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Marole TA, Sibanda T, Buys EM. Assessing probiotic viability in mixed species yogurt using a novel propidium monoazide (PMAxx)-quantitative PCR method. Front Microbiol 2024; 15:1325268. [PMID: 38389538 PMCID: PMC10882272 DOI: 10.3389/fmicb.2024.1325268] [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: 10/20/2023] [Accepted: 01/29/2024] [Indexed: 02/24/2024] Open
Abstract
Viability is a prerequisite for any therapeutic benefits associated with the ingestion of probiotic bacteria. Current culture-based techniques are inadequate for the enumeration of probiotics in mixed-species food products. This study utilized a quantitative PCR (qPCR) method coupled with propidium monoazide (PMAxx), and novel species-specific tuf gene primers to selectively enumerate Lacticaseibacillus rhamnosus, Bifidobacterium spp., and yogurt starter cultures in mixed-species probiotic yogurt. The method was optimized for PMAxx concentration and specificity and evaluated for efficiency and applicability. PMAxx-qPCR showed high specificity to the target organisms in mixed-species yogurt, quantifying only viable cells. The linear dynamic ranges were established over five to seven orders of magnitude. The assay was reliable with an efficiency of 91-99%, R2 values > 0.99, and a good correlation to the plate count method (r = 0.882). The results of this study demonstrate the high selectivity, improved lead time, and reliability of PMAxx-qPCR over the culture-dependent method, making it a valuable tool for inline viability verification during processing and improving probiotic quality assurance for processors and consumers.
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Affiliation(s)
- Tlaleo A Marole
- Department of Consumer and Food Sciences, University of Pretoria, Pretoria, South Africa
| | - Thulani Sibanda
- Department of Consumer and Food Sciences, University of Pretoria, Pretoria, South Africa
| | - Elna M Buys
- Department of Consumer and Food Sciences, University of Pretoria, Pretoria, South Africa
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2
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Laroute V, Aubry N, Audonnet M, Mercier-Bonin M, Daveran-Mingot ML, Cocaign-Bousquet M. Natural diversity of lactococci in γ-aminobutyric acid (GABA) production and genetic and phenotypic determinants. Microb Cell Fact 2023; 22:178. [PMID: 37689693 PMCID: PMC10492284 DOI: 10.1186/s12934-023-02181-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 08/18/2023] [Indexed: 09/11/2023] Open
Abstract
BACKGROUND γ-aminobutyric acid (GABA) is a bioactive compound produced by lactic acid bacteria (LAB). The diversity of GABA production in the Lactococcus genus is poorly understood. Genotypic and phenotypic approaches were therefore combined in this study to shed light on this diversity. A comparative genomic study was performed on the GAD-system genes (gadR, gadC and gadB) involved in GABA production in 36 lactococci including L. lactis and L. cremoris species. In addition, 132 Lactococcus strains were screened for GABA production in culture medium supplemented with 34 mM L-glutamic acid with or without NaCl (0.3 M). RESULTS Comparative analysis of the nucleotide sequence alignments revealed the same genetic organization of the GAD system in all strains except one, which has an insertion sequence element (IS981) into the PgadCB promoter. This analysis also highlighted several deletions including a 3-bp deletion specific to the cremoris species located in the PgadR promoter, and a second 39-bp deletion specific to L. cremoris strains with a cremoris phenotype. Phenotypic analysis revealed that GABA production varied widely, but it was higher in L. lactis species than in L. cremoris, with an exceptional GABA production of up to 14 and 24 mM in two L. lactis strains. Moreover, adding chloride increased GABA production in some L. cremoris and L. lactis strains by a factor of up to 16 and GAD activity correlated well with GABA production. CONCLUSIONS This genomic analysis unambiguously characterized the cremoris phenotype of L. cremoris species and modified GadB and GadR proteins explain why the corresponding strains do not produce GABA. Finally, we found that glutamate decarboxylase activity revealing GadB protein amount, varied widely between the strains and correlated well with GABA production both with and without chloride. As this protein level is associated to gene expression, the regulation of GAD gene expression was identified as a major contributor to this diversity.
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Affiliation(s)
- Valérie Laroute
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.
| | - Nathalie Aubry
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Marjorie Audonnet
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Muriel Mercier-Bonin
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Marie-Line Daveran-Mingot
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.
| | - Muriel Cocaign-Bousquet
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.
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3
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Mahony J, Bottacini F, van Sinderen D. Towards the diversification of lactococcal starter and non-starter species in mesophilic dairy culture systems. Microb Biotechnol 2023; 16:1745-1754. [PMID: 37606352 PMCID: PMC10443329 DOI: 10.1111/1751-7915.14320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 07/04/2023] [Accepted: 07/06/2023] [Indexed: 08/23/2023] Open
Abstract
Lactococcus is one of the earliest identified fermentative bacterial genera and among its member species, the dairy-associated Lactococcus lactis and Lactococcus cremoris are undoubtedly the best studied. These two species are believed to have evolved from plant-associated lactococci and through genome decay and acquisition of plasmids, have adapted to the dairy niche. The past decade has witnessed a surge of activity in novel lactococcal species identification from insect, plant and animal sources. Currently, 22 Lactococcus species are described and in this review, we summarise the genome characteristics of and phylogenetic relationships among these species. Furthermore, we explore the role of mobile elements including plasmids and bacteriophages in the diversification of lactococcal species. The pace of identification of novel lactococcal species suggests that the number of lactococcal species is likely to continue to grow. With additional sequence data for the emerging species, it will be possible to perform pathogenicity/virulence risk evaluations and generate extensive insights into the niche adaptation strategies through which they have evolved.
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Affiliation(s)
- Jennifer Mahony
- School of MicrobiologyUniversity College CorkCorkIreland
- APC Microbiome IrelandUniversity College CorkCorkIreland
| | - Francesca Bottacini
- APC Microbiome IrelandUniversity College CorkCorkIreland
- Department of Biological SciencesMunster Technological UniversityCorkIreland
| | - Douwe van Sinderen
- School of MicrobiologyUniversity College CorkCorkIreland
- APC Microbiome IrelandUniversity College CorkCorkIreland
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4
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Chen L, Wang Y, Li X, MacAdam JW, Zhang Y. Interaction between plants and epiphytic lactic acid bacteria that affect plant silage fermentation. Front Microbiol 2023; 14:1164904. [PMID: 37362945 PMCID: PMC10290204 DOI: 10.3389/fmicb.2023.1164904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 05/17/2023] [Indexed: 06/28/2023] Open
Abstract
Lactic acid bacteria (LAB) have the ability to ferment water-soluble carbohydrates, resulting in the production of significant amounts of lactic acid. When utilized as additives in silage fermentation and feed, they have been shown to enhance the quality of these products. Epiphytic LAB of plants play a major role in the fermentation of silage plants. Plant species in turn affect the community structure of epiphytic LAB. In recent years, an increasing number of studies have suggested that epiphytic LAB are more effective than exogenous LAB when applied to silage. Inoculating silage plants with epiphytic LAB has attracted extensive attention because of the potential to improve the fermentation quality of silages. This review discusses the interaction of epiphytic LAB with plants during silage fermentation and compares the effects of exogenous and epiphytic LAB on plant fermentation. Overall, this review provides insight into the potential benefits of using epiphytic LAB as an inoculant and proposes a theoretical basis for improving silage quality.
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Affiliation(s)
- Lijuan Chen
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Yili Wang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Xi Li
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Jennifer W. MacAdam
- College of Agriculture and Applied Sciences, Utah State University, Logan, UT, United States
| | - Yunhua Zhang
- College of Resources and Environment, Anhui Agricultural University, Hefei, China
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5
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Ruiz MJ, Salatti-Dorado JA, Cardador MJ, Frizzo L, Jordano R, Arce L, Medina LM. Relationship between Volatile Organic Compounds and Microorganisms Isolated from Raw Sheep Milk Cheeses Determined by Sanger Sequencing and GC-IMS. Foods 2023; 12:foods12020372. [PMID: 36673464 PMCID: PMC9858180 DOI: 10.3390/foods12020372] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/04/2023] [Accepted: 01/09/2023] [Indexed: 01/15/2023] Open
Abstract
Recently, the interest of consumers regarding artisan cheeses worldwide has increased. The ability of different autochthonous and characterized lactic acid bacteria (LAB) to produce aromas and the identification of the volatile organic compounds (VOCs) responsible for flavor in cheeses are important aspects to consider when selecting strains with optimal aromatic properties, resulting in the diversification of cheese products. The objective of this work is to determine the relationship between VOCs and microorganisms isolated (Lacticaseibacillus paracasei, Lactiplantibacillus plantarum, Leuconostoc mesenteroides and Lactococcus lactis subsp. hordniae) from raw sheep milk cheeses (matured and creamy natural) using accuracy and alternative methods. On combining Sanger sequencing for LAB identification with Gas Chromatography coupled to Ion Mobility Spectrometry (GC−IMS) to determinate VOCs, we describe cheeses and differentiate the potential role of each microorganism in their volatilome. The contribution of each LAB can be described according to their different VOC profile. Differences between LAB behavior in each cheese are shown, especially between LAB involved in creamy cheeses. Only L. lactis subsp. hordniae and L. mesenteroides show the same VOC profile in de Man Rogosa and Sharpe (MRS) cultures, but for different cheeses, and show two differences in VOC production in skim milk cultures. The occurrence of Lactococcus lactis subsp. hordniae from cheese is reported for first time.
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Affiliation(s)
- María J. Ruiz
- Laboratory of Food Analysis “Rodolfo Oscar Dalla Santina”, Institute of Veterinary Science (ICiVet Litoral), National University of the Litoral-National Council of Scientific and Technical Research (UNL/CONICET), Esperanza 3080, Province of Santa Fe, Argentina
| | - José A. Salatti-Dorado
- Analytical Chemistry Department, Institute of Fine Chemistry and Nanochemistry, International Agrifood Campus of Excellence, Marie Curie Annex Building, Campus de Rabanales, University of Cordoba, E-14071 Cordoba, Spain
| | - María J. Cardador
- Analytical Chemistry Department, Institute of Fine Chemistry and Nanochemistry, International Agrifood Campus of Excellence, Marie Curie Annex Building, Campus de Rabanales, University of Cordoba, E-14071 Cordoba, Spain
| | - Laureano Frizzo
- Laboratory of Food Analysis “Rodolfo Oscar Dalla Santina”, Institute of Veterinary Science (ICiVet Litoral), National University of the Litoral-National Council of Scientific and Technical Research (UNL/CONICET), Esperanza 3080, Province of Santa Fe, Argentina
| | - Rafael Jordano
- Food Science and Technology Department, International Agrifood Campus of Excellence, Charles Darwin Annex Building, Campus de Rabanales, University of Córdoba, E-14071 Cordoba, Spain
| | - Lourdes Arce
- Analytical Chemistry Department, Institute of Fine Chemistry and Nanochemistry, International Agrifood Campus of Excellence, Marie Curie Annex Building, Campus de Rabanales, University of Cordoba, E-14071 Cordoba, Spain
| | - Luis M. Medina
- Food Science and Technology Department, International Agrifood Campus of Excellence, Charles Darwin Annex Building, Campus de Rabanales, University of Córdoba, E-14071 Cordoba, Spain
- Correspondence:
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6
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Gorrasi S, Pasqualetti M, Muñoz-Palazon B, Novello G, Mazzucato A, Campiglia E, Fenice M. Comparison of the Peel-Associated Epiphytic Bacteria of Anthocyanin-Rich "Sun Black" and Wild-Type Tomatoes under Organic and Conventional Farming. Microorganisms 2022; 10:2240. [PMID: 36422310 PMCID: PMC9694333 DOI: 10.3390/microorganisms10112240] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 07/30/2023] Open
Abstract
Tomatoes are among the most consumed vegetables worldwide and represent a source of health-beneficial substances. Our study represents the first investigating the peel-associated epiphytic bacteria of red and purple (anthocyanin-rich) tomatoes subjected to organic and conventional farming systems. Proteobacteria was the dominant phylum (relative abundances 79-91%) in all experimental conditions. Enterobacteriaceae represented a large fraction (39.3-47.5%) of the communities, with Buttiauxella and Atlantibacter as the most represented genera. The core microbiota was composed of 59 operational taxonomic units (OTUs), including the majority of the most abundant ones. The occurrence of the most abundant OTUs differed among the experimental conditions. OTU 1 (Buttiauxella), OTU 2 (Enterobacteriales), and OTU 6 (Bacillales) were higher in red and purple tomatoes grown under organic farming. OTU 5 (Acinetobacter) had the highest abundance in red tomatoes subjected to organic farming. OTU 3 (Atlantibacter) was among the major OTUs in red tomatoes under both farming conditions. OTU 7 (Clavibacter) and OTU 8 (Enterobacteriaceae) had abundances ≥1% only in red tomatoes grown under conventional farming. PCA and clustering analysis highlighted a high similarity between the bacterial communities of red and purple tomatoes grown under organic farming. Furthermore, the bacterial communities of purple tomatoes grown under organic farming showed the lowest diversity and evenness. This work paves the way to understand the role of nutritional superior tomato genotypes, combined with organic farming, to modulate the presence of beneficial/harmful bacteria and supply healthier foods within a sustainable agriculture.
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Affiliation(s)
- Susanna Gorrasi
- Department of Ecological and Biological Sciences (DEB), University of Tuscia, Largo Università snc, 01100 Viterbo, Italy
| | - Marcella Pasqualetti
- Department of Ecological and Biological Sciences (DEB), University of Tuscia, Largo Università snc, 01100 Viterbo, Italy
- Laboratory of Ecology of Marine Fungi, CoNISMa, Department of Ecological and Biological Sciences, University of Tuscia, Largo Università snc, 01100 Viterbo, Italy
| | - Barbara Muñoz-Palazon
- Department of Ecological and Biological Sciences (DEB), University of Tuscia, Largo Università snc, 01100 Viterbo, Italy
- Institute of Water Research, University of Granada, 18071 Granada, Spain
| | - Giorgia Novello
- Department of Science, Technology and Innovation (DISIT), Università del Piemonte Orientale, Viale Teresa Michel, 11, 15121 Alessandria, Italy
| | - Andrea Mazzucato
- Department of Agricultural and Forest Sciences (DAFNE), University of Tuscia, Via San Camillo de Lellis snc, 01100 Viterbo, Italy
| | - Enio Campiglia
- Department of Agricultural and Forest Sciences (DAFNE), University of Tuscia, Via San Camillo de Lellis snc, 01100 Viterbo, Italy
| | - Massimiliano Fenice
- Department of Ecological and Biological Sciences (DEB), University of Tuscia, Largo Università snc, 01100 Viterbo, Italy
- Laboratory of Applied Marine Microbiology, CoNISMa, University of Tuscia, Largo Università snc, 01100 Viterbo, Italy
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7
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Pechenov PY, Garagulya DA, Stanovov DS, Letarov AV. New Effective Method of Lactococcus Genome Editing Using Guide RNA-Directed Transposition. Int J Mol Sci 2022; 23:13978. [PMID: 36430465 PMCID: PMC9696066 DOI: 10.3390/ijms232213978] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
Lactococcus lactis is an important industrial microorganism and a widely used model object for research in the field of lactic acid bacteria (LAB) biology. The development of new L. lactis and related LAB strains with improved properties, including phage-resistant strains for dairy fermentation, LAB-based vaccines or strains with altered genotypes for research purposes, are hindered by the lack of genome-editing tools that allow for the easy and straightforward incorporation of a significant amount of the novel genetic material, such as large genes or operons, into the chromosomes of these bacteria. We recently employed a suggested system based on the CRISPR-Cas-associated transposon for the editing of the L. lactis genome. After the in-depth redesign of the system, we were able to achieve the stable incorporation of the fragments that were sized up to 10 kbp into the L. lactis beta-galactosidase gene. The efficiency of editing under the optimized conditions were 2 × 10-4 and 4 × 10-5 for 1 kbp and 10 kbp, respectively, which are sufficient for fast and easy modifications if a positive selection marker can be used.
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Affiliation(s)
- Pavel Yu Pechenov
- Federal Research Center “Fundamentals of Biotechnology” of Russian Academy of Sciences, Leninsky Prospect, 33, Build. 2, 119071 Moscow, Russia
| | | | | | - Andrey V. Letarov
- Federal Research Center “Fundamentals of Biotechnology” of Russian Academy of Sciences, Leninsky Prospect, 33, Build. 2, 119071 Moscow, Russia
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8
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Rodríguez J, Vázquez L, Flórez AB, Mayo B. Phenotype testing, genome analysis, and metabolic interactions of three lactic acid bacteria strains existing as a consortium in a naturally fermented milk. Front Microbiol 2022; 13:1000683. [PMID: 36212860 PMCID: PMC9539746 DOI: 10.3389/fmicb.2022.1000683] [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: 07/22/2022] [Accepted: 09/06/2022] [Indexed: 11/13/2022] Open
Abstract
This work reports the characterization of three lactic acid bacteria (LAB) strains -Lactococcus lactis LA1, Lactococcus cremoris LA10, and Lactiplantibacillus plantarum LA30- existing as a stable consortium in a backslopping-inoculated, naturally fermented milk (NFM). This study aimed at uncovering the biochemical and genetic basis of the stability of the consortium and the cooperativity among the strains during milk fermentation. All three strains were subjected to phenotyping, covering the utilization of carbohydrates, enzyme activity, and antibiotic resistance. The strains were grown in milk individually, as well as in all possible combinations, and the resulting fermented product was analyzed for sugars, organic acids, and volatile compounds. Finally, the genomes of the three strains were sequenced and analyzed for genes associated with technological and safety properties. As expected, wide phenotypic diversity was seen between the strains. Lactococcus cremoris LA10 was the only strain to reach high cell densities and coagulate milk alone after incubation at 22°C for 24 h; congruently, it possessed a gene coding for a PrtP type II caseinolytic protease. Compared to any other fermentation, acetaldehyde concentrations were greater by a factor of six when all three strains grew together in milk, suggesting that its production might be the result of an interaction between them. Lactococcus lactis LA1, which carried a plasmid-encoded citQRP operon, was able to utilize milk citrate producing diacetyl and acetoin. No genes encoding virulence traits or pathogenicity factors were identified in any of the strains, and none produced biogenic amines from amino acid precursors, suggesting them to be safe. Lactiplantibacillus plantarum LA30 was susceptible to tetracycline, although it harbors a disrupted antibiotic resistance gene belonging to the tetM/tetW/tetO/tetS family. All three strains contained large numbers of pseudogenes, suggesting that they are well adapted ("domesticated") to the milk environment. The consortium as a whole or its individual strains might have a use as a starter or as starter components for dairy fermentations. The study of simple consortia, such as that existing in this NFM, can help reveal how microorganisms interact with one another, and what influence they may have on the sensorial properties of fermented products.
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Affiliation(s)
- Javier Rodríguez
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Villaviciosa, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Lucía Vázquez
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Villaviciosa, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Ana Belén Flórez
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Villaviciosa, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Baltasar Mayo
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Villaviciosa, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
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9
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Zhai Y, Wei C. Open pangenome of Lactococcus lactis generated by a combination of metagenome-assembled genomes and isolate genomes. Front Microbiol 2022; 13:948138. [PMID: 36081802 PMCID: PMC9445621 DOI: 10.3389/fmicb.2022.948138] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 07/05/2022] [Indexed: 11/29/2022] Open
Abstract
Lactococcus lactis (L. lactis) is a well isolated and cultured lactic acid bacterium, but if utilizing the isolate genomes alone, the genome-based analysis of this taxon would be incomplete, because there are still uncultured strains in some ecological niches. In this study, we recovered 93 high-quality metagenome-assembled genomes (MAGs) of L. lactis from food and human gut metagenomes with a culture-independent method. We then constructed a unified genome catalog of L. lactis by integrating these MAGs with 70 publicly available isolated genomes. Having this comprehensive resource, we assessed the genomic diversity and phylogenetic relationships to further explore the genetic and functional properties of L. lactis. An open pangenome of L. lactis was generated using our genome catalog, consisting of 13,066 genes in total, from which 5,448 genes were not identified in the isolate genomes. The core genome-based phylogenetic analysis showed that L. lactis strains we collected were separated into two main subclades corresponding to two subspecies, with some uncultured phylogenetic lineages discovered. The species disparity was also indicated in PCA analysis based on accessory genes of our pangenome. These various analyzes shed further light on unexpectedly high diversity within the taxon at both genome and gene levels and gave clues about its population structure and evolution. Lactococcus lactis has a long history of safe use in food fermentations and is considered as one of the important probiotic microorganisms. Obtaining the complete genetic information of L. lactis is important to the food and health industry. However, it can naturally inhabit many environments other than dairy products, including drain water and human gut samples. Here we presented an open pan-genome of L. lactis constructed from 163 high-quality genomes obtained from various environments, including MAGs recovered from environmental metagenomes and isolate genomes. This study expanded the genetic information of L. lactis about one third, including more than 5,000 novel genes found in uncultured strains. This more complete gene repertoire of L. lactis is crucial to further understanding the genetic and functional properties. These properties may be harnessed to impart additional value to dairy fermentation or other industries.
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10
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Couderc C, Laroute V, Coddeville M, Caillaud MA, Jard G, Raynaud C, Cocaign-Bousquet M, Tormo H, Daveran-Mingot ML. Harnessing diversity of Lactococcus lactis from raw goat milk: Design of an indigenous starter for the production of Rocamadour, a French PDO cheese. Int J Food Microbiol 2022; 379:109837. [PMID: 35872491 DOI: 10.1016/j.ijfoodmicro.2022.109837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 06/24/2022] [Accepted: 07/10/2022] [Indexed: 11/20/2022]
Abstract
Twenty-four strains of Lactococcus lactis isolated from raw goat milk collected in the Rocamadour PDO area were analysed by MLST typing and phenotypic characterisation. The strains were combined to design an indigenous starter for the production of Rocamadour PDO cheese. The strains were divided into three classes based on their technological properties: acidifying and proteolytic strains in class I (12/24 strains), slightly acidifying and non-proteolytic strains in class II (2/24 strains), and non-acidifying and non-proteolytic strains in class III (10/24 strains). Interestingly, all but three strains (21/24) produced diacetyl/acetoin despite not having citrate metabolism genes, as would classically be expected for the production of these aroma compounds. Three strains (EIP07A, EIP13D, and EIP20B) were selected for the indigenous starter based on the following inclusion/exclusion criteria: (i) no negative interactions between included strains, (ii) ability to metabolize lactose and at least one strain with the prtP gene and/or capable of producing diacetyl/acetoin, and (iii) selected strains derived from different farms to maximise genetic and phenotypic diversity. Despite consisting exclusively of L. lactis strains, the designed indigenous starter allowed reproducible cheese production with performances similar to those obtained with an industrial starter and with the sensory qualities expected of Rocamadour PDO cheese.
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Affiliation(s)
- Christel Couderc
- Université de Toulouse, Ecole d'Ingénieurs de Purpan, INPT, Toulouse, France.
| | - Valérie Laroute
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | | | | | - Gwenaelle Jard
- Université de Toulouse, Ecole d'Ingénieurs de Purpan, INPT, Toulouse, France
| | - Christine Raynaud
- Laboratoire de Chimie Agro-industrielle (LCA), Université de Toulouse, INRAE, INP-ENSIACET, Toulouse, France; Centre d'Application et de traitement des Agroressources (CATAR), INP-ENSIACET, Toulouse, France
| | | | - Hélène Tormo
- Université de Toulouse, Ecole d'Ingénieurs de Purpan, INPT, Toulouse, France
| | - Marie-Line Daveran-Mingot
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France; Université Toulouse 3 - Paul Sabatier, Université de Toulouse, Toulouse, France
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11
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MLST analysis of genetic diversity of Bacillus coagulans strains to evaluate effects on constipation model. FOOD SCIENCE AND HUMAN WELLNESS 2022. [DOI: 10.1016/j.fshw.2022.03.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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12
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Laroute V, Beaufrand C, Gomes P, Nouaille S, Tondereau V, Daveran-Mingot ML, Theodorou V, Eutamene H, Mercier-Bonin M, Cocaign-Bousquet M. Lactococcus lactis NCDO2118 exerts visceral antinociceptive properties in rat via GABA production in the gastro-intestinal tract. eLife 2022; 11:77100. [PMID: 35727704 PMCID: PMC9213000 DOI: 10.7554/elife.77100] [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: 01/15/2022] [Accepted: 06/01/2022] [Indexed: 12/01/2022] Open
Abstract
Gut disorders associated to irritable bowel syndrome (IBS) are combined with anxiety and depression. Evidence suggests that microbially produced neuroactive molecules, like γ-aminobutyric acid (GABA), can modulate the gut-brain axis. Two natural strains of Lactococcus lactis and one mutant were characterized in vitro for their GABA production and tested in vivo in rat by oral gavage for their antinociceptive properties. L. lactis NCDO2118 significantly reduced visceral hypersensitivity induced by stress due to its glutamate decarboxylase (GAD) activity. L. lactis NCDO2727 with similar genes for GABA metabolism but no detectable GAD activity had no in vivo effect, as well as the NCDO2118 ΔgadB mutant. The antinociceptive effect observed for the NCDO2118 strain was mediated by the production of GABA in the gastro-intestinal tract and blocked by GABAB receptor antagonist. Only minor changes in the faecal microbiota composition were observed after the L. lactis NCDO2118 treatment. These findings reveal the crucial role of the microbial GAD activity of L. lactis NCDO2118 to deliver GABA into the gastro-intestinal tract for exerting antinociceptive properties in vivo and open avenues for this GRAS (Generally Recognized As safe) bacterium in the management of visceral pain and anxious profile of IBS patients.
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Affiliation(s)
- Valérie Laroute
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Catherine Beaufrand
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Pedro Gomes
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.,Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Sébastien Nouaille
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Valérie Tondereau
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | | | - Vassilia Theodorou
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Hélène Eutamene
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Muriel Mercier-Bonin
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Muriel Cocaign-Bousquet
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
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13
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CHENG T, WANG L, GUO Z, LI B. Technological characterization and antibacterial activity of Lactococcus lactis subsp. cremoris strains for potential use as starter culture for cheddar cheese manufacture. FOOD SCIENCE AND TECHNOLOGY 2022. [DOI: 10.1590/fst.13022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Tianfu CHENG
- Northeast Agricultural University, China; Heilongjiang Beidahuang Green Health Food Co., Ltd, China
| | - Lin WANG
- Northeast Agricultural University, China
| | | | - Bailiang LI
- Northeast Agricultural University, China; Northeast Agricultural University, China
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14
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Abstract
The growing need for industrial production of bio-based acetoin and 2,3-butanediol (2,3-BD) is due to both environmental concerns, and their widespread use in the food, pharmaceutical, and chemical industries. Acetoin is a common spice added to many foods, but also a valuable reagent in many chemical syntheses. Similarly, 2,3-BD is an indispensable chemical on the platform in the production of synthetic rubber, printing inks, perfumes, antifreeze, and fuel additives. This state-of-the-art review focuses on representatives of the genus Bacillus as prospective producers of acetoin and 2,3-BD. They have the following important advantages: non-pathogenic nature, unpretentiousness to growing conditions, and the ability to utilize a huge number of substrates (glucose, sucrose, starch, cellulose, and inulin hydrolysates), sugars from the composition of lignocellulose (cellobiose, mannose, galactose, xylose, and arabinose), as well as waste glycerol. In addition, these strains can be improved by genetic engineering, and are amenable to process optimization. Bacillus spp. are among the best acetoin producers. They also synthesize 2,3-BD in titer and yield comparable to those of the pathogenic producers. However, Bacillus spp. show relatively lower productivity, which can be increased in the course of challenging future research.
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15
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Song X, Liu L, Liu XX, Xiong ZQ, Xie CL, Wang SJ, Ai LZ. Single-plasmid systems based on CRISPR-Cas9 for gene editing in Lactococcus lactis. J Dairy Sci 2021; 104:10576-10585. [PMID: 34275631 DOI: 10.3168/jds.2020-19901] [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: 11/11/2020] [Accepted: 03/15/2021] [Indexed: 01/20/2023]
Abstract
Lactococcus lactis is a food-grade lactic acid bacterial species that is widely used in food and medical industries. Due to its relatively small genome and simple metabolism, L. lactis is commonly engineered to produce large quantities of recombinant proteins. The most common single-gene knockout strategy in L. lactis involves RecA-dependent homologous double-crossover recombination, which is relatively time-consuming and laborious. In this study, a precise and efficient genome-editing plasmid for L. lactis NZ9000 genome engineering, pLL, was established based on clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 technology. By studying the effects of different single guide RNA (sgRNA) promoters, the efficiency of gene deletion was optimized. For LLNZ_02045 (ldh), gene deletion efficiency of up to 50% was achieved. Effective sequential gene deletion of LLNZ_11240 (upp) and LLNZ_04580 (upp1) was also demonstrated using this tool. Additionally, the gene that encodes for uracil phosphoribosyltransferase was identified using this system. Similar robust gene deletion efficiencies of sgRNA that targeted different regions of a single gene suggested that gene deletion was not affected by the location of sgRNA binding. Thus, our study established a new gene-editing tool that may allow further investigation and understanding of the L. lactis NZ9000 genome.
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Affiliation(s)
- Xin Song
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Lu Liu
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Xin-Xin Liu
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Zhi-Qiang Xiong
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Chun-Liang Xie
- Institute of Bast Fiber Crop, Chinese Academy of Agricultural Sciences, Changsha 410205, China
| | - Shij-Jie Wang
- College of Bioscience and Bioengineering, Hebei University of Science and Technology, Shijiazhuang 050018, Hebei, China; Shijiazhuang Junlebao Dairy Co. Ltd., Shijiazhuang 050211, China
| | - Lian-Zhong Ai
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China.
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16
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Ramos-Vivas J, Elexpuru-Zabaleta M, Samano ML, Barrera AP, Forbes-Hernández TY, Giampieri F, Battino M. Phages and Enzybiotics in Food Biopreservation. Molecules 2021; 26:molecules26175138. [PMID: 34500572 PMCID: PMC8433972 DOI: 10.3390/molecules26175138] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/10/2021] [Accepted: 08/20/2021] [Indexed: 12/27/2022] Open
Abstract
Presently, biopreservation through protective bacterial cultures and their antimicrobial products or using antibacterial compounds derived from plants are proposed as feasible strategies to maintain the long shelf-life of products. Another emerging category of food biopreservatives are bacteriophages or their antibacterial enzymes called "phage lysins" or "enzybiotics", which can be used directly as antibacterial agents due to their ability to act on the membranes of bacteria and destroy them. Bacteriophages are an alternative to antimicrobials in the fight against bacteria, mainly because they have a practically unique host range that gives them great specificity. In addition to their potential ability to specifically control strains of pathogenic bacteria, their use does not generate a negative environmental impact as in the case of antibiotics. Both phages and their enzymes can favor a reduction in antibiotic use, which is desirable given the alarming increase in resistance to antibiotics used not only in human medicine but also in veterinary medicine, agriculture, and in general all processes of manufacturing, preservation, and distribution of food. We present here an overview of the scientific background of phages and enzybiotics in the food industry, as well as food applications of these biopreservatives.
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Affiliation(s)
- José Ramos-Vivas
- Research Group on Foods, Nutritional Biochemistry and Health, Universidad Europea del Atlántico, 39011 Santander, Spain; (J.R.-V.); (M.E.-Z.); (M.L.S.)
- Department of Project Management, Universidad Internacional Iberoamericana, Campeche 24560, Mexico;
| | - María Elexpuru-Zabaleta
- Research Group on Foods, Nutritional Biochemistry and Health, Universidad Europea del Atlántico, 39011 Santander, Spain; (J.R.-V.); (M.E.-Z.); (M.L.S.)
| | - María Luisa Samano
- Research Group on Foods, Nutritional Biochemistry and Health, Universidad Europea del Atlántico, 39011 Santander, Spain; (J.R.-V.); (M.E.-Z.); (M.L.S.)
- Department of Project Management, Universidad Internacional Iberoamericana, Campeche 24560, Mexico;
| | - Alina Pascual Barrera
- Department of Project Management, Universidad Internacional Iberoamericana, Campeche 24560, Mexico;
| | | | - Francesca Giampieri
- Department of Clinical Sciences, Polytechnic University of Marche, 60131 Ancona, Italy
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Correspondence: (F.G.); (M.B.); Tel.: +339-071-220-4136 (F.G.); +339-071-220-4646 (M.B.)
| | - Maurizio Battino
- Department of Clinical Sciences, Polytechnic University of Marche, 60131 Ancona, Italy
- International Research Center for Food Nutrition and Safety, Jiangsu University, Zhenjiang 212013, China
- Correspondence: (F.G.); (M.B.); Tel.: +339-071-220-4136 (F.G.); +339-071-220-4646 (M.B.)
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Gustaw K, Niedźwiedź I, Rachwał K, Polak-Berecka M. New Insight into Bacterial Interaction with the Matrix of Plant-Based Fermented Foods. Foods 2021; 10:foods10071603. [PMID: 34359473 PMCID: PMC8304663 DOI: 10.3390/foods10071603] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 06/24/2021] [Accepted: 07/08/2021] [Indexed: 12/12/2022] Open
Abstract
Microorganisms have been harnessed to process raw plants into fermented foods. The adaptation to a variety of plant environments has resulted in a nearly inseparable association between the bacterial species and the plant with a characteristic chemical profile. Lactic acid bacteria, which are known for their ability to adapt to nutrient-rich niches, have altered their genomes to dominate specific habitats through gene loss or gain. Molecular biology approaches provide a deep insight into the evolutionary process in many bacteria and their adaptation to colonize the plant matrix. Knowledge of the adaptive characteristics of microorganisms facilitates an efficient use thereof in fermentation to achieve desired final product properties. With their ability to acidify the environment and degrade plant compounds enzymatically, bacteria can modify the textural and organoleptic properties of the product and increase the bioavailability of plant matrix components. This article describes selected microorganisms and their competitive survival and adaptation in fermented fruit and vegetable environments. Beneficial changes in the plant matrix caused by microbial activity and their beneficial potential for human health are discussed as well.
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18
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Ma S, Cao J, Liliu R, Li N, Zhao J, Zhang H, Chen W, Zhai Q. Effects of Bacillus coagulans as an adjunct starter culture on yogurt quality and storage. J Dairy Sci 2021; 104:7466-7479. [PMID: 33896630 DOI: 10.3168/jds.2020-19876] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 03/19/2021] [Indexed: 11/19/2022]
Abstract
Bacillus coagulans has been widely studied for its probiotic properties. Therefore, identifying a strain that can be used as an adjunct starter culture for yogurt production would have commercial value. In this study, 30 B. coagulans strains were isolated from vegetable samples from 11 provinces or autonomous regions in China, and their pan-genomic and phylogenetic characteristics were analyzed. Phylogenetic analysis categorized 30 strains into 4 different subphylotypes, including subtype I (11 isolates), subtype II (7 isolates), subtype III (11 isolates), and subtype IV (1 isolate). Four B. coagulans strains (B. coagulans-70, B. coagulans-78, B. coagulans-79, and B. coagulans-100) were randomly selected from each subphylotype of the phylogenetic tree as adjunct starter cultures. Compared with the other tested strains, B. coagulans-70 showed the highest count in yogurt at the end of the manufacturing period. Comparative genome analysis indicated that the different bacterial levels of B. coagulans strains in yogurt may be associated with the abundance of genes related to carbohydrate transport and metabolism (e.g., sucrose utilization). Finally, differences in texture and volatile flavor compound profiles were observed between the yogurt samples. Compared with the other groups, the addition of B. coagulans-70 exerted a positive effect on the appearance and texture of yogurt products. Volatile analysis showed increased quantities of 2-heptanone, 2-nonanone, amyl alcohol, and 2-hydroxy-3-pentanone in the B. coagulans-70 group compared with control yogurts. These results above combined with the results of a sensory evaluation indicated that B. coagulans-70 is the most suitable strain for further use in functional dairy product development.
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Affiliation(s)
- Shenyan Ma
- State Key Laboratory of Dairy Biotechnology, Shanghai Engineering Research Center of Dairy Biotechnology, Dairy Research Institute, Bright Dairy & Food Co., Ltd., Shanghai 200436, China; State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Jiang Cao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Ruolan Liliu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Nan Li
- State Key Laboratory of Dairy Biotechnology, Shanghai Engineering Research Center of Dairy Biotechnology, Dairy Research Institute, Bright Dairy & Food Co., Ltd., Shanghai 200436, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, PR China; Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi, Jiangsu 214122, PR China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China.
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Characteristics of the Proteolytic Enzymes Produced by Lactic Acid Bacteria. Molecules 2021; 26:molecules26071858. [PMID: 33806095 PMCID: PMC8037685 DOI: 10.3390/molecules26071858] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 03/17/2021] [Accepted: 03/23/2021] [Indexed: 12/20/2022] Open
Abstract
Over the past several decades, we have observed a very rapid development in the biotechnological use of lactic acid bacteria (LAB) in various branches of the food industry. All such areas of activity of these bacteria are very important and promise enormous economic and industrial successes. LAB are a numerous group of microorganisms that have the ability to ferment sugars into lactic acid and to produce proteolytic enzymes. LAB proteolytic enzymes play an important role in supplying cells with the nitrogen compounds necessary for their growth. Their nutritional requirements in this regard are very high. Lactic acid bacteria require many free amino acids to grow. The available amount of such compounds in the natural environment is usually small, hence the main function of these enzymes is the hydrolysis of proteins to components absorbed by bacterial cells. Enzymes are synthesized inside bacterial cells and are mostly secreted outside the cell. This type of proteinase remains linked to the cell wall structure by covalent bonds. Thanks to advances in enzymology, it is possible to obtain and design new enzymes and their preparations that can be widely used in various biotechnological processes. This article characterizes the proteolytic activity, describes LAB nitrogen metabolism and details the characteristics of the peptide transport system. Potential applications of proteolytic enzymes in many industries are also presented, including the food industry.
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Mayo B, Rodríguez J, Vázquez L, Flórez AB. Microbial Interactions within the Cheese Ecosystem and Their Application to Improve Quality and Safety. Foods 2021; 10:602. [PMID: 33809159 PMCID: PMC8000492 DOI: 10.3390/foods10030602] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 03/09/2021] [Indexed: 12/26/2022] Open
Abstract
The cheese microbiota comprises a consortium of prokaryotic, eukaryotic and viral populations, among which lactic acid bacteria (LAB) are majority components with a prominent role during manufacturing and ripening. The assortment, numbers and proportions of LAB and other microbial biotypes making up the microbiota of cheese are affected by a range of biotic and abiotic factors. Cooperative and competitive interactions between distinct members of the microbiota may occur, with rheological, organoleptic and safety implications for ripened cheese. However, the mechanistic details of these interactions, and their functional consequences, are largely unknown. Acquiring such knowledge is important if we are to predict when fermentations will be successful and understand the causes of technological failures. The experimental use of "synthetic" microbial communities might help throw light on the dynamics of different cheese microbiota components and the interplay between them. Although synthetic communities cannot reproduce entirely the natural microbial diversity in cheese, they could help reveal basic principles governing the interactions between microbial types and perhaps allow multi-species microbial communities to be developed as functional starters. By occupying the whole ecosystem taxonomically and functionally, microbiota-based cultures might be expected to be more resilient and efficient than conventional starters in the development of unique sensorial properties.
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Affiliation(s)
- Baltasar Mayo
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Spain; (J.R.); (L.V.); (A.B.F.)
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21
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Kleerebezem M, Bachmann H, van Pelt-KleinJan E, Douwenga S, Smid EJ, Teusink B, van Mastrigt O. Lifestyle, metabolism and environmental adaptation in Lactococcus lactis. FEMS Microbiol Rev 2021; 44:804-820. [PMID: 32990728 DOI: 10.1093/femsre/fuaa033] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 09/28/2020] [Indexed: 12/14/2022] Open
Abstract
Lactococcus lactis serves as a paradigm organism for the lactic acid bacteria (LAB). Extensive research into the molecular biology, metabolism and physiology of several model strains of this species has been fundamental for our understanding of the LAB. Genomic studies have provided new insights into the species L. lactis, including the resolution of the genetic basis of its subspecies division, as well as the control mechanisms involved in the fine-tuning of growth rate and energy metabolism. In addition, it has enabled novel approaches to study lactococcal lifestyle adaptations to the dairy application environment, including its adjustment to near-zero growth rates that are particularly relevant in the context of cheese ripening. This review highlights various insights in these areas and exemplifies the strength of combining experimental evolution with functional genomics and bacterial physiology research to expand our fundamental understanding of the L. lactis lifestyle under different environmental conditions.
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Affiliation(s)
- Michiel Kleerebezem
- Host-Microbe Interactomics Group, Animal Sciences Department, Wageningen University, De Elst 1, 6708 WD Wageningen, the Netherlands
| | - Herwig Bachmann
- Systems Bioinformatics, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, the Netherlands.,NIZO food research, Kernhemseweg 2, 6718 ZB Ede, the Netherlands
| | - Eunice van Pelt-KleinJan
- Systems Bioinformatics, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, the Netherlands.,TiFN Food & Nutrition, Nieuwe Kanaal 9A, 6709 PA Wageningen, the Netherlands
| | - Sieze Douwenga
- Systems Bioinformatics, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, the Netherlands.,TiFN Food & Nutrition, Nieuwe Kanaal 9A, 6709 PA Wageningen, the Netherlands
| | - Eddy J Smid
- Laboratory of Food Microbiology, Wageningen University, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands
| | - Bas Teusink
- Systems Bioinformatics, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, the Netherlands
| | - Oscar van Mastrigt
- Laboratory of Food Microbiology, Wageningen University, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands
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22
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Higdon SM, Huang BC, Bennett AB, Weimer BC. Identification of Nitrogen Fixation Genes in Lactococcus Isolated from Maize Using Population Genomics and Machine Learning. Microorganisms 2020; 8:microorganisms8122043. [PMID: 33419343 PMCID: PMC7768417 DOI: 10.3390/microorganisms8122043] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/08/2020] [Accepted: 12/17/2020] [Indexed: 02/06/2023] Open
Abstract
Sierra Mixe maize is a landrace variety from Oaxaca, Mexico, that utilizes nitrogen derived from the atmosphere via an undefined nitrogen fixation mechanism. The diazotrophic microbiota associated with the plant’s mucilaginous aerial root exudate composed of complex carbohydrates was previously identified and characterized by our group where we found 23 lactococci capable of biological nitrogen fixation (BNF) without containing any of the proposed essential genes for this trait (nifHDKENB). To determine the genes in Lactococcus associated with this phenotype, we selected 70 lactococci from the dairy industry that are not known to be diazotrophic to conduct a comparative population genomic analysis. This showed that the diazotrophic lactococcal genomes were distinctly different from the dairy isolates. Examining the pangenome followed by genome-wide association study and machine learning identified genes with the functions needed for BNF in the maize isolates that were absent from the dairy isolates. Many of the putative genes received an ‘unknown’ annotation, which led to the domain analysis of the 135 homologs. This revealed genes with molecular functions needed for BNF, including mucilage carbohydrate catabolism, glycan-mediated host adhesion, iron/siderophore utilization, and oxidation/reduction control. This is the first report of this pathway in this organism to underpin BNF. Consequently, we proposed a model needed for BNF in lactococci that plausibly accounts for BNF in the absence of the nif operon in this organism.
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Affiliation(s)
- Shawn M. Higdon
- Department of Plant Sciences, University of California, Davis, CA 95616, USA; (S.M.H.); (A.B.B.)
| | - Bihua C. Huang
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616, USA;
- 100 K Pathogen Genome Project, University of California, Davis, CA 95616, USA
| | - Alan B. Bennett
- Department of Plant Sciences, University of California, Davis, CA 95616, USA; (S.M.H.); (A.B.B.)
| | - Bart C. Weimer
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616, USA;
- 100 K Pathogen Genome Project, University of California, Davis, CA 95616, USA
- Correspondence:
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Choo SW, Rishik S, Wee WY. Comparative genome analyses of Mycobacteroides immunogenum reveals two potential novel subspecies. Microb Genom 2020; 6. [PMID: 33295861 PMCID: PMC8116688 DOI: 10.1099/mgen.0.000495] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mycobacteroides immunogenum is an emerging opportunistic pathogen implicated in nosocomial infections. Comparative genome analyses may provide better insights into its genomic structure, functions and evolution. The present analysis showed that M. immunogenum has an open pan-genome. Approximately 36.8% of putative virulence genes were identified in the accessory regions of M. immunogenum. Phylogenetic analyses revealed two potential novel subspecies of M. immunogenum, supported by evidence from ANIb (average nucleotide identity using blast) and GGDC (Genome to Genome Distance Calculator) analyses. We identified 74 genomic islands (GIs) in Subspecies 1 and 23 GIs in Subspecies 2. All Subspecies 2-harboured GIs were not found in Subspecies 1, indicating that they might have been acquired by Subspecies 2 after their divergence. Subspecies 2 has more defence genes than Subspecies 1, suggesting that it might be more resistant to the insertion of foreign DNA and probably explaining why Subspecies 2 has fewer GIs. Positive selection analysis suggest that M. immunogenum has a lower selection pressure compared to non-pathogenic mycobacteria. Thirteen genes were positively selected and many were involved in virulence.
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Affiliation(s)
- Siew Woh Choo
- College of Science and Technology, Wenzhou-Kean University, 88 Daxue Rd, Ouhai District Wenzhou, Zhejiang CN 325027, PR China
- *Correspondence: Siew Woh Choo,
| | - Shusruto Rishik
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Subang Jaya, Bandar Sunway, Selangor, MY 46150, Malaysia
| | - Wei Yee Wee
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Subang Jaya, Bandar Sunway, Selangor, MY 46150, Malaysia
- *Correspondence: Wei Yee Wee,
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Linares-Morales JR, Cuellar-Nevárez GE, Rivera-Chavira BE, Gutiérrez-Méndez N, Pérez-Vega SB, Nevárez-Moorillón GV. Selection of Lactic Acid Bacteria Isolated from Fresh Fruits and Vegetables Based on Their Antimicrobial and Enzymatic Activities. Foods 2020; 9:foods9101399. [PMID: 33023126 PMCID: PMC7599564 DOI: 10.3390/foods9101399] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 09/29/2020] [Accepted: 09/30/2020] [Indexed: 02/07/2023] Open
Abstract
Lactic acid bacteria (LAB) are an important source of bioactive metabolites and enzymes. LAB isolates from fresh vegetable sources were evaluated to determine their antimicrobial, enzymatic, and adhesion activities. A saline solution from the rinse of each sample was inoculated in De Man, Rogosa and Sharpe Agar (MRS Agar) for isolates recovery. Antimicrobial activity of cell-free supernatants from presumptive LAB isolates was evaluated by microtitration against Gram-positive, Gram-negative, LAB, mold, and yeast strains. Protease, lipase, amylase, citrate metabolism and adhesion activities were also evaluated. Data were grouped using cluster analysis, with 85% of similarity. A total of 76 LAB isolates were recovered, and 13 clusters were formed based on growth inhibition of the tested microorganisms. One cluster had antimicrobial activity against Gram-positive bacteria, molds and yeasts. Several LAB strains, PIM4, ELO8, PIM5 and CAL14 strongly inhibited the growth of L. monocytogenes and JAV15 and TOV9 strongly inhibited the growth of F. oxysporum. Based on enzymatic activities, 5 clusters were formed. Seven isolates hydrolyzed starch, 46 proteins, 14 lipids, and 36 metabolized citrate. LAB isolates with the best activities were molecularly identified as Leuconostoc mesenteroides, Enterococcus mundtii and Enterococcus faecium. Overall, LAB isolated from vegetables showed potential technological applications and should be further evaluated.
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Draft Genome Sequences of Six Strains of Lactococcus lactis (Phylum Firmicutes), Spanning the Seeds of Cucumis sativus L. (Cucumber), Cucumis melo L. (Cantaloupe), and Cucurbita pepo var. turbinate (Acorn Squash). Microbiol Resour Announc 2020; 9:9/37/e00665-20. [PMID: 32912910 PMCID: PMC7484069 DOI: 10.1128/mra.00665-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
We announce the draft genome sequences of six strains of Lactococcus lactis (EKM101L, EKM102L, EKM201L, EKM203L, EKM501L, and EKM502L). These candidate plant probiotics were isolated from surface-sterilized seeds of Cucumis sativus L. (cucumber), Cucumis melo L. (cantaloupe), and Cucurbita pepo var. turbinate (acorn squash). They display beneficial activities, including biocontrol. We announce the draft genome sequences of six strains of Lactococcus lactis (EKM101L, EKM102L, EKM201L, EKM203L, EKM501L, and EKM502L). These candidate plant probiotics were isolated from surface-sterilized seeds of Cucumis sativus L. (cucumber), Cucumis melo L. (cantaloupe), and Cucurbita pepo var. turbinate (acorn squash). They display beneficial activities, including biocontrol.
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Kristensen LS, Siegumfeldt H, Larsen N, Jespersen L. Diversity in NaCl tolerance of Lactococcus lactis strains from dl-starter cultures for production of semi-hard cheeses. Int Dairy J 2020. [DOI: 10.1016/j.idairyj.2020.104673] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Draft Genome Sequences of Three Amino Acid-Secreting Lactococcus lactis Strains. Microbiol Resour Announc 2020; 9:9/16/e00158-20. [PMID: 32299876 PMCID: PMC7163014 DOI: 10.1128/mra.00158-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Three Lactococcus lactis strains with the ability to secrete various amino acids (leucine, isoleucine, methionine, valine, glutamic acid, and histidine) were sequenced in order to identify the mechanisms involved in the secretion. Amino acids contribute to flavor formation; therefore, bacterial strains with this ability are relevant for the food industry. Three Lactococcus lactis strains with the ability to secrete various amino acids (leucine, isoleucine, methionine, valine, glutamic acid, and histidine) were sequenced in order to identify the mechanisms involved in the secretion. Amino acids contribute to flavor formation; therefore, bacterial strains with this ability are relevant for the food industry.
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Martins MCDF, Fusieger A, Freitas RD, Valence F, Nero LA, Carvalho AF. Novel sequence types of Lactococcus lactis subsp. lactis obtained from Brazilian dairy production environments. Lebensm Wiss Technol 2020. [DOI: 10.1016/j.lwt.2020.109146] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Tracking of Intentionally Inoculated Lactic Acid Bacteria Strains in Yogurt and Probiotic Powder. Microorganisms 2019; 8:microorganisms8010005. [PMID: 31861385 PMCID: PMC7022703 DOI: 10.3390/microorganisms8010005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/15/2019] [Accepted: 12/16/2019] [Indexed: 12/20/2022] Open
Abstract
The present work aimed at tracking intentionally inoculated lactic acid bacteria (LAB) strains in yogurt and probiotic powder. Leuconostoc (Leu.) mesenteroides (11251), Lactobacillus (L.) brevis (B151), and Lactobacillus plantarum (LB41K) strains were tracked in yogurt, and L. plantarum (LB41P) was tracked in a commercial probiotic powder. The yogurt was intentionally inoculated with the selected bacterial strains. Two types of yogurt with known and unknown bacterial pools were utilized. The standard 16S rRNA gene sequencing was used to evaluate the initial screening. The molecular typing tools, random amplified polymorphic DNA (RAPD), repetitive element palindromic PCR (rep-PCR), and comparative gene sequence analysis of selected housekeeping loci were used to track the inoculated dubious strains. Out of 30 random selections for each inoculation, the developed method identified seven (11251), nine (B151), and five (LB41K) colonies in the yogurt. The validation was performed by identifying 7 colonies (LB41P) out of 30 in the probiotic powder. The DNA banding profiles and the gene sequence alignments led to the identification of the correct inoculated strains. Overall, the study summarizes the use of molecular tools to identify the deliberately inoculated LAB strains. In conclusion, the proposed polyphasic approach effectively tracked the intentionally inoculated strains: Leu. mesenteroides, L. brevis, and L. plantarum (LB41K) in yogurt and L. plantarum (LB41P) in probiotic powder. The study demonstrates how to track industrially relevant misused LAB strains in marketable food products.
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Investigation of genomic characteristics and carbohydrates' metabolic activity of Lactococcus lactis subsp. lactis during ripening of a Swiss-type cheese. Food Microbiol 2019; 87:103392. [PMID: 31948633 DOI: 10.1016/j.fm.2019.103392] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 10/04/2019] [Accepted: 11/20/2019] [Indexed: 01/08/2023]
Abstract
Genetic diversity and metabolic properties of Lactococcus lactis subsp. lactis were explored using phylogenetic, pan-genomic and metatranscriptomic analysis. The genomes, used in the current study, were available and downloaded from the GenBank which were primarily related with microorganisms isolated from dairy products and secondarily from other foodstuffs. To study the genetic diversity of the microorganism, various bioinformatics tools were employed such as average nucleotide identity, digital DNA-DNA hybridization, phylogenetic analysis, clusters of orthologous groups analysis, KEGG orthology analysis and pan-genomic analysis. The results showed that Lc. lactis subsp. lactis strains cannot be sufficiently separated into phylogenetic lineages based on the 16S rRNA gene sequences and core genome-based phylogenetic analysis was more appropriate. Pan-genomic analysis of the strains indicated that the core, accessory and unique genome comprised of 1036, 3146 and 1296 genes, respectively. Considering the results of pan-genomic and KEGG orthology analyses, the metabolic network of Lc. lactis subsp. lactis was rebuild regarding its carbohydrates' metabolic capabilities. Based on the metatranscriptomic data during the ripening of the Swiss-type Maasdam cheese at 20 °C and 5 °C, it was shown that the microorganism performed mixed acid fermentation producing lactate, formate, acetate, ethanol and 2,3-butanediol. Mixed acid fermentation was more pronounced at higher ripening temperatures. At lower ripening temperatures, the genes involved in mixed acid fermentation were repressed while lactate production remained unaffected resembling to a homolactic fermentation. Comparative genomics and metatranscriptomic analysis are powerful tools to gain knowledge on the genomic diversity of the lactic acid bacteria used as starter cultures as well as on the metabolic activities occurring in fermented dairy products.
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Fusieger A, Martins MCF, de Freitas R, Nero LA, de Carvalho AF. Technological properties of Lactococcus lactis subsp. lactis bv. diacetylactis obtained from dairy and non-dairy niches. Braz J Microbiol 2019; 51:313-321. [PMID: 31734902 DOI: 10.1007/s42770-019-00182-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 10/25/2019] [Indexed: 12/29/2022] Open
Abstract
Lactococcus lactis subsp. lactis bv. diacetylactis strains are often used as starter cultures by the dairy industry due to their production of acetoin and diacetyl, important substances that add buttery flavor notes in dairy products. Twenty-three L. lactis subsp. lactis isolates were obtained from dairy products (milk and cheese) and dairy farms (silage), identified at a biovar level, fingerprinted by rep-PCR and characterized for some technological features. Fifteen isolates presented molecular and phenotypical (diacetyl and citrate) characteristics coherent with L. lactis subsp. lactis bv. diacetylactis and rep-PCR allowed the identification of 12 distinct profiles (minimum similarity of 90%). Based on technological features, only two isolates were not able to coagulate skim milk and 10 were able to produce proteases. All isolates were able to acidify skim milk: two isolates, in special, presented high acidifying ability due to their ability in reducing more than two pH units after 24 h. All isolates were also able to grow at different NaCl concentrations (0 to 10%, w/v), and isolates obtained from peanut and grass silages presented the highest NaCl tolerance (10%, w/v). These results indicate that the L. lactis subsp. lactis bv. diacetylactis isolates presented interesting technological features for potential application in fermented foods production. Despite presenting promising technological features, the isolates must be assessed according to their safety before being considered as starter cultures.
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Affiliation(s)
- Andressa Fusieger
- Departamento de Tecnologia de Alimentos, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | | | - Rosângela de Freitas
- Departamento de Tecnologia de Alimentos, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Luís Augusto Nero
- Departamento de Veterinária, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil.
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Zhao F, Song S, Ma Y, Xu X, Zhou G, Li C. A Short-Term Feeding of Dietary Casein Increases Abundance of Lactococcus lactis and Upregulates Gene Expression Involving Obesity Prevention in Cecum of Young Rats Compared With Dietary Chicken Protein. Front Microbiol 2019; 10:2411. [PMID: 31708891 PMCID: PMC6824296 DOI: 10.3389/fmicb.2019.02411] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Accepted: 10/07/2019] [Indexed: 02/06/2023] Open
Abstract
Casein and chicken are assessed to contain high quality proteins, which are essential for human health. Studies have shown that ingestion of the two dietary proteins resulted in distinct effects on physiology, liver transcriptome and gut microbiota. However, its underlying mechanism is not fully understood, in particular for a crosstalk between gut microbiota and host under a specific diet intervention. We fed young rats with a casein or a chicken protein-based diet (CHPD) for 7 days, and characterized cecal microbiota composition and cecal gene expression. We found that a short-term intervention with a casein-based diet (CAD) induced a higher relative abundance of beneficial bacterium Lactococcus lactis as well as Bifidobacterium pseudolongum, which upregulated galactose metabolism of the microbiome compared with a CHPD. The CAD also upregulated gene expression involved in obesity associated pathways (e.g., Adipoq and Irs1) in cecal tissue of rats. These genes and the bacterial taxon were reported to play an important role in protecting development of obesity. Furthermore, the differentially represented bacterial taxon L. lactis was positively associated with these differentially expressed genes in the gut tissue. Our results provide a new insight into the crosstalk between gut microbiota and host in response to dietary proteins, indicating a potential mechanism of obesity prevention function by casein.
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Affiliation(s)
- Fan Zhao
- College of Food Science and Technology, Nanjing Agricultural University, Key Laboratory of Meat Products Processing, Ministry of Agriculture and Rural Affairs, Jiangsu Collaborative Innovation Center of Meat Production and Processing, Quality and Safety Control, Nanjing, China
| | - Shangxin Song
- School of Food Science, Nanjing Xiaozhuang University, Nanjing, China
| | - Yafang Ma
- College of Food Science and Technology, Nanjing Agricultural University, Key Laboratory of Meat Products Processing, Ministry of Agriculture and Rural Affairs, Jiangsu Collaborative Innovation Center of Meat Production and Processing, Quality and Safety Control, Nanjing, China
| | - Xinglian Xu
- College of Food Science and Technology, Nanjing Agricultural University, Key Laboratory of Meat Products Processing, Ministry of Agriculture and Rural Affairs, Jiangsu Collaborative Innovation Center of Meat Production and Processing, Quality and Safety Control, Nanjing, China
| | - Guanghong Zhou
- College of Food Science and Technology, Nanjing Agricultural University, Key Laboratory of Meat Products Processing, Ministry of Agriculture and Rural Affairs, Jiangsu Collaborative Innovation Center of Meat Production and Processing, Quality and Safety Control, Nanjing, China
| | - Chunbao Li
- College of Food Science and Technology, Nanjing Agricultural University, Key Laboratory of Meat Products Processing, Ministry of Agriculture and Rural Affairs, Jiangsu Collaborative Innovation Center of Meat Production and Processing, Quality and Safety Control, Nanjing, China
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Fessard A, Remize F. Genetic and technological characterization of lactic acid bacteria isolated from tropically grown fruits and vegetables. Int J Food Microbiol 2019; 301:61-72. [PMID: 31100643 DOI: 10.1016/j.ijfoodmicro.2019.05.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 01/23/2019] [Accepted: 05/06/2019] [Indexed: 10/26/2022]
Abstract
Phyllosphere microorganisms are common contaminants of fruit or vegetable containing foods. The aim of this study was to identify and characterize lactic acid bacteria isolated from fruits and vegetables from Reunion Island, regarding possible application in food. Among 77 isolates, a large diversity of species was observed, with isolates belonging to Lactobacillus plantarum (3 isolates), other species of Lactobacillus (3), Lactococcus lactis (13), Leuconostoc pseudomesenteroides (25), Leuconostoc lactis (1), Leuconostoc mesenteroides (7), Leuconostoc citreum (14), Weissella cibaria (4), Weissella confusa (4), other species of Weissella (2) and Fructobacillus tropaeoli (1). Several of these species, although belonging to lactic acid bacteria, are poorly characterized, because of their low occurrence in dairy products. Lactobacillus, Lactococcus, Leuconostoc and Weissella isolates were classified by (GTG)5 fingerprinting in 3, 6, 21 and 10 genetic groups, respectively, suggesting a large intra-species diversity. Several Weissella and Lactobacillus isolates were particularly tolerant to acid and osmotic stress, whereas Lc. pseudomesenteroides 60 was highly tolerant to oxidative stress. Isolates of Weissella 30, 64 and 58, Leuconostoc 60 and 12b, Lactobacillus 75 and Fructobacillus 77 present relevant characteristics for their use as starters or as preservative cultures for fruits and vegetables.
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Affiliation(s)
- Amandine Fessard
- UMR QualiSud, Université de La Réunion, CIRAD, Université Montpellier, Montpellier SupAgro, Université d'Avignon, ESIROI, 2 rue J. Wetzell, Parc Technologique Universitaire, F-97490 Sainte Clotilde, France.
| | - Fabienne Remize
- UMR QualiSud, Université de La Réunion, CIRAD, Université Montpellier, Montpellier SupAgro, Université d'Avignon, ESIROI, 2 rue J. Wetzell, Parc Technologique Universitaire, F-97490 Sainte Clotilde, France.
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Tran TD, Huynh S, Parker CT, Han R, Hnasko R, Gorski L, McGarvey JA. Complete Genome Sequence of Lactococcus lactis subsp . lactis Strain 14B4, Which Inhibits the Growth of Salmonella enterica Serotype Poona In Vitro. Microbiol Resour Announc 2018; 7:e01364-18. [PMID: 30533785 PMCID: PMC6256472 DOI: 10.1128/mra.01364-18] [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: 10/02/2018] [Accepted: 10/22/2018] [Indexed: 11/20/2022] Open
Abstract
We present here the complete genome sequence of Lactococcus lactis strain 14B4, isolated from almond drupes in northern California. This strain was observed to inhibit the growth of Salmonella enterica serotype Poona strain RM3363 in vitro.
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Affiliation(s)
- Thao D. Tran
- Department of Plant Sciences, University of California, Davis, California, USA
| | - Steven Huynh
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, California, USA
| | - Craig T. Parker
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, California, USA
| | - Ruyang Han
- Department of Plant Sciences, University of California, Davis, California, USA
| | - Robert Hnasko
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, California, USA
| | - Lisa Gorski
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, California, USA
| | - Jeffery A. McGarvey
- Foodborne Toxin Detection and Prevention Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, California, USA
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Torres Manno M, Zuljan F, Alarcón S, Esteban L, Blancato V, Espariz M, Magni C. Genetic and phenotypic features defining industrial relevant Lactococcus lactis, L. cremoris and L. lactis biovar. diacetylactis strains. J Biotechnol 2018; 282:25-31. [DOI: 10.1016/j.jbiotec.2018.06.345] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 06/22/2018] [Accepted: 06/22/2018] [Indexed: 12/11/2022]
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Vinogradov E, Sadovskaya I, Courtin P, Kulakauskas S, Grard T, Mahony J, van Sinderen D, Chapot-Chartier MP. Determination of the cell wall polysaccharide and teichoic acid structures from Lactococcus lactis IL1403. Carbohydr Res 2018; 462:39-44. [DOI: 10.1016/j.carres.2018.04.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 04/09/2018] [Accepted: 04/09/2018] [Indexed: 10/17/2022]
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Berlec A, Škrlec K, Kocjan J, Olenic M, Štrukelj B. Single plasmid systems for inducible dual protein expression and for CRISPR-Cas9/CRISPRi gene regulation in lactic acid bacterium Lactococcus lactis. Sci Rep 2018; 8:1009. [PMID: 29343791 PMCID: PMC5772564 DOI: 10.1038/s41598-018-19402-1] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 12/29/2017] [Indexed: 12/17/2022] Open
Abstract
Lactococcus lactis is a food-grade lactic acid bacterium that is used in the dairy industry as a cell factory and as a host for recombinant protein expression. The nisin-controlled inducible expression (NICE) system is frequently applied in L. lactis; however new tools for its genetic modification are highly desirable. In this work NICE was adapted for dual protein expression. Plasmid pNZDual, that contains two nisin promoters and multiple cloning sites (MCSs), and pNZPolycist, that contains a single nisin promoter and two MCSs separated by the ribosome binding site, were constructed. Genes for the infrared fluorescent protein and for the human IgG-binding DARPin were cloned in all possible combinations to assess the protein yield. The dual promoter plasmid pNZDual enabled balanced expression of the two model proteins. It was exploited for the development of a single-plasmid inducible CRISPR-Cas9 system (pNZCRISPR) by using a nisin promoter, first to drive Cas9 expression and, secondly, to drive single guide RNA transcription. sgRNAs against htrA and ermR directed Cas9 against genomic or plasmid DNA and caused changes in bacterial growth and survival. Replacing Cas9 by dCas9 enabled CRISPR interference-mediated silencing of the upp gene. The present study introduces a new series of plasmids for advanced genetic modification of lactic acid bacterium L. lactis.
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Affiliation(s)
- Aleš Berlec
- Department of Biotechnology, Jožef Stefan Institute, Jamova 39, SI-1000, Ljubljana, Slovenia.
| | - Katja Škrlec
- Department of Biotechnology, Jožef Stefan Institute, Jamova 39, SI-1000, Ljubljana, Slovenia
- Graduate School of Biomedicine, Faculty of Medicine, University of Ljubljana, SI-1000, Ljubljana, Slovenia
| | - Janja Kocjan
- Department of Biotechnology, Jožef Stefan Institute, Jamova 39, SI-1000, Ljubljana, Slovenia
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000, Ljubljana, Slovenia
| | - Maria Olenic
- Department of Biotechnology, Jožef Stefan Institute, Jamova 39, SI-1000, Ljubljana, Slovenia
- Faculty of Pharmacy, Charles University in Prague, 500 05, Hradec Králové, Czech Republic
| | - Borut Štrukelj
- Department of Biotechnology, Jožef Stefan Institute, Jamova 39, SI-1000, Ljubljana, Slovenia
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000, Ljubljana, Slovenia
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Mercier-Bonin M, Chapot-Chartier MP. Surface Proteins of Lactococcus lactis: Bacterial Resources for Muco-adhesion in the Gastrointestinal Tract. Front Microbiol 2017; 8:2247. [PMID: 29218032 PMCID: PMC5703838 DOI: 10.3389/fmicb.2017.02247] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 10/31/2017] [Indexed: 01/13/2023] Open
Abstract
Food and probiotic bacteria, in particular lactic acid bacteria, are ingested in large amounts by humans and are part of the transient microbiota which is increasingly considered to be able to impact the resident microbiota and thus possibly the host health. The lactic acid bacterium Lactococcus lactis is extensively used in starter cultures to produce dairy fermented food. Also because of a generally recognized as safe status, L. lactis has been considered as a possible vehicle to deliver in vivo therapeutic molecules with anti-inflammatory properties in the gastrointestinal tract. One of the key factors that may favor health effects of beneficial bacteria to the host is their capacity to colonize transiently the gut, notably through close interactions with mucus, which covers and protects the intestinal epithelium. Several L. lactis strains have been shown to exhibit mucus-binding properties and bacterial surface proteins have been identified as key determinants of such capacity. In this review, we describe the different types of surface proteins found in L. lactis, with a special focus on mucus-binding proteins and pili. We also review the different approaches used to investigate the adhesion of L. lactis to mucus, and particularly to mucins, one of its major components, and we present how these approaches allowed revealing the role of surface proteins in muco-adhesion.
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Affiliation(s)
- Muriel Mercier-Bonin
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, Toulouse, France
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Talon R, Zagorec M. Special Issue: Beneficial Microorganisms for Food Manufacturing-Fermented and Biopreserved Foods and Beverages. Microorganisms 2017; 5:microorganisms5040071. [PMID: 29137179 PMCID: PMC5748580 DOI: 10.3390/microorganisms5040071] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 11/06/2017] [Accepted: 11/07/2017] [Indexed: 11/16/2022] Open
Abstract
Food fermentation is an ancient technology, disseminated worldwide, which harness microorganisms and their enzymes to improve and diversify the human diet [...].
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Affiliation(s)
- Régine Talon
- Université Clermont-Auvergne, INRA, MEDIS, F-63000 Clermont-Ferrand, France.
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40
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Lu Y, Yan H, Deng J, Huang Z, Jin X, Yu Y, Hu Q, Hu F, Wang J. Development and evaluation of an efficient heterologous gene knock-in reporter system in Lactococcus lactis. Microb Cell Fact 2017; 16:154. [PMID: 28923077 PMCID: PMC5604289 DOI: 10.1186/s12934-017-0770-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 09/09/2017] [Indexed: 02/07/2023] Open
Abstract
Background Lactococcus lactis is a food grade probiotics and widely used to express heterologous proteins. Generally, target genes are knocked into the L. lactis genome through double-crossover recombination to express heterologous proteins stably. However, creating marker-less heterologous genes knocked-in clones is laborious. In this study, an efficient heterologous gene knock-in reporter system was developed in L. lactis NZ9000. Results Our knock-in reporter system consists of a temperature-sensitive plasmid pJW and a recombinant L. lactis strain named NZB. The pJW contains homologous arms, and was constructed to knock-in heterologous genes at a fixed locus of NZ9000 genome. lacZ (β-galactosidase) gene was knocked into the chromosome of NZ9000 as a counter-selective marker through the plasmid pJW to generate NZB. The engineered NZB strain formed blue colonies on X-Gal plate. The desired double-crossover mutants formed white colonies distinctive from the predominantly blue colonies (parental and plasmid-integrated clones) when the embedded lacZ was replaced with the target heterologous genes carried by pJW in NZB. Conclusions By using the system, the heterologous gene knocked-in clones are screened by colony phenotype change rather than by checking colonies individually. Our new knock-in reporter system provides an efficient method to create heterologous genes knocked-in clones. Electronic supplementary material The online version of this article (doi:10.1186/s12934-017-0770-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yifei Lu
- Department of Microbiology, Third Military Medical University, Chongqing, 400038, China
| | - Hongxiang Yan
- Department of Microbiology, Third Military Medical University, Chongqing, 400038, China
| | - Jiezhong Deng
- Department of Microbiology, Third Military Medical University, Chongqing, 400038, China
| | - Zhigang Huang
- Department of Microbiology, Third Military Medical University, Chongqing, 400038, China
| | - Xurui Jin
- Department of Microbiology, Third Military Medical University, Chongqing, 400038, China
| | - Yanlan Yu
- Department of Microbiology, Third Military Medical University, Chongqing, 400038, China
| | - Qiwen Hu
- Department of Microbiology, Third Military Medical University, Chongqing, 400038, China
| | - Fuquan Hu
- Department of Microbiology, Third Military Medical University, Chongqing, 400038, China
| | - Jing Wang
- Department of Microbiology, Third Military Medical University, Chongqing, 400038, China.
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