1
|
Propionic acid production via two-step sequential repeated batch fermentations on whey and flour. Biochem Eng J 2023. [DOI: 10.1016/j.bej.2023.108816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
|
2
|
Food-Grade Bacteria Combat Pathogens by Blocking AHL-Mediated Quorum Sensing and Biofilm Formation. Foods 2022; 12:foods12010090. [PMID: 36613306 PMCID: PMC9818890 DOI: 10.3390/foods12010090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 12/15/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022] Open
Abstract
Disrupting bacterial quorum sensing (QS) signaling is a promising strategy to combat pathogenic biofilms without the development of antibiotic resistance. Here, we report that food-associated bacteria can interfere with the biofilm formation of a Gram-negative pathogenic bacterium by targeting its AHL (acyl-homoserine lactone) QS system. This was demonstrated by screening metabolic end-products of different lactobacilli and propionibacteria using Gram-negative and biofilm-forming Chromobacterium violaceum as the QS reporter and our anti-QS microscale screening platform with necessary modifications. The method was optimized in terms of the inoculation technique and the concentrations of D-glucose and L-tryptophan, two key factors controlling the synthesis of violacein, a purple pigment indicating the activation of the QS system in C. violaceum. These improvements resulted in ca. 16-times higher violacein yields and enabled revealing anti-QS effects of Lactobacillus acidophilus, Lentilactobacillus kefiri, Lacticaseibacillus rhamnosus and Propionibacterium freudenreichii, including new cheese-associated strains. Our findings also suggest that acetate and propionate excreted by these species are the main factors that interrupt the QS-mediated signaling and subsequent biofilm growth without affecting the cell viability of the C. violaceum reporter. Thus, the present study reports a revised anti-QS screening method to accurately define new bacteria with an ability to combat pathogens in a safe and sustainable way.
Collapse
|
3
|
The Antimicrobial Effect of Various Single-Strain and Multi-Strain Probiotics, Dietary Supplements or Other Beneficial Microbes against Common Clinical Wound Pathogens. Microorganisms 2022; 10:microorganisms10122518. [PMID: 36557771 PMCID: PMC9781324 DOI: 10.3390/microorganisms10122518] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/09/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
The skin is the largest organ in the human body and is colonized by a diverse microbiota that works in harmony to protect the skin. However, when skin damage occurs, the skin microbiota is also disrupted, and pathogens can invade the wound and cause infection. Probiotics or other beneficial microbes and their metabolites are one possible alternative treatment for combating skin pathogens via their antimicrobial effectiveness. The objective of our study was to evaluate the antimicrobial effect of seven multi-strain dietary supplements and eleven single-strain microbes that contain probiotics against 15 clinical wound pathogens using the agar spot assay, co-culturing assay, and agar well diffusion assay. We also conducted genera-specific and species-specific molecular methods to detect the DNA in the dietary supplements and single-strain beneficial microbes. We found that the multi-strain dietary supplements exhibited a statistically significant higher antagonistic effect against the challenge wound pathogens than the single-strain microbes and that lactobacilli-containing dietary supplements and single-strain microbes were significantly more efficient than the selected propionibacteria and bacilli. Differences in results between methods were also observed, possibly due to different mechanisms of action. Individual pathogens were susceptible to different dietary supplements or single-strain microbes. Perhaps an individual approach such as a 'probiogram' could be a possibility in the future as a method to find the most efficient targeted probiotic strains, cell-free supernatants, or neutralized cell-free supernatants that have the highest antagonistic effect against individual clinical wound pathogens.
Collapse
|
4
|
Benito-Vaquerizo S, Parera Olm I, de Vroet T, Schaap PJ, Sousa DZ, Martins Dos Santos VAP, Suarez-Diez M. Genome-scale metabolic modelling enables deciphering ethanol metabolism via the acrylate pathway in the propionate-producer Anaerotignum neopropionicum. Microb Cell Fact 2022; 21:116. [PMID: 35710409 PMCID: PMC9205015 DOI: 10.1186/s12934-022-01841-1] [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: 04/12/2022] [Accepted: 05/26/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Microbial production of propionate from diluted streams of ethanol (e.g., deriving from syngas fermentation) is a sustainable alternative to the petrochemical production route. Yet, few ethanol-fermenting propionigenic bacteria are known, and understanding of their metabolism is limited. Anaerotignum neopropionicum is a propionate-producing bacterium that uses the acrylate pathway to ferment ethanol and CO2 to propionate and acetate. In this work, we used computational and experimental methods to study the metabolism of A. neopropionicum and, in particular, the pathway for conversion of ethanol into propionate. RESULTS Our work describes iANEO_SB607, the first genome-scale metabolic model (GEM) of A. neopropionicum. The model was built combining the use of automatic tools with an extensive manual curation process, and it was validated with experimental data from this and published studies. The model predicted growth of A. neopropionicum on ethanol, lactate, sugars and amino acids, matching observed phenotypes. In addition, the model was used to implement a dynamic flux balance analysis (dFBA) approach that accurately predicted the fermentation profile of A. neopropionicum during batch growth on ethanol. A systematic analysis of the metabolism of A. neopropionicum combined with model simulations shed light into the mechanism of ethanol fermentation via the acrylate pathway, and revealed the presence of the electron-transferring complexes NADH-dependent reduced ferredoxin:NADP+ oxidoreductase (Nfn) and acryloyl-CoA reductase-EtfAB, identified for the first time in this bacterium. CONCLUSIONS The realisation of the GEM iANEO_SB607 is a stepping stone towards the understanding of the metabolism of the propionate-producer A. neopropionicum. With it, we have gained insight into the functioning of the acrylate pathway and energetic aspects of the cell, with focus on the fermentation of ethanol. Overall, this study provides a basis to further exploit the potential of propionigenic bacteria as microbial cell factories.
Collapse
Affiliation(s)
- Sara Benito-Vaquerizo
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, Wageningen, 6708WE, The Netherlands
| | - Ivette Parera Olm
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, Wageningen, 6708WE, The Netherlands
| | - Thijs de Vroet
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, Wageningen, 6708WE, The Netherlands
| | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, Wageningen, 6708WE, The Netherlands
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, Wageningen, 6708WE, The Netherlands.,Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, Vening Meinesz building C, Princetonlaan 6, Utrecht, 3584 CB, The Netherlands
| | - Vitor A P Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, Wageningen, 6708WE, The Netherlands.,Bioprocess Engineering, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, Wageningen, 6708WE, The Netherlands.
| |
Collapse
|
5
|
Turgay M, Falentin H, Irmler S, Fröhlich-Wyder MT, Meola M, Oberhaensli S, Berthoud-dit-Gallon Marchand H. Genomic rearrangements in the aspA-dcuA locus of Propionibacterium freudenreichii are associated with aspartase activity. Food Microbiol 2022; 106:104030. [DOI: 10.1016/j.fm.2022.104030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 02/02/2022] [Accepted: 03/20/2022] [Indexed: 11/25/2022]
|
6
|
Anastasiou R, Kazou M, Georgalaki M, Aktypis A, Zoumpopoulou G, Tsakalidou E. Omics Approaches to Assess Flavor Development in Cheese. Foods 2022; 11:188. [PMID: 35053920 PMCID: PMC8775153 DOI: 10.3390/foods11020188] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/03/2022] [Accepted: 01/09/2022] [Indexed: 12/27/2022] Open
Abstract
Cheese is characterized by a rich and complex microbiota that plays a vital role during both production and ripening, contributing significantly to the safety, quality, and sensory characteristics of the final product. In this context, it is vital to explore the microbiota composition and understand its dynamics and evolution during cheese manufacturing and ripening. Application of high-throughput DNA sequencing technologies have facilitated the more accurate identification of the cheese microbiome, detailed study of its potential functionality, and its contribution to the development of specific organoleptic properties. These technologies include amplicon sequencing, whole-metagenome shotgun sequencing, metatranscriptomics, and, most recently, metabolomics. In recent years, however, the application of multiple meta-omics approaches along with data integration analysis, which was enabled by advanced computational and bioinformatics tools, paved the way to better comprehension of the cheese ripening process, revealing significant associations between the cheese microbiota and metabolites, as well as their impact on cheese flavor and quality.
Collapse
Affiliation(s)
- Rania Anastasiou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 118 55 Athens, Greece; (M.K.); (M.G.); (A.A.); (G.Z.); (E.T.)
| | | | | | | | | | | |
Collapse
|
7
|
Fermentative production of propionic acid: prospects and limitations of microorganisms and substrates. Appl Microbiol Biotechnol 2021; 105:6199-6213. [PMID: 34410439 DOI: 10.1007/s00253-021-11499-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 07/30/2021] [Accepted: 08/03/2021] [Indexed: 12/17/2022]
Abstract
Propionic acid is an important organic acid with wide industrial applications, especially in the food industry. It is currently produced from petrochemicals via chemical routes. Increasing concerns about greenhouse gas emissions from fossil fuels and a growing consumer preference for bio-based products have led to interest in fermentative production of propionic acid, but it is not yet competitive with chemical production. To improve the economic feasibility and sustainability of bio-propionic acid, fermentation performance in terms of concentration, yield, and productivity must be improved and the cost of raw materials must be reduced. These goals require robust microbial producers and inexpensive renewable feedstocks, so the present review focuses on bacterial producers of propionic acid and promising sources of substrates as carbon sources. Emphasis is placed on assessing the capacity of propionibacteria and the various approaches pursued in an effort to improve their performance through metabolic engineering. A wide range of substrates employed in propionic acid fermentation is analyzed with particular interest in the prospects of inexpensive renewable feedstocks, such as cellulosic biomass and industrial residues, to produce cost-competitive bio-propionic acid. KEY POINTS: • Fermentative propionic acid production emerges as competitor to chemical synthesis. • Various bacteria synthesize propionic acid, but propionibacteria are the best producers. • Biomass substrates hold promise to reduce propionic acid fermentation cost.
Collapse
|
8
|
Surachat K, Deachamag P, Kantachote D, Wonglapsuwan M, Jeenkeawpiam K, Chukamnerd A. In silico comparative genomics analysis of Lactiplantibacillus plantarum DW12, a potential gamma-aminobutyric acid (GABA)-producing strain. Microbiol Res 2021; 251:126833. [PMID: 34352473 DOI: 10.1016/j.micres.2021.126833] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/21/2021] [Accepted: 07/26/2021] [Indexed: 01/22/2023]
Abstract
Gamma-aminobutyric acid (GABA) is an amino that plays a major role as a neurotransmitter. It iscommonly produced by lactic acid bacteria (LAB) naturally found in fermented food and fruit. Lactiplantibacillus plantarum DW12 is a high potential GABA-producing strain isolated from a fermented beverage. In this study, to highlight its ability to produce GABA, we sequenced the genome of L. plantarum DW12 and then performed comprehensive bioinformatics and meta-analysis to compare the genomic data of previously published genomes. Also, the evolutionary analysis among L. plantarum species was demonstrated using pan-genome analysis against 576 genomes from the database. As a result, the DW12 genome comprises one circular chromosome of 3,217,574 bp. It contains several genes that encode for the production of antimicrobial compounds including plantaricin A, E, F, J, K, and N. The glutamic acid decarboxylase (GAD) operon was found in the DW12 genome, suggests a high potential of producing GABA in this strain. Therefore, L. plantarum DW12 could be a good candidate as a starter culture in the beverage and food industries due to its safety aspects and ability to produce GABA.
Collapse
Affiliation(s)
- Komwit Surachat
- Division of Computational Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand; Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand.
| | - Panchalika Deachamag
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand.
| | - Duangporn Kantachote
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand.
| | - Monwadee Wonglapsuwan
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand.
| | - Kongpop Jeenkeawpiam
- Division of Computational Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand; Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand.
| | - Arnon Chukamnerd
- Department of Biomedical Sciences, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, Thailand.
| |
Collapse
|
9
|
Balabanova L, Averianova L, Marchenok M, Son O, Tekutyeva L. Microbial and Genetic Resources for Cobalamin (Vitamin B12) Biosynthesis: From Ecosystems to Industrial Biotechnology. Int J Mol Sci 2021; 22:ijms22094522. [PMID: 33926061 PMCID: PMC8123684 DOI: 10.3390/ijms22094522] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 04/23/2021] [Accepted: 04/23/2021] [Indexed: 12/12/2022] Open
Abstract
Many microbial producers of coenzyme B12 family cofactors together with their metabolically interdependent pathways are comprehensively studied and successfully used both in natural ecosystems dominated by auxotrophs, including bacteria and mammals, and in the safe industrial production of vitamin B12. Metabolic reconstruction for genomic and metagenomic data and functional genomics continue to mine the microbial and genetic resources for biosynthesis of the vital vitamin B12. Availability of metabolic engineering techniques and usage of affordable and renewable sources allowed improving bioprocess of vitamins, providing a positive impact on both economics and environment. The commercial production of vitamin B12 is mainly achieved through the use of the two major industrial strains, Propionobacterium shermanii and Pseudomonas denitrificans, that involves about 30 enzymatic steps in the biosynthesis of cobalamin and completely replaces chemical synthesis. However, there are still unresolved issues in cobalamin biosynthesis that need to be elucidated for future bioprocess improvements. In the present work, we review the current state of development and challenges for cobalamin (vitamin B12) biosynthesis, describing the major and novel prospective strains, and the studies of environmental factors and genetic tools effecting on the fermentation process are reported.
Collapse
Affiliation(s)
- Larissa Balabanova
- Department of Bioeconomy and Food Security, School of Economics and Management, Far Eastern Federal University, 690922 Vladivostok, Russia; (L.A.); (M.M.); (O.S.); (L.T.)
- Laboratory of Marine Biochemistry, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 690022 Vladivostok, Russia
- ARNIKA, Territory of PDA Nadezhdinskaya, 692481 Primorskiy Region, Russia
- Correspondence:
| | - Liudmila Averianova
- Department of Bioeconomy and Food Security, School of Economics and Management, Far Eastern Federal University, 690922 Vladivostok, Russia; (L.A.); (M.M.); (O.S.); (L.T.)
- ARNIKA, Territory of PDA Nadezhdinskaya, 692481 Primorskiy Region, Russia
| | - Maksim Marchenok
- Department of Bioeconomy and Food Security, School of Economics and Management, Far Eastern Federal University, 690922 Vladivostok, Russia; (L.A.); (M.M.); (O.S.); (L.T.)
- ARNIKA, Territory of PDA Nadezhdinskaya, 692481 Primorskiy Region, Russia
| | - Oksana Son
- Department of Bioeconomy and Food Security, School of Economics and Management, Far Eastern Federal University, 690922 Vladivostok, Russia; (L.A.); (M.M.); (O.S.); (L.T.)
- ARNIKA, Territory of PDA Nadezhdinskaya, 692481 Primorskiy Region, Russia
| | - Liudmila Tekutyeva
- Department of Bioeconomy and Food Security, School of Economics and Management, Far Eastern Federal University, 690922 Vladivostok, Russia; (L.A.); (M.M.); (O.S.); (L.T.)
- ARNIKA, Territory of PDA Nadezhdinskaya, 692481 Primorskiy Region, Russia
| |
Collapse
|
10
|
Hasebe F. MetW regulates the enzymatic activity of MetX in Pseudomonas. Biosci Biotechnol Biochem 2021; 85:351-358. [PMID: 33604638 DOI: 10.1093/bbb/zbaa044] [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: 08/13/2020] [Accepted: 10/05/2020] [Indexed: 11/13/2022]
Abstract
Methionine is a canonical amino acid. The protein MetX is a homoserine O-acyltransferase utilized in the methionine biosynthetic pathway. The metW gene is found adjacent to the metX gene in some bacteria, but its functions are unclear. In this study, I focused on the function of MetW and MetX from Pseudomonas aeruginosa (PaMetW and PaMetX). I demonstrated that PaMetW interacted with and activated the homoserine O-succinyltransferase (HST) activity of PaMetX. Furthermore, I elucidated that the HST activity of PaMetX in complex with PaMetW was inhibited by the addition of S-adenosyl-l-homocysteine (SAH), although PaMetX alone showed no feedback inhibition. Since PaMetW possesses a glycine-rich sequence annotated as a SAM/SAH binding site, I also investigated the relationship between this glycine-rich sequence and the inhibition caused by SAH. I revealed that alanine mutation of PaMetW Gly24 reduced the inhibitory effect of SAH. These results suggest that MetW is a regulatory protein of MetX.
Collapse
Affiliation(s)
- Fumihito Hasebe
- Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, Shizuoka, Japan
| |
Collapse
|
11
|
Piwowarek K, Lipińska E, Hać-Szymańczuk E, Kieliszek M, Kot AM. Sequencing and Analysis of the Genome of Propionibacterium Freudenreichii T82 Strain: Importance for Industry. Biomolecules 2020; 10:E348. [PMID: 32102319 PMCID: PMC7072396 DOI: 10.3390/biom10020348] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/11/2020] [Accepted: 02/20/2020] [Indexed: 01/12/2023] Open
Abstract
The genome of Propionibacterium freudenreichii ssp. freudenreichii T82, which has a chromosome containing 2,585,340 nucleotides with 67.3% GC content (guanine-cytosine content), is described in this paper. The total number of genes is 2308, of which 2260 are protein-coding genes and 48 are RNA genes. According to the genome analysis and the obtained results, the T82 strain can produce various compounds such as propionic acid, trehalose, glycogen, and B group vitamins (e.g., B6, B9, and B12). From protein-coding sequences (CDSs), genes related to stress adaptation, biosynthesis, metabolism, transport, secretion, and defense machinery were detected. In the genome of the T82 strain, sequences corresponding to the CRISPR loci (Clustered Regularly Interspaced Short Palindromic Repeats), antibiotic resistance, and restriction-modification system were found.
Collapse
Affiliation(s)
- Kamil Piwowarek
- Department of Food Biotechnology and Microbiology, Institute of Food Sciences, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159 c, 02-776 Warsaw, Poland; (E.L.); (E.H.-S.); (M.K.); (A.M.K.)
| | | | | | | | | |
Collapse
|
12
|
Hedayati R, Hosseini M, Najafpour GD. Optimization of semi-anaerobic vitamin B12 (cyanocobalamin) production from rice bran oil using Propionibacterium freudenreichii PTCC1674. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2020. [DOI: 10.1016/j.bcab.2019.101444] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
13
|
Deptula P, Loivamaa I, Smolander OP, Laine P, Roberts RJ, Piironen V, Paulin L, Savijoki K, Auvinen P, Varmanen P. Red-Brown Pigmentation of Acidipropionibacterium jensenii Is Tied to Haemolytic Activity and cyl-Like Gene Cluster. Microorganisms 2019; 7:microorganisms7110512. [PMID: 31671651 PMCID: PMC6920887 DOI: 10.3390/microorganisms7110512] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 10/21/2019] [Accepted: 10/29/2019] [Indexed: 01/28/2023] Open
Abstract
The novel Acidipropionibacterium genus encompasses species of industrial importance but also those associated with food spoilage. In particular, Acidipropionibacterium acidipropionici, Acidipropionibacterium thoenii, and Acidipropionibacterium jensenii play an important role in food fermentation, as biopreservatives, or as potential probiotics. Notably, A. jensenii and A. thoenii can cause brown spot defects in Swiss-type cheeses, which have been tied to the rhamnolipid pigment granadaene. In the pathogenic bacterium Streptococcus agalactiae, production of granadaene depends on the presence of a cyl gene cluster, an important virulence factor linked with haemolytic activity. Here, we show that the production of granadaene in pigmented Acidipropionibacterium, including A. jensenii, A. thoenii, and Acidipropionibacterium virtanenii, is tied to haemolytic activity and the presence of a cyl-like gene cluster. Furthermore, we propose a PCR-based test, which allows pinpointing acidipropionibacteria with the cyl-like gene cluster. Finally, we present the first two whole genome sequence analyses of the A. jensenii strains as well as testing phenotypic characteristics important for industrial applications. In conclusion, the present study sheds light on potential risks associated with the presence of pigmented Acidipropionibacterium strains in food fermentation. In addition, the results presented here provide ground for development of a quick and simple diagnostic test instrumental in avoiding potential negative effects of Acidipropionibacterium strains with haemolytic activity on food quality.
Collapse
Affiliation(s)
- Paulina Deptula
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland.
- Department of Food Sciences, University of Copenhagen, Rolighedsvej 26, DK-1958 Frederiksberg C, Denmark.
| | - Iida Loivamaa
- Department of Food and Nutrition, University of Helsinki, 00014 Helsinki, Finland.
| | | | - Pia Laine
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland.
| | | | - Vieno Piironen
- Department of Food and Nutrition, University of Helsinki, 00014 Helsinki, Finland.
| | - Lars Paulin
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland.
| | - Kirsi Savijoki
- Division of Pharmaceutical Biosciences, University of Helsinki, 00014 Helsinki, Finland.
| | - Petri Auvinen
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland.
| | - Pekka Varmanen
- Department of Food and Nutrition, University of Helsinki, 00014 Helsinki, Finland.
| |
Collapse
|
14
|
Whole-Genome Sequences of Propionibacterium australiense NML (LCDC) 98A072 T and NML (LCDC) 98A078, Associated with Granulomatous Bovine Lesions. Microbiol Resour Announc 2018; 7:MRA01445-18. [PMID: 30533813 PMCID: PMC6256612 DOI: 10.1128/mra.01445-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 10/26/2018] [Indexed: 12/02/2022] Open
Abstract
Draft genome sequences of Propionibacterium australiense isolates NML 98A072T and NML 98A078, derived from granulomatous lesions of infected bovines, were assembled and studied. Respectively, the genome sizes were 2.99 and 3.01 Mb, with G+C contents of 68.4% and 68.5%. Draft genome sequences of Propionibacterium australiense isolates NML 98A072T and NML 98A078, derived from granulomatous lesions of infected bovines, were assembled and studied. Respectively, the genome sizes were 2.99 and 3.01 Mb, with G+C contents of 68.4% and 68.5%.
Collapse
|
15
|
Deptula P, Smolander OP, Laine P, Roberts RJ, Edelmann M, Peltola P, Piironen V, Paulin L, Storgårds E, Savijoki K, Laitila A, Auvinen P, Varmanen P. Acidipropionibacterium virtanenii sp. nov., isolated from malted barley. Int J Syst Evol Microbiol 2018; 68:3175-3183. [PMID: 30156530 DOI: 10.1099/ijsem.0.002965] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
A Gram-stain-positive, catalase-positive and pleomorphic rod organism was isolated from malted barley in Finland, classified initially by partial 16S rRNA gene sequencing and originally deposited in the VTT Culture Collection as a strain of Propionibacterium acidipropionici (currently Acidipropionibacterium acidipropionici). The subsequent comparison of the whole 16S rRNA gene with other representatives of the genus Acidipropionibacterium revealed that the strain belongs to a novel species, most closely related to Acidipropionibacterium microaerophilum and Acidipropionibacterium acidipropionici, with similarity values of 98.46 and 98.31 %, respectively. The whole genome sequencing using PacBio RS II platform allowed further comparison of the genome with all of the other DNA sequences available for the type strains of the Acidipropionibacterium species. Those comparisons revealed the highest similarity of strain JS278T to A. acidipropionici, which was confirmed by the average nucleotide identity analysis. The genome of strain JS278T is intermediate in size compared to the A. acidipropionici and Acidipropionibacterium jensenii at 3 432 872 bp, the G+C content is 68.4 mol%. The strain fermented a wide range of carbon sources, and produced propionic acid as the major fermentation product. Besides its poor ability to grow at 37 °C and positive catalase reaction, the observed phenotype was almost indistinguishable from those of A. acidipropionici and A. jensenii. Based on our findings, we conclude that the organism represents a novel member of the genus Acidipropionibacterium, for which we propose the name Acidipropionibacteriumvirtanenii sp. nov. The type strain is JS278T (=VTT E-113202T=DSM 106790T).
Collapse
Affiliation(s)
- Paulina Deptula
- 1Department of Food and Nutrition, University of Helsinki, 00014 Helsinki, Finland
| | | | - Pia Laine
- 2Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | | | - Minnamari Edelmann
- 1Department of Food and Nutrition, University of Helsinki, 00014 Helsinki, Finland
| | | | - Vieno Piironen
- 1Department of Food and Nutrition, University of Helsinki, 00014 Helsinki, Finland
| | - Lars Paulin
- 2Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Erna Storgårds
- 5VTT Technical Research Centre of Finland, 02044 VTT, Finland
| | - Kirsi Savijoki
- 1Department of Food and Nutrition, University of Helsinki, 00014 Helsinki, Finland
| | - Arja Laitila
- 5VTT Technical Research Centre of Finland, 02044 VTT, Finland
| | | | - Pekka Varmanen
- 1Department of Food and Nutrition, University of Helsinki, 00014 Helsinki, Finland
| |
Collapse
|
16
|
Frohnmeyer E, Deptula P, Nyman TA, Laine PKS, Vihinen H, Paulin L, Auvinen P, Jokitalo E, Piironen V, Varmanen P, Savijoki K. Secretome profiling of Propionibacterium freudenreichii reveals highly variable responses even among the closely related strains. Microb Biotechnol 2018; 11:510-526. [PMID: 29488359 PMCID: PMC5902329 DOI: 10.1111/1751-7915.13254] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 01/19/2018] [Indexed: 12/20/2022] Open
Abstract
This study compared the secretomes (proteins exported out of the cell) of Propionibacterium freudenreichii of different origin to identify plausible adaptation factors. Phylosecretomics indicated strain‐specific variation in secretion of adhesins/invasins (SlpA, InlA), cell‐wall hydrolysing (NlpC60 peptidase, transglycosylase), protective (RpfB) and moonlighting (DnaK, GroEL, GaPDH, IDH, ENO, ClpB) enzymes and/or proteins. Detailed secretome comparison suggested that one of the cereal strains (JS14) released a tip fimbrillin (FimB) in to the extracellular milieu, which was in line with the electron microscopy and genomic analyses, indicating the lack of surface‐associated fimbrial‐like structures, predicting a mutated type‐2 fimbrial gene cluster (fimB‐fimA‐srtC2) and production of anchorless FimB. Instead, the cereal strain produced high amounts of SlpB that tentatively mediated adherent growth on hydrophilic surface and adherence to hydrophobic material. One of the dairy strains (JS22), producing non‐covalently bound surface‐proteins (LspA, ClpB, AraI) and releasing SlpA and InlA into the culture medium, was found to form clumps under physiological conditions. The JS22 strain lacked SlpB and displayed a non‐clumping and biofilm‐forming phenotype only under conditions of increased ionic strength (300 mM NaCl). However, this strain cultured under the same conditions was not adherent to hydrophobic support, which supports the contributory role of SlpB in mediating hydrophobic interactions. Thus, this study reports significant secretome variation in P. freudenreichii and suggests that strain‐specific differences in protein export, modification and protein–protein interactions have been the driving forces behind the adaptation of this bacterial species.
Collapse
Affiliation(s)
- Esther Frohnmeyer
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki 00014, Finland
| | - Paulina Deptula
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki 00014, Finland
| | - Tuula A Nyman
- Department of Immunology, Institute of Clinical Medicine, University of Oslo, 0424 Oslo, Norway
| | - Pia K S Laine
- DNA Sequencing and Genomics Lab, Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - Helena Vihinen
- Electron Microscopy Unit, Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - Lars Paulin
- DNA Sequencing and Genomics Lab, Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - Petri Auvinen
- DNA Sequencing and Genomics Lab, Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - Eija Jokitalo
- Electron Microscopy Unit, Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - Vieno Piironen
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki 00014, Finland
| | - Pekka Varmanen
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki 00014, Finland
| | - Kirsi Savijoki
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki 00014, Finland
| |
Collapse
|
17
|
Deptula P, Laine PK, Roberts RJ, Smolander OP, Vihinen H, Piironen V, Paulin L, Jokitalo E, Savijoki K, Auvinen P, Varmanen P. De novo assembly of genomes from long sequence reads reveals uncharted territories of Propionibacterium freudenreichii. BMC Genomics 2017; 18:790. [PMID: 29037147 PMCID: PMC5644110 DOI: 10.1186/s12864-017-4165-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 10/05/2017] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Propionibacterium freudenreichii is an industrially important bacterium granted the Generally Recognized as Safe (the GRAS) status, due to its long safe use in food bioprocesses. Despite the recognized role in the food industry and in the production of vitamin B12, as well as its documented health-promoting potential, P. freudenreichii remained poorly characterised at the genomic level. At present, only three complete genome sequences are available for the species. RESULTS We used the PacBio RS II sequencing platform to generate complete genomes of 20 P. freudenreichii strains and compared them in detail. Comparative analyses revealed both sequence conservation and genome organisational diversity among the strains. Assembly from long reads resulted in the discovery of additional circular elements: two putative conjugative plasmids and three active, lysogenic bacteriophages. It also permitted characterisation of the CRISPR-Cas systems. The use of the PacBio sequencing platform allowed identification of DNA modifications, which in turn allowed characterisation of the restriction-modification systems together with their recognition motifs. The observed genomic differences suggested strain variation in surface piliation and specific mucus binding, which were validated by experimental studies. The phenotypic characterisation displayed large diversity between the strains in ability to utilise a range of carbohydrates, to grow at unfavourable conditions and to form a biofilm. CONCLUSION The complete genome sequencing allowed detailed characterisation of the industrially important species, P. freudenreichii by facilitating the discovery of previously unknown features. The results presented here lay a solid foundation for future genetic and functional genomic investigations of this actinobacterial species.
Collapse
Affiliation(s)
- Paulina Deptula
- Department of Food and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland
| | - Pia K. Laine
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | | | | | - Helena Vihinen
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Vieno Piironen
- Department of Food and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland
| | - Lars Paulin
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Eija Jokitalo
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Kirsi Savijoki
- Department of Food and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland
| | - Petri Auvinen
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Pekka Varmanen
- Department of Food and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland
| |
Collapse
|
18
|
Deutsch SM, Mariadassou M, Nicolas P, Parayre S, Le Guellec R, Chuat V, Peton V, Le Maréchal C, Burati J, Loux V, Briard-Bion V, Jardin J, Plé C, Foligné B, Jan G, Falentin H. Identification of proteins involved in the anti-inflammatory properties of Propionibacterium freudenreichii by means of a multi-strain study. Sci Rep 2017; 7:46409. [PMID: 28406170 PMCID: PMC5390290 DOI: 10.1038/srep46409] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 03/09/2017] [Indexed: 12/29/2022] Open
Abstract
Propionibacterium freudenreichii, a dairy starter, can reach a population of almost 109 propionibacteria per gram in Swiss-type cheese at the time of consumption. Also consumed as a probiotic, it displays strain-dependent anti-inflammatory properties mediated by surface proteins that induce IL-10 in leukocytes. We selected 23 strains with varied anti-inflammatory potentials in order to identify the protein(s) involved. After comparative genomic analysis, 12 of these strains were further analysed by surface proteomics, eight of them being further submitted to transcriptomics. The omics data were then correlated to the anti-inflammatory potential evaluated by IL-10 induction. This comparative omics strategy highlighted candidate genes that were further subjected to gene-inactivation validation. This validation confirmed the contribution of surface proteins, including SlpB and SlpE, two proteins with SLH domains known to mediate non-covalent anchorage to the cell-wall. Interestingly, HsdM3, predicted as cytoplasmic and involved in DNA modification, was shown to contribute to anti-inflammatory activity. Finally, we demonstrated that a single protein cannot explain the anti-inflammatory properties of a strain. These properties therefore result from different combinations of surface and cytoplasmic proteins, depending on the strain. Our enhanced understanding of the molecular bases for immunomodulation will enable the relevant screening for bacterial resources with anti-inflammatory properties.
Collapse
Affiliation(s)
| | | | | | | | | | - Victoria Chuat
- STLO, UMR 1253, INRA, Agrocampus Ouest, 35000, Rennes, France
| | - Vincent Peton
- STLO, UMR 1253, INRA, Agrocampus Ouest, 35000, Rennes, France
| | | | | | | | | | - Julien Jardin
- STLO, UMR 1253, INRA, Agrocampus Ouest, 35000, Rennes, France
| | - Coline Plé
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 8204 - CIIL - Center for Infection and Immunity of Lille, 59000 Lille, France
| | - Benoît Foligné
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 8204 - CIIL - Center for Infection and Immunity of Lille, 59000 Lille, France
| | - Gwénaël Jan
- STLO, UMR 1253, INRA, Agrocampus Ouest, 35000, Rennes, France
| | - Hélène Falentin
- STLO, UMR 1253, INRA, Agrocampus Ouest, 35000, Rennes, France
| |
Collapse
|
19
|
Deptula P, Kylli P, Chamlagain B, Holm L, Kostiainen R, Piironen V, Savijoki K, Varmanen P. BluB/CobT2 fusion enzyme activity reveals mechanisms responsible for production of active form of vitamin B₁₂ by Propionibacterium freudenreichii. Microb Cell Fact 2015; 14:186. [PMID: 26597297 PMCID: PMC4657239 DOI: 10.1186/s12934-015-0363-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 10/18/2015] [Indexed: 01/02/2023] Open
Abstract
Background Propionibacterium freudenreichii is a food grade bacterium that has gained attention as a producer of appreciable amounts of cobalamin, a cobamide with activity of vitamin B12. Production of active form of vitamin is a prerequisite for attempts to naturally fortify foods with B12 by microbial fermentation. Active vitamin B12 is distinguished from the pseudovitamin by the presence of 5,6-dimethylbenzimidazole (DMBI) as the lower ligand. Genomic data indicate that P. freudenreichii possesses a fusion gene, bluB/cobT2, coding for a predicted phosphoribosyltransferase/nitroreductase, which is presumably involved in production of vitamin B12. Understanding the mechanisms affecting the synthesis of different vitamin forms is useful for rational strain selection and essential for engineering of strains with improved B12 production properties. Results Here, we investigated the activity of heterologously expressed and purified fusion enzyme BluB/CobT2. Our results show that BluB/CoBT2 is responsible for the biosynthesis of the DMBI base and its activation into α-ribazole phosphate, preparing it for attachment as the lower ligand of cobalamin. The fusion enzyme was found to be efficient in metabolite channeling and the enzymes’ inability to react with adenine, a lower ligand present in the pseudovitamin, revealed a mechanism favoring the production of the active form of the vitamin. P. freudenreichii did not produce cobalamin under strictly anaerobic conditions, confirming the requirement of oxygen for DMBI synthesis. In vivo experiments also revealed a clear preference for incorporating DMBI over adenine into cobamide under both microaerobic and anaerobic conditions. Conclusions The herein described BluB/CobT2 is responsible for the production and activation of DMBI. Fusing those two activities results in high pressure towards production of the true vitamin B12 by efficiently activating DMBI formed within the same enzymatic complex. This indicates that BluB/CobT2 is the crucial enzyme in the B12 biosynthetic pathway of P. freudenreichii. The GRAS organism status and the preference for synthesizing active vitamin form make P. freudenreichii a unique candidate for the in situ production of vitamin B12 within food products. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0363-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Paulina Deptula
- Department of Food and Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland.
| | - Petri Kylli
- Division of Pharmaceutical Chemistry and Technology, University of Helsinki, 00014, Helsinki, Finland.
| | - Bhawani Chamlagain
- Department of Food and Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland.
| | - Liisa Holm
- Institute of Biotechnology, University of Helsinki, 00014, Helsinki, Finland.
| | - Risto Kostiainen
- Division of Pharmaceutical Chemistry and Technology, University of Helsinki, 00014, Helsinki, Finland.
| | - Vieno Piironen
- Department of Food and Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland.
| | - Kirsi Savijoki
- Department of Food and Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland.
| | - Pekka Varmanen
- Department of Food and Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland.
| |
Collapse
|