jia-Zhou Li
- Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Livestock and Poultry Breeding, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Maoming Branch of Guangdong Laboratory for Lingnan Modern Agriculture, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Ming-Fei Sun
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Maoming Branch of Guangdong Laboratory for Lingnan Modern Agriculture, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Qiao Yang
- Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Livestock and Poultry Breeding, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Maoming Branch of Guangdong Laboratory for Lingnan Modern Agriculture, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China. .,ABI Group, GPM Project, Zhejiang Ocean University, Zhoushan, 316022, China.
| | - Chun-Tian Zheng
- Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Livestock and Poultry Breeding, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Maoming Branch of Guangdong Laboratory for Lingnan Modern Agriculture, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
| | - Shen-Quan Liao
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Maoming Branch of Guangdong Laboratory for Lingnan Modern Agriculture, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
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7
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Zheng J, Wittouck S, Salvetti E, Franz CMAP, Harris HMB, Mattarelli P, O'Toole PW, Pot B, Vandamme P, Walter J, Watanabe K, Wuyts S, Felis GE, Gänzle MG, Lebeer S. A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae. Int J Syst Evol Microbiol 2020; 70:2782-2858. [PMID: 32293557 DOI: 10.1099/ijsem.0.004107] [Citation(s) in RCA: 1570] [Impact Index Per Article: 392.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The genus Lactobacillus comprises 261 species (at March 2020) that are extremely diverse at phenotypic, ecological and genotypic levels. This study evaluated the taxonomy of Lactobacillaceae and Leuconostocaceae on the basis of whole genome sequences. Parameters that were evaluated included core genome phylogeny, (conserved) pairwise average amino acid identity, clade-specific signature genes, physiological criteria and the ecology of the organisms. Based on this polyphasic approach, we propose reclassification of the genus Lactobacillus into 25 genera including the emended genus Lactobacillus, which includes host-adapted organisms that have been referred to as the Lactobacillus delbrueckii group, Paralactobacillus and 23 novel genera for which the names Holzapfelia, Amylolactobacillus, Bombilactobacillus, Companilactobacillus, Lapidilactobacillus, Agrilactobacillus, Schleiferilactobacillus, Loigolactobacilus, Lacticaseibacillus, Latilactobacillus, Dellaglioa, Liquorilactobacillus, Ligilactobacillus, Lactiplantibacillus, Furfurilactobacillus, Paucilactobacillus, Limosilactobacillus, Fructilactobacillus, Acetilactobacillus, Apilactobacillus, Levilactobacillus, Secundilactobacillus and Lentilactobacillus are proposed. We also propose to emend the description of the family Lactobacillaceae to include all genera that were previously included in families Lactobacillaceae and Leuconostocaceae. The generic term 'lactobacilli' will remain useful to designate all organisms that were classified as Lactobacillaceae until 2020. This reclassification reflects the phylogenetic position of the micro-organisms, and groups lactobacilli into robust clades with shared ecological and metabolic properties, as exemplified for the emended genus Lactobacillus encompassing species adapted to vertebrates (such as Lactobacillus delbrueckii, Lactobacillus iners, Lactobacillus crispatus, Lactobacillus jensensii, Lactobacillus johnsonii and Lactobacillus acidophilus) or invertebrates (such as Lactobacillus apis and Lactobacillus bombicola).
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Affiliation(s)
- Jinshui Zheng
- Huazhong Agricultural University, State Key Laboratory of Agricultural Microbiology, Hubei Key Laboratory of Agricultural Bioinformatics, Wuhan, Hubei, PR China
| | - Stijn Wittouck
- Research Group Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Elisa Salvetti
- Dept. of Biotechnology, University of Verona, Verona, Italy
| | - Charles M A P Franz
- Max Rubner-Institut, Department of Microbiology and Biotechnology, Kiel, Germany
| | - Hugh M B Harris
- School of Microbiology & APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
| | - Paola Mattarelli
- University of Bologna, Dept. of Agricultural and Food Sciences, Bologna, Italy
| | - Paul W O'Toole
- School of Microbiology & APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
| | - Bruno Pot
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Vrije Universiteit Brussel, Brussels, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Jens Walter
- Department of Biological Sciences, University of Alberta, Edmonton, Canada.,Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, Canada
| | - Koichi Watanabe
- Food Industry Research and Development Institute, Bioresource Collection and Research Center, Hsinchu, Taiwan, ROC.,National Taiwan University, Dept. of Animal Science and Technology, Taipei, Taiwan, ROC
| | - Sander Wuyts
- Research Group Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | | | - Michael G Gänzle
- Hubei University of Technology, College of Bioengineering and Food Science, Wuhan, Hubei, PR China.,Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, Canada
| | - Sarah Lebeer
- Research Group Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
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