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Lei J, Ran X, Guo M, Liu J, Yang F, Chen D. Screening, Identification, and Probiotic Properties of Bacillus Pumilus From Yak. Probiotics Antimicrob Proteins 2024; 16:531-540. [PMID: 36995549 DOI: 10.1007/s12602-023-10054-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/02/2023] [Indexed: 03/31/2023]
Abstract
The yak has a unique physiological structure suited to life in anoxic and cold environments at high altitudes. The aim of this study was to isolate Bacillus species with good probiotic properties from yak feces. A series of tests were performed on the isolated Bacillus: 16S rRNA identification, antibacterial activity, tolerance to gastroenteric fluid, hydrophobicity, auto-aggregation, antibiotic sensitivity, growth performance, antioxidants, and immune indexes. A safe and harmless Bacillus pumilus DX24 strain with good survival rate, hydrophobicity, auto-aggregation, and antibacterial activity was identified in the yak feces. Feeding mice with Bacillus pumilus DX24 increased their daily weight gain, jejunal villus length, villi/Crypt ratio, blood IgG levels, and jejunum sIgA levels. This study confirmed the probiotic effects of Bacillus pumilus isolated from yak feces and provides the theoretical basis for the clinical application and development of new feed additives.
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Affiliation(s)
- Jiangying Lei
- College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu, 610041, China
| | - Xuan Ran
- College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu, 610041, China
| | - Minghao Guo
- College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu, 610041, China
| | - Jiahao Liu
- College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu, 610041, China
| | - Falong Yang
- College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu, 610041, China
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization (Southwest Minzu University), Ministry of Education, Chengdu, 610041, China
| | - Dechun Chen
- College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu, 610041, China.
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization (Southwest Minzu University), Ministry of Education, Chengdu, 610041, China.
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Sánchez-Díaz R, Molina-Garza ZJ, Cruz-Suárez LE, Selvin J, Kiran GS, Gómez-Gil B, Galaviz-Silva L, Ibarra-Gámez JC. Draft genome sequences of Bacillus pumilus 36R ATNSAL and B. safensis 13L LOBSAL, two potential candidate probiotic strains for shrimp aquaculture. J Glob Antimicrob Resist 2022; 31:304-308. [PMID: 36272706 DOI: 10.1016/j.jgar.2022.10.002] [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: 04/08/2020] [Revised: 09/21/2022] [Accepted: 10/06/2022] [Indexed: 11/08/2022] Open
Abstract
OBJECTIVES This work aimed to isolate bacterial strains with antagonist activity against Vibrio parahaemolyticus, the causative agent of acute hepatopancreatic necrosis disease (VPAHPND) that was isolated from outbreaks in Mexico. Here, we report the draft genome sequences of two antagonistic strains, isolated from saline sediment in Sonora, Mexico. METHODS Cross-streak and well diffusion tests were employed to find the bacterial strains with higher inhibitory activity against VPAHPND. The whole genomes of B. pumilus 36R ATNSAL and B. safensis 13L LOBSAL were sequenced using Ion TorrentTM (PGM) and Illumina MiseqTM platforms, respectively. Annotation was performed using the RAST server, and the genes involved in the biosynthesis of bacterial secondary metabolites were predicted using antiSMASH. RESULTS Two bacterial isolates, B. safensis 13L LOBSAL and B. pumilus 36R ATNSAL, were chosen based on their strong antagonistic profiles. The genome of 36R ATNSAL was 3.94 Mbp in length and contained 3824 genes and a total of 4116 coding sequences (CDSs); the genome of 13L LOBSAL was 3.68 Mbp and contained 3619 genes and 3688 CDSs. Twenty-eight and 32 biosynthetic gene clusters responsible for putative antimicrobial metabolite production were identified in 36R ATNSAL and 13L LOBSAL, respectively. CONCLUSIONS The two strains 13L LOBSAL and 36R ATNSAL showed excellent probiotic profiles in vitro. The genome sequences will help with the mining and reconstruction of metabolic pathways in Bacillus strains. Genome sequence-guided strain improvement could augment the probiotic potential of Bacillus strains for applications in shrimp aquaculture.
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Affiliation(s)
- Ricardo Sánchez-Díaz
- Technological Institute of Sonora (ITSON), 5 de Febrero 818 Sur, Col. Centro, Ciudad Obregón, Sonora,CP 85000, México
| | - Zinnia Judith Molina-Garza
- Autonomous University of Nuevo Leon (UANL), Ave. Universidad S/N, Cd. Universitaria, San Nicolás de los Garza, Nuevo León, CP 66455, Mexico
| | - Lucía Elizabeth Cruz-Suárez
- Autonomous University of Nuevo Leon (UANL), Ave. Universidad S/N, Cd. Universitaria, San Nicolás de los Garza, Nuevo León, CP 66455, Mexico
| | - Joseph Selvin
- Department of Microbiology, Pondicherry University, Puducherry, India
| | - George Seghal Kiran
- Department of Food Science and Technology, Pondicherry University, Puducherry, India
| | - Bruno Gómez-Gil
- Research Center for Food and Development (CIAD), Mazatlan Unit, Av. Sábalo Cerritos S/N, Mazatlán, Sinaloa, C.P. 82112. Mexico
| | - Lucio Galaviz-Silva
- Autonomous University of Nuevo Leon (UANL), Ave. Universidad S/N, Cd. Universitaria, San Nicolás de los Garza, Nuevo León, CP 66455, Mexico.
| | - José Cuauhtémoc Ibarra-Gámez
- Technological Institute of Sonora (ITSON), 5 de Febrero 818 Sur, Col. Centro, Ciudad Obregón, Sonora,CP 85000, México.
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Wu YP, Liu DM, Liang MH, Huang YY, Lin J, Xiao LF. Genome-guided purification and characterization of polymyxin A1 from Paenibacillus thiaminolyticus SY20: A rarely explored member of polymyxins. Front Microbiol 2022; 13:962507. [DOI: 10.3389/fmicb.2022.962507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 10/14/2022] [Indexed: 11/16/2022] Open
Abstract
Polymyxin A1 was a rarely investigated member in the polymyxins family produced by Bacillus aerosporus. As a cyclic non-ribosomal lipopeptide, it was purified from Paenibacillus thiaminolyticus for the first time. The producing strain SY20 was screened from Chinese natural fermented bamboo shoots and identified as P. thiaminolyticus SY20 using 16S rRNA homology along with whole genome sequencing. The optimum incubation time was 32 h by the growth kinetics of antimicrobial agent production. The proteinaceous nature of antimicrobial agents was characterized according to the physicochemical properties of the cell-free supernatant. Subsequently, the active antimicrobial agent was purified from the supernatant using ammonium sulfate–graded precipitation, ion-exchange chromatography, and C18-H chromatography. The active agent was identified as polymyxin A1 with a molecular weight 1156.7 Da and antimicrobial activity mainly against Gram-negative bacteria. The molecular structure, a cyclic heptapeptide and a tripeptide side chain acylated by a fatty acid at the amino terminus, was elucidated using the combination of liquid chromatography-tandem mass spectrometry (LC-MS/MS), matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS), amino acid analysis, and whole genome mining tool. Meanwhile, the biosynthetic gene cluster of polymyxin A1 including five open reading frames (ORFs) was demonstrated in the genome. The compound should be further explored for its efficacy and toxicity in vivo to develop its application.
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Antimicrobial Bacillus: Metabolites and Their Mode of Action. Antibiotics (Basel) 2022; 11:antibiotics11010088. [PMID: 35052965 PMCID: PMC8772736 DOI: 10.3390/antibiotics11010088] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/07/2022] [Accepted: 01/08/2022] [Indexed: 12/12/2022] Open
Abstract
The agricultural industry utilizes antibiotic growth promoters to promote livestock growth and health. However, the World Health Organization has raised concerns over the ongoing spread of antibiotic resistance transmission in the populace, leading to its subsequent ban in several countries, especially in the European Union. These restrictions have translated into an increase in pathogenic outbreaks in the agricultural industry, highlighting the need for an economically viable, non-toxic, and renewable alternative to antibiotics in livestock. Probiotics inhibit pathogen growth, promote a beneficial microbiota, regulate the immune response of its host, enhance feed conversion to nutrients, and form biofilms that block further infection. Commonly used lactic acid bacteria probiotics are vulnerable to the harsh conditions of the upper gastrointestinal system, leading to novel research using spore-forming bacteria from the genus Bacillus. However, the exact mechanisms behind Bacillus probiotics remain unexplored. This review tackles this issue, by reporting antimicrobial compounds produced from Bacillus strains, their proposed mechanisms of action, and any gaps in the mechanism studies of these compounds. Lastly, this paper explores omics approaches to clarify the mechanisms behind Bacillus probiotics.
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A new, reliable, and high-throughput strategy to screen bacteria for antagonistic activity against Staphylococcus aureus. BMC Microbiol 2021; 21:189. [PMID: 34167492 PMCID: PMC8228506 DOI: 10.1186/s12866-021-02265-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/10/2021] [Indexed: 01/20/2023] Open
Abstract
Background Antibiotic-resistant Staphylococcus aureus clones have emerged globally over the last few decades. Probiotics have been actively studied as an alternative to antibiotics to prevent and treat S. aureus infections, but identifying new probiotic bacteria, that have antagonistic activity against S. aureus, is difficult since traditional screening strategies are time-consuming and expensive. Here, we describe a new plasmid-based method which uses highly stable plasmids to screen bacteria with antagonistic activity against S. aureus. Results We have created two recombinant plasmids (pQS1 and pQS3) which carry either gfpbk or mCherry under the control of a S. aureus quorum-sensing (QS) promoter (agrP3). Using this recombinant plasmid pair, we tested 81 bacteria isolated from Holstein dairy milk to identify bacteria that had growth-inhibiting activity against S. aureus and suggest potential explanations for the growth inhibition. The stability test illustrated that pQS1 and pQS3 remained highly stable for at least 24 h in batch culture conditions without selection pressure from antibiotics. This allowed co-culturing of S. aureus with other bacteria. Using the newly developed pQS plasmids, we found commensal bacteria, isolated from raw bovine milk, which had growth-inhibiting activity (n = 13) and quorum-quenching (QQ) activity (n = 13) towards both S. aureus Sa25 (CC97) and Sa27 (CC151). The pQS-based method is efficient and effective for simultaneously screening growth-inhibiting and QQ bacteria against S. aureus on agar media. Conclusions It was shown that growth-inhibiting and QQ activity toward pQS plasmid transformants of S. aureus can be simultaneously monitored by observing the zone of growth inhibition and reporter protein inhibition on agar plates. Newly identified antagonistic bacteria and their functional biomolecules are promising candidates for future development of probiotic drugs and prophylactics/therapeutics for bacterial infections including S. aureus. Furthermore, this new approach can be a useful method to find bacteria that can be used to prevent and treat S. aureus infections in both humans and animals. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02265-4.
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Eveno M, Belguesmia Y, Bazinet L, Gancel F, Fliss I, Drider D. In silico analyses of the genomes of three new bacteriocin-producing bacteria isolated from animal's faeces. Arch Microbiol 2020; 203:205-217. [PMID: 32803347 DOI: 10.1007/s00203-020-02016-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 08/02/2020] [Accepted: 08/05/2020] [Indexed: 10/23/2022]
Abstract
Here, we have analysed and explored the genome sequences of three newly isolated bacteria that were recently characterised for their probiotic activities and ability to produce bacteriocins. These strains, isolated from faeces of animals living in captivity at the zoological garden of Lille (France), are Escherichia coli ICVB443, Enterococcus faecalis ICVB501 and Pediococcus pentosaceus ICVB491. Their genomes have been analysed and compared to those of their pathogenic or probiotic counterparts. The genome analyses of E. coli ICVB443 and Ent. faecalis ICVB501 displayed similarities to those of probiotics E. coli 1917 Nissle, and Ent. faecalis Symbioflor 1, respectively. Furthermore, E. coli ICVB443 shares at least 89 genes with the enteroaggregative E. coli 55989 (EAEC), and Ent. faecalis ICVB501 shares at least 315 genes with the pathogenic Ent. faecalis V583 strain. Unlike Ped. pentosaceus ICVB491, which is devoid of virulence genes, E. coli ICVB443 and Ent. faecalis ICVB501 both carry genes encoding virulence factors on their genomes. Of note, the bioinformatics analysis of these two genomes located the bsh gene, which codes for bile salt hydrolase (BSH). The presence of BSH is of major importance, as it can help to increase the viability of these two strains in the gastrointestinal tract (GIT). The genome analysis of Ped. pentosaceus ICVB491 confirmed its GRAS status (Generally Recognised As Safe), as no genomic virulence factor determinant was found.
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Affiliation(s)
- Mégane Eveno
- UMR Transfrontalière BioEcoAgro INRAE 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, YNCREA, Univ. Artois, Univ. Littoral Côte d'Opale, ICV - Institut Charles Viollette, 59000, Lille, France.,Department of Food Sciences, Institute of Nutrition and Functional Foods (INAF), Dairy Research Center (STELA), Pavillon Paul-Comtois, Université Laval, 2425, rue de l'Agriculture, Québec, G1V 0A6, Canada
| | - Yanath Belguesmia
- UMR Transfrontalière BioEcoAgro INRAE 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, YNCREA, Univ. Artois, Univ. Littoral Côte d'Opale, ICV - Institut Charles Viollette, 59000, Lille, France
| | - Laurent Bazinet
- Department of Food Sciences, Institute of Nutrition and Functional Foods (INAF), Dairy Research Center (STELA), Pavillon Paul-Comtois, Université Laval, 2425, rue de l'Agriculture, Québec, G1V 0A6, Canada
| | - Frédérique Gancel
- UMR Transfrontalière BioEcoAgro INRAE 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, YNCREA, Univ. Artois, Univ. Littoral Côte d'Opale, ICV - Institut Charles Viollette, 59000, Lille, France
| | - Ismail Fliss
- Department of Food Sciences, Institute of Nutrition and Functional Foods (INAF), Dairy Research Center (STELA), Pavillon Paul-Comtois, Université Laval, 2425, rue de l'Agriculture, Québec, G1V 0A6, Canada
| | - Djamel Drider
- UMR Transfrontalière BioEcoAgro INRAE 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, YNCREA, Univ. Artois, Univ. Littoral Côte d'Opale, ICV - Institut Charles Viollette, 59000, Lille, France.
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