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Kim YH, Lee DH, Seo HS, Eun SH, Lee DS, Choi YK, Lee SH, Kim TY. Genome-based taxonomic identification and safety assessment of an Enterococcus strain isolated from a homemade dairy product. Int Microbiol 2024; 27:1513-1525. [PMID: 38466360 DOI: 10.1007/s10123-024-00496-9] [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: 12/31/2023] [Revised: 02/24/2024] [Accepted: 03/05/2024] [Indexed: 03/13/2024]
Abstract
The aim of this study was to explore the taxonomic identification and evaluate the safety of a bacterium, Enterococcus lactis IDCC 2105, isolated from homemade cheese in Korea, using whole genome sequence (WGS) analysis. It sought to identify the species level of this Enterococcus spp., assess its antibiotic resistance, and evaluate its virulence potential. WGS analysis confirmed the bacterial strain IDCC 2105 as E. lactis and identified genes responsible for resistance to erythromycin and clindamycin, specifically msrC, and eatAv, which are chromosomally located, indicating a minimal risk for horizontal gene transfer. The absence of plasmids in E. lactis IDCC 2105 further diminishes the likelihood of resistance gene dissemination. Additionally, our investigation into seven virulence factors, including hemolysis, platelet aggregation, biofilm formation, hyaluronidase, gelatinase, ammonia production, and β-glucuronidase activity, revealed no detectable virulence traits. Although bioinformatic analysis suggested the presence of collagen adhesion genes acm and scm, these were not corroborated by phenotypic virulence assays. Based on these findings, E. lactis IDCC 2105 presents as a safe strain for potential applications, contributing valuable information on its taxonomy, antibiotic resistance profile, and lack of virulence factors, supporting its use in food products.
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Affiliation(s)
- Young-Hoo Kim
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, 05029, South Korea
| | | | - Han Sol Seo
- Yunovia Co., Ltd, Hwaseong, 18449, South Korea
| | | | - Do Sup Lee
- Yunovia Co., Ltd, Hwaseong, 18449, South Korea
| | | | - Sang Hyun Lee
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, 05029, South Korea
| | - Tae-Yoon Kim
- Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Seongnam, 13488, Republic of Korea.
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Mendonça AA, Pinto-Neto WDP, da Paixão GA, Santos DDS, De Morais MA, De Souza RB. Journey of the Probiotic Bacteria: Survival of the Fittest. Microorganisms 2022; 11:95. [PMID: 36677387 PMCID: PMC9861974 DOI: 10.3390/microorganisms11010095] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 12/26/2022] [Accepted: 12/27/2022] [Indexed: 01/03/2023] Open
Abstract
This review aims to bring a more general view of the technological and biological challenges regarding production and use of probiotic bacteria in promoting human health. After a brief description of the current concepts, the challenges for the production at an industrial level are presented from the physiology of the central metabolism to the ability to face the main forms of stress in the industrial process. Once produced, these cells are processed to be commercialized in suspension or dried forms or added to food matrices. At this stage, the maintenance of cell viability and vitality is of paramount for the quality of the product. Powder products requires the development of strategies that ensure the integrity of components and cellular functions that allow complete recovery of cells at the time of consumption. Finally, once consumed, probiotic cells must face a very powerful set of physicochemical mechanisms within the body, which include enzymes, antibacterial molecules and sudden changes in pH. Understanding the action of these agents and the induction of cellular tolerance mechanisms is fundamental for the selection of increasingly efficient strains in order to survive from production to colonization of the intestinal tract and to promote the desired health benefits.
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Affiliation(s)
- Allyson Andrade Mendonça
- Laboratory of Microbial Genetics, Department of Genetics, Federal University of Pernambuco, Recife 50670-901, Brazil
| | - Walter de Paula Pinto-Neto
- Laboratory of Microbial Genetics, Department of Genetics, Federal University of Pernambuco, Recife 50670-901, Brazil
| | - Giselle Alves da Paixão
- Laboratory of Microbial Metabolism, Institute of Biological Sciences, University of Pernambuco, Recife 50100-130, Brazil
| | - Dayane da Silva Santos
- Laboratory of Microbial Genetics, Department of Genetics, Federal University of Pernambuco, Recife 50670-901, Brazil
| | - Marcos Antonio De Morais
- Laboratory of Microbial Genetics, Department of Genetics, Federal University of Pernambuco, Recife 50670-901, Brazil
| | - Rafael Barros De Souza
- Laboratory of Microbial Metabolism, Institute of Biological Sciences, University of Pernambuco, Recife 50100-130, Brazil
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Domínguez-Maqueda M, Pérez-Gómez O, Grande-Pérez A, Esteve C, Seoane P, Tapia-Paniagua ST, Balebona MC, Moriñigo MA. Pathogenic strains of Shewanella putrefaciens contain plasmids that are absent in the probiotic strain Pdp11. PeerJ 2022; 10:e14248. [PMID: 36312754 PMCID: PMC9610664 DOI: 10.7717/peerj.14248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 09/26/2022] [Indexed: 01/24/2023] Open
Abstract
Shewanella putrefaciens Pdp11 is a strain described as a probiotic for use in aquaculture. However, S. putrefaciens includes strains reported to be pathogenic or saprophytic to fish. Although the probiotic trait has been related to the presence of a group of genes in its genome, the existence of plasmids that could determine the probiotic or pathogenic character of this bacterium is unknown. In the present work, we searched for plasmids in several strains of S. putrefaciens that differ in their pathogenic and probiotic character. Under the different conditions tested, plasmids were only found in two of the five pathogenic strains, but not in the probiotic strain nor in the two saprophytic strains tested. Using a workflow integrating Sanger and Illumina reads, the complete consensus sequences of the plasmids were obtained. Plasmids differed in one ORF and encoded a putative replication initiator protein of the repB family, as well as proteins related to plasmid stability and a toxin-antitoxin system. Phylogenetic analysis showed some similarity to functional repB proteins of other Shewanella species. The implication of these plasmids in the probiotic or pathogenic nature of S. putrefaciens is discussed.
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Affiliation(s)
| | | | - Ana Grande-Pérez
- Área de Genética, Universidad de Málaga, Málaga, Spain,Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”-Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Universidad de Málaga, Málaga, Spain
| | - Consuelo Esteve
- Departmento de Microbiología y Ecología, Universidad de Valencia, Valencia, Spain
| | - Pedro Seoane
- Centro de Investigación Biomédica en Red de Enfermedades Raras, CIBERER, Madrid, Spain,Departmento de Biología Molecular y Bioquímica, Universidad de Málaga, Málaga, Spain
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Bajagai YS, Petranyi F, J Yu S, Lobo E, Batacan R, Kayal A, Horyanto D, Ren X, M Whitton M, Stanley D. Phytogenic supplement containing menthol, carvacrol and carvone ameliorates gut microbiota and production performance of commercial layers. Sci Rep 2022; 12:11033. [PMID: 35773309 PMCID: PMC9246849 DOI: 10.1038/s41598-022-14925-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 06/15/2022] [Indexed: 11/17/2022] Open
Abstract
Consumer push towards open and free-range production systems makes biosecurity on farms challenging, leading to increased disease and animal welfare issues. Phytogenic products are increasingly becoming a viable alternative for the use of antibiotics in livestock production. Here we present a study of the effects of commercial phytogenic supplement containing menthol, carvacrol and carvone on intestinal microbiota of layer hens, microbial functional capacity, and intestinal morphology. A total of 40,000 pullets were randomly assigned to two sides of the experimental shed. Growth performance, mortality, egg production and egg quality parameters were recorded throughout the trial period (18–30 weeks of age). Microbial community was investigated using 16S amplicon sequencing and functional difference using metagenomic sequencing. Phytogen supplemented birds had lower mortality and number of dirty eggs, and their microbial communities showed reduced richness. Although phytogen showed the ability to control the range of poultry pathogens, its action was not restricted to pathogenic taxa, and it involved functional remodelling the intestinal community towards increased cofactor production, heterolactic fermentation and salvage and recycling of metabolites. The phytogen did not alter the antimicrobial resistance profile or the number of antibiotic resistance genes. The study indicates that phytogenic supplementation can mimic the action of antibiotics in altering the gut microbiota and be used as their alternative in industry-scale layer production.
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Affiliation(s)
- Yadav S Bajagai
- Institute for Future Farming Systems, Central Queensland University, Rockhampton, QLD, 4702, Australia
| | - Friedrich Petranyi
- Institute for Future Farming Systems, Central Queensland University, Rockhampton, QLD, 4702, Australia
| | - Sung J Yu
- Institute for Future Farming Systems, Central Queensland University, Rockhampton, QLD, 4702, Australia
| | - Edina Lobo
- Institute for Future Farming Systems, Central Queensland University, Rockhampton, QLD, 4702, Australia
| | - Romeo Batacan
- Institute for Future Farming Systems, Central Queensland University, Rockhampton, QLD, 4702, Australia
| | - Advait Kayal
- Institute for Future Farming Systems, Central Queensland University, Rockhampton, QLD, 4702, Australia
| | - Darwin Horyanto
- Institute for Future Farming Systems, Central Queensland University, Rockhampton, QLD, 4702, Australia
| | - Xipeng Ren
- Institute for Future Farming Systems, Central Queensland University, Rockhampton, QLD, 4702, Australia
| | - Maria M Whitton
- Institute for Future Farming Systems, Central Queensland University, Rockhampton, QLD, 4702, Australia
| | - Dragana Stanley
- Institute for Future Farming Systems, Central Queensland University, Rockhampton, QLD, 4702, Australia.
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Cadmium stress triggers significant metabolic reprogramming in Enterococcus faecium CX 2-6. Comput Struct Biotechnol J 2021; 19:5678-5687. [PMID: 34765088 PMCID: PMC8554106 DOI: 10.1016/j.csbj.2021.10.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 10/09/2021] [Accepted: 10/12/2021] [Indexed: 12/13/2022] Open
Abstract
A cadmium resistant strain of Enterococcus faecium CX 2–6 is sequenced. Differential expression analysis found 47% of CX 2–6 genes are significantly affected by Cd treatment. Differentially expressed genes (DEGs) form physically linked gene clusters in the CX 2–6 genome. A prophage is unique to CX 2–6 and is strongly activated by high Cd concentration. A majority of DEGs responding to Cd treatment are present in the core genome.
Heavy metal pollutions in the soils are increasingly threatening the global crop and food production. Using plant associated bacteria to remediate heavy metal contamination is a promising approach. We have isolated a cadmium (Cd) resistant Enterococcus faecium strain CX 2–6 from a heavy metal contaminated farmland. We have shown that: (i) CX 2–6 can tolerate cadmium (Cd) with a slower growth rate; (ii) The CX 2–6 complete genome is fully assembled using PacBio long reads; (iii) Differential expression analysis found 47% of CX 2–6 genes are significantly affected by Cd treatment and form three gene groups with distinct expression profiles; (iv) Differentially expressed genes (DEGs) form physically linked gene clusters in the CX 2–6 genome, and one of the gene clusters corresponds to a prophage that is unique to CX 2–6 and is strongly activated when Cd concentration is higher; (v) A majority of DEGs responding to Cd treatment are present in the core genome; and (vi) 55 noncoding RNA genes are identified and 49 of them are DEGs responding to cadmium stress. Our pan-genome analysis and comparative RNA-seq data analysis has significantly improved our understanding of the metabolic reprogramming of E. faecium CX 2–6 under Cd stress.
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Coutinho JOPA, Quintanilha MF, Campos MRA, Ferreira E, de Menezes GCA, Rosa LH, Rosa CA, Vital KD, Fernandes SOA, Cardoso VN, Nicoli JR, Tiago FCP, Martins FS. Antarctic Strain of Rhodotorula mucilaginosa UFMGCB 18,377 Attenuates Mucositis Induced by 5-Fluorouracil in Mice. Probiotics Antimicrob Proteins 2021; 14:486-500. [PMID: 34255281 DOI: 10.1007/s12602-021-09817-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2021] [Indexed: 12/17/2022]
Abstract
Mucositis is one of the most strenuous side effects caused by chemotherapy drugs, such as 5-fluorouracil (5-FU), during the treatment of several types of cancers. The disease is so prevalent and aggressive that many patients cannot resist such symptoms. However, despite its frequency and clinical significance, there is no effective treatment to prevent or treat mucositis. Thus, the use of probiotics as an adjuvant for the treatment has gained prominence. In the present study, we evaluated the effectiveness of oral administration of the Antarctic strain of Rhodotorula mucilaginosa UFMGCB 18,377 as an alternative to minimize side effects of 5-FU-induced mucositis in mice. Body weight, food consumption, stool consistency, and presence of blood in the feces were assessed daily in mice orally treated or not with the yeast and submitted or not to experimental mucositis. Blood, bones, and intestinal tissues and fluid were used to determine intestinal permeability and immunological, microbiological, and histopathological parameters. Treatment with R. mucilaginosa UFMGCB 18,377 was able to decrease clinical signs of the disease, such as reduction of food intake and body weight loss, and also decreased the number of intestinal enterobacteria and intestinal length shortening. Additionally, treatment was able to decrease the levels of MPO and EPO activities and inflammatory infiltrates, as well as the histopathological lesions characteristic of mucositis in the jejunum and ileum. Results of the present study showed that the oral administration of R. mucilaginosa UFMGCB 18,377 protected mice against mucositis induced by 5-FU.
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Affiliation(s)
- Joana O P A Coutinho
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Mônica F Quintanilha
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Marina R A Campos
- Departamento de Patologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Enio Ferreira
- Departamento de Patologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Graciéle C A de Menezes
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Luiz H Rosa
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Carlos A Rosa
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Katia D Vital
- Departamento de Análises Clínicas E Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Simone O A Fernandes
- Departamento de Análises Clínicas E Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Valbert N Cardoso
- Departamento de Análises Clínicas E Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Jacques R Nicoli
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Fabiana C P Tiago
- Centro Federal de Educação Tecnológica de Minas Gerais (CEFET-MG), Belo Horizonte, MG, Brazil
| | - Flaviano S Martins
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil. .,Laboratório de Agentes Bioterapêuticos, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, Belo Horizonte, MG, 30270-901, Brazil.
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