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Yang Y, Shao Y, Pei C, Liu Y, Zhang M, Zhu X, Li J, Feng L, Li G, Li K, Liang Y, Li Y. Pangenome analyses of Clostridium butyricum provide insights into its genetic characteristics and industrial application. Genomics 2024; 116:110855. [PMID: 38703968 DOI: 10.1016/j.ygeno.2024.110855] [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: 02/22/2024] [Revised: 04/29/2024] [Accepted: 05/01/2024] [Indexed: 05/06/2024]
Abstract
Clostridium butyricum is a Gram-positive anaerobic bacterium known for its ability to produce butyate. In this study, we conducted whole-genome sequencing and assembly of 14C. butyricum industrial strains collected from various parts of China. We performed a pan-genome comparative analysis of the 14 assembled strains and 139 strains downloaded from NCBI. We found that the genes related to critical industrial production pathways were primarily present in the core and soft-core gene categories. The phylogenetic analysis revealed that strains from the same clade of the phylogenetic tree possessed similar antibiotic resistance and virulence factors, with most of these genes present in the shell and cloud gene categories. Finally, we predicted the genes producing bacteriocins and botulinum toxins as well as CRISPR systems responsible for host defense. In conclusion, our research provides a desirable pan-genome database for the industrial production, food application, and genetic research of C. butyricum.
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Affiliation(s)
- Yicheng Yang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuan Shao
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Chenchen Pei
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yangyang Liu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Min Zhang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xi Zhu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinshan Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Lifei Feng
- Henan Jinbaihe Biotechnology Co., Ltd., Tangyin, Anyang 455000, China
| | - Guanghua Li
- Henan Jinbaihe Biotechnology Co., Ltd., Tangyin, Anyang 455000, China
| | - Keke Li
- Henan Jinbaihe Biotechnology Co., Ltd., Tangyin, Anyang 455000, China
| | - Yunxiang Liang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yingjun Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
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Azevedo I, Barbosa J, Albano H, Nogueira T, Teixeira P. Lactic Acid Bacteria isolated from traditional and innovative alheiras as potential biocontrol agents. Food Microbiol 2024; 119:104450. [PMID: 38225051 DOI: 10.1016/j.fm.2023.104450] [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: 08/10/2023] [Revised: 12/07/2023] [Accepted: 12/09/2023] [Indexed: 01/17/2024]
Abstract
From a selection of seven traditional and 14 innovative alheiras, 491 lactic acid bacteria (LAB) were isolated and tested for their antimicrobial activity against several food-borne pathogens. Among these, six strains revealed antimicrobial activity through potential bacteriocin production against 14 Listeria monocytogenes strains, Enterococcus faecalis ATCC 29212, Clostridium sporogenes ESB050, and Clostridium perfringens ESB054. Through whole genome sequencing (WGS), these strains were identified as Lactiplantibacillus plantarum (2), Leuconostoc mesenteroides (1), and Pediococcus acidilactici (3). Furthermore, several orthologues of class II bacteriocins genes were identified, including Plantaricin E, Plantaricin F, Pediocin PA, Enterocin X, Leucocin A, and Coagulin A. No virulence or antibiotic resistance genes' orthologues were detected by WGS analysis. However, the selected LAB strains showed variable phenotypic patterns related to virulence genes and antibiotic resistance when assessed through classical methodologies. None of these strains demonstrated the production of biogenic amines, gelatinase or DNase. Additionally, no hemolytic activity or lipase enzyme production was observed. However, only Lpb. plantarum 9A3 was sensitive to all tested antibiotics and was thus chosen for further examination. The bacteriocins produced by Lpb. plantarum (9A3) exhibited stability across a broad range of conditions, including temperatures from 4 to 100 °C, pH values ranging from 2 to 8, exposure to surfactants and detergents (Tween 20 and 80, SDS, EDTA 0.1, 2 and 5 mM, urea and sodium deoxycholate), and enzymes (papain and catalase). Their maximum activity (AU/mL = 12,800) against four L. monocytogenes strains was observed between 21 and 36 h of growth of Lbp. plantarum 9A3, indicating a bacteriostatic mode of action. Therefore, this strain appears to be a robust candidate for potential application as a protective strain to be used in the food industry. Not only is it safe, but it also produces stable bacteriocins (harbouring genes encoding for the production of three) effectively inhibiting significant pathogens such as L. monocytogenes and C. perfringens.
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Affiliation(s)
- Inês Azevedo
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Porto, Portugal
| | - Joana Barbosa
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Porto, Portugal.
| | - Helena Albano
- Escola Superior de Enfermagem de Coimbra, Portugal; Instituto Politécnico de Viana do Castelo, Escola Superior Agrária, Refóios, 4990-706 Ponte de Lima, Portugal
| | - Teresa Nogueira
- Instituto Nacional de Investigação Agrária e Veterinária, I.P., 2780-157, Oeiras, 4485-655, Vairão, Portugal; CE3c - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Faculdade de Ciências da Universidade de Lisboa, 1749-016, Lisboa, Portugal
| | - Paula Teixeira
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Porto, Portugal
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Frota EG, Pessoa ARS, Souza de Azevedo POD, Dias M, Veríssimo NVP, Zanin MHA, Tachibana L, de Souza Oliveira RP. Symbiotic microparticles produced through spray-drying-induced in situ alginate crosslinking for the preservation of Pediococcus pentosaceus viability. Int J Biol Macromol 2024; 261:129818. [PMID: 38290636 DOI: 10.1016/j.ijbiomac.2024.129818] [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: 09/21/2023] [Revised: 01/03/2024] [Accepted: 01/26/2024] [Indexed: 02/01/2024]
Abstract
Probiotic microorganisms are a promising alternative to antibiotics in preventing and treating bacterial infections. Within the probiotic group, the lactic acid bacteria (LAB)stand out for their health benefits and for being recognized as safe by regulatory agencies. However, these microorganisms are sensitive to various environmental conditions, including the acidic environment of the stomach. Faced with these obstacles, this work aimed to promote the symbiotic microencapsulation of LAB in a composite matrix of alginate and prebiotics to enhance their survival and improve their probiotic activity during gastrointestinal transit. We evaluated the effect of inulin, fructo-oligosaccharides (FOS) and mannan-oligosaccharides (MOS) as prebiotic sources on the growth of Pediococcus pentosaceus LBM34 strain, finding that MOS favored LAB growth and maintenance of microencapsulated cell viability. The symbiotic microparticles were produced using the spray-drying technique with an average size of 10 μm, a smooth surface, and a composition that favored the stabilization of live cells according to the FTIR and the thermal analysis of the material. The best formulation was composed of 1 % of alginate, 10 % MOS and 1 % M10 (% w/v), which presented notable increases in the survival rates of the probiotic strain in both alkaline and acidic conditions. Therefore, this industrially scalable approach to symbiotic LAB microencapsulation can facilitate their growth and colonization within the host. This effort aims to contribute to reducing antibiotic reliance and mitigating the emergence of new zoonotic diseases, which pose significant challenges to public health.
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Affiliation(s)
- Elionio Galvão Frota
- Laboratory of Microbial Biomolecules, School of Pharmaceutical Sciences, University of São Paulo, Rua Do Lago, 250, Cidade Universitária, São Paulo 05508-000, Brazil
| | - Amanda Romana Santos Pessoa
- Laboratory of Microbial Biomolecules, School of Pharmaceutical Sciences, University of São Paulo, Rua Do Lago, 250, Cidade Universitária, São Paulo 05508-000, Brazil
| | - Pamela Oliveira de Souza de Azevedo
- Laboratory of Microbial Biomolecules, School of Pharmaceutical Sciences, University of São Paulo, Rua Do Lago, 250, Cidade Universitária, São Paulo 05508-000, Brazil
| | - Meriellen Dias
- Laboratory of Microbial Biomolecules, School of Pharmaceutical Sciences, University of São Paulo, Rua Do Lago, 250, Cidade Universitária, São Paulo 05508-000, Brazil
| | - Nathalia Vieira Porphirio Veríssimo
- Laboratory of Microbial Biomolecules, School of Pharmaceutical Sciences, University of São Paulo, Rua Do Lago, 250, Cidade Universitária, São Paulo 05508-000, Brazil; Department of Engineering of Bioprocesses and Biotechnology, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Rodovia Araraquara-Jaú/Km 01, 14800-903 Araraquara, SP, Brazil
| | - Maria Helena Ambrosio Zanin
- Institute for Technological Research (IPT), Bionanomanufacturing Nucleus, Prof. Almeida Prado Avenue, 532, Butantã, São Paulo, SP 05508-901, Brazil.
| | - Leonardo Tachibana
- Aquaculture Research Center, Scientific Research of Fisheries Institute/APTA/SAA, São Paulo, Brazil.
| | - Ricardo Pinheiro de Souza Oliveira
- Laboratory of Microbial Biomolecules, School of Pharmaceutical Sciences, University of São Paulo, Rua Do Lago, 250, Cidade Universitária, São Paulo 05508-000, Brazil.
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