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Harlé O, Niay J, Parayre S, Nicolas A, Henry G, Maillard MB, Valence F, Thierry A, Guédon É, Falentin H, Deutsch SM. Deciphering the metabolism of Lactobacillus delbrueckii subsp. delbrueckii during soy juice fermentation using phenotypic and transcriptional analysis. Appl Environ Microbiol 2024; 90:e0193623. [PMID: 38376234 PMCID: PMC10952386 DOI: 10.1128/aem.01936-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 01/03/2024] [Indexed: 02/21/2024] Open
Abstract
In the context of sustainable diet, the development of soy-based yogurt fermented with lactic acid bacteria is an attractive alternative to dairy yogurts. To decipher the metabolism of Lactobacillus delbrueckii subsp. delbrueckii during soy juice (SJ) fermentation, the whole genome of the strain CIRM-BIA865 (Ld865) was sequenced and annotated. Then Ld865 was used to ferment SJ. Samples were analyzed throughout fermentation for their cell number, carbohydrate, organic acid, free amino acid, and volatile compound contents. Despite acidification, the number of Ld865 cells did not rise, and microscopic observations revealed the elongation of cells from 3.6 µm (inoculation) to 36.9 µm (end of fermentation). This elongation was observed in SJ but not in laboratory-rich medium MRS. Using transcriptomic analysis, we showed that the biosynthesis genes of peptidoglycan and membrane lipids were stably expressed, in line with the cell elongation observed, whereas no genes implicated in cell division were upregulated. Among the main sugars available in SJ (sucrose, raffinose, and stachyose), Ld865 only used sucrose. The transcriptomic analysis showed that Ld865 implemented the two transport systems that it contains to import sucrose: a PTS system and an ABC transporter. To fulfill its nitrogen needs, Ld865 probably first consumed the free amino acids of the SJ and then implemented different oligopeptide transporters and proteolytic/peptidase enzymes. In conclusion, this study showed that Ld865 enables fast acidification of SJ, despite the absence of cell division, leads to a product rich in free amino acids, and also leads to the production of aromatic compounds of interest. IMPORTANCE To reduce the environmental and health concerns related to food, an alternative diet is recommended, containing 50% of plant-based proteins. Soy juice, which is protein rich, is a relevant alternative to animal milk, for the production of yogurt-like products. However, soy "beany" and "green" off-flavors limit the consumption of such products. The lactic acid bacteria (LAB) used for fermentation can help to improve the organoleptic properties of soy products. But metabolic data concerning LAB adapted to soy juice are lacking. The aim of this study was, thus, to decipher the metabolism of Lactobacillus delbrueckii subsp. delbrueckii during fermentation of a soy juice, based on a multidisciplinary approach. This result will contribute to give tracks for a relevant selection of starter. Indeed, the improvement of the organoleptic properties of these types of products could help to promote plant-based proteins in our diet.
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Affiliation(s)
- Olivier Harlé
- INRAE, Institut Agro, STLO, Rennes, France
- Olga-Triballat Noyal, R&D UF, Noyal-sur-Vilaine, France
| | - Jérôme Niay
- Olga-Triballat Noyal, R&D UF, Noyal-sur-Vilaine, France
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Penland M, Pawtowski A, Pioli A, Maillard MB, Debaets S, Deutsch SM, Falentin H, Mounier J, Coton M. Brine salt concentration reduction and inoculation with autochthonous consortia: Impact on Protected Designation of Origin Nyons black table olive fermentations. Food Res Int 2022; 155:111069. [DOI: 10.1016/j.foodres.2022.111069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 11/04/2022]
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Cao W, Aubert J, Maillard MB, Boissel F, Leduc A, Thomas JL, Deutsch SM, Camier B, Kerjouh A, Parayre S, Harel-Oger M, Garric G, Thierry A, Falentin H. Fine-Tuning of Process Parameters Modulates Specific Metabolic Bacterial Activities and Aroma Compound Production in Semi-Hard Cheese. J Agric Food Chem 2021; 69:8511-8529. [PMID: 34283609 DOI: 10.1021/acs.jafc.1c01634] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The formation of cheese flavor mainly results from the production of volatile compounds by microorganisms. We investigated how fine-tuning cheese-making process parameters changed the cheese volatilome in a semi-hard cheese inoculated with Lactococcus (L.) lactis, Lactiplantibacillus (L.) plantarum, and Propionibacterium (P.) freudenreichii. A standard (Std) cheese was compared with three variants of technological itineraries: a shorter salting time (7 h vs 10 h, Salt7h), a shorter stirring time (15 min vs 30 min, Stir15min), or a higher ripening temperature (16 °C vs 13 °C, Rip16°C). Bacterial counts were similar in the four cheese types, except for a 1.4 log10 reduction of L. lactis counts in Rip16°C cheeses after 7 weeks of ripening. Compared to Std, Stir15min and Rip16°C increased propionibacterial activity, causing higher concentrations of acetic, succinic, and propanoic acids and lower levels of lactic acid. Rip16°C accelerated secondary proteolysis and volatile production. We thus demonstrated that fine-tuning process parameters could modulate the cheese volatilome by influencing specific bacterial metabolisms.
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Affiliation(s)
- Wenfan Cao
- UMR STLO, INRAE, Institut Agro, 35042 Rennes, France
| | - Julie Aubert
- Université Paris-Saclay, AgroParisTech, INRAE, MIA-Paris, 75005 Paris, France
| | | | | | - Arlette Leduc
- UMR STLO, INRAE, Institut Agro, 35042 Rennes, France
| | | | | | | | - Ali Kerjouh
- UMR STLO, INRAE, Institut Agro, 35042 Rennes, France
| | | | | | - Gilles Garric
- UMR STLO, INRAE, Institut Agro, 35042 Rennes, France
| | - Anne Thierry
- UMR STLO, INRAE, Institut Agro, 35042 Rennes, France
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Penland M, Mounier J, Pawtowski A, Tréguer S, Deutsch SM, Coton M. Use of metabarcoding and source tracking to identify desirable or spoilage autochthonous microorganism sources during black olive fermentations. Food Res Int 2021; 144:110344. [PMID: 34053540 DOI: 10.1016/j.foodres.2021.110344] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 03/03/2021] [Accepted: 03/19/2021] [Indexed: 12/01/2022]
Abstract
This study aimed at investigating the influence of the process environment and raw materials as sources of microorganisms during Nyons black table olive fermentations. Fermented olives and/or brine from spoiled fermentation tanks were analyzed and compared to good quality samples from fermentations collected during 3 consecutive harvest years. Fresh olives, salt and different process environment samples were also analyzed. Microbial diversity of all samples was analyzed using 16S and ITS2 amplicon sequencing and SourceTracker tool was used to investigate links between environment, raw materials and fermentation samples. First, comparison of microbial diversity in control and most spoiled fermentations revealed striking differences in bacterial composition with an overall higher diversity in spoiled fermentations especially for lactic acid bacteria with Lentilactobacillus buchneri, Lentilactobacillus parafarraginis dominating in brine and Pediococcus parvulus, Pediococcus ethanolidurans dominating in olive fruits. Fungal communities were similar in composition although higher abundances of Pichia membranifaciens and Penicillium carneum/roqueforti were observed in spoiled samples. Secondly, process environment samples were characterized by high bacterial and fungal diversity, especially compared to fresh olive fruits. Overall, dominant fungal species in control fermentations were also found in most environmental samples revealing a "house mycobiota". SourceTracker analysis further highlighted the contribution of brine and water from the optical sorter as a source of fungi. Most interestingly, spoilage fungi and most bacteria were retrieved in brine and environmental samples while others such as P. ethanolidurans were only found in environmental samples indicating that the studied spoilage originated from a fermentation deviation rather than a punctual contamination. Taken altogether, these results highlighted the positive and negative influence of the process environment and emphasized the relevance of studying it to better understand microbial vectors occurring during food fermentations, especially natural ones.
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Affiliation(s)
- Marine Penland
- Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280 Plouzané, France; STLO, INRAE, Institut Agro, 35042 Rennes, France
| | - Jérôme Mounier
- Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280 Plouzané, France
| | - Audrey Pawtowski
- Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280 Plouzané, France
| | - Sylvie Tréguer
- Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280 Plouzané, France
| | | | - Monika Coton
- Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280 Plouzané, France.
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Penland M, Falentin H, Parayre S, Pawtowski A, Maillard MB, Thierry A, Mounier J, Coton M, Deutsch SM. Linking Pélardon artisanal goat cheese microbial communities to aroma compounds during cheese-making and ripening. Int J Food Microbiol 2021; 345:109130. [PMID: 33735781 DOI: 10.1016/j.ijfoodmicro.2021.109130] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 11/27/2020] [Accepted: 02/23/2021] [Indexed: 11/17/2022]
Abstract
Pélardon is an artisanal French raw goat's milk cheese, produced using natural whey as a backslop. The aim of this study was to identify key microbial players involved in the acidification and aroma production of this Protected Designation of Origin cheese. Microbial diversity of samples, collected from the raw milk to 3-month cheese ripening, was determined by culture-dependent (MALDI-TOF analysis of 2877 isolates) and -independent (ITS2 and 16S metabarcoding) approaches and linked to changes in biochemical profiles (volatile compounds and acids). In parallel, potential dominant autochthonous microorganism reservoirs were also investigated by sampling the cheese-factory environment. Complex and increasing microbial diversity was observed by both approaches during ripening although major discrepancies were observed regarding Lactococcus lactis and Lacticaseibacillus paracasei fate. By correlating microbial shifts to biochemical changes, Lactococcus lactis was identified as the main acidifying bacterium, while L. mesenteroides and Geotrichum candidum were prevalent and associated with amino acids catabolism after the acidification step. The three species were dominant in the whey (backslop). In contrast, L. paracasei, Enterococcus faecalis, Penicillium commune and Scopulariopsis brevicaulis, which dominated during ripening, likely originated from the cheese-making environment. All these four species were positively correlated to major volatile compounds responsible for the goaty and earthy Pélardon cheese aroma. Overall, this work highlighted the power of MALDI-TOF and molecular techniques combined with volatilome analyses to dynamically follow and identify microbial communities during cheese-making and successively identify the key-players involved in aroma production and contributing to the typicity of Pélardon cheese.
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Affiliation(s)
- Marine Penland
- STLO, INRAE, Institut Agro, 35042 Rennes, France; Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280 Plouzané, France
| | | | | | - Audrey Pawtowski
- Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280 Plouzané, France
| | | | - Anne Thierry
- STLO, INRAE, Institut Agro, 35042 Rennes, France
| | - Jérôme Mounier
- Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280 Plouzané, France
| | - Monika Coton
- Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280 Plouzané, France
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Penland M, Deutsch SM, Falentin H, Pawtowski A, Poirier E, Visenti G, Le Meur C, Maillard MB, Thierry A, Mounier J, Coton M. Deciphering Microbial Community Dynamics and Biochemical Changes During Nyons Black Olive Natural Fermentations. Front Microbiol 2020; 11:586614. [PMID: 33133054 PMCID: PMC7578400 DOI: 10.3389/fmicb.2020.586614] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 09/02/2020] [Indexed: 12/15/2022] Open
Abstract
French PDO Nyons black table olives are produced according to a traditional slow spontaneous fermentation in brine. The manufacture and unique sensorial properties of these olives thus only rely on the autochthonous complex microbiota. This study aimed at unraveling the microbial communities and dynamics of Nyons olives during a 1.5-year-long spontaneous fermentation to determine the main microbial drivers and link microbial species to key metabolites. Fermentations were monitored at a local producer plant at regular time intervals for two harvests and two olive types (organically and conventionally grown) using culture-dependent and metabarcoding (ITS2 for fungi, V3-V4 region for bacteria) approaches. Olives and brines were also sampled for volatiles, organic acids and phenolic compounds. No major differences in microbiota composition were observed according to olive type or harvest period. Throughout the fermentation, yeasts were clearly the most dominant. ITS2 sequencing data revealed complex fungal diversity dominated by Citeromyces nyonsensis, Wickerhamomyces anomalus, Zygotorulaspora mrakii, Candida boidinii and Pichia membranifaciens species. Bacterial communities were dominated by the Celerinatantimonas genus, while lactic acid bacteria remained scarce. Clear shifts in microbial communities and biochemical profiles were observed during fermentation and, by correlating metabolites and microbiota changes, four different phases were distinguished. During the first 7 days, phase I, a fast decrease of filamentous fungal and bacterial populations was observed. Between days 21 and 120, phase II, W. anomalus and C. nyonsensis for fungi and Celerinatantimonas diazotrophica for bacteria dominated the fermentation and were linked to the pH decrease and citric acid production. Phase III, between 120 and 183 days, was characterized by an increase in acids and esters and correlated to increased abundances of Z. mrakii, P. membranifaciens and C. boidinii. During the last months of fermentation, phase IV, microbial communities were dominated by P. membranifaciens and C. boidinii. Both species were strongly correlated to an increase in fruity esters and alcohol abundances. Overall, this study provides an in-depth understanding about microbial species succession and how the microbiota shapes the final distinct olive characteristics. It also constitutes a first step to identify key drivers of this fermentation.
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Affiliation(s)
- Marine Penland
- Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, Plouzané, France.,STLO, INRAE, Institut Agro, Rennes, France
| | | | | | - Audrey Pawtowski
- Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, Plouzané, France
| | - Elisabeth Poirier
- Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, Plouzané, France
| | - Giorgia Visenti
- Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, Plouzané, France
| | - Christophe Le Meur
- Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, Plouzané, France
| | | | | | - Jérôme Mounier
- Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, Plouzané, France
| | - Monika Coton
- Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, Plouzané, France
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Guyomarc'h F, Francius G, Parayre S, Madec MN, Deutsch SM. Surface properties associated with the production of polysaccharides in the food bacteria Propionibacterium freudenreichii. Food Microbiol 2020; 92:103579. [PMID: 32950163 DOI: 10.1016/j.fm.2020.103579] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 05/20/2020] [Accepted: 06/20/2020] [Indexed: 10/24/2022]
Abstract
This study explores the production of polysaccharides (PS) in the strain Pf2289 of the food species Propionibacterium freudenreichii. Pf2289 presents characteristics atypical of the species: a molar-shaped morphotype upon plating, and cells strongly aggregative in liquid medium. When plating Pf2289, another morphotype was observed with a 4% frequency of appearance: round-shaped colonies, typical of the species. A clone was isolated, designated Pf456. No reversibility of Pf456 towards the molar-shaped morphotype was observed. Pf2289 was shown to produce a surface polysaccharide (PS) bound to the cell wall, mainly during the stationary growth phase. Meanwhile, Pf456 had lost the ability to produce the PS. AFM images of Pf2289 showed that entangled filaments spread over the whole surface of the bacteria, whereas Pf456 exhibited a smooth surface. Adhesion force maps, performed with concanavalin-A grafted probes, revealed twice as much adhesion of Pf2289 to concanavalin-A compared to Pf456. Furthermore, the length of PS molecules surrounding Pf2289 measured at least 7 μm, whereas it only reached 1 μm in Pf456. Finally, the presence of PS had a strong impact on adhesion properties: Pf2289 did not adhere to hydrophobic surfaces, whereas Pf456 showed strong adhesion.
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Affiliation(s)
| | - Grégory Francius
- Université de Lorraine, LCPME, Laboratoire de Chimie Physique et Microbiologie pour l'Environnement, UMR 7564, 54600, Villers-lès-Nancy, France
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Harlé O, Falentin H, Niay J, Valence F, Courselaud C, Chuat V, Maillard MB, Guédon É, Deutsch SM, Thierry A. Diversity of the metabolic profiles of a broad range of lactic acid bacteria in soy juice fermentation. Food Microbiol 2020; 89:103410. [PMID: 32138982 DOI: 10.1016/j.fm.2019.103410] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 11/14/2019] [Accepted: 12/26/2019] [Indexed: 12/31/2022]
Abstract
This study explores the ability of lactic acid bacteria (LAB) to ferment soy juice. The ability of 276 LAB strains from 25 species to ferment the principal soy carbohydrates, sucrose, raffinose or stachyose was tested in synthetic media and a soy juice. Fermented soy juices (FSJs) were characterized for their odor. Selected FSJs were characterized by targeted metabolomics. All Streptococcus, 83% of Leuconostoc and Lactobacillus and 41% of Lactococcus strains were sucrose-positive, while only 36% of all the LAB strains tested were raffinose-positive and 6% stachyose-positive. Nearly all (97%) the sucrose-positive strains fermented soy juice, indicating that an ability to use sucrose is a good criterion to select strains for soy juice fermentation. Among the most efficient acidifying strains, 46 FSJs had an odor deemed to be acceptable. FSJ composition was dependent on both species and strains: 17/46 strains deglycosylated soy juice isoflavones, the 27 S. thermophilus strains converted a mean 4.4 ± 0.1 g/L of sucrose into 3.0 ± 0.1 g/L of lactic acid versus 5.2 ± 0.1 g/L into 2.2 ± 0.1 g/L for the 18 Lactobacillus and one Lactococcus strains. This study highlights the diversity of the metabolic profiles of LAB strains in soy juice fermentation.
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Affiliation(s)
- Olivier Harlé
- STLO, INRAE, Agrocampus Ouest, Rennes, France; Triballat Noyal, Noyal-sur-Vilaine, France.
| | | | | | | | | | | | | | - Éric Guédon
- STLO, INRAE, Agrocampus Ouest, Rennes, France.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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Aburjaile FF, Rohmer M, Parrinello H, Maillard MB, Beaucher E, Henry G, Nicolas A, Madec MN, Thierry A, Parayre S, Deutsch SM, Cocaign-Bousquet M, Miyoshi A, Azevedo V, Le Loir Y, Falentin H. Adaptation of Propionibacterium freudenreichii to long-term survival under gradual nutritional shortage. BMC Genomics 2016; 17:1007. [PMID: 27931189 PMCID: PMC5146858 DOI: 10.1186/s12864-016-3367-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 12/02/2016] [Indexed: 11/23/2022] Open
Abstract
Background Propionibacterium freudenreichii is an Actinobacterium widely used in the dairy industry as a ripening culture for Swiss-type cheeses, for vitamin B12 production and some strains display probiotic properties. It is reportedly a hardy bacterium, able to survive the cheese-making process and digestive stresses. Results During this study, P. freudenreichii CIRM-BIA 138 (alias ITG P9), which has a generation time of five hours in Yeast Extract Lactate medium at 30 °C under microaerophilic conditions, was incubated for 11 days (9 days after entry into stationary phase) in a culture medium, without any adjunct during the incubation. The carbon and free amino acids sources available in the medium, and the organic acids produced by the strain, were monitored throughout growth and survival. Although lactate (the preferred carbon source for P. freudenreichii) was exhausted three days after inoculation, the strain sustained a high population level of 9.3 log10 CFU/mL. Its physiological adaptation was investigated by RNA-seq analysis and revealed a complete disruption of metabolism at the entry into stationary phase as compared to exponential phase. Conclusions P. freudenreichii adapts its metabolism during entry into stationary phase by down-regulating oxidative phosphorylation, glycolysis, and the Wood-Werkman cycle by exploiting new nitrogen (glutamate, glycine, alanine) sources, by down-regulating the transcription, translation and secretion of protein. Utilization of polyphosphates was suggested. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3367-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Flavia Figueira Aburjaile
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.,INRA, UMR 1253, Science et Technologie du Lait et de l' Œuf, 35000, Rennes, France.,AGROCAMPUS OUEST, UMR1253, UMR Science et Technologie du Lait et de l'Œuf, 35000, Rennes, France
| | - Marine Rohmer
- UMS BioCampus- MGX Montpellier GenomiX, Institut de Génomique Fonctionelle, 141, rue de la Cardonnille, 34094, Montpellier Cedex 05, France
| | - Hugues Parrinello
- UMS BioCampus- MGX Montpellier GenomiX, Institut de Génomique Fonctionelle, 141, rue de la Cardonnille, 34094, Montpellier Cedex 05, France
| | - Marie-Bernadette Maillard
- INRA, UMR 1253, Science et Technologie du Lait et de l' Œuf, 35000, Rennes, France.,AGROCAMPUS OUEST, UMR1253, UMR Science et Technologie du Lait et de l'Œuf, 35000, Rennes, France
| | - Eric Beaucher
- INRA, UMR 1253, Science et Technologie du Lait et de l' Œuf, 35000, Rennes, France.,AGROCAMPUS OUEST, UMR1253, UMR Science et Technologie du Lait et de l'Œuf, 35000, Rennes, France
| | - Gwénaële Henry
- INRA, UMR 1253, Science et Technologie du Lait et de l' Œuf, 35000, Rennes, France.,AGROCAMPUS OUEST, UMR1253, UMR Science et Technologie du Lait et de l'Œuf, 35000, Rennes, France
| | - Aurélie Nicolas
- INRA, UMR 1253, Science et Technologie du Lait et de l' Œuf, 35000, Rennes, France.,AGROCAMPUS OUEST, UMR1253, UMR Science et Technologie du Lait et de l'Œuf, 35000, Rennes, France
| | - Marie-Noëlle Madec
- INRA, UMR 1253, Science et Technologie du Lait et de l' Œuf, 35000, Rennes, France.,AGROCAMPUS OUEST, UMR1253, UMR Science et Technologie du Lait et de l'Œuf, 35000, Rennes, France
| | - Anne Thierry
- INRA, UMR 1253, Science et Technologie du Lait et de l' Œuf, 35000, Rennes, France.,AGROCAMPUS OUEST, UMR1253, UMR Science et Technologie du Lait et de l'Œuf, 35000, Rennes, France
| | - Sandrine Parayre
- INRA, UMR 1253, Science et Technologie du Lait et de l' Œuf, 35000, Rennes, France.,AGROCAMPUS OUEST, UMR1253, UMR Science et Technologie du Lait et de l'Œuf, 35000, Rennes, France
| | - Stéphanie-Marie Deutsch
- INRA, UMR 1253, Science et Technologie du Lait et de l' Œuf, 35000, Rennes, France.,AGROCAMPUS OUEST, UMR1253, UMR Science et Technologie du Lait et de l'Œuf, 35000, Rennes, France
| | - Muriel Cocaign-Bousquet
- LISBP, Université de Toulouse, CNRS, INRA, INSA, 135 avenue de Rangueil, Toulouse, 31077, France
| | - Anderson Miyoshi
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Vasco Azevedo
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Yves Le Loir
- INRA, UMR 1253, Science et Technologie du Lait et de l' Œuf, 35000, Rennes, France.,AGROCAMPUS OUEST, UMR1253, UMR Science et Technologie du Lait et de l'Œuf, 35000, Rennes, France
| | - Hélène Falentin
- INRA, UMR 1253, Science et Technologie du Lait et de l' Œuf, 35000, Rennes, France. .,AGROCAMPUS OUEST, UMR1253, UMR Science et Technologie du Lait et de l'Œuf, 35000, Rennes, France.
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11
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Falentin H, Deutsch SM, Loux V, Hammani A, Buratti J, Parayre S, Chuat V, Barbe V, Aury JM, Jan G, Le Loir Y. Permanent draft genome sequence of the probiotic strain Propionibacterium freudenreichii CIRM-BIA 129 (ITG P20). Stand Genomic Sci 2016; 11:6. [PMID: 26779303 PMCID: PMC4714504 DOI: 10.1186/s40793-015-0120-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 12/03/2015] [Indexed: 11/25/2022] Open
Abstract
Propionibacterium freudenreichii belongs to the class Actinobacteria (Gram positive with a high GC content). This “Generally Recognized As Safe” (GRAS) species is traditionally used as (i) a starter for Swiss-type cheeses where it is responsible for holes and aroma production, (ii) a vitamin B12 and propionic acid producer in white biotechnologies, and (iii) a probiotic for use in humans and animals because of its bifidogenic and anti-inflammatory properties. Until now, only strain CIRM-BIA1T had been sequenced, annotated and become publicly available. Strain CIRM-BIA129 (commercially available as ITG P20) has considerable anti-inflammatory potential. Its gene content was compared to that of CIRM-BIA1 T. This strain contains 2384 genes including 1 ribosomal operon, 45 tRNA and 30 pseudogenes.
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Affiliation(s)
- Hélène Falentin
- INRA, UMR 1253, Science et Technologie du Lait et de l'Oeuf, 35000 Rennes, France ; AGROCAMPUS OUEST, UMR1253, UMR Science et Technologie du Lait et de l'Oeuf, 35000 Rennes, France
| | - Stéphanie-Marie Deutsch
- INRA, UMR 1253, Science et Technologie du Lait et de l'Oeuf, 35000 Rennes, France ; AGROCAMPUS OUEST, UMR1253, UMR Science et Technologie du Lait et de l'Oeuf, 35000 Rennes, France
| | - Valentin Loux
- INRA, UR1077 Unité Mathématique Informatique et Génome, Jouy-en-Josas, France
| | - Amal Hammani
- INRA, UR1077 Unité Mathématique Informatique et Génome, Jouy-en-Josas, France
| | - Julien Buratti
- INRA, UR1077 Unité Mathématique Informatique et Génome, Jouy-en-Josas, France
| | - Sandrine Parayre
- INRA, UMR 1253, Science et Technologie du Lait et de l'Oeuf, 35000 Rennes, France ; AGROCAMPUS OUEST, UMR1253, UMR Science et Technologie du Lait et de l'Oeuf, 35000 Rennes, France
| | - Victoria Chuat
- INRA, UMR 1253, Science et Technologie du Lait et de l'Oeuf, 35000 Rennes, France ; AGROCAMPUS OUEST, UMR1253, UMR Science et Technologie du Lait et de l'Oeuf, 35000 Rennes, France
| | - Valérie Barbe
- CEA Genoscope CNRS and université d'Evry, 91 006 Evry, France
| | - Jean-Marc Aury
- CEA Genoscope CNRS and université d'Evry, 91 006 Evry, France
| | - Gwenaël Jan
- INRA, UMR 1253, Science et Technologie du Lait et de l'Oeuf, 35000 Rennes, France ; AGROCAMPUS OUEST, UMR1253, UMR Science et Technologie du Lait et de l'Oeuf, 35000 Rennes, France
| | - Yves Le Loir
- INRA, UMR 1253, Science et Technologie du Lait et de l'Oeuf, 35000 Rennes, France ; AGROCAMPUS OUEST, UMR1253, UMR Science et Technologie du Lait et de l'Oeuf, 35000 Rennes, France
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12
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Plé C, Breton J, Richoux R, Nurdin M, Deutsch SM, Falentin H, Hervé C, Chuat V, Lemée R, Maguin E, Jan G, Van de Guchte M, Foligné B. Combining selected immunomodulatory Propionibacterium freudenreichii
and Lactobacillus delbrueckii
strains: Reverse engineering development of an anti-inflammatory cheese. Mol Nutr Food Res 2015; 60:935-48. [DOI: 10.1002/mnfr.201500580] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 11/25/2015] [Accepted: 11/29/2015] [Indexed: 12/14/2022]
Affiliation(s)
- Coline Plé
- Institut Pasteur de Lille, Lactic Acid Bacteria & Mucosal Immunity; Center for Infection and Immunity of Lille; Lille France
| | - Jérôme Breton
- Institut Pasteur de Lille, Lactic Acid Bacteria & Mucosal Immunity; Center for Infection and Immunity of Lille; Lille France
| | - Romain Richoux
- Actalia Produits Laitiers; Agrocampus Ouest; Rennes cedex France
| | - Marine Nurdin
- Actalia Produits Laitiers; Agrocampus Ouest; Rennes cedex France
| | - Stéphanie-Marie Deutsch
- Science et Technologie du Lait et de l’Œuf; INRA; Rennes France
- Agrocampus Ouest; Rennes France
| | - Hélène Falentin
- Science et Technologie du Lait et de l’Œuf; INRA; Rennes France
- Agrocampus Ouest; Rennes France
| | | | - Victoria Chuat
- Science et Technologie du Lait et de l’Œuf; INRA; Rennes France
- Agrocampus Ouest; Rennes France
- CIRM-BIA; Centre Internationale de Ressources Microbiennes-Bactéries d'Intérêt Alimentaire; Rennes France
| | | | - Emmanuelle Maguin
- INRA; Jouy-en-Josas France
- AgroParisTech; UMR Micalis; Jouy-en-Josas France
| | - Gwénaël Jan
- Science et Technologie du Lait et de l’Œuf; INRA; Rennes France
- Agrocampus Ouest; Rennes France
| | | | - Benoit Foligné
- Institut Pasteur de Lille, Lactic Acid Bacteria & Mucosal Immunity; Center for Infection and Immunity of Lille; Lille France
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13
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Plé C, Richoux R, Jardin J, Nurdin M, Briard-Bion V, Parayre S, Ferreira S, Pot B, Bouguen G, Deutsch SM, Falentin H, Foligné B, Jan G. Single-strain starter experimental cheese reveals anti-inflammatory effect of Propionibacterium freudenreichii CIRM BIA 129 in TNBS-colitis model. J Funct Foods 2015. [DOI: 10.1016/j.jff.2015.08.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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14
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Le Maréchal C, Peton V, Plé C, Vroland C, Jardin J, Briard-Bion V, Durant G, Chuat V, Loux V, Foligné B, Deutsch SM, Falentin H, Jan G. Data from an integrative approach decipher the surface proteome of Propionibacterium freudenreichii. Data Brief 2015. [PMID: 26217685 PMCID: PMC4459863 DOI: 10.1016/j.dib.2014.08.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
The surface proteins of the probiotic Propionibacterium freudenreichii were inventoried by an integrative approach that combines in silico protein localization prediction, surface protein extraction, shaving and fluorescent CyDye labeling. Proteins that were extracted and/or shaved and/or labeled were identified by nano-LC-MS/MS following trypsinolysis. This method's combination allowed to confirm detection of true surface proteins involved in host/probiotic interactions. The data, supplied in this article, are related to the research article entitled "Surface proteins of P. freudenreichii are involved in its anti-inflammatory properties" (Le Maréchal et al., 2014 [6]).
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Affiliation(s)
- Caroline Le Maréchal
- INRA, UMR1253 STLO, Science et Technologie du Lait et de l׳Œuf, F-35042 Rennes, France ; GROCAMPUS OUEST, UMR1253 STLO, F-35042 Rennes, France
| | - Vincent Peton
- INRA, UMR1253 STLO, Science et Technologie du Lait et de l׳Œuf, F-35042 Rennes, France ; GROCAMPUS OUEST, UMR1253 STLO, F-35042 Rennes, France
| | - Coline Plé
- Lactic acid Bacteria & Mucosal Immunity, Center for Infection and Immunity of Lille, Institut Pasteur de Lille, U 1019, UMR 8204 Université Lille Nord de France, 1 rue du Pr Calmette, BP 245, F-59019 Lille, France
| | - Christophe Vroland
- INRA, UMR1253 STLO, Science et Technologie du Lait et de l׳Œuf, F-35042 Rennes, France ; GROCAMPUS OUEST, UMR1253 STLO, F-35042 Rennes, France
| | - Julien Jardin
- INRA, UMR1253 STLO, Science et Technologie du Lait et de l׳Œuf, F-35042 Rennes, France ; GROCAMPUS OUEST, UMR1253 STLO, F-35042 Rennes, France
| | - Valérie Briard-Bion
- INRA, UMR1253 STLO, Science et Technologie du Lait et de l׳Œuf, F-35042 Rennes, France ; GROCAMPUS OUEST, UMR1253 STLO, F-35042 Rennes, France
| | - Gaël Durant
- INRA, UMR1253 STLO, Science et Technologie du Lait et de l׳Œuf, F-35042 Rennes, France ; GROCAMPUS OUEST, UMR1253 STLO, F-35042 Rennes, France
| | - Victoria Chuat
- INRA, UMR1253 STLO, Science et Technologie du Lait et de l׳Œuf, F-35042 Rennes, France ; GROCAMPUS OUEST, UMR1253 STLO, F-35042 Rennes, France ; INRA, UMR1253 STLO, CIRM-BIA, F-35042 Rennes, France
| | | | - Benoit Foligné
- Lactic acid Bacteria & Mucosal Immunity, Center for Infection and Immunity of Lille, Institut Pasteur de Lille, U 1019, UMR 8204 Université Lille Nord de France, 1 rue du Pr Calmette, BP 245, F-59019 Lille, France
| | - Stéphanie-Marie Deutsch
- INRA, UMR1253 STLO, Science et Technologie du Lait et de l׳Œuf, F-35042 Rennes, France ; GROCAMPUS OUEST, UMR1253 STLO, F-35042 Rennes, France
| | - Hélène Falentin
- INRA, UMR1253 STLO, Science et Technologie du Lait et de l׳Œuf, F-35042 Rennes, France ; GROCAMPUS OUEST, UMR1253 STLO, F-35042 Rennes, France
| | - Gwénaël Jan
- INRA, UMR1253 STLO, Science et Technologie du Lait et de l׳Œuf, F-35042 Rennes, France ; GROCAMPUS OUEST, UMR1253 STLO, F-35042 Rennes, France
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15
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Foligné B, Parayre S, Cheddani R, Famelart MH, Madec MN, Plé C, Breton J, Dewulf J, Jan G, Deutsch SM. Immunomodulation properties of multi-species fermented milks. Food Microbiol 2015; 53:60-9. [PMID: 26611170 DOI: 10.1016/j.fm.2015.04.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 03/24/2015] [Accepted: 04/07/2015] [Indexed: 12/25/2022]
Abstract
Dairy propionibacteria (PAB) are used as a ripening starter in combination with Lactic acid bacteria (LAB) for dairy products such as Swiss-type cheese. LAB and PAB have also been studied for their probiotic properties but little is still known about their individual and/or synergistic beneficial effects within dairy matrices. In the context of a rising incidence of Inflammatory Bowel Diseases, it has become crucial to evaluate the immunomodulatory potential of bacteria ingested in large numbers via dairy products. We therefore selected different strains and combinations of technological LAB and PAB. We determined their immunomodulatory potential by IL-10 and IL-12 induction, in human peripheral blood mononuclear cells, on either single or mixed cultures, grown on laboratory medium or directly in milk. Milk was fermented with selected anti-inflammatory strains of LAB or PAB/LAB mixed cultures and the resulting bacterial fractions were also evaluated for these properties, together with starter viability and optimum technological aspects. The most promising fermented milks were evaluated in the context of TNBS- or DSS-induced colitis in mice. The improvement in inflammatory parameters evidenced an alleviation of colitis symptoms as a result of fermented milk consumption. This effect was clearly strain-dependent and modulated by growth within a fermented dairy product. These findings offer new tools and perspectives for the development of immunomodulatory fermented dairy products for targeted populations.
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Affiliation(s)
- Benoît Foligné
- Lactic Acid Bacteria & Mucosal Immunity, Center for Infection and Immunity of Lille, Institut Pasteur de Lille, INSERM-U 1019, CNRS UMR 8204 Université de Lille, 1 rue du Pr Calmette, BP 245, F-59019 Lille, France
| | - Sandrine Parayre
- INRA, UMR 1253 Science et Technologie du Lait et de l'Œuf, F-35042 Rennes, France; AGROCAMPUS OUEST, UMR1253 UMR Science et Technologie du Lait et de l' Œuf, F-35042 Rennes, France
| | - Redouane Cheddani
- INRA, UMR 1253 Science et Technologie du Lait et de l'Œuf, F-35042 Rennes, France; AGROCAMPUS OUEST, UMR1253 UMR Science et Technologie du Lait et de l' Œuf, F-35042 Rennes, France
| | - Marie-Hélène Famelart
- INRA, UMR 1253 Science et Technologie du Lait et de l'Œuf, F-35042 Rennes, France; AGROCAMPUS OUEST, UMR1253 UMR Science et Technologie du Lait et de l' Œuf, F-35042 Rennes, France
| | - Marie-Noëlle Madec
- INRA, UMR 1253 Science et Technologie du Lait et de l'Œuf, F-35042 Rennes, France; AGROCAMPUS OUEST, UMR1253 UMR Science et Technologie du Lait et de l' Œuf, F-35042 Rennes, France
| | - Coline Plé
- Lactic Acid Bacteria & Mucosal Immunity, Center for Infection and Immunity of Lille, Institut Pasteur de Lille, INSERM-U 1019, CNRS UMR 8204 Université de Lille, 1 rue du Pr Calmette, BP 245, F-59019 Lille, France
| | - Jérôme Breton
- Lactic Acid Bacteria & Mucosal Immunity, Center for Infection and Immunity of Lille, Institut Pasteur de Lille, INSERM-U 1019, CNRS UMR 8204 Université de Lille, 1 rue du Pr Calmette, BP 245, F-59019 Lille, France
| | - Joëlle Dewulf
- Lactic Acid Bacteria & Mucosal Immunity, Center for Infection and Immunity of Lille, Institut Pasteur de Lille, INSERM-U 1019, CNRS UMR 8204 Université de Lille, 1 rue du Pr Calmette, BP 245, F-59019 Lille, France
| | - Gwénaël Jan
- INRA, UMR 1253 Science et Technologie du Lait et de l'Œuf, F-35042 Rennes, France; AGROCAMPUS OUEST, UMR1253 UMR Science et Technologie du Lait et de l' Œuf, F-35042 Rennes, France
| | - Stéphanie-Marie Deutsch
- INRA, UMR 1253 Science et Technologie du Lait et de l'Œuf, F-35042 Rennes, France; AGROCAMPUS OUEST, UMR1253 UMR Science et Technologie du Lait et de l' Œuf, F-35042 Rennes, France
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16
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Loux V, Mariadassou M, Almeida S, Chiapello H, Hammani A, Buratti J, Gendrault A, Barbe V, Aury JM, Deutsch SM, Parayre S, Madec MN, Chuat V, Jan G, Peterlongo P, Azevedo V, Le Loir Y, Falentin H. Mutations and genomic islands can explain the strain dependency of sugar utilization in 21 strains of Propionibacterium freudenreichii. BMC Genomics 2015; 16:296. [PMID: 25886522 PMCID: PMC4437456 DOI: 10.1186/s12864-015-1467-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 02/27/2015] [Indexed: 01/11/2023] Open
Abstract
Background Propionibacterium freudenreichii (PF) is an actinobacterium used in cheese technology and for its probiotic properties. PF is also extremely adaptable to several ecological niches and can grow on a variety of carbon and nitrogen sources. The aim of this work was to discover the genetic basis for strain-dependent traits related to its ability to use specific carbon sources. High-throughput sequencing technologies were ideal for this purpose as they have the potential to decipher genomic diversity at a moderate cost. Results 21 strains of PF were sequenced and the genomes were assembled de novo. Scaffolds were ordered by comparison with the complete reference genome CIRM-BIA1, obtained previously using traditional Sanger sequencing. Automatic functional annotation and manual curation were performed. Each gene was attributed to either the core genome or an accessory genome. The ability of the 21 strains to degrade 50 different sugars was evaluated. Thirty-three sugars were degraded by none of the sequenced strains whereas eight sugars were degraded by all of them. The corresponding genes were present in the core genome. Lactose, melibiose and xylitol were only used by some strains. In this case, the presence/absence of genes responsible for carbon uptake and degradation correlated well with the phenotypes, with the exception of xylitol. Furthermore, the simultaneous presence of these genes was in line the metabolic pathways described previously in other species. We also considered the genetic origin (transduction, rearrangement) of the corresponding genomic islands. Ribose and gluconate were degraded to a greater or lesser extent (quantitative phenotype) by some strains. For these sugars, the phenotypes could not be explained by the presence/absence of a gene but correlated with the premature appearance of a stop codon interrupting protein synthesis and preventing the catabolism of corresponding carbon sources. Conclusion These results illustrate (i) the power of correlation studies to discover the genetic basis of binary strain-dependent traits, and (ii) the plasticity of PF chromosomes, probably resulting from horizontal transfers, duplications, transpositions and an accumulation of mutations. Knowledge of the genetic basis of nitrogen and sugar degradation opens up new strategies for the screening of PF strain collections to enable optimum cheese starter, probiotic and white biotechnology applications. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1467-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Valentin Loux
- INRA Mathématique Informatique et Génome, France Institute of Biological, Jouy en Josas, 78352, France.
| | - Mahendra Mariadassou
- INRA Mathématique Informatique et Génome, France Institute of Biological, Jouy en Josas, 78352, France.
| | - Sintia Almeida
- INRA, UMR 1253, Science et Technologie du Lait et de l'Oeuf, Rennes, 35000, France. .,AGROCAMPUS OUEST, UMR1253, UMR Science et Technologie du Lait et de l'Oeuf, Rennes, 35000, France. .,Sciences, Federal University of Minas Gerais Belo Horizonte, Minas Gerais, Brazil.
| | - Hélène Chiapello
- INRA Mathématique Informatique et Génome, France Institute of Biological, Jouy en Josas, 78352, France.
| | - Amal Hammani
- INRA Mathématique Informatique et Génome, France Institute of Biological, Jouy en Josas, 78352, France.
| | - Julien Buratti
- INRA Mathématique Informatique et Génome, France Institute of Biological, Jouy en Josas, 78352, France.
| | - Annie Gendrault
- INRA Mathématique Informatique et Génome, France Institute of Biological, Jouy en Josas, 78352, France.
| | - Valérie Barbe
- CEA Genoscope CNRS and université d'Evry, Evry, 91006, France.
| | - Jean-Marc Aury
- CEA Genoscope CNRS and université d'Evry, Evry, 91006, France.
| | - Stéphanie-Marie Deutsch
- INRA, UMR 1253, Science et Technologie du Lait et de l'Oeuf, Rennes, 35000, France. .,AGROCAMPUS OUEST, UMR1253, UMR Science et Technologie du Lait et de l'Oeuf, Rennes, 35000, France.
| | - Sandrine Parayre
- INRA, UMR 1253, Science et Technologie du Lait et de l'Oeuf, Rennes, 35000, France. .,AGROCAMPUS OUEST, UMR1253, UMR Science et Technologie du Lait et de l'Oeuf, Rennes, 35000, France.
| | - Marie-Noëlle Madec
- INRA, UMR 1253, Science et Technologie du Lait et de l'Oeuf, Rennes, 35000, France. .,AGROCAMPUS OUEST, UMR1253, UMR Science et Technologie du Lait et de l'Oeuf, Rennes, 35000, France.
| | - Victoria Chuat
- INRA, UMR 1253, Science et Technologie du Lait et de l'Oeuf, Rennes, 35000, France. .,AGROCAMPUS OUEST, UMR1253, UMR Science et Technologie du Lait et de l'Oeuf, Rennes, 35000, France.
| | - Gwenaël Jan
- INRA, UMR 1253, Science et Technologie du Lait et de l'Oeuf, Rennes, 35000, France. .,AGROCAMPUS OUEST, UMR1253, UMR Science et Technologie du Lait et de l'Oeuf, Rennes, 35000, France.
| | | | - Vasco Azevedo
- Sciences, Federal University of Minas Gerais Belo Horizonte, Minas Gerais, Brazil.
| | - Yves Le Loir
- INRA, UMR 1253, Science et Technologie du Lait et de l'Oeuf, Rennes, 35000, France. .,AGROCAMPUS OUEST, UMR1253, UMR Science et Technologie du Lait et de l'Oeuf, Rennes, 35000, France.
| | - Hélène Falentin
- INRA, UMR 1253, Science et Technologie du Lait et de l'Oeuf, Rennes, 35000, France. .,AGROCAMPUS OUEST, UMR1253, UMR Science et Technologie du Lait et de l'Oeuf, Rennes, 35000, France.
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de sa Peixoto P, Roiland C, Thomas D, Briard-Bion V, Le Guellec R, Parayre S, Deutsch SM, Jan G, Guyomarc'h F. Recrystallized S-layer protein of a probiotic Propionibacterium: structural and nanomechanical changes upon temperature or pH shifts probed by solid-state NMR and AFM. Langmuir 2014; 31:199-208. [PMID: 25479375 DOI: 10.1021/la503735z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Surface protein layers (S layers) are common constituents of the bacterial cell wall and originate from the assembly of strain-dependent surface layer proteins (Slps). These proteins are thought to play important roles in the bacteria's biology and to have very promising technological applications as biomaterials or as part of cell-host cross-talk in probiotic mechanism. The SlpA from Propionibacterium freudenreichii PFCIRM 118 strain was isolated and recrystallized to investigate organization and assembly of the protein using atomic force microscopy and solid-state (1)H and (13)C-nuclear magnetic resonance. SlpA was found to form hexagonal p1 monolayer lattices where the protein exhibited high proportions of disordered regions and of bound water. The lattice structure was maintained, but softened, upon mild heating or acidification, probably in relation with the increasing mobilities of the disordered protein regions. These results gave structural insights on the mobile protein regions exposed by S layer films, upon physiologically relevant changes of their environmental conditions.
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Affiliation(s)
- Paulo de sa Peixoto
- INRA-AGROCAMPUS OUEST UMR 1253 Science et Technologie du Lait et de l'Œuf, 35042 Rennes, France
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Cousin FJ, Louesdon S, Maillard MB, Parayre S, Falentin H, Deutsch SM, Boudry G, Jan G. The first dairy product exclusively fermented by Propionibacterium freudenreichii: A new vector to study probiotic potentialities in vivo. Food Microbiol 2012; 32:135-46. [DOI: 10.1016/j.fm.2012.05.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Revised: 03/14/2012] [Accepted: 05/14/2012] [Indexed: 01/17/2023]
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Cousin FJ, Foligné B, Deutsch SM, Massart S, Parayre S, Le Loir Y, Boudry G, Jan G. Assessment of the probiotic potential of a dairy product fermented by Propionibacterium freudenreichii in piglets. J Agric Food Chem 2012; 60:7917-7927. [PMID: 22823107 DOI: 10.1021/jf302245m] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Dairy propionibacteria, including Propionibacterium freudenreichii , display promising probiotic properties, including immunomodulation. These properties are highly strain-dependent and rarely studied in a fermented dairy product. We screened 10 strains, grown in a newly developed fermented milk ultrafiltrate, for immunomodulatory properties in vitro. The most anti-inflammatory strain, P. freudenreichii BIA129, was further tested on piglets. P. freudenreichii -fermented product improved food intake and growth of piglets. Colonic mucosa explants of treated pigs secreted less interleukin 8 (-25%, P < 0.05) and tumor necrosis factor α (-20%, P < 0.05), either in basal conditions or after a lipopolysaccharide challenge. By contrast, the gut structure, barrier function (measured ex vivo in Ussing chambers), microbial diversity (assessed by 16S rRNA pyrosequencing), and colonic short-chain fatty acid content were unchanged, assuming maintenance of normal intestinal physiology. In conclusion, this work confirms in vivo probiotic properties of dairy propionibacteria-fermented products, which are promising for the prevention or healing of inflammatory bowel diseases.
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Affiliation(s)
- Fabien J Cousin
- UMR 1253, Science et Technologie du Lait et de l'Œuf, INRA, F-35042 Rennes, France
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Falentin H, Henaff N, Le Bivic P, Deutsch SM, Parayre S, Richoux R, Sohier D, Thierry A, Lortal S, Postollec F. Reverse transcription quantitative PCR revealed persistency of thermophilic lactic acid bacteria metabolic activity until the end of the ripening of Emmental cheese. Food Microbiol 2011; 29:132-40. [PMID: 22029927 DOI: 10.1016/j.fm.2011.09.009] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2011] [Revised: 09/13/2011] [Accepted: 09/14/2011] [Indexed: 11/16/2022]
Abstract
For Emmental manufacture two kinds of adjunct culture are added: (i) thermophilic lactic acid bacteria (starters) such as Lactobacillus helveticus (LH), and Streptococcus thermophilus (ST) growing the first day of the manufacture and (ii) ripening culture. ST and LH have a key role in curd acidification and proteolysis at the beginning of the manufacture but are considered to be lyzed for a great part of them at the ripening step. The aim of this work was to assess the metabolic activity of these bacteria throughout manufacture and ripening. During Emmental cheesemaking, LH and ST were subjected to i) population quantification by numerations and by quantitative PCR (qPCR) ii) reverse transcription (RT) Temporal Temperature Gel Electrophoresis (TTGE) iii) transcript quantification by RT-qPCR targeting 16S rRNA, tuf and groL mRNAs to evaluate bacterial metabolic activity. During ripening, ST and LH numerations showed a 2.5 log(10) loss of culturability whereas qPCR on pelleted cells revealed only one log(10) of decrease for both of these species. 10(9) ST and 10(8) LH cells/g of cheese still remained. They contained a stable number of 16S transcript and at least 10(6) copies of mRNAs per 10(9) cells until the end of ripening. These results prove the unexpected persistency of thermophilic lactic acid bacteria starters (ST and LH) metabolic activity until the end of ripening and open new perspectives in term of their involvement in the quality of cheeses during ripening.
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Affiliation(s)
- Hélène Falentin
- INRA, UMR 1253, Science et Technologie du Lait et de l'Oeuf, F-35000, Rennes, France.
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Thierry A, Deutsch SM, Falentin H, Dalmasso M, Cousin FJ, Jan G. New insights into physiology and metabolism of Propionibacterium freudenreichii. Int J Food Microbiol 2011; 149:19-27. [DOI: 10.1016/j.ijfoodmicro.2011.04.026] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2010] [Revised: 04/14/2011] [Accepted: 04/29/2011] [Indexed: 01/25/2023]
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Falentin H, Deutsch SM, Jan G, Loux V, Thierry A, Parayre S, Maillard MB, Dherbécourt J, Cousin FJ, Jardin J, Siguier P, Couloux A, Barbe V, Vacherie B, Wincker P, Gibrat JF, Gaillardin C, Lortal S. The complete genome of Propionibacterium freudenreichii CIRM-BIA1, a hardy actinobacterium with food and probiotic applications. PLoS One 2010; 5:e11748. [PMID: 20668525 PMCID: PMC2909200 DOI: 10.1371/journal.pone.0011748] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Accepted: 06/29/2010] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Propionibacterium freudenreichii is essential as a ripening culture in Swiss-type cheeses and is also considered for its probiotic use. This species exhibits slow growth, low nutritional requirements, and hardiness in many habitats. It belongs to the taxonomic group of dairy propionibacteria, in contrast to the cutaneous species P. acnes. The genome of the type strain, P. freudenreichii subsp. shermanii CIRM-BIA1 (CIP 103027(T)), was sequenced with an 11-fold coverage. METHODOLOGY/PRINCIPAL FINDINGS The circular chromosome of 2.7 Mb of the CIRM-BIA1 strain has a GC-content of 67% and contains 22 different insertion sequences (3.5% of the genome in base pairs). Using a proteomic approach, 490 of the 2439 predicted proteins were confirmed. The annotation revealed the genetic basis for the hardiness of P. freudenreichii, as the bacterium possesses a complete enzymatic arsenal for de novo biosynthesis of aminoacids and vitamins (except panthotenate and biotin) as well as sequences involved in metabolism of various carbon sources, immunity against phages, duplicated chaperone genes and, interestingly, genes involved in the management of polyphosphate, glycogen and trehalose storage. The complete biosynthesis pathway for a bifidogenic compound is described, as well as a high number of surface proteins involved in interactions with the host and present in other probiotic bacteria. By comparative genomics, no pathogenicity factors found in P. acnes or in other pathogenic microbial species were identified in P. freudenreichii, which is consistent with the Generally Recognized As Safe and Qualified Presumption of Safety status of P. freudenreichii. Various pathways for formation of cheese flavor compounds were identified: the Wood-Werkman cycle for propionic acid formation, amino acid degradation pathways resulting in the formation of volatile branched chain fatty acids, and esterases involved in the formation of free fatty acids and esters. CONCLUSIONS/SIGNIFICANCE With the exception of its ability to degrade lactose, P. freudenreichii seems poorly adapted to dairy niches. This genome annotation opens up new prospects for the understanding of the P. freudenreichii probiotic activity.
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Affiliation(s)
- Hélène Falentin
- INRA, UMR 1253, Science et Technologie du Lait et de l'OEuf, Rennes, France.
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Deutsch SM, Falentin H, Dols-Lafargue M, Lapointe G, Roy D. Capsular exopolysaccharide biosynthesis gene of Propionibacterium freudenreichii subsp. shermanii. Int J Food Microbiol 2008; 125:252-8. [PMID: 18524407 DOI: 10.1016/j.ijfoodmicro.2008.04.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2008] [Revised: 04/16/2008] [Accepted: 04/16/2008] [Indexed: 11/27/2022]
Abstract
In the dairy industry, exopolysaccharides (EPS) contribute to improving the texture and viscosity of cheese and yoghurt and also receive increasing attention because of their beneficial properties for health. For lactic acid bacteria, the production of EPS is well studied. However, for dairy propionibacteria the biosynthesis of EPS is poorly documented. A polysaccharide synthase-encoding gene was identified in the genome of Propionibacterium freudenreichii subsp. shermanii TL 34 (CIP 103027). This gene best aligns with Tts, the polysaccharide synthase gene of Streptococcus pneumoniae type 37 that is responsible for the production of a beta-glucan capsular polysaccharide. PCR amplification showed the presence of an internal fragment of this gene in twelve strains of P. freudenreichii subsp. shermanii with a ropy phenotype in YEL+ medium. The gene sequence is highly conserved, as less than 1% of nucleotides differed among the 10 strains containing the complete gtf gene. The same primers failed to detect the gene in Propionibacterium acidipropionici strain TL 47, which is known to excrete exopolysaccharides in milk. The presence of (1-->3, 1-->2)-beta-d-glucan capsule was demonstrated for 7 out of 12 strains by agglutination with a S. pneumoniae-type 37-specific antiserum. The presence of mRNA corresponding to the gene was detected by RT-PCR in three strains at both exponential and stationary growth phases. This work represents the first identification of a polysaccharide synthase gene of P. freudenreichii, and further studies will be undertaken to elucidate the role of capsular EPS.
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Deutsch SM, Guezenec S, Piot M, Foster S, Lortal S. Mur-LH, the broad-spectrum endolysin of Lactobacillus helveticus temperate bacteriophage phi-0303. Appl Environ Microbiol 2004; 70:96-103. [PMID: 14711630 PMCID: PMC321252 DOI: 10.1128/aem.70.1.96-103.2004] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2003] [Accepted: 09/28/2003] [Indexed: 11/20/2022] Open
Abstract
phi-0303 is a temperate bacteriophage isolated from Lactobacillus helveticus CNRZ 303 strain after mitomycin C induction. In this work, the gene coding for a lytic protein of this bacteriophage was cloned using a library of phi-0303 in Escherichia coli DH5alpha. The lytic activity was detected by its expression, using whole cells of the sensitive strain L. helveticus CNRZ 892 as the substrate. The lysin gene was within a 4.1-kb DNA fragment of phi-0303 containing six open reading frames (ORFs) and two truncated ORFs. No sequence homology with holin genes was found within the cloned fragment. An integrase-encoding gene was also present in the fragment, but it was transcribed in a direction opposite that of the lysin gene. The lysin-encoding lys gene was verified by PCR amplification from the total phage DNA and subcloned. The lys gene is a 1,122-bp sequence encoding a protein of 373 amino acids (Mur-LH), whose product had a deduced molecular mass of 40,207 Da. Comparisons with sequences in sequence databases showed homology with numerous endolysins of other bacteriophages. Mur-LH was expressed in E. coli BL21, and by renaturing sodium dodecyl sulfate-polyacrylamide gel electrophoresis with L. helveticus CNRZ 892 as the substrate, the recombinant protein showed an apparent molecular mass of 40 kDa. The N-terminal sequence of the protein confirmed the start codon. Hydrolysis of cell walls of L. helveticus CNRZ 303 by the endolysin and biochemical analysis of the residues produced demonstrated that Mur-LH has N-acetylmuramidase activity. Last, the endolysin exhibited a broad spectrum of lytic activity, as it was active on different species, mainly thermophilic lactobacilli but also lactococci, pediococci, Bacillus subtilis, Brevibacterium linens, and Enterococcus faecium.
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Affiliation(s)
- Stéphanie-Marie Deutsch
- Laboratoire de Recherches de Technologie Laitière, Institut National de la Recherche Agronomique, 35042 Rennes Cédex, France.
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Deutsch SM, Molle D, Gagnaire V, Piot M, Atlan D, Lortal S. Hydrolysis of sequenced beta-casein peptides provides new insight into peptidase activity from thermophilic lactic acid bacteria and highlights intrinsic resistance of phosphopeptides. Appl Environ Microbiol 2000; 66:5360-7. [PMID: 11097915 PMCID: PMC92469 DOI: 10.1128/aem.66.12.5360-5367.2000] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The peptidases of thermophilic lactic acid bacteria have a key role in the proteolysis of Swiss cheeses during warm room ripening. To compare their peptidase activities toward a dairy substrate, a tryptic/chymotryptic hydrolysate of purified beta-casein was used. Thirty-four peptides from 3 to 35 amino acids, including three phosphorylated peptides, constitute the beta-casein hydrolysate, as shown by tandem mass spectrometry. Cell extracts prepared from Lactobacillus helveticus ITG LH1, ITG LH77, and CNRZ 32, Lactobacillus delbrueckii subsp. lactis ITG LL14 and ITG LL51, L. delbrueckii subsp. bulgaricus CNRZ 397 and NCDO 1489, and Streptococcus thermophilus CNRZ 385, CIP 102303, and TA 060 were standardized in protein. The peptidase activities were assessed with the beta-casein hydrolysate as the substrate at pH 5.5 and 24 degrees C (conditions of warm room ripening) by (i) free amino acid release, (ii) reverse-phase chromatography, and (iii) identification of undigested peptides by mass spectrometry. Regardless of strain, L. helveticus was the most efficient in hydrolyzing beta-casein peptides. Interestingly, cell extracts of S. thermophilus were not able to release a significant level of free proline from the beta-casein hydrolysate, which was consistent with the identification of numerous dipeptides containing proline. With the three lactic acid bacteria tested, the phosphorylated peptides remained undigested or weakly hydrolyzed indicating their high intrinsic resistance to peptidase activities. Finally, several sets of peptides differing by a single amino acid in a C-terminal position revealed the presence of at least one carboxypeptidase in the cell extracts of these species.
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Affiliation(s)
- S M Deutsch
- Institut National de la Recherche Agronomique, Laboratoire de Recherches de Technologie Laitière, 35042 Rennes Cédex, France
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Abstract
Intracellular peptidases of Lactobacillus helveticus may play a major role in the proteolysis of Swiss cheeses, provided that they are released through bacterial lysis. Experimental Swiss cheeses were manufactured on a small scale from thermized and microfiltered milk using as starters (in addition to Streptococcus thermophilus and Propionibacterium freudenreichii) one of two Lb. helveticus strains, ITGLH1 and ITGLH77, which undergo lysis to different extents in vitro. All the cheeses were biochemically identical after pressing. The viability of Lb. helveticus ITGLH1 and ITGLH77 decreased to a similar extent (96-98%) while in the cold room, but the concomitant release of intracellular lactate dehydrogenase in cheeses made with strain ITGLH1 was 5-7-fold that in cheeses made with ITGLH77. Protein profiles and immunoblot detection of the dipeptidase PepD confirmed a greater degree of lysis of the ITGLH1 strain. Free active peptidases were detected in aqueous extracts of cheese for both strains, and proteolysis occurred principally in the warm room. Reversed-phase HPLC revealed a more extensive peptide hydrolysis for ITGLH1, which was confirmed by the greater release of free NH2 groups (+33%) and free amino acids (+75%) compared with ITGLH77. As the intracellular peptidase activities of ITGLH1 and ITGLH77 have previously been shown to be similar, our results indicated that the extent of lysis of Lb. helveticus could have a direct impact on the degree of proteolysis in Swiss cheeses.
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Affiliation(s)
- F Valence
- Institut National de la Recherche Agronomique, Laboratoire de Recherche de Technologie Laitière, Rennes, France
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