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Somerville V, Thierer N, Schmidt RS, Roetschi A, Braillard L, Haueter M, Berthoud H, Shani N, von Ah U, Mazel F, Engel P. Genomic and phenotypic imprints of microbial domestication on cheese starter cultures. Nat Commun 2024; 15:8642. [PMID: 39366947 PMCID: PMC11452379 DOI: 10.1038/s41467-024-52687-7] [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: 03/29/2024] [Accepted: 09/16/2024] [Indexed: 10/06/2024] Open
Abstract
Domestication - the artificial selection of wild species to obtain variants with traits of human interest - was integral to the rise of complex societies. The oversupply of food was probably associated with the formalization of food preservation strategies through microbial fermentation. While considerable literature exists on the antiquity of fermented food, only few eukaryotic microbes have been studied so far for signs of domestication, less is known for bacteria. Here, we tested if cheese starter cultures harbour typical hallmarks of domestication by characterising over 100 community samples and over 100 individual strains isolated from historical and modern traditional Swiss cheese starter cultures. We find that cheese starter cultures have low genetic diversity both at the species and strain-level and maintained stable phenotypic traits. Molecular clock dating further suggests that the evolutionary origin of the bacteria approximately coincided with the first archaeological records of cheese making. Finally, we find evidence for ongoing genome decay and pseudogenization via transposon insertion related to a reduction of their niche breadth. Future work documenting the prevalence of these hallmarks across diverse fermented food systems and geographic regions will be key to unveiling the joint history of humanity with fermented food microbes.
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Affiliation(s)
- Vincent Somerville
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
- Agroscope, Liebefeld, Switzerland.
- Université Laval, Quebec, Canada.
- McGill, Montréal, Canada.
| | | | | | | | | | | | | | | | | | - Florent Mazel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
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2
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Carlino N, Blanco-Míguez A, Punčochář M, Mengoni C, Pinto F, Tatti A, Manghi P, Armanini F, Avagliano M, Barcenilla C, Breselge S, Cabrera-Rubio R, Calvete-Torre I, Coakley M, Cobo-Díaz JF, De Filippis F, Dey H, Leech J, Klaassens ES, Knobloch S, O'Neil D, Quijada NM, Sabater C, Skírnisdóttir S, Valentino V, Walsh L, Alvarez-Ordóñez A, Asnicar F, Fackelmann G, Heidrich V, Margolles A, Marteinsson VT, Rota Stabelli O, Wagner M, Ercolini D, Cotter PD, Segata N, Pasolli E. Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome. Cell 2024; 187:5775-5795.e15. [PMID: 39214080 DOI: 10.1016/j.cell.2024.07.039] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 05/17/2024] [Accepted: 07/23/2024] [Indexed: 09/04/2024]
Abstract
Complex microbiomes are part of the food we eat and influence our own microbiome, but their diversity remains largely unexplored. Here, we generated the open access curatedFoodMetagenomicData (cFMD) resource by integrating 1,950 newly sequenced and 583 public food metagenomes. We produced 10,899 metagenome-assembled genomes spanning 1,036 prokaryotic and 108 eukaryotic species-level genome bins (SGBs), including 320 previously undescribed taxa. Food SGBs displayed significant microbial diversity within and between food categories. Extension to >20,000 human metagenomes revealed that food SGBs accounted on average for 3% of the adult gut microbiome. Strain-level analysis highlighted potential instances of food-to-gut transmission and intestinal colonization (e.g., Lacticaseibacillus paracasei) as well as SGBs with divergent genomic structures in food and humans (e.g., Streptococcus gallolyticus and Limosilactobabillus mucosae). The cFMD expands our knowledge on food microbiomes, their role in shaping the human microbiome, and supports future uses of metagenomics for food quality, safety, and authentication.
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Affiliation(s)
- Niccolò Carlino
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Aitor Blanco-Míguez
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Michal Punčochář
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Claudia Mengoni
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Federica Pinto
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Alessia Tatti
- Scuola Universitaria Superiore IUSS Pavia, Pavia, Italy; Centre for Agriculture Food Environment, University of Trento, Trento, Italy; Research and Innovation Centre, Fondazione Edmund Mach, San Michele All'Adige, Italy
| | - Paolo Manghi
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Federica Armanini
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Michele Avagliano
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Portici, Italy
| | - Coral Barcenilla
- Department of Food Hygiene and Technology, Universidad de León, León, Spain
| | - Samuel Breselge
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland; APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Raul Cabrera-Rubio
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland; Department of Biotechnology, Institute of Agrochemistry and Food Technology - National Research Council (IATA-CSIC), Paterna, Valencia, Spain
| | - Inés Calvete-Torre
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Villaviciosa, Spain; Microhealth Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Mairéad Coakley
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - José F Cobo-Díaz
- Department of Food Hygiene and Technology, Universidad de León, León, Spain
| | - Francesca De Filippis
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Portici, Italy; Task Force on Microbiome Studies, University of Naples Federico II, Portici, Italy
| | - Hrituraj Dey
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - John Leech
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | | | | | | | - Narciso M Quijada
- Austrian Competence Centre for Feed and Food Quality, Safety, and Innovation, FFoQSI GmbH, Tulln an der Donau, Austria; Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria; Institute for Agribiotechnology Research (CIALE), Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain
| | - Carlos Sabater
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Villaviciosa, Spain; Microhealth Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | | | - Vincenzo Valentino
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Portici, Italy
| | - Liam Walsh
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland; APC Microbiome Ireland, University College Cork, Cork, Ireland; School of Microbiology, University College Cork, Cork, Ireland
| | | | - Francesco Asnicar
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Gloria Fackelmann
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Vitor Heidrich
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Abelardo Margolles
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Villaviciosa, Spain; Microhealth Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Viggó Thór Marteinsson
- Microbiology Research Group, Matís, Reykjavík, Iceland; University of Iceland, Faculty of Food Science and Nutrition, Reykjavík, Iceland
| | - Omar Rota Stabelli
- Centre for Agriculture Food Environment, University of Trento, Trento, Italy; Research and Innovation Centre, Fondazione Edmund Mach, San Michele All'Adige, Italy
| | - Martin Wagner
- Austrian Competence Centre for Feed and Food Quality, Safety, and Innovation, FFoQSI GmbH, Tulln an der Donau, Austria; Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Danilo Ercolini
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Portici, Italy; Task Force on Microbiome Studies, University of Naples Federico II, Portici, Italy
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland; APC Microbiome Ireland, University College Cork, Cork, Ireland; VistaMilk SFI Research Centre, Teagasc, Moorepark, Fermoy, Co. Cork, Ireland
| | - Nicola Segata
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy; IEO, Istituto Europeo di Oncologia IRCSS, Milan, Italy; Department of Twins Research and Genetic Epidemiology, King's College London, London, UK.
| | - Edoardo Pasolli
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Portici, Italy; Task Force on Microbiome Studies, University of Naples Federico II, Portici, Italy
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Yamane K, Tanizawa Y, Kobayashi H, Kamizono T, Kojima Y, Takagi H, Tohno M. Proposal of Lactobacillus amylovorus subsp. animalis subsp. nov. and an emended description of Lactobacillus amylovorus. Int J Syst Evol Microbiol 2024; 74. [PMID: 39264830 DOI: 10.1099/ijsem.0.006517] [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] [Indexed: 09/14/2024] Open
Abstract
Seven novel lactic acid bacterial strains (BF125T, BF186, TKL145, YK3, YK6, YK10 and NSK) were isolated from the fresh faeces of Japanese black beef cattle and weanling piglets, spent mushroom substrates, or steeping water of a corn starch production plant. These strains are rod-shaped, Gram-stain-positive, non-motile, non-spore-forming, catalase-negative, cytochrome oxidase-negative, facultatively anaerobic, and homofermentative. Strain BF125T did not produce any gas from glucose; both d- and l-lactate were produced as end-products of glucose (D/L, 40 : 60). Growth occurred at 30-45 °C (optimum, 37 °C), pH 5.0-8.0 (optimum, pH 6.0), and with NaCl concentration of 1.0-3.0% (w/v). The G+C content of genomic DNA of strain BF125T was 37.8 mol% (whole-genome analysis). The major fatty acids were C16 : 0, C18 : 1 ω9c, C19 cyclopropane 9, 10, and summed feature 10. The 16S rRNA gene in strain BF125T showed high similarity to that of the type strain of Lactobacillus amylovorus (99.93%), and the other isolates were also identified as L. amylovorus based on these similarities. A phylogenetic tree based on the core genomes of L. amylovorus strains (n=54), including the seven isolates, showed that they could be divided into two clusters. Strains YK3, YK6, YK10, and NSK were in the first cluster, along with the type strain DSM 20531T, while the second cluster included isolates BF125T, BF186, TKL145, and other strains isolated from various animal origins. Phenotypic differences in fermentability were observed for lactose, salicin, and gentiobiose between these two groups. The intergroup digital DNA-DNA hybridization values (72.9-78.6%) and intergroup average nucleotide identity values (95.64-96.92%) were comparable to values calculated using datasets of other valid subspecies of the genus (ex-) Lactobacillus. In light of the physiological, genotypic, and phylogenetic evidence, we propose a novel subspecies of L. amylovorus, named Lactobacillus amylovorus subsp. animalis subsp. nov. (type strain BF125T=MAFF 212522T=DSM 115528T). Our findings also led to the automatic creation of Lactobacillus amylovorus subsp. amylovorus subsp. nov. and an emended description of the species L. amylovorus.
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Affiliation(s)
- Kenji Yamane
- Innovative Animal Production System, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8571, Japan
- Nihon Shokuhin Kako Co. LTD, 30, Tajima, Fuji, Shizuoka 417-8530, Japan
| | - Yasuhiro Tanizawa
- Department of Informatics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Hisami Kobayashi
- Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization, Nasushiobara, Tochigi 329-2793, Japan
| | - Tomomi Kamizono
- Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization, Nasushiobara, Tochigi 329-2793, Japan
| | - Yoichiro Kojima
- Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization, Nasushiobara, Tochigi 329-2793, Japan
| | - Hiroki Takagi
- Nihon Shokuhin Kako Co. LTD, 30, Tajima, Fuji, Shizuoka 417-8530, Japan
| | - Masanori Tohno
- Innovative Animal Production System, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8571, Japan
- Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization, Nasushiobara, Tochigi 329-2793, Japan
- Research Center of Genetic Resources, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8602, Japan
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Jakaria Al-Mujahidy SM, Kryukov K, Ikeo K, Saito K, Uddin ME, Ibn Sina AA. Functional genomic analysis of the isolated potential probiotic Lactobacillus delbrueckii subsp. indicus TY-11 and its comparison with other Lactobacillus delbrueckii strains. Microbiol Spectr 2024; 12:e0347023. [PMID: 38771133 PMCID: PMC11218508 DOI: 10.1128/spectrum.03470-23] [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: 11/01/2023] [Accepted: 04/10/2024] [Indexed: 05/22/2024] Open
Abstract
Probiotics refer to living microorganisms that exert a variety of beneficial effects on human health. On the contrary, they also can cause infection, produce toxins within the body, and transfer antibiotic-resistant genes to the other microorganisms in the digestive tract necessitating a comprehensive safety assessment. This study aimed to conduct functional genomic analysis and some relevant biochemical tests to uncover the probiotic potentials of Lactobacillus delbrueckii subsp. indicus TY-11 isolated from native yogurt in Bangladesh. We also performed transmission electron microscopic (TEM) analysis, comparative genomic study as well as phylogenetic tree construction with 332 core genes from 262 genomes. The strain TY-11 was identified as Lactobacillus delbrueckii subsp. indicus, whose genome (1,916,674 bp) contained 1911 CDS, and no gene was identified for either antibiotic resistance or toxic metabolites. It carried genes for the degradation of toxic metabolites, treatment of lactose intolerance, toll-like receptor 2-dependent innate immune response, heat and cold shock, bile salts tolerance, and acidic pH tolerance. Genes were annotated for inhibiting pathogenic bacteria by inhibitory substances [bacteriocin: Helveticin-J (331 bp) and Enterolysin-A (275 bp), hydrogen peroxide, and acid]; blockage of adhesion sites; and competition for nutrients. The genes involved in its metabolic pathway were detected as suitable for digesting indigestible nutrients in the human gut. The TY-11 genome possessed an additional 37 core genes of subspecies indicus which were deficient in the core genome of the most popular subsp. bulgaricus. During the phenotypic testing, the isolate TY-11 demonstrated high antagonistic activity (inhibition zone of 21.33 ± 1.53 mm) against Escherichia coli ATCC 8739 and was not sensitive to any of the 10 tested antibiotics. This study was the first study to explore the molecular insights into probiotic roles, including antimicrobial activities and antibiotic sensitivity, of a representative strain (TY-11) of Lactobacillus delbrueckii subsp. indicus. IMPORTANCE This study aimed to conduct functional genomic analysis to uncover the probiotic potential of Lactobacillus delbrueckii subsp. indicus TY-11 isolated from native yogurt in Bangladesh. We also performed transmission electron microscopic (TEM) analysis, comparative genomic study as well as phylogenetic tree construction with 332 core genes from 262 genomes. In our current investigation, we revealed a number of common and unique excellences of the probiotic Lactobacillus delbrueckii subsp. indicus TY-11 that are likely to be important to illustrate its intestinal residence and probiotic roles. This is the first study to explore the molecular insights into intestinal residence and probiotic roles, including antimicrobial activities and antibiotic sensitivity, of a representative strain (TY-11) of Lactobacillus delbrueckii subsp. indicus.
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Affiliation(s)
- Sk. Md. Jakaria Al-Mujahidy
- DNA Data Analysis Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Kirill Kryukov
- Center for Genome Informatics, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Mishima, Shizuoka, Japan
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Kazuho Ikeo
- DNA Data Analysis Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Kei Saito
- Laboratory of Physics and Cell Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Md. Ekhlas Uddin
- Department of Biochemistry and Molecular Biology, Gono Bishwabidyalay, Savar, Dhaka, Bangladesh
| | - Abu Ali Ibn Sina
- Australian Institute for Bioengineering & Nanotechnology (AIBN), The University of Queensland, Brisbane, Queensland, Australia
- Department of Systems Biology, Columbia University Irving Medical Center, New York, New York, USA
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Quaresma LS, Santos RCV, Gomes GC, Américo MF, Campos GM, Laguna JG, Barroso FAL, Azevedo V, de Jesus LCL. Multidrug resistance profile in Lactobacillus delbrueckii: a food industry species with probiotic properties. World J Microbiol Biotechnol 2024; 40:235. [PMID: 38850338 DOI: 10.1007/s11274-024-04046-3] [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: 04/10/2024] [Accepted: 06/03/2024] [Indexed: 06/10/2024]
Abstract
Lactobacillus delbrueckii, a widely used lactic acid bacterium in the food industry, has been studied for its probiotic properties and reservoir of antibiotic-resistant genes, raising safety concerns for probiotic formulations and fermented products. This review consolidates findings from 60 articles published between 2012 and 2023, focusing on the global antibiotic resistance profile and associated genetic factors in L. delbrueckii strains. Resistance to aminoglycosides, particularly streptomycin, kanamycin, and gentamicin, as well as resistance to glycopeptides (vancomycin), fluoroquinolones (ciprofloxacin), and tetracyclines was predominant. Notably, although resistance genes have been identified, they have not been linked to mobile genetic elements, reducing the risk of dissemination. However, a significant limitation is the insufficient exploration of responsible genes or mobile elements in 80% of studies, hindering safety assessments. Additionally, most articles originated from Asian and Middle Eastern countries, with strains often isolated from fermented dairy foods. Therefore, these findings underscore the necessity for comprehensive analyses of new strains of L. delbrueckii for potential industrial and biotherapeutic applications and in combating the rise of antibiotic-resistant pathogens.
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Affiliation(s)
- Ludmila Silva Quaresma
- Department of Genetics, Ecology, and Evolution, Federal University of Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | | | - Gabriel Camargos Gomes
- Department of Genetics, Ecology, and Evolution, Federal University of Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Monique Ferrary Américo
- Department of Genetics, Ecology, and Evolution, Federal University of Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Gabriela Munis Campos
- Department of Genetics, Ecology, and Evolution, Federal University of Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Juliana Guimarães Laguna
- Department of Genetics, Ecology, and Evolution, Federal University of Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | | | - Vasco Azevedo
- Department of Genetics, Ecology, and Evolution, Federal University of Minas Gerais, Belo Horizonte, 31270-901, Brazil.
| | - Luís Cláudio Lima de Jesus
- Department of Genetics, Ecology, and Evolution, Federal University of Minas Gerais, Belo Horizonte, 31270-901, Brazil.
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Harlé O, Niay J, Parayre S, Nicolas A, Henry G, Maillard MB, Valence F, Thierry A, Guédon É, Falentin H, Deutsch SM. Deciphering the metabolism of Lactobacillus delbrueckii subsp. delbrueckii during soy juice fermentation using phenotypic and transcriptional analysis. Appl Environ Microbiol 2024; 90:e0193623. [PMID: 38376234 PMCID: PMC10952386 DOI: 10.1128/aem.01936-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 01/03/2024] [Indexed: 02/21/2024] Open
Abstract
In the context of sustainable diet, the development of soy-based yogurt fermented with lactic acid bacteria is an attractive alternative to dairy yogurts. To decipher the metabolism of Lactobacillus delbrueckii subsp. delbrueckii during soy juice (SJ) fermentation, the whole genome of the strain CIRM-BIA865 (Ld865) was sequenced and annotated. Then Ld865 was used to ferment SJ. Samples were analyzed throughout fermentation for their cell number, carbohydrate, organic acid, free amino acid, and volatile compound contents. Despite acidification, the number of Ld865 cells did not rise, and microscopic observations revealed the elongation of cells from 3.6 µm (inoculation) to 36.9 µm (end of fermentation). This elongation was observed in SJ but not in laboratory-rich medium MRS. Using transcriptomic analysis, we showed that the biosynthesis genes of peptidoglycan and membrane lipids were stably expressed, in line with the cell elongation observed, whereas no genes implicated in cell division were upregulated. Among the main sugars available in SJ (sucrose, raffinose, and stachyose), Ld865 only used sucrose. The transcriptomic analysis showed that Ld865 implemented the two transport systems that it contains to import sucrose: a PTS system and an ABC transporter. To fulfill its nitrogen needs, Ld865 probably first consumed the free amino acids of the SJ and then implemented different oligopeptide transporters and proteolytic/peptidase enzymes. In conclusion, this study showed that Ld865 enables fast acidification of SJ, despite the absence of cell division, leads to a product rich in free amino acids, and also leads to the production of aromatic compounds of interest. IMPORTANCE To reduce the environmental and health concerns related to food, an alternative diet is recommended, containing 50% of plant-based proteins. Soy juice, which is protein rich, is a relevant alternative to animal milk, for the production of yogurt-like products. However, soy "beany" and "green" off-flavors limit the consumption of such products. The lactic acid bacteria (LAB) used for fermentation can help to improve the organoleptic properties of soy products. But metabolic data concerning LAB adapted to soy juice are lacking. The aim of this study was, thus, to decipher the metabolism of Lactobacillus delbrueckii subsp. delbrueckii during fermentation of a soy juice, based on a multidisciplinary approach. This result will contribute to give tracks for a relevant selection of starter. Indeed, the improvement of the organoleptic properties of these types of products could help to promote plant-based proteins in our diet.
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Affiliation(s)
- Olivier Harlé
- INRAE, Institut Agro, STLO, Rennes, France
- Olga-Triballat Noyal, R&D UF, Noyal-sur-Vilaine, France
| | - Jérôme Niay
- Olga-Triballat Noyal, R&D UF, Noyal-sur-Vilaine, France
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Zhao K, Qiu L, Tao X, Zhang Z, Wei H. Genome Analysis for Cholesterol-Lowing Action and Bacteriocin Production of Lactiplantibacillus plantarum WLPL21 and ZDY04 from Traditional Chinese Fermented Foods. Microorganisms 2024; 12:181. [PMID: 38258009 PMCID: PMC10820322 DOI: 10.3390/microorganisms12010181] [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: 12/18/2023] [Revised: 01/07/2024] [Accepted: 01/11/2024] [Indexed: 01/24/2024] Open
Abstract
Lactiplantibacillus plantarum, a typical ecological species against pathogens, used due to its bacteriocin yield in fermented foods, was proven to have the capacity to lower cholesterol. In this study, using L. plantarum ATCC8014 as the control, L. plantarum WLPL21 and ZDY04 were probed with whole-genome sequencing to ascertain their potential ability to lower cholesterol and yield bacteriocins, as well as to further evaluate their survival capacity in vitro. Our results showed 386 transport-system genes in both L. plantarum WLPL21 and ZDY04. Correspondingly, the in vitro results showed that L. plantarum WLPL21 and ZDY04 could remove cholesterol at 49.23% and 41.97%, respectively, which is 1.89 and 1.61 times that of L. plantarum ATCC8014. The survival rates of L. plantarum WLPL21 and ZDY04 in 1% H2O2, pH 3.0, and 0.3% bile salt were higher than those of L. plantarum ATCC8014. Our results exhibited a complete gene cluster for bacteriocin production encoded by L. plantarum WLPL21 and ZDY04, including plnJKR, plnPQAB, plnEFI, plnSUVWY, and plnJK; and plnMN, plnPQA and plnEFI, respectively, compared with only plnEF in L. plantarum ATCC8014. The present study suggests that the combination of genomic analysis with in vitro evaluations might be useful for exploring the potential functions of probiotics.
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Affiliation(s)
- Kui Zhao
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China; (K.Z.); (X.T.); (Z.Z.)
| | - Liang Qiu
- Centre for Translational Medicine, Jiangxi University of Traditional Chinese Medicine, Nanchang 330006, China;
| | - Xueying Tao
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China; (K.Z.); (X.T.); (Z.Z.)
| | - Zhihong Zhang
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China; (K.Z.); (X.T.); (Z.Z.)
| | - Hua Wei
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China; (K.Z.); (X.T.); (Z.Z.)
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8
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Bae WY, Lee YJ, Jung WH, Shin SL, Kim TR, Sohn M. Draft genome sequence and probiotic functional property analysis of Lactobacillus gasseri LM1065 for food industry applications. Sci Rep 2023; 13:12212. [PMID: 37500806 PMCID: PMC10374649 DOI: 10.1038/s41598-023-39454-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 07/25/2023] [Indexed: 07/29/2023] Open
Abstract
Probiotics are defined as live organisms in the host that contribute to health benefits. Lactobacillus gasseri LM1065, isolated from human breast milk, was investigated for its probiotic properties based on its genome. Draft genome map and de novo assembly were performed using the PacBio RS II system and hierarchical genome assembly process (HGAP). Probiotic properties were determined by the resistance to gastric conditions, adherence ability, enzyme production, safety assessment and mobile genetic elements. The fungistatic effect and inhibition of hyphae transition were studied using the cell-free supernatant (CFS). L. gasseri LM1065 showed high gastric pepsin tolerance and mild tolerance to bile salts. Auto-aggregation and hydrophobicity were measured to be 61.21% and 61.55%, respectively. The adherence to the human intestinal epithelial cells was measured to be 2.02%. Antibiotic-resistance genes and putative virulence genes were not predicted in the genomic analysis, and antibiotic susceptibility was satisfied by the criteria of the European Food Safety Authority. CFS showed a fungistatic effect and suppressed the tricarboxylic acid cycle in Candida albicans (29.02%). CFS also inhibited the transition to true hyphae and damaged the blastoconidia. This study demonstrates the essential properties of this novel probiotic, L. gasseri LM1065, and potential to inhibit vaginal C. albicans infection.
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Affiliation(s)
- Won-Young Bae
- Microbiome R&D Center, Lactomason, Seoul, 06620, Republic of Korea.
| | - Young Jin Lee
- Microbiome R&D Center, Lactomason, Seoul, 06620, Republic of Korea
| | - Woo-Hyun Jung
- Microbiome R&D Center, Lactomason, Seoul, 06620, Republic of Korea
| | - So Lim Shin
- Microbiome R&D Center, Lactomason, Seoul, 06620, Republic of Korea
| | - Tae-Rahk Kim
- Microbiome R&D Center, Lactomason, Seoul, 06620, Republic of Korea
| | - Minn Sohn
- Microbiome R&D Center, Lactomason, Seoul, 06620, Republic of Korea
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Bazukyan I, Georgieva-Miteva D, Velikova T, Dimov SG. In Silico Probiogenomic Characterization of Lactobacillus delbrueckii subsp. lactis A4 Strain Isolated from an Armenian Honeybee Gut. INSECTS 2023; 14:540. [PMID: 37367356 DOI: 10.3390/insects14060540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 06/07/2023] [Accepted: 06/08/2023] [Indexed: 06/28/2023]
Abstract
A Lactobacillus delbrueckii ssp. lactis strain named A4, isolated from the gut of an Armenian honeybee, was subjected to a probiogenomic characterization because of its unusual origin. A whole-genome sequencing was performed, and the bioinformatic analysis of its genome revealed a reduction in the genome size and the number of the genes-a process typical for the adaptation to endosymbiotic conditions. Further analysis of the genome revealed that Lactobacillus delbrueckii ssp. lactis strain named A4 could play the role of a probiotic endosymbiont because of the presence of intact genetic sequences determining antioxidant properties, exopolysaccharides synthesis, adhesion properties, and biofilm formation, as well as an antagonistic activity against some pathogens which is not due to pH or bacteriocins production. Additionally, the genomic analysis revealed significant potential for stress tolerance, such as extreme pH, osmotic stress, and high temperature. To our knowledge, this is the first report of a potentially endosymbiotic Lactobacillus delbrueckii ssp. lactis strain adapted to and playing beneficial roles for its host.
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Affiliation(s)
- Inga Bazukyan
- Faculty of Biology, Yerevan State University, Yerevan 0025, Armenia
| | | | - Tsvetelina Velikova
- Medical Faculty, Sofia University St. Kliment Ohridski, 1 Kozyak Str., 1407 Sofia, Bulgaria
| | - Svetoslav G Dimov
- Faculty of Biology, Sofia University St. Kliment Ohridski, 8 Dragan Tzankov Str., 1164 Sofia, Bulgaria
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