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Kompramool S, Singkhamanan K, Pomwised R, Chaichana N, Suwannasin S, Wonglapsuwan M, Jitpakdee J, Kantachote D, Yaikhan T, Surachat K. Genomic Insights into Pediococcus pentosaceus ENM104: A Probiotic with Potential Antimicrobial and Cholesterol-Reducing Properties. Antibiotics (Basel) 2024; 13:813. [PMID: 39334988 PMCID: PMC11428213 DOI: 10.3390/antibiotics13090813] [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: 08/07/2024] [Revised: 08/22/2024] [Accepted: 08/26/2024] [Indexed: 09/30/2024] Open
Abstract
Pediococcus pentosaceus, which often occurs in fermented foods, is characterized by numerous positive effects on the human health, such as the presence of possible probiotic abilities, the reduction of cholesterol levels, satisfactory antimicrobial activity, and certain therapeutic functions. This study was conducted with the goal of describing the genomic content of Pediococcus pentosaceus ENM104, a strain known for its inhibitory effects against pathogenic bacteria and its remarkable probiotic potential, including the induction of significant reductions in cholesterol levels and the production of γ-aminobutyric acid (GABA). The P. pentosaceus ENM104 chromosome is circular. The chromosome is 1,734,928 bp with a GC content of 37.2%. P. pentosaceus also harbors a circular plasmid, pENM104, that is 71,811 bp with a GC content of 38.1%. Functional annotations identified numerous genes associated with probiotic traits, including those involved in stress adaptation (e.g., heat stress: htpX, dnaK, and dnaJ), bile tolerance (e.g., ppaC), vitamin biosynthesis (e.g., ribU, ribZ, ribF, and btuD), immunomodulation (e.g., dltA, dltC, and dltD), and bacteriocin production (e.g., pedA). Notably, genes responsible for lowering cholesterol levels (bile salt hydrolase, bsh) and GABA synthesis (glutamate/GABA antiporter, gadC) were also identified. The in vitro assay results using cell-free supernatants of P. pentosaceus ENM104 revealed antibacterial activity against carbapenem-resistant bacteria, such as Pseudomonas aeruginosa, Klebsiella pneumoniae, and Acinetobacter baumannii, and the inhibition zone diameter increased progressively over time. This comprehensive study provides valuable insights into the molecular characteristics of P. pentosaceus ENM104, emphasizing its potential as a probiotic. Its notable cholesterol-lowering, GABA-producing, and antimicrobial capabilities suggest promising applications in the pharmaceutical and food industries. Future research should focus on further exploring these functional properties and assessing the strain's efficacy in clinical settings.
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Affiliation(s)
- Siriwan Kompramool
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand; (S.K.); (K.S.); (N.C.); (S.S.); (T.Y.)
| | - Kamonnut Singkhamanan
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand; (S.K.); (K.S.); (N.C.); (S.S.); (T.Y.)
| | - Rattanaruji Pomwised
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand; (R.P.); (M.W.); (J.J.); (D.K.)
| | - Nattarika Chaichana
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand; (S.K.); (K.S.); (N.C.); (S.S.); (T.Y.)
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand; (R.P.); (M.W.); (J.J.); (D.K.)
| | - Sirikan Suwannasin
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand; (S.K.); (K.S.); (N.C.); (S.S.); (T.Y.)
| | - Monwadee Wonglapsuwan
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand; (R.P.); (M.W.); (J.J.); (D.K.)
| | - Jirayu Jitpakdee
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand; (R.P.); (M.W.); (J.J.); (D.K.)
| | - Duangporn Kantachote
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand; (R.P.); (M.W.); (J.J.); (D.K.)
| | - Thunchanok Yaikhan
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand; (S.K.); (K.S.); (N.C.); (S.S.); (T.Y.)
| | - Komwit Surachat
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand; (S.K.); (K.S.); (N.C.); (S.S.); (T.Y.)
- Translational Medicine Research Center, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand
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Lu K, Wang X, Zhou Y, Zhu Q. Genomic characterization and probiotic potential assessment of an exopolysaccharide-producing strain Pediococcus pentosaceus LL-07 isolated from fermented meat. BMC Microbiol 2024; 24:142. [PMID: 38664612 PMCID: PMC11044368 DOI: 10.1186/s12866-024-03304-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 04/12/2024] [Indexed: 04/29/2024] Open
Abstract
BACKGROUND The genomic information available for Pediococcus pentosaceus is primarily derived from fermented fruits and vegetables, with less information available from fermented meat. P. pentosaceus LL-07, a strain isolated from fermented meat, has the capability of producing exopolysaccharides (EPS). To assess the probiotic attributes of P. pentosaceus LL-07, we conducted whole-genome sequencing (WGS) using the PacBio SequelIIe and Illumina MiSeq platforms, followed by in vitro experiments to explore its probiotic potential. RESULTS The genome size of P. pentosaceus LL-07 is 1,782,685 bp, comprising a circular chromosome and a circular plasmid. Our investigation revealed the absence of a CRISPR/Cas system. Sugar fermentation experiments demonstrated the characteristics of carbohydrate metabolism. P. pentosaceus LL-07 contains an EPS synthesis gene cluster consisting of 13 genes, which is different from the currently known gene cluster structure. NO genes associated with hemolysis or toxin synthesis were detected. Additionally, eighty-six genes related to antibiotic resistance were identified but not present in the prophage, transposon or plasmid. In vitro experiments demonstrated that P. pentosaceus LL-07 was comparable to the reference strain P. pentosaceus ATCC25745 in terms of tolerance to artificial digestive juice and bile, autoaggregation and antioxidation, and provided corresponding genomic evidence. CONCLUSION This study confirmed the safety and probiotic properties of P. pentosaceus LL-07 via complete genome and phenotype analysis, supporting its characterization as a potential probiotic candidate.
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Affiliation(s)
- Kuan Lu
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guizhou Province, Guiyang, 550025, China
- Guizhou Province Key Laboratory of Agricultural and Animal Products Storage and Processing, School of Liquor and Food Engineering, Guizhou University, Guizhou, Guiyang, 550025, China
| | - Xueya Wang
- Chili Pepper Research Institute, Guizhou Provincial Academy of Agricultural Sciences, Guizhou, Guiyang, 550006, China
| | - Ying Zhou
- Guizhou Province Key Laboratory of Agricultural and Animal Products Storage and Processing, School of Liquor and Food Engineering, Guizhou University, Guizhou, Guiyang, 550025, China
| | - Qiujin Zhu
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guizhou Province, Guiyang, 550025, China.
- Guizhou Province Key Laboratory of Agricultural and Animal Products Storage and Processing, School of Liquor and Food Engineering, Guizhou University, Guizhou, Guiyang, 550025, China.
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Tathode MS, Bonomo MG, Zappavigna S, Mang SM, Bocchetti M, Camele I, Caraglia M, Salzano G. Whole-genome analysis suggesting probiotic potential and safety properties of Pediococcus pentosaceus DSPZPP1, a promising LAB strain isolated from traditional fermented sausages of the Basilicata region (Southern Italy). Front Microbiol 2024; 15:1268216. [PMID: 38638895 PMCID: PMC11024341 DOI: 10.3389/fmicb.2024.1268216] [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: 07/27/2023] [Accepted: 03/07/2024] [Indexed: 04/20/2024] Open
Abstract
Introduction Many lactic acid bacteria (LAB) strains are currently gaining attention in the food industry and various biological applications because of their harmless and functional properties. Given the growing consumer demand for safe food, further research into potential probiotic bacteria is beneficial. Therefore, we aimed to characterize Pediococcus pentosaceus DSPZPP1, a LAB strain isolated from traditional fermented sausages from the Basilicata region of Southern Italy. Methods In this study, we analyzed the whole genome of the P. pentosaceus DSPZPP1 strain and performed in silico characterization to evaluate its applicability for probiotics and use in the food industry. Results and Discussion The whole-genome assembly and functional annotations revealed many interesting characteristics of the DSPZPP1 strain. Sequencing raw reads were assembled into a draft genome of size 1,891,398 bp, with a G + C content of 37.3%. Functional annotation identified 1930 protein-encoding genes and 58 RNAs including tRNA, tmRNA, and 16S, 23S, and 5S rRNAs. The analysis shows the presence of genes that encode water-soluble B-group vitamins such as biotin, folate, coenzyme A, and riboflavin. Furthermore, the analysis revealed that the DSPZPP1 strain can synthesize class II bacteriocin, penocin A, adding importance to the food industry for bio-enriched food. The DSPZPP1 genome does not show the presence of plasmids, and no genes associated with antimicrobial resistance and virulence were found. In addition, two intact bacteriophages were identified. Importantly, the lowest probability value in pathogenicity analysis indicates that this strain is non-pathogenic to humans. 16 s rRNA-based phylogenetic analysis and comparative analysis based on ANI and Tetra reveal that the DSPZPP1 strain shares the closest evolutionary relationship with P. pentosaceus DSM 20336 and other Pediococcus strains. Analysis of carbohydrate active enzymes (CAZymes) identified glycosyl transferases (GT) as a main class of enzymes followed by glycoside hydrolases (GH). Our study shows several interesting characteristics of the isolated DSPZPP1 strain from fermented Italian sausages, suggesting its potential use as a promising probiotic candidate and making it more appropriate for selection as a future additive in biopreservation.
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Affiliation(s)
- Madhura S. Tathode
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Maria Grazia Bonomo
- Department of Science, Università degli Studi della Basilicata, Potenza, Italy
- Spinoff TNcKILLERS, Potenza, Italy
| | - Silvia Zappavigna
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Stefania Mirela Mang
- School of Agricultural, Forestry, Food and Environmental Sciences (SAFE), Università degli Studi della Basilicata, Potenza, Italy
| | - Marco Bocchetti
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy
- Laboratory of Molecular and Precision Oncology, Biogem Scarl, Institute of Genetic Research, Ariano Irpino, Italy
| | - Ippolito Camele
- School of Agricultural, Forestry, Food and Environmental Sciences (SAFE), Università degli Studi della Basilicata, Potenza, Italy
| | - Michele Caraglia
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy
- Laboratory of Molecular and Precision Oncology, Biogem Scarl, Institute of Genetic Research, Ariano Irpino, Italy
| | - Giovanni Salzano
- Department of Science, Università degli Studi della Basilicata, Potenza, Italy
- Spinoff TNcKILLERS, Potenza, Italy
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Su X, Fang T, Fang L, Wang D, Jiang X, Liu C, Zhang H, Guo R, Wang J. Effects of short-term exposure to simulated microgravity on the physiology of Bacillus subtilis and multiomic analysis. Can J Microbiol 2023; 69:464-478. [PMID: 37463516 DOI: 10.1139/cjm-2023-0061] [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: 07/20/2023]
Abstract
In our study, Bacillus subtilis was disposed to a simulated microgravity (SMG) environment in high-aspect ratio rotating-wall vessel bioreactors for 14 days, while the control group was disposed to the same bioreactors in a normal gravity (NG) environment for 14 days. The B. subtilis strain exposed to the SMG (labeled BSS) showed an enhanced growth ability, increased biofilm formation ability, increased sensitivity to ampicillin sulbactam and cefotaxime, and some metabolic alterations compared with the B. subtilis strain under NG conditions (labeled BSN) and the original strain of B. subtilis (labeled BSO). The differentially expressed proteins (DEPs) associated with an increased growth rate, such as DNA strand exchange activity, oxidoreductase activity, proton-transporting ATP synthase complex, and biosynthetic process, were significantly upregulated in BSS. The enhanced biofilm formation ability may be related with the DEPs of spore germination and protein processing in BSS, and differentially expressed genes involved in protein localization and peptide secretion were also significantly enriched. The results revealed that SMG may increase the level of related functional proteins by upregulating or downregulating affiliated genes to change physiological characteristics and modulate growth ability, biofilm formation ability (epsB, epsC, epsN), antibiotic sensitivity (penP) and metabolism. Our experiment may gives new ideas for the study of space microbiology.
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Affiliation(s)
- Xiaolei Su
- Department of Otorhinolaryngology Head and Neck Surgery, Air Force Medical Center, PLA, Beijing, China
| | - Tingzheng Fang
- Sixth Department of Health Care, The Second Medical Center and National Clinical Research Center for Geriatric Disease, Chinese PLA General Hospital, Beijing, China
| | - Lin Fang
- Department of Otorhinolaryngology Head and Neck Surgery, Air Force Medical Center, PLA, Beijing, China
| | - Dapeng Wang
- Department of Respiratory and Critical Care Medicine, The Second Medical Center and National Clinical Research Center for Geriatric Disease, Chinese PLA General Hospital, Beijing, China
| | - Xuege Jiang
- Department of Respiratory and Critical Care Medicine, The Second Medical Center and National Clinical Research Center for Geriatric Disease, Chinese PLA General Hospital, Beijing, China
| | - Changting Liu
- Department of Respiratory and Critical Care Medicine, The Second Medical Center and National Clinical Research Center for Geriatric Disease, Chinese PLA General Hospital, Beijing, China
| | - Honglei Zhang
- Department of Otorhinolaryngology Head and Neck Surgery, Air Force Medical Center, PLA, Beijing, China
| | - Rui Guo
- Department of Otorhinolaryngology Head and Neck Surgery, Air Force Medical Center, PLA, Beijing, China
| | - Junfeng Wang
- Department of Respiratory and Critical Care Medicine, The Second Medical Center and National Clinical Research Center for Geriatric Disease, Chinese PLA General Hospital, Beijing, China
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Deng X, Yuan J, Chen L, Chen H, Wei C, Nielsen PH, Wuertz S, Qiu G. CRISPR-Cas phage defense systems and prophages in Candidatus Accumulibacter. WATER RESEARCH 2023; 235:119906. [PMID: 37004306 DOI: 10.1016/j.watres.2023.119906] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 02/27/2023] [Accepted: 03/21/2023] [Indexed: 06/19/2023]
Abstract
Candidatus Accumulibacter plays a major role in enhanced biological phosphorus removal (EBPR) from wastewater. Although bacteriophages have been shown to represent fatal threats to Ca. Accumulibacter organisms and thus interfere with the stability of the EBPR process, little is known about the ability of different Ca. Accumulibacter strains to resist phage infections. We conducted a systematic analysis of the occurrence and characteristics of clustered regularly interspaced short palindromic repeats and associated proteins (CRISPR-Cas) systems and prophages in Ca. Accumulibacter lineage members (43 in total, including 10 newly recovered genomes). Results indicate that 28 Ca. Accumulibacter genomes encode CRISPR-Cas systems. They were likely acquired via horizontal gene transfer, conveying a distinct adaptivity to phage predation to different Ca. Accumulibacter members. Major differences in the number of spacers show the unique phage resistance of these members. A comparison of the spacers in closely related Ca. Accumulibacter members from distinct geographical locations indicates that habitat isolation may have resulted in the acquisition of resistance to different phages by different Ca. Accumulibacter. Long-term operation of three laboratory-scale EBPR bioreactors revealed high relative abundances of Ca. Accumulibacter with CRISPSR-Cas systems. Their specific resistance to phages in these reactors was indicated by spacer analysis. Metatranscriptomic analyses showed the activation of the CRISPR-Cas system under both anaerobic and aerobic conditions. Additionally, 133 prophage regions were identified in 43 Ca. Accumulibacter genomes. Twenty-seven of them (in 19 genomes) were potentially active. Major differences in the occurrence of CRISPR-Cas systems and prophages in Ca. Accumulibacter will lead to distinct responses to phage predation. This study represents the first systematic analysis of CRISPR-Cas systems and prophages in the Ca. Accumulibacter lineage, providing new perspectives on the potential impacts of phages on Ca. Accumulibacter and EBPR systems.
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Affiliation(s)
- Xuhan Deng
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Jing Yuan
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Liping Chen
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Hang Chen
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Chaohai Wei
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China; The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, Guangzhou 510006, China
| | - Per H Nielsen
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore; Centre for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg DK-9220, Denmark
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore; School of Civil and Environmental Engineering, Nanyang Technological University, Singapore 639798, Singapore.
| | - Guanglei Qiu
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China; Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore; Guangdong Provincial Key Laboratory of Solid Wastes Pollution Control and Recycling, Guangzhou 510006, China.
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Phuengjayaem S, Pakdeeto A, Kingkaew E, Tunvongvinis T, Somphong A, Tanasupawat S. Genome sequences and functional analysis of Levilactobacillus brevis LSF9-1 and Pediococcus acidilactici LSF1-1 from fermented fish cake (Som-fak) with gamma-aminobutyric acid (GABA) production. Funct Integr Genomics 2023; 23:158. [PMID: 37171680 DOI: 10.1007/s10142-023-01085-1] [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: 03/12/2023] [Revised: 05/02/2023] [Accepted: 05/02/2023] [Indexed: 05/13/2023]
Abstract
Gamma-aminobutyric acid (GABA) is a crucial inhibitory neurotransmitter in the sympathetic nervous system that exerts regulatory effects on the blood, immune, and nervous systems. GABA production in som-fak, a traditional fermented fish of Thailand, has been attributed to the activity of lactic acid bacteria (LAB). The present study aims to characterize the LAB isolates and compare the genomes and GABA synthesis genes of selected isolates capable of GABA production. Thirteen isolates demonstrating GABA synthesis capability were identified based on their phenotypic and genotypic characteristics. Seven isolates (group I: LSF3-3, LSF8-3, LSF9-1, LSF9-3, LSF9-6, LSF9-7, and LSF10-14) were identified as Levilactobacillus brevis with 99.78-100% similarity. LSF2-1, LSF3-2, LSF5-4, and LSF6-5 (group II) were identified as Lactiplantibacillus pentosus with 99.86-100% similarity. Strain LSF1-1 (group III) was identified as Pediococcus acidilactici (99.47%), and LSF10-4 (group IV) was identified as Pediococcus pentosaceus with 99.93% similarity. The GABA production of isolates ranged from 0.087 to 16.935 g/L. The maximum production of 16.935 g/L from 3% monosodium glutamate was obtained from strain LSF9-1. Gene and genome analysis revealed that L. brevis LSF9-1 has multiple gad genes in the genome, such as gadB1, gadB2, gadC1, and gadC2, making it the potential strain for GABA production. Additionally, the genome analysis of P. acidilactici LSF1-1 consists of gadA, gadB, and gadC, which respond to controlling GABA production and export. Furthermore, strain LSF1-1 was considered safe, containing no virulence factors. Thus, Levilactobacillus brevis LSF9-1 and Pediococcus acidilactici LSF1-1 have the potential for GABA production and probiotic use in future studies.
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Affiliation(s)
- Sukanya Phuengjayaem
- Department of Microbiology, Faculty of Science, King Mongkut's University of Technology Thonburi, Bangkok, 10140, Thailand
| | - Amnat Pakdeeto
- Program in Food Science and Technology, Faculty of Agriculture and Life Sciences, Chandrakasem Rajabhat University, Bangkok, 10900, Thailand
| | - Engkarat Kingkaew
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Tuangrat Tunvongvinis
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Achiraya Somphong
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, 10330, Thailand.
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Borowska M, Ispiryan L, Neylon E, Sahin AW, Murphy CP, Zannini E, Arendt EK, Coffey A. Screening and Application of Novel Homofermentative Lactic Acid Bacteria Results in Low-FODMAP Whole-Wheat Bread. FERMENTATION-BASEL 2023. [DOI: 10.3390/fermentation9040336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
FODMAPs are fermentable oligo-, di-, monosaccharides, and polyols. The application of homofermentative lactic acid bacteria (LAB) has been investigated as a promising approach for producing low-FODMAP whole-wheat bread. The low-FODMAP diet is recommended to treat irritable bowel syndrome (IBS). Wheat flour is staple to many diets and is a significant source of fructans, which are considered FODMAPs. The reduction of fructans via sourdough fermentation, generally associated with heterofermentative lactic acid bacteria (LAB), often leads to the accumulation of other FODMAPs. A collection of 244 wild-type LAB strains was isolated from different environments and their specific FODMAP utilisation profiles established. Three homofermentative strains were selected for production of whole-wheat sourdough bread. These were Lactiplantibacillus plantarum FST1.7 (FST1.7), Lacticaseibacillus paracasei R3 (R3), and Pediococcus pentosaceus RYE106 (RYE106). Carbohydrate levels in flour, sourdoughs (before and after 48 h fermentation), and resulting breads were analysed via HPAEC-PAD and compared with whole-wheat bread leavened with baker’s yeast. While strain R3 was the most efficient in FODMAP reduction, breads produced with all three test strains had FODMAP content below cut-off levels that would trigger IBS symptoms. Results of this study highlighted the potential of homofermentative LAB in producing low-FODMAP whole-wheat bread.
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Favaro L, Campanaro S, Fugaban JII, Treu L, Jung ES, d'Ovidio L, de Oliveira DP, Liong MT, Ivanova IV, Todorov SD. Genomic, metabolomic, and functional characterisation of beneficial properties of Pediococcus pentosaceus ST58, isolated from human oral cavity. Benef Microbes 2023; 14:57-72. [PMID: 36815495 DOI: 10.3920/bm2022.0067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Bacteriocins produced by lactic acid bacteria are proteinaceous antibacterial metabolites that normally exhibit bactericidal or bacteriostatic activity against genetically closely related bacteria. In this work, the bacteriocinogenic potential of Pediococcus pentosaceus strain ST58, isolated from oral cavity of a healthy volunteer was evaluated. To better understand the biological role of this strain, its technological and safety traits were deeply investigated through a combined approach considering physiological, metabolomic and genomic properties. Three out of 14 colonies generating inhibition zones were confirmed to be bacteriocin producers and, according to repPCR and RAPD-PCR, differentiation assays, and 16S rRNA sequencing it was confirmed to be replicates of the same strain, identified as P. pentosaceus, named ST58. Based on multiple isolation of the same strain (P. pentosaceus ST58) over the 26 weeks in screening process for the potential bacteriocinogenic strains from the oral cavity of the same volunteer, strain ST58 can be considered a persistent component of oral cavity microbiota. Genomic analysis of P. pentosaceus ST58 revealed the presence of operons encoding for bacteriocins pediocin PA-1 and penocin A. The produced bacteriocin(s) inhibited the growth of Listeria monocytogenes, Enterococcus spp. and some Lactobacillus spp. used to determine the activity spectrum. The highest levels of production (6400 AU/ml) were recorded against L. monocytogenes strains after 24 h of incubation and the antimicrobial activity was inhibited after treatment of the cell-free supernatants with proteolytic enzymes. Noteworthy, P. pentosaceus ST58 also presented antifungal activity and key metabolites potentially involved in these properties were identified. Overall, this strain can be of great biotechnological interest towards the development of effective bio-preservation cultures as well as potential health promoting microbes.
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Affiliation(s)
- L Favaro
- Department of Agronomy Food Natural Resources Animals and Environment (DAFNAE), Università degli Studi di Padova, Agripolis, Viale dell'Università 16, 35020 Legnaro, Italy
| | - S Campanaro
- Department of Biology, Università degli Studi di Padova, Via U. Bassi 58/b, 35121 Padova, Italy.,CRIBI Biotechnology Center, Università degli Studi di Padova, 35121 Padova, Italy
| | - J I I Fugaban
- ProBacLab, Department of Advanced Convergence, Handong Global University, Pohang, Gyeongbuk 791-708, South Korea.,National Food Institute, Technical University of Denmark, Building 202, Rm. 3.234, Kemitorvet, 2800 Kongens, Lyngby, Denmark
| | - L Treu
- Department of Biology, Università degli Studi di Padova, Via U. Bassi 58/b, 35121 Padova, Italy
| | - E S Jung
- HEM Pharma Inc., Suwon, Gyeonggi 16229, Republic of Korea
| | - L d'Ovidio
- Laboratório de Microbiologia de Alimentos, Departamento de Alimentos e Nutrição Experimental, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo (SP), Brazil
| | - D P de Oliveira
- Laboratório de Microbiologia de Alimentos, Departamento de Alimentos e Nutrição Experimental, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo (SP), Brazil
| | - M-T Liong
- School of Industrial Technology, University Sains Malaysia, 11800 Penang, Malaysia
| | - I V Ivanova
- Department of General and Applied Microbiology, Faculty of Biology, Sofia University St. Kliment Ohridski, 8 Dragan Tzankov Blvd., 1164 Sofia, Bulgaria
| | - S D Todorov
- ProBacLab, Department of Advanced Convergence, Handong Global University, Pohang, Gyeongbuk 791-708, South Korea.,Laboratório de Microbiologia de Alimentos, Departamento de Alimentos e Nutrição Experimental, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo (SP), Brazil
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Gumustop I, Ortakci F. Analyzing the genetic diversity and biotechnological potential of Leuconostoc pseudomesenteroides by comparative genomics. Front Microbiol 2023; 13:1074366. [PMID: 36713205 PMCID: PMC9875049 DOI: 10.3389/fmicb.2022.1074366] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 12/14/2022] [Indexed: 01/12/2023] Open
Abstract
Leuconostoc pseudomesenteroides is a lactic acid bacteria species widely exist in fermented dairy foods, cane juice, sourdough, kimchi, apple dumpster, caecum, and human adenoid. In the dairy industry, Ln. pseudomesenteroides strains are usually found in mesophilic starter cultures with lactococci. This species plays a crucial role in the production of aroma compounds such as acetoin, acetaldehyde, and diacetyl, thus beneficially affecting dairy technology. We performed genomic characterization of 38 Ln. pseudomesenteroides from diverse ecological niches to evaluate this species' genetic diversity and biotechnological potential. A mere ~12% of genes conserved across 38 Ln. pseudomesenteroides genomes indicate that accessory genes are the driving force for genotypic distinction in this species. Seven main clades were formed with variable content surrounding mobile genetic elements, namely plasmids, transposable elements, IS elements, prophages, and CRISPR-Cas. All but three genomes carried CRISPR-Cas system. Furthermore, a type IIA CRISPR-Cas system was found in 80% of the CRISPR-Cas positive strains. AMBR10, CBA3630, and MGBC116435 were predicted to encode bacteriocins. Genes responsible for citrate metabolism were found in all but five strains belonging to cane juice, sourdough, and unknown origin. On the contrary, arabinose metabolism genes were only available in nine strains isolated from plant-related systems. We found that Ln. pseudomesenteroides genomes show evolutionary adaptation to their ecological environment due to niche-specific carbon metabolism and forming closely related phylogenetic clades based on their isolation source. This species was found to be a reservoir of type IIA CRISPR-Cas system. The outcomes of this study provide a framework for uncovering the biotechnological potential of Ln. pseudomesenteroides and its future development as starter or adjunct culture for dairy industry.
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Comparative Genomics of Lentilactobacillus parabuchneri isolated from dairy, KEM complex, Makgeolli, and Saliva Microbiomes. BMC Genomics 2022; 23:803. [PMID: 36471243 PMCID: PMC9724434 DOI: 10.1186/s12864-022-09053-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Lentilactobacillus parabuchneri is of particular concern in fermented food bioprocessing due to causing unwanted gas formation, cracks, and off-flavor in fermented dairy foods. This species is also a known culprit of histamine poisonings because of decarboxylating histidine to histamine in ripening cheese. Twenty-eight genomes in NCBI GenBank were evaluated via comparative analysis to determine genomic diversity within this species and identify potential avenues for reducing health associated risks and economic losses in the food industry caused by these organisms. RESULT Core genome-based phylogenetic analysis revealed four distinct major clades. Eight dairy isolates, two strains from an unknown source, and a saliva isolate formed the first clade. Three out of five strains clustered on clade 2 belonged to dairy, and the remaining two strains were isolated from the makgeolli and Korean effective microorganisms (KEM) complex. The third and fourth clade members were isolated from Tete de Moine and dairy-associated niches, respectively. Whole genome analysis on twenty-eight genomes showed ~ 40% of all CDS were conserved across entire strains proposing a considerable diversity among L. parabuchneri strains analyzed. After assigning CDS to their corresponding function, ~ 79% of all strains were predicted to carry putative intact prophages, and ~ 43% of the strains harbored at least one plasmid; however, all the strains were predicted to encode genomic island, insertion sequence, and CRISPR-Cas system. A type I-E CRISPR-Cas subgroup was identified in all the strains, with the exception of DSM15352, which carried a type II-A CRISPR-Cas system. Twenty strains were predicted to encode histidine decarboxylase gene cluster that belongs to not only dairy but also saliva, KEM complex, and unknown source. No bacteriocin-encoding gene(s) or antibiotic resistome was found in any of the L. parabuchneri strains screened. CONCLUSION The findings of the present work provide in-depth knowledge of the genomics of L. parabuchneri by comparing twenty-eight genomes available to date. For example, the hdc gene cluster was generally reported in cheese isolates; however, our findings in the current work indicated that it could also be encoded in those strains isolated from saliva, KEM complex, and unknown source. We think prophages are critical mobile elements of L. parabuchneri genomes that could pave the way for developing novel tools to reduce the occurrence of this unwanted species in the food industry.
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Genomic analysis and in vivo efficacy of Pediococcus acidilactici as a potential probiotic to prevent hyperglycemia, hypercholesterolemia and gastrointestinal infections. Sci Rep 2022; 12:20429. [PMID: 36443433 PMCID: PMC9705362 DOI: 10.1038/s41598-022-24791-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 11/21/2022] [Indexed: 11/29/2022] Open
Abstract
Lactic acid bacteria are the well acknowledged probiotics that can cure a variety of diseases. In this study, we observed the in vivo potentials of Pediococcus to treat hyperglycemia, hypercholesterolemia and gastrointestinal infections. A total of 77 Lactobacillus were isolated from the milk of 10 cows and 10 goats, four of those strains inhibited both carbohydrates-hydrolyzing enzymes, α-glucosidase, and α-amylase. They all showed antagonistic effects on pathogenic E. coli and S. Typhimurium which were confirmed by performing pathogen challenge test and visualizing on Electron microscopy. 16S rRNA gene sequence identified that all four strains belong to Pediococcus genus which were further distinguished as Pediococcus acidilactici by pheS gene sequence. Whole genome sequence analysis revealed their non-pathogenic properties for human and the presence of probiotic genes responsible for stress resistance, immunomodulation, adhesion, metal and drug resistance. In vivo trial with diabetes-induced mice ascertained that all Pediococcus acidilactici had significant potentials to reduce elevated glucose and low-density lipoprotein level in blood. Interestingly, two out of four strains were significantly more effective (p < 0.0001 each) than metformin in reducing the blood glucose level. This in vivo study demonstrated that Pediococcus acidilactici might be a promising probiotic to prevent hyperglycemia, hypercholesterolemia and gastrointestinal infections.
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Al-Surrayai T, Al-Khalaifah H, Al-Mansour H, Kishk M, Al-Mutairi A, Sultan H, Al-Saleem H. Evaluation of the lactic acid bacteria based formulated probiotic product for poultry. FRONTIERS IN ANIMAL SCIENCE 2022. [DOI: 10.3389/fanim.2022.1026958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
This study evaluated the effectiveness of a new probiotic product developed to reduce the effect of Salmonella infections and compared it to the efficacy of commercial probiotics in broiler chicken. Based on the in vitro assessment of the growth characteristics and safety to human health, four bacterial isolates were isolated, characterized, and identified as excellent candidates for the development of commercial probiotic feed additives for poultry. Compatibility and interactions among the four selected strains were investigated. After that, a preliminary study was conducted in which the selected isolates were evaluated individually in vivo with three different methods of application (water, feed, and oral gavage). The cycle included N = 312 chicks, which were divided into 13 groups, including control, distributed into four batteries, with 78 broiler chickens in each battery. There were eight replicates with 24 chicks in each replicate, and the analysis was randomly done in triplicate. The intentional parameters were growth performance, microbial analysis and humoral immune response. The results of the preliminary study assisted in formulating the new probiotic product. Then In vivo evaluations for the newly formulated product were performed with the comparison with two imported commercial products (Alterion and Galli pro fit) used in poultry farms in Kuwait. The second cycle included N = 96 chicks that were divided into four groups, including control. Each group has three replicates and each replicate has eight chicks, and the analysis was randomly done in triplicate. The results showed that although antibiotics were not used, all the growth parameters were similar and sometimes better than the control. The new product inhibited the growth of salmonella as a control and all chickens in different treatment gained a high mass of meat. The statistical analysis showed that no differences were observed in bird weight, weight gain, feed consumption, and feed efficiency between bacterial strains p>0.05. Also, the different probiotic treatments did not affect the total antibody IgM titers significantly in the broilers (P > 0.05). Thus, the newly formulated product was effective in reducing the salmonella.
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13
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Rodrigues Blanco I, José Luduverio Pizauro L, Victor dos Anjos Almeida J, Miguel Nóbrega Mendonça C, de Mello Varani A, Pinheiro de Souza Oliveira R. Pan-genomic and comparative analysis of Pediococcus pentosaceus focused on the in silico assessment of pediocin-like bacteriocins. Comput Struct Biotechnol J 2022; 20:5595-5606. [PMID: 36284702 PMCID: PMC9568690 DOI: 10.1016/j.csbj.2022.09.041] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 11/29/2022] Open
Abstract
Bacteriocins are antimicrobial peptides produced by different species of bacteria, especially the Gram-positive lactic acid bacteria (LAB). Pediococcus pentosaceus is widely applied in the industry and stands out as Bacteriocin-Like Inhibitory Substances (BLIS) producer known to inhibit pathogens commonly considered a concern in the food industries. This study aimed to perform in silico comparisons of P. pentosaceus genomes available in the public GenBank database focusing on their pediocin-like bacteriocins repertoire. The pan-genome analysis evidenced a temporal signal in the pattern of gene gain and loss, supporting the hypothesis that the complete genetic repertoire of this group of bacteria is still uncovered. Thirteen bacteriocin genes from Class II and III were predicted in the accessory genome. Four pediocin-like bacteriocins (54% of the detected bacteriocin repertoire) and their accompanying immunity genes are highlighted; penocin A, coagulin A, pediocin PA-1, and plantaricin 423. Additionally, in silico, modeling of the pediocin-like bacteriocins revealed different configurations of the helix motif compared to other physically determined pediocin-like structures. Comparative and phylogenomic analyses support the hypothesis that a dynamic mechanism of bacteriocin acquisition and purging is not dependent on the bacterial isolation source origin. Synteny analysis revealed that while coagulin A, pediocin PA-1, and Plantaricin 423 loci are associated with insertion sequences mainly from the IS30 family and are likely of plasmid origin, penocin A lies in a conserved chromosomal locus. The results presented here provide insights into the unique pediocin-like bacteriocin peptide fold, genomic diversity, and the evolution of the bacteriocin genetic repertoire of P. pentosaceus, shedding new insights into the role of these biomolecules for application in inhibiting bacterial pathogens, and suggesting that prospecting and sequencing new strains is still an alternative to mining for new probiotic compounds.
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Affiliation(s)
- Iago Rodrigues Blanco
- Department of Biochemical and Pharmaceutical Technology, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Lucas José Luduverio Pizauro
- Department of Agricultural and Environmental Biotechnology, School of Agricultural and Veterinary Sciences (FCAV), UNESP, Jaboticabal, Brazil
| | - João Victor dos Anjos Almeida
- Department of Agricultural and Environmental Biotechnology, School of Agricultural and Veterinary Sciences (FCAV), UNESP, Jaboticabal, Brazil
| | - Carlos Miguel Nóbrega Mendonça
- Department of Biochemical and Pharmaceutical Technology, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Alessandro de Mello Varani
- Department of Agricultural and Environmental Biotechnology, School of Agricultural and Veterinary Sciences (FCAV), UNESP, Jaboticabal, Brazil
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14
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Draft Genome Sequence of Pediococcus pentosaceus Strain PP16CC, Isolated from Oyster Crassostrea corteziensis. Microbiol Resour Announc 2022; 11:e0039522. [PMID: 36098530 PMCID: PMC9584201 DOI: 10.1128/mra.00395-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pediococcus pentosaceus strain PP16CC comes from the intestine of Crassostrea corteziensis. A 1.82-Mbp draft genome of this strain was assembled using A5-miseq from illumina reads, resulting in 4 contigs and 1,856 predicted protein coding genes. Additionally, 23 proteins belonging to various glycosyl hydrolase families and 6 prophage regions were identified.
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15
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Surachat K, Kantachote D, Wonglapsuwan M, Chukamnerd A, Deachamag P, Mittraparp-arthorn P, Jeenkeawpiam K. Complete Genome Sequence of Weissella cibaria NH9449 and Comprehensive Comparative-Genomic Analysis: Genomic Diversity and Versatility Trait Revealed. Front Microbiol 2022; 13:826683. [PMID: 35663880 PMCID: PMC9161744 DOI: 10.3389/fmicb.2022.826683] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 04/12/2022] [Indexed: 11/13/2022] Open
Abstract
Lactic acid bacteria (LAB) in the genus Weissella spp. contain traits in their genome that confer versatility. In particular, Weissella cibaria encodes several beneficial genes that are useful in biotechnological applications. The complete genome of W. cibaria NH9449 was sequenced and an in silico comparative analysis was performed to gain insight into the genomic diversity among members of the genus Weissella. A total of 219 Weissella genomes were used in a bioinformatics analysis of pan-genomes, phylogenetics, self-defense mechanisms, virulence factors, antimicrobial resistance, and carbohydrate-active enzymes. These investigations showed that the strain NH9449 encodes several restriction-modification-related genes and a CRISPR-Cas region in its genome. The identification of carbohydrate-active enzyme-encoding genes indicated that this strain could be beneficial in biotechnological applications. The comparative genomic analysis reveals the very high genomic diversity in this genus, and some marked differences in genetic variation and genes among Weissella species. The calculated average amino acid identity (AAI) and phylogenetic analysis of core and accessory genes shows the possible existence of three new species in this genus. These new genomic insights into Weissella species and their biological functions could be useful in the food industry and other applications.
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Affiliation(s)
- Komwit Surachat
- Division of Computational Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
- Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
- *Correspondence: Komwit Surachat,
| | - Duangporn Kantachote
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Monwadee Wonglapsuwan
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Arnon Chukamnerd
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
| | - Panchalika Deachamag
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Pimonsri Mittraparp-arthorn
- Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Kongpop Jeenkeawpiam
- Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
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Ranaivo H, Thirion F, Béra-Maillet C, Guilly S, Simon C, Sothier M, Van Den Berghe L, Feugier-Favier N, Lambert-Porcheron S, Dussous I, Roger L, Roume H, Galleron N, Pons N, Le Chatelier E, Ehrlich SD, Laville M, Doré J, Nazare JA. Increasing the diversity of dietary fibers in a daily-consumed bread modifies gut microbiota and metabolic profile in subjects at cardiometabolic risk. Gut Microbes 2022; 14:2044722. [PMID: 35311446 PMCID: PMC8942430 DOI: 10.1080/19490976.2022.2044722] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Some cardiometabolic risk factors such as dyslipidemia and insulin resistance are known to be associated with low gut microbiota richness. A link between gut microbiota richness and the diversity of consumed dietary fibers (DF) has also been reported. We introduced a larger diversity of consumed DF by using a daily consumed bread in subjects at cardiometabolic risk and assessed the impacts on the composition and functions of gut microbiota as well as on cardiometabolic profile. Thirty-nine subjects at cardiometabolic risk were included in a double-blind, randomized, cross-over, twice 8-week study, and consumed daily 150 g of standard bread or enriched with a 7-dietary fiber mixture (5.55 g and 16.05 g of fibers, respectively). Before and after intervention, stool samples were collected for gut microbiota analysis from species determination down to gene-level abundance using shotgun metagenomics, and cardiometabolic profile was assessed. Multi-fiber bread consumption significantly decreased Bacteroides vulgatus, whereas it increased Parabacteroides distasonis, Fusicatenibacter saccharivorans, an unclassified Acutalibacteraceae and an unclassified Eisenbergiella (q < 0.1). The fraction of gut microbiota carrying the gene coding for five families/subfamilies of glycoside hydrolases (CAZymes) were also increased and negatively correlated with peaks and total/incremental area under curve (tAUC/iAUC) of postprandial glycemia and insulinemia. Compared to control bread, multi-fiber bread decreased total cholesterol (-0.42 mM; q < 0.01), LDL cholesterol (-0.36 mM; q < 0.01), insulin (-2.77 mIU/l; q < 0.05), and HOMA (-0.78; q < 0.05). In conclusion, increasing the diversity of DF in a daily consumed product modifies gut microbiota composition and function and could be a relevant nutritional tool to improve cardiometabolic profile.
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Affiliation(s)
- Harimalala Ranaivo
- Univ-Lyon, CarMeN Laboratory, Inserm, Inrae, Université Claude Bernard Lyon-1, Oullins, France,Centre de Recherche En Nutrition Humaine Rhône-Alpes, Univ-Lyon, CarMeN Laboratory, Université Claude Bernard Lyon1, Hospices Civils de Lyon, Cens, Fcrin/force Network, Pierre-Bénite, France
| | | | - Christel Béra-Maillet
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Susie Guilly
- Université Paris-Saclay, INRAE, MGP, Jouy-en-Josas, France
| | - Chantal Simon
- Univ-Lyon, CarMeN Laboratory, Inserm, Inrae, Université Claude Bernard Lyon-1, Oullins, France,Centre de Recherche En Nutrition Humaine Rhône-Alpes, Univ-Lyon, CarMeN Laboratory, Université Claude Bernard Lyon1, Hospices Civils de Lyon, Cens, Fcrin/force Network, Pierre-Bénite, France
| | - Monique Sothier
- Univ-Lyon, CarMeN Laboratory, Inserm, Inrae, Université Claude Bernard Lyon-1, Oullins, France,Centre de Recherche En Nutrition Humaine Rhône-Alpes, Univ-Lyon, CarMeN Laboratory, Université Claude Bernard Lyon1, Hospices Civils de Lyon, Cens, Fcrin/force Network, Pierre-Bénite, France
| | - Laurie Van Den Berghe
- Univ-Lyon, CarMeN Laboratory, Inserm, Inrae, Université Claude Bernard Lyon-1, Oullins, France,Centre de Recherche En Nutrition Humaine Rhône-Alpes, Univ-Lyon, CarMeN Laboratory, Université Claude Bernard Lyon1, Hospices Civils de Lyon, Cens, Fcrin/force Network, Pierre-Bénite, France
| | - Nathalie Feugier-Favier
- Univ-Lyon, CarMeN Laboratory, Inserm, Inrae, Université Claude Bernard Lyon-1, Oullins, France,Centre de Recherche En Nutrition Humaine Rhône-Alpes, Univ-Lyon, CarMeN Laboratory, Université Claude Bernard Lyon1, Hospices Civils de Lyon, Cens, Fcrin/force Network, Pierre-Bénite, France
| | - Stéphanie Lambert-Porcheron
- Univ-Lyon, CarMeN Laboratory, Inserm, Inrae, Université Claude Bernard Lyon-1, Oullins, France,Centre de Recherche En Nutrition Humaine Rhône-Alpes, Univ-Lyon, CarMeN Laboratory, Université Claude Bernard Lyon1, Hospices Civils de Lyon, Cens, Fcrin/force Network, Pierre-Bénite, France
| | | | | | - Hugo Roume
- Université Paris-Saclay, INRAE, MGP, Jouy-en-Josas, France
| | | | - Nicolas Pons
- Université Paris-Saclay, INRAE, MGP, Jouy-en-Josas, France
| | | | - Stanislav Dusko Ehrlich
- Univ-Lyon, CarMeN Laboratory, Inserm, Inrae, Université Claude Bernard Lyon-1, Oullins, France,Centre de Recherche En Nutrition Humaine Rhône-Alpes, Univ-Lyon, CarMeN Laboratory, Université Claude Bernard Lyon1, Hospices Civils de Lyon, Cens, Fcrin/force Network, Pierre-Bénite, France
| | - Martine Laville
- Univ-Lyon, CarMeN Laboratory, Inserm, Inrae, Université Claude Bernard Lyon-1, Oullins, France,Centre de Recherche En Nutrition Humaine Rhône-Alpes, Univ-Lyon, CarMeN Laboratory, Université Claude Bernard Lyon1, Hospices Civils de Lyon, Cens, Fcrin/force Network, Pierre-Bénite, France
| | - Joël Doré
- Université Paris-Saclay, INRAE, MGP, Jouy-en-Josas, France,Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Julie-Anne Nazare
- Univ-Lyon, CarMeN Laboratory, Inserm, Inrae, Université Claude Bernard Lyon-1, Oullins, France,Centre de Recherche En Nutrition Humaine Rhône-Alpes, Univ-Lyon, CarMeN Laboratory, Université Claude Bernard Lyon1, Hospices Civils de Lyon, Cens, Fcrin/force Network, Pierre-Bénite, France,CONTACT Julie-Anne Nazare CRNH Rhône-Alpes (Centre de recherche en Nutrition Humaine) Centre Hospitalier Lyon Sud – Secteur 2 Bâtiment 2D - CENS ELI 165 chemin du grand Revoyet 69310 – Pierre Bénite France
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Okoye CO, Dong K, Wang Y, Gao L, Li X, Wu Y, Jiang J. Comparative genomics reveals the organic acid biosynthesis metabolic pathways among five lactic acid bacterial species isolated from fermented vegetables. N Biotechnol 2022; 70:73-83. [PMID: 35525431 DOI: 10.1016/j.nbt.2022.05.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 02/28/2022] [Accepted: 05/02/2022] [Indexed: 10/18/2022]
Abstract
Lactic acid bacteria (LAB) comprise a widespread bacterial group, inhabiting the niches of fermented vegetables and capable of producing beneficial organic acids. In the present study, several bioinformatics approaches were used to perform whole-genome sequencing and comparative genomics of five LAB species, Lactobacillus plantarum PC1-1, Pediococcus pentosaceus PC2-1(F2), Weissella hellenica PC1A, Lactobacillus buchneri PC-C1, and Enterococcus sp. YC2-6, to enhance understanding of their different genetic functionalities and organic acid biosynthesis. The results revealed major carbohydrate-active enzymes, putative operons and unique mobile genetic elements, including plasmids, resistance genes, insertion sequences and composite transposons involved in organic acid biosynthesis. The metabolic pathways of organic acid biosynthesis emphasize the key genes encoding specific enzymes required for organic acid metabolism. The five genomes were found to contain various regions of secondary metabolite biosynthetic gene clusters, including the type III polyketide synthases (T3PKS) enriched with unique genes encoding a hydroxymethylglutaryl-CoA synthase, capable of exhibiting specific antimicrobial activity with biopreservative potential, and a cyclic AMP receptor protein (CPR) transcription factor acting as a glucose sensor in organic acid biosynthesis. This could enable the organisms to prevail in the fermentation process, suggesting potential industrial applications.
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Affiliation(s)
- Charles Obinwanne Okoye
- Biofuels Institute, Jiangsu University, Zhenjiang 212013, China; School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, China; Department of Zoology & Environmental Biology, University of Nigeria, Nsukka 410001, Nigeria
| | - Ke Dong
- Biofuels Institute, Jiangsu University, Zhenjiang 212013, China; School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Yongli Wang
- Biofuels Institute, Jiangsu University, Zhenjiang 212013, China; School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Lu Gao
- Biofuels Institute, Jiangsu University, Zhenjiang 212013, China; School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Xia Li
- Biofuels Institute, Jiangsu University, Zhenjiang 212013, China; School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Yanfang Wu
- Biofuels Institute, Jiangsu University, Zhenjiang 212013, China; School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Jianxiong Jiang
- Biofuels Institute, Jiangsu University, Zhenjiang 212013, China; School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, China.
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18
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Queiroz LL, Hoffmann C, Lacorte GA, de Melo Franco BDG, Todorov SD. Genomic and functional characterization of bacteriocinogenic lactic acid bacteria isolated from Boza, a traditional cereal-based beverage. Sci Rep 2022; 12:1460. [PMID: 35087086 PMCID: PMC8795150 DOI: 10.1038/s41598-022-05086-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 12/31/2021] [Indexed: 11/17/2022] Open
Abstract
Boza is a traditional low-alcohol fermented beverage from the Balkan Peninsula, frequently explored as a functional food product. The product is rich in Lactic Acid Bacteria (LAB) and some of them can produce bacteriocins. In this study, a sample of Boza from Belogratchik, Bulgaria, was analyzed for the presence of bacteriocinogenic LAB, and after analyses by RAPD-PCR, three representative isolates were characterized by genomic analyses, using whole genome sequencing. Isolates identified as Pediococcus pentosaceus ST75BZ and Pediococcus pentosaceus ST87BZ contained operons encoding for bacteriocins pediocin PA-1 and penocin A, while isolate identified as Pediococcus acidilactici ST31BZ contained only the operon for pediocin PA-1 and a CRISPR/Cas system for protection against bacteriophage infection. The antimicrobial activity of bacteriocins produced by the three isolates was inhibited by treatment of the cell-free supernatants with proteolytic enzymes. The produced bacteriocins inhibited the growth of Listeria monocytogenes, Enterococcus spp. and some Lactobacillus spp., among other tested species. The levels of bacteriocin production varied from 3200 to 12,800 AU/ml recorded against L. monocytogenes 104, 637 and 711, measured at 24 h of incubation at 37 °C. All bacteriocins remained active after incubation at pH 2.0-10.0. The activity mode of the studied bacteriocins was bactericidal, as determined against L. monocytogenes 104, 637 and 711. In addition, bactericidal activity was demonstrated using a cell leakage β-galactosidase assay, indicating a pore formation mechanism as a mode of action. The present study highlights the importance of combining genomic analyses and traditional microbiological approaches as way of characterizing microbial interactions in fermented foods.
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Affiliation(s)
- Luciano Lopes Queiroz
- Microbiology Graduate Program, Department of Microbiology, Institute of Biomedical Science, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Christian Hoffmann
- Faculdade de Ciências Farmacêuticas, Food Research Center (FoRC), Universidade de São Paulo, São Paulo, SP, Brazil.
| | - Gustavo Augusto Lacorte
- Faculdade de Ciências Farmacêuticas, Food Research Center (FoRC), Universidade de São Paulo, São Paulo, SP, Brazil
- Instituto Federal de Minas Gerais, Bambuí, MG, Brazil
| | | | - Svetoslav Dimitrov Todorov
- Laboratório de Microbiologia de Alimentos, Departamento de Alimentos e Nutrição Experimental, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, SP, Brazil.
- ProBacLab, Department of Advanced Convergence, Handong Global University, Pohang, Gyeongbuk, 37554, Republic of Korea.
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19
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Liu X, Mao B, Gu J, Wu J, Cui S, Wang G, Zhao J, Zhang H, Chen W. Blautia-a new functional genus with potential probiotic properties? Gut Microbes 2022; 13:1-21. [PMID: 33525961 PMCID: PMC7872077 DOI: 10.1080/19490976.2021.1875796] [Citation(s) in RCA: 598] [Impact Index Per Article: 299.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Blautia is a genus of anaerobic bacteria with probiotic characteristics that occur widely in the feces and intestines of mammals. Based on phenotypic and phylogenetic analyses, some species in the genera Clostridium and Ruminococcus have been reclassified as Blautia, so to date, there are 20 new species with valid published names in this genus. An extensive body of research has recently focused on the probiotic effects of this genus, such as biological transformation and its ability to regulate host health and alleviate metabolic syndrome. This article reviews the origin and biological characteristics of Blautia and the factors that affect its abundance and discusses its role in host health, thus laying a theoretical foundation for the development of new functional microorganisms with probiotic properties.
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Affiliation(s)
- Xuemei Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Bingyong Mao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China,CONTACT Bingyong Mao
| | - Jiayu Gu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Jiaying Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Shumao Cui
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China,Shumao Cui School of Food Science and Technology, Jiangnan University, Lihu Avenue 1800, Wuxi214122, China
| | - Gang Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu, China,Beijing Innovation Center of Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing, China
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20
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Oliveira FS, da Silva Rodrigues R, de Carvalho AF, Nero LA. Genomic Analyses of Pediococcus pentosaceus ST65ACC, a Bacteriocinogenic Strain Isolated from Artisanal Raw-Milk Cheese. Probiotics Antimicrob Proteins 2022; 15:630-645. [PMID: 34984631 DOI: 10.1007/s12602-021-09894-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2021] [Indexed: 12/12/2022]
Abstract
Pediococcus pentosaceus ST65ACC was obtained from a Brazilian artisanal cheese (BAC) and characterized as bacteriocinogenic. This strain presented beneficial properties in previous studies, indicating its potential as a probiotic candidate. In this study, we aimed to carry out a genetic characterization based on whole-genome sequencing (WGS), including taxonomy, biotechnological properties, bacteriocin clusters and safety-related genes. WGS was performed using the Illumina MiSeq platform and the genome was annotated with the Prokaryotic Genome Annotation (Prokka). P. pentosaceus ST65ACC taxonomy was investigated and bacteriocin genes clusters were identified by BAGEL4, metabolic pathways were analyzed by Kyoto Encyclopedia of Genes and Genomes (KEGG) and safety-related genes were checked. P. pentosaceus ST65ACC had a total draft genome size of 1,933,194 bp with a GC content of 37.00%, and encoded 1950 protein coding sequences (CDSs), 6 rRNA, 55 tRNA, 1 tmRNA and no plasmids were detected. The analysis revealed absence of a CRISPR/Cas system, bacteriocin gene clusters for pediocin PA-1/AcH and penocin-A were identified. Genes related to beneficial properties, such as stress adaptation genes and adhesion genes, were identified. Furthermore, genes related to biogenic amines and virulence-related genes were not detected. Genes related to antibiotic resistance were identified, but not in prophage regions. Based on the obtained results, the beneficial potential of P. pentosaceus ST65ACC was confirmed, allowing its characterization as a potential probiotic candidate.
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Affiliation(s)
- Francielly Soares Oliveira
- InsPOA - Laboratório de Inspeção de Produtos de Origem Animal, Departamento de Veterinária, Universidade Federal de Viçosa, Viçosa, MG, 36570 900, Brazil.,Inovaleite - Laboratório de Pesquisa Em Leite E Derivados, Departamento de Tecnologia de Alimentos, Universidade Federal de Viçosa, Viçosa, MG, 36570 900, Brazil
| | - Rafaela da Silva Rodrigues
- InsPOA - Laboratório de Inspeção de Produtos de Origem Animal, Departamento de Veterinária, Universidade Federal de Viçosa, Viçosa, MG, 36570 900, Brazil.,Inovaleite - Laboratório de Pesquisa Em Leite E Derivados, Departamento de Tecnologia de Alimentos, Universidade Federal de Viçosa, Viçosa, MG, 36570 900, Brazil
| | - Antônio Fernandes de Carvalho
- Inovaleite - Laboratório de Pesquisa Em Leite E Derivados, Departamento de Tecnologia de Alimentos, Universidade Federal de Viçosa, Viçosa, MG, 36570 900, Brazil
| | - Luís Augusto Nero
- InsPOA - Laboratório de Inspeção de Produtos de Origem Animal, Departamento de Veterinária, Universidade Federal de Viçosa, Viçosa, MG, 36570 900, Brazil.
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21
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Qi Y, Huang L, Zeng Y, Li W, Zhou D, Xie J, Xie J, Tu Q, Deng D, Yin J. Pediococcus pentosaceus: Screening and Application as Probiotics in Food Processing. Front Microbiol 2021; 12:762467. [PMID: 34975787 PMCID: PMC8716948 DOI: 10.3389/fmicb.2021.762467] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 11/17/2021] [Indexed: 11/13/2022] Open
Abstract
Lactic acid bacteria (LAB) are vital probiotics in the food processing industry, which are widely spread in food additives and products, such as meat, milk, and vegetables. Pediococcus pentosaceus (P. pentosaceus), as a kind of LAB, has numerous probiotic effects, mainly including antioxidant, cholesterol-lowering, and immune effects. Recently, the applications in the probiotic- fermentation products have attracted progressively more attentions. However, it is necessary to screen P. pentosaceus with abundant functions from diverse sources due to the limitation about the source and species of P. pentosaceus. This review summarized the screening methods of P. pentosaceus and the exploration methods of probiotic functions in combination with the case study. The screening methods included primary screening and rescreening including gastric acidity resistance, bile resistance, adhesion, antibacterial effects, etc. The application and development prospects of P. pentosaceus were described in detail, and the shortcomings in the practical application of P. pentosaceus were evaluated to make better application of P. pentosaceus in the future.
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Affiliation(s)
- Yining Qi
- Key Laboratory of Protein Chemistry and Developmental Biology of Fish of Ministry of Education, Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Hunan Normal University, Changsha, China
| | - Le Huang
- Key Laboratory of Protein Chemistry and Developmental Biology of Fish of Ministry of Education, Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Hunan Normal University, Changsha, China
| | - Yan Zeng
- Key Laboratory of Protein Chemistry and Developmental Biology of Fish of Ministry of Education, Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Hunan Normal University, Changsha, China
| | - Wen Li
- Key Laboratory of Protein Chemistry and Developmental Biology of Fish of Ministry of Education, Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Hunan Normal University, Changsha, China
| | - Diao Zhou
- Key Laboratory of Protein Chemistry and Developmental Biology of Fish of Ministry of Education, Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Hunan Normal University, Changsha, China
| | | | - Junyan Xie
- CAS Key Laboratory of Agro-ecological Processes in Subtropical Region, Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Qiang Tu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- *Correspondence: Qiang Tu,
| | - Dun Deng
- Tangrenshen Group Co., Ltd., Zhuzhou, China
- Dun Deng,
| | - Jia Yin
- Key Laboratory of Protein Chemistry and Developmental Biology of Fish of Ministry of Education, Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Hunan Normal University, Changsha, China
- Jia Yin,
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22
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Zou W, Ye G, Liu C, Zhang K, Li H, Yang J. Comparative genome analysis of Clostridium beijerinckii strains isolated from pit mud of Chinese strong flavor baijiu ecosystem. G3 (BETHESDA, MD.) 2021; 11:6364901. [PMID: 34542586 PMCID: PMC8527462 DOI: 10.1093/g3journal/jkab317] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 08/26/2021] [Indexed: 12/24/2022]
Abstract
Clostridium beijerinckii is a well-known anaerobic solventogenic bacterium which inhabits a wide range of different niches. Previously, we isolated five butyrate-producing C. beijerinckii strains from pit mud (PM) of strong-flavor baijiu (SFB) ecosystems. Genome annotation of the five strains showed that they could assimilate various carbon sources as well as ammonium to produce acetate, butyrate, lactate, hydrogen, and esters but did not produce the undesirable flavors isopropanol and acetone, making them useful for further exploration in SFB production. Our analysis of the genomes of an additional 233 C. beijerinckii strains revealed an open pangenome based on current sampling and will likely change with additional genomes. The core genome, accessory genome, and strain-specific genes comprised 1567, 8851, and 2154 genes, respectively. A total of 298 genes were found only in the five C. beijerinckii strains from PM, among which only 77 genes were assigned to Clusters of Orthologous Genes categories. In addition, 15 transposase and 12 phage integrase families were found in all five C. beijerinckii strains from PM. Between 18 and 21 genome islands were predicted for the five C. beijerinckii genomes. The existence of a large number of mobile genetic elements indicated that the genomes of the five C. beijerinckii strains evolved with the loss or insertion of DNA fragments in the PM of SFB ecosystems. This study presents a genomic framework of C. beijerinckii strains from PM that could be used for genetic diversification studies and further exploration of these strains.
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Affiliation(s)
- Wei Zou
- College of Bioengineering, Sichuan University of Science & Engineering, Yibin, Sichuan 644005, China
| | - Guangbin Ye
- College of Bioengineering, Sichuan University of Science & Engineering, Yibin, Sichuan 644005, China
| | - Chaojie Liu
- College of Bioengineering, Sichuan University of Science & Engineering, Yibin, Sichuan 644005, China
| | - Kaizheng Zhang
- College of Bioengineering, Sichuan University of Science & Engineering, Yibin, Sichuan 644005, China
| | - Hehe Li
- Beijing Key Laboratory of Flavor Chemistry, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Jiangang Yang
- College of Bioengineering, Sichuan University of Science & Engineering, Yibin, Sichuan 644005, China
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23
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Kuniyoshi TM, Mendonça CMN, Vieira VB, Robl D, de Melo Franco BDG, Todorov SD, Tomé E, O'Connor PM, Converti A, Araújo WL, Vasconcellos LPSP, Varani ADM, Cotter PD, Rabelo SC, Oliveira RPDS. Pediocin PA-1 production by Pediococcus pentosaceus ET34 using non-detoxified hemicellulose hydrolysate obtained from hydrothermal pretreatment of sugarcane bagasse. BIORESOURCE TECHNOLOGY 2021; 338:125565. [PMID: 34315131 DOI: 10.1016/j.biortech.2021.125565] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 07/09/2021] [Accepted: 07/10/2021] [Indexed: 06/13/2023]
Abstract
Listeria monocytogenes is one of the foodborne pathogens of most concern for food safety. To limit its presence in foods, bacteriocins have been proposed as natural bio-preservatives. Herein, a bacteriocin was produced on hemicellulose hydrolysate of sugarcane bagasse by Pediococcus pentosaceous ET34, whose genome sequencing revealed an operon with 100% similarity to that of pediocin PA-1. ET34 grown on hydrolysate-containing medium led to an increase in the expression of PA-1 genes and a non-optimized purification step sequence resulted in a yield of 0.8 mg·L-1 of pure pediocin (purity > 95%). Culture conditions were optimized according to a central composite design using temperature and hydrolysate % as independent variables and validated in 3-L Erlenmeyers. Finally, a process for scaled-up implementation by sugar-ethanol industry was proposed, considering green chemistry and biorefinery concepts. This work stands up as an approach addressing a future proper sugarcane bagasse valorisation for pediocin production.
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Affiliation(s)
- Taís Mayumi Kuniyoshi
- Department of Biochemical and Pharmaceutical Technology, School of Pharmaceutical Sciences, University of São Paulo, 05508-000 São Paulo, Brazil
| | - Carlos Miguel Nóbrega Mendonça
- Department of Biochemical and Pharmaceutical Technology, School of Pharmaceutical Sciences, University of São Paulo, 05508-000 São Paulo, Brazil
| | - Viviane Borges Vieira
- Department of Biochemical and Pharmaceutical Technology, School of Pharmaceutical Sciences, University of São Paulo, 05508-000 São Paulo, Brazil
| | - Diogo Robl
- Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina (UFSC), 88040-900, Florianópolis, Santa Catarina, Brazil
| | - Bernadette Dora Gombossy de Melo Franco
- FoRC (Food Research Center), Food and Experimental Nutrition Department, School of Pharmaceutical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | - Svetoslav Dimitrov Todorov
- Food and Experimental Nutrition Department, School of Pharmaceutical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; ProBacLab, Advanced Convergence, Handong Global University, Pohang, Gyeongbuk 37554, South Korea
| | - Elisabetta Tomé
- Instituto de Ciencias y Tecnología de Alimentos. Escuela de Biología. Universidad Central de Venezuela, Apartado 47.097 - Caracas 1041 A, Venezuela
| | - Paula Mary O'Connor
- Food Bioscience Department Teagasc Food Research Centre, Moorepark, Fermoy, Cork, T12 YN60 Ireland; APC Microbiome Ireland, University College Cork, T12YT20, Cork, Ireland
| | - Attilio Converti
- Department of Civil, Chemical and Environmental Engineering, Genoa University, I-16145 Genoa, Italy
| | - Welington Luiz Araújo
- Microbiology Department - Biomedical Sciences Institute, University of São Paulo, São Paulo 05508-900, Brazil
| | | | - Alessandro de Mello Varani
- Department of Technology, School of Agricultural and Veterinary Sciences, Faculdade de Ciências Agrarias e Veterinária, São Paulo State University, Jaboticabal, SP 14884000, Brazil
| | - Paul David Cotter
- Food Bioscience Department Teagasc Food Research Centre, Moorepark, Fermoy, Cork, T12 YN60 Ireland; APC Microbiome Ireland, University College Cork, T12YT20, Cork, Ireland; School of Microbiology, University College Cork, T12YT20, Cork, Ireland
| | - Sarita Cândida Rabelo
- Department of Bioprocess and Biotechnology, College of Agricultural Sciences, São Paulo State University, 18610-034, São Paulo, Brazil
| | - Ricardo Pinheiro de Souza Oliveira
- Department of Biochemical and Pharmaceutical Technology, School of Pharmaceutical Sciences, University of São Paulo, 05508-000 São Paulo, Brazil.
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24
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Wanna W, Surachat K, Kaitimonchai P, Phongdara A. Evaluation of probiotic characteristics and whole genome analysis of Pediococcus pentosaceus MR001 for use as probiotic bacteria in shrimp aquaculture. Sci Rep 2021; 11:18334. [PMID: 34526534 PMCID: PMC8443617 DOI: 10.1038/s41598-021-96780-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 08/12/2021] [Indexed: 02/08/2023] Open
Abstract
The development of non-antibiotic and environmentally friendly agents is a key consideration for health management in shrimp aquaculture. In this study, the probiotic potential in shrimp aquaculture of Pediococcus pentosaceus MR001, isolated from Macrobrachium rosenbergii, was investigated by means of feeding trial and genetic characterization. In the feeding trial, dietary supplementation with P. pentosaceus MR001 significantly increased weight gain and digestive enzyme activity (p < 0.05) in shrimp, Litopenaeus vannamei. The intestinal histology showed that shrimp given the probiotic diet had healthier guts than the control group. Also, the immune gene expression and the survival rate in the treatment group were significantly increased when compared with the control group. The genetic characteristics of P. pentosaceus strain MR001 were explored by performing whole-genome sequencing (WGS) using the HiSeq 2500 platform and PacBio system, revealing the complete circular genome of 1,804,896 bp. We also identified 1789 coding genes and subsequently characterized genes related to the biosynthesis of bacteriocins, stress resistance, and bile tolerance. Our findings suggest that insights in the functional and genetic characteristics of P. pentosaceus strain MR001 could provide opportunities for applications of such strain in shrimp diet supplementation.
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Affiliation(s)
- Warapond Wanna
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand.
- Center for Genomics and Bioinformatics Research, Faculty of Science, Prince of Songkla University, Songkhla, 90110, Thailand.
| | - Komwit Surachat
- Division of Computational Science, Faculty of Science, Prince of Songkla University, Songkhla, 90110, Thailand
- Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Hat Yai, 90110, Songkhla, Thailand
| | - Panmile Kaitimonchai
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Amornrat Phongdara
- Center for Genomics and Bioinformatics Research, Faculty of Science, Prince of Songkla University, Songkhla, 90110, Thailand
- Faculty of Medical Technology, Prince of Songkla University, Songkhla, 90110, Thailand
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25
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Su X, Guo Y, Fang T, Jiang X, Wang D, Li D, Bai P, Zhang B, Wang J, Liu C. Effects of Simulated Microgravity on the Physiology of Stenotrophomonas maltophilia and Multiomic Analysis. Front Microbiol 2021; 12:701265. [PMID: 34512577 PMCID: PMC8429793 DOI: 10.3389/fmicb.2021.701265] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/29/2021] [Indexed: 11/13/2022] Open
Abstract
Many studies have shown that the space environment plays a pivotal role in changing the characteristics of conditional pathogens, especially their pathogenicity and virulence. However, Stenotrophomonas maltophilia, a type of conditional pathogen that has shown to a gradual increase in clinical morbidity in recent years, has rarely been reported for its impact in space. In this study, S. maltophilia was exposed to a simulated microgravity (SMG) environment in high-aspect ratio rotating-wall vessel bioreactors for 14days, while the control group was exposed to the same bioreactors in a normal gravity (NG) environment. Then, combined phenotypic, genomic, transcriptomic, and proteomic analyses were conducted to compare the influence of the SMG and NG on S. maltophilia. The results showed that S. maltophilia in simulated microgravity displayed an increased growth rate, enhanced biofilm formation ability, increased swimming motility, and metabolic alterations compared with those of S. maltophilia in normal gravity and the original strain of S. maltophilia. Clusters of Orthologous Groups (COG) annotation analysis indicated that the increased growth rate might be related to the upregulation of differentially expressed genes (DEGs) involved in energy metabolism and conversion, secondary metabolite biosynthesis, transport and catabolism, intracellular trafficking, secretion, and vesicular transport. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses showed that the increased motility might be associated the upregulation of differentially expressed proteins (DEPs) involved in locomotion, localization, biological adhesion, and binding, in accordance with the upregulated DEGs in cell motility according to COG classification, including pilP, pilM, flgE, flgG, and ronN. Additionally, the increased biofilm formation ability might be associated with the upregulation of DEPs involved in biofilm formation, the bacterial secretion system, biological adhesion, and cell adhesion, which were shown to be regulated by the differentially expressed genes (chpB, chpC, rpoN, pilA, pilG, pilH, and pilJ) through the integration of transcriptomic and proteomic analyses. These results suggested that simulated microgravity might increase the level of corresponding functional proteins by upregulating related genes to alter physiological characteristics and modulate growth rate, motility, biofilm formation, and metabolism. In conclusion, this study is the first general analysis of the phenotypic, genomic, transcriptomic, and proteomic changes in S. maltophilia under simulated microgravity and provides some suggestions for future studies of space microbiology.
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Affiliation(s)
- Xiaolei Su
- Medical School of Chinese PLA, Beijing, China.,Department of Respiratory and Critical Care Medicine, The Second Medical Center and National Clinical Research Center for Geriatric Disease, Chinese PLA General Hospital, Beijing, China
| | - Yinghua Guo
- Medical School of Chinese PLA, Beijing, China.,College of Pulmonary and Critical Care Medicine, The Eighth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Tingzheng Fang
- Medical School of Chinese PLA, Beijing, China.,Department of Respiratory and Critical Care Medicine, The Second Medical Center and National Clinical Research Center for Geriatric Disease, Chinese PLA General Hospital, Beijing, China
| | - Xuege Jiang
- Department of Respiratory and Critical Care Medicine, The Second Medical Center and National Clinical Research Center for Geriatric Disease, Chinese PLA General Hospital, Beijing, China
| | - Dapeng Wang
- Medical School of Chinese PLA, Beijing, China.,Department of Respiratory and Critical Care Medicine, The Second Medical Center and National Clinical Research Center for Geriatric Disease, Chinese PLA General Hospital, Beijing, China
| | - Diangeng Li
- Department of Academic Research, Beijing Chaoyang Hospital Affiliated to Capital Medical University, Beijing, China
| | - Po Bai
- Respiratory Diseases Department, PLA Rocket Force Characteristic Medical Center, Beijing, China
| | - Bin Zhang
- Department of Respiratory and Critical Care Medicine, Binzhou Medical University Hospital, Binzhou, China
| | - Junfeng Wang
- Department of Respiratory and Critical Care Medicine, The Second Medical Center and National Clinical Research Center for Geriatric Disease, Chinese PLA General Hospital, Beijing, China
| | - Changting Liu
- Department of Respiratory and Critical Care Medicine, The Second Medical Center and National Clinical Research Center for Geriatric Disease, Chinese PLA General Hospital, Beijing, China
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26
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Comparative Genomics Analyses Reveal the Differences between B. longum subsp. infantis and B. longum subsp. longum in Carbohydrate Utilisation, CRISPR-Cas Systems and Bacteriocin Operons. Microorganisms 2021; 9:microorganisms9081713. [PMID: 34442792 PMCID: PMC8399906 DOI: 10.3390/microorganisms9081713] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/08/2021] [Accepted: 08/09/2021] [Indexed: 11/24/2022] Open
Abstract
Bifidobacterium longum is one of the most widely distributed and abundant Bifidobacterium in the human intestine, and has been proven to have a variety of physiological functions. In this study, 80 strains of B. longum isolated from human subjects were classified into subspecies by ANI and phylogenetic analyses, and the functional genes were compared. The results showed that there were significant differences in carbohydrate metabolism between the two subspecies, which determined their preference for human milk oligosaccharides or plant-derived carbohydrates. The predicted exopolysaccharide (EPS) gene clusters had large variability within species but without difference at the subspecies level. Four subtype CRISPR-Cas systems presented in B. longum, while the subtypes I-U and II-C only existed in B. longum subsp. longum. The bacteriocin operons in B. longum subsp. infantis were more widely distributed compared with B. longum subsp. longum. In conclusion, this study revealed the similarities and differences between B. longum subsp. infantis and B. longum subsp. longum, which could provide a theoretical basis for further exploring the probiotic characteristics of B. longum.
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27
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Integrated Phenotypic-Genotypic Analysis of Latilactobacillus sakei from Different Niches. Foods 2021; 10:foods10081717. [PMID: 34441495 PMCID: PMC8393274 DOI: 10.3390/foods10081717] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 11/16/2022] Open
Abstract
Increasing attention has been paid to the potential probiotic effects of Latilactobacillus sakei. To explore the genetic diversity of L. sakei, 14 strains isolated from different niches (feces, fermented kimchi, and meat products) and 54 published strains were compared and analyzed. The results showed that the average genome size and GC content of L. sakei were 1.98 Mb and 41.22%, respectively. Its core genome mainly encodes translation and transcription, amino acid synthesis, glucose metabolism, and defense functions. L. sakei has open pan-genomic characteristics, and its pan-gene curve shows an upward trend. The genetic diversity of L. sakei is mainly reflected in carbohydrate utilization, antibiotic tolerance, and immune/competition-related factors, such as clustering regular interval short palindromic repeat sequence (CRISPR)-Cas. The CRISPR system is mainly IIA type, and a few are IIC types. This work provides a basis for the study of this species.
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28
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Li Z, Song Q, Wang M, Ren J, Liu S, Zhao S. Comparative genomics analysis of Pediococcus acidilactici species. J Microbiol 2021; 59:573-583. [PMID: 33990913 DOI: 10.1007/s12275-021-0618-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 02/05/2021] [Accepted: 02/23/2021] [Indexed: 01/24/2023]
Abstract
Pediococcus acidilactici is a reliable bacteriocin producer and a promising probiotic species with wide application in the food and health industry. However, the underlying genetic features of this species have not been analyzed. In this study, we performed a comprehensive comparative genomic analysis of 41 P. acidilactici strains from various ecological niches. The bacteriocin production of 41 strains were predicted and three kinds of bacteriocin encoding genes were identified in 11 P. acidilactici strains, namely pediocin PA-1, enterolysin A, and colicin-B. Moreover, whole-genome analysis showed a high genetic diversity within the population, mainly related to a large proportion of variable genomes, mobile elements, and hypothetical genes obtained through horizontal gene transfer. In addition, comparative genomics also facilitated the genetic explanation of the adaptation for host environment, which specify the protection mechanism against the invasion of foreign DNA (i.e. CRISPR/Cas locus), as well as carbohydrate fermentation. The 41 strains of P. acidilactici can metabolize a variety of carbon sources, which enhances the adaptability of this species and survival in different environments. This study evaluated the antibacterial ability, genome evolution, and ecological flexibility of P. acidilactici from the perspective of genetics and provides strong supporting evidence for its industrial development and application.
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Affiliation(s)
- Zhenzhen Li
- BGI College, Zhengzhou University, Zhengzhou, 450052, China
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, China
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, 518120, China
| | - Qi Song
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, 518120, China
- Key Laboratory of Genomics, Ministry of Agriculture, BGI-Shenzhen, Shenzhen, 518120, China
| | - Mingming Wang
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, 518120, China
| | - Junli Ren
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, 518120, China
| | - Songling Liu
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, 518120, China
- Key Laboratory of Genomics, Ministry of Agriculture, BGI-Shenzhen, Shenzhen, 518120, China
| | - Shancen Zhao
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, 518120, China.
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29
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Diversity and technological characterization of Pediococcus pentosaceus strains isolated from Nigerian traditional fermented foods. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2020.110697] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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30
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Cui S, Jiang J, Li B, Ross RP, Stanton C, Zhao J, Zhang H, Yang B, Chen W. Effects of the short-term administration of Pediococcus pentosaceus on physiological characteristics, inflammation, and intestinal microecology in mice. Food Funct 2021; 12:1695-1707. [PMID: 33502422 DOI: 10.1039/d0fo02948c] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The role of Pediococcus pentosaceus in the gastrointestinne has received considerable attention in recent decades. This study aimed to investigate the effects of the short-term administration of P. pentosaceus on physiological characteristics, inflammation, and intestinal microecology in mice. In this study, 90 male C57BL/6J mice were divided into 15 groups, with 14 groups treated with a daily intragastric administration of different genotypes of P. pentosaceus. After three weeks of intragastric administration P. pentosaceus had a mild effect on mice. It could be seen that different P. pentosaceus strains had different effects on the gut microbiota and intestinal microecology. P. pentosaceus VCQYC5144M12 possessing an Enterolysin A operon may have been harmful, activating the expression of inflammatory factors, while P. pentosaceus DYNDL69M8 consisting of only a pediocin-like operon increased the abundance of beneficial bacteria and increased the content of acetic acid. The presence of various genotypes of bacteriocin may have been the explanation for variations among strains. This may provide theoretical support for further exploring the probiotic effect and patterns of P. pentosaceus.
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Affiliation(s)
- Shumao Cui
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China and School of Food Science and Technology, Jiangnan University, Wuxi, China.
| | - Jie Jiang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China and School of Food Science and Technology, Jiangnan University, Wuxi, China.
| | - Bowen Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China and School of Food Science and Technology, Jiangnan University, Wuxi, China.
| | - R Paul Ross
- International Joint Research Laboratory for Pharmabiotics & Antibiotic Resistance, Jiangnan University, Wuxi, China and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Catherine Stanton
- International Joint Research Laboratory for Pharmabiotics & Antibiotic Resistance, Jiangnan University, Wuxi, China and Teagasc Food Research Centre, Moorepark, Co. Cork, Ireland
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China and School of Food Science and Technology, Jiangnan University, Wuxi, China. and National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China and School of Food Science and Technology, Jiangnan University, Wuxi, China. and National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China and Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, China
| | - Bo Yang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China and School of Food Science and Technology, Jiangnan University, Wuxi, China. and International Joint Research Laboratory for Pharmabiotics & Antibiotic Resistance, Jiangnan University, Wuxi, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China and School of Food Science and Technology, Jiangnan University, Wuxi, China. and National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China
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31
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Jiang S, Cai L, Lv L, Li L. Pediococcus pentosaceus, a future additive or probiotic candidate. Microb Cell Fact 2021; 20:45. [PMID: 33593360 PMCID: PMC7885583 DOI: 10.1186/s12934-021-01537-y] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 02/04/2021] [Indexed: 12/12/2022] Open
Abstract
Background Pediococcus pentosaceus, a promising strain of lactic acid bacteria (LAB), is gradually attracting attention, leading to a rapid increase in experimental research. Due to increased demand for practical applications of microbes, the functional and harmless P. pentosaceus might be a worthwhile LAB strain for both the food industry and biological applications. Results As an additive, P. pentosaceus improves the taste and nutrition of food, as well as the storage of animal products. Moreover, the antimicrobial abilities of Pediococcus strains are being highlighted. Evidence suggests that bacteriocins or bacteriocin-like substances (BLISs) produced by P. pentosaceus play effective antibacterial roles in the microbial ecosystem. In addition, various strains of P. pentosaceus have been highlighted for probiotic use due to their anti-inflammation, anticancer, antioxidant, detoxification, and lipid-lowering abilities. Conclusions Therefore, it is necessary to continue studying P. pentosaceus for further use. Thorough study of several P. pentosaceus strains should clarify the benefits and drawbacks in the future.
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Affiliation(s)
- Shiman Jiang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Lingzhi Cai
- The Infectious Diseases Department, The First People's Hospital of Wenling, The Affiliated Wenling Hospital of Wenzhou Medical University, Taizhou, China
| | - Longxian Lv
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.
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32
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Han D, Shi R, Yan Q, Shi Y, Ma J, Jiang Z. Global transcriptomic analysis of functional oligosaccharide metabolism in Pediococcus pentosaceus. Appl Microbiol Biotechnol 2021; 105:1601-1614. [PMID: 33511444 DOI: 10.1007/s00253-021-11120-5] [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: 09/28/2020] [Revised: 12/31/2020] [Accepted: 01/16/2021] [Indexed: 11/27/2022]
Abstract
Lactic acid bacteria (LAB) are important in food fermentation and may enhance overall host health. Previous studies to explore LAB metabolism mainly focused on the genera Lacticaseibacillus and Lactococcus. Pediococcus pentosaceus, historically recognized as an important food fermentation bacterial strain, can produce bacteriocins and occasionally demonstrated probiotic functionalities. This study thoroughly surveyed the growth kinetic of three P. pentosaceus isolates in various culture formulations, especially in fructooligosaccharide (FOS), xylooligosaccharide (XOS), or konjac mannooligosaccharide (KMOS) conditions. Results showed that P. pentosaceus effectively metabolized KMOS, the culture of which led to 23.6-fold population increase. However, FOS and XOS were less metabolized by P. pentosaceus. On functional oligosaccharide cultures, P. pentosaceus could result in higher population proliferation, more acidified fermentation environment, and higher glycoside hydrolysis activities in the culture. RNA-Seq analysis classified 1572 out of 1708 putative genes as mRNA-coding genes. The dataset also revealed that the three functional oligosaccharides led to extensive global functional gene regulations. Phosphate conservation and utilization efficiency enhancement may serve as a leading transcriptional regulation direction in functional oligosaccharide metabolisms. In summary, these discovered metabolic characteristics could be employed to support future studies. KEY POINTS: • Konjac mannooligosaccharides effectively promoted P. pentosaceus proliferation. • Functional genes were highly regulated in functional oligosaccharide utilization. • Phosphate conservation was an important transcriptional regulation direction.
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Affiliation(s)
- Dong Han
- Key Laboratory of Food Bioengineering (China National Light Industry), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Ran Shi
- Key Laboratory of Food Bioengineering (China National Light Industry), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Qiaojuan Yan
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Engineering, China Agricultural University, Beijing, China
| | - Yuqin Shi
- Key Laboratory of Food Bioengineering (China National Light Industry), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Junwen Ma
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Engineering, China Agricultural University, Beijing, China
| | - Zhengqiang Jiang
- Key Laboratory of Food Bioengineering (China National Light Industry), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China.
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33
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Surachat K, Kantachote D, Deachamag P, Wonglapsuwan M. Genomic Insight into Pediococcus acidilactici HN9, a Potential Probiotic Strain Isolated from the Traditional Thai-Style Fermented Beef Nhang. Microorganisms 2020; 9:microorganisms9010050. [PMID: 33375492 PMCID: PMC7823806 DOI: 10.3390/microorganisms9010050] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/17/2020] [Accepted: 12/24/2020] [Indexed: 12/31/2022] Open
Abstract
Pediococcus acidilactici HN9 is a beneficial lactic acid bacterium isolated from Nhang, a traditional Thai-style fermented beef. In this study, the molecular properties of P. acidilactici HN9 were characterized to provide insights into its potential probiotic activity. Specifically, this work sought to report the complete genome of P. acidilactici HN9 and perform a comparative genome analysis with other bacterial strains belonging to the genus Pediococcus. Genomic features of HN9 were compared with those of all other bacterial Pediococcus strains to examine the adaptation, evolutionary relationships, and diversity within this genus. Additionally, several bioinformatic approaches were used to investigate phylogenetic relationships, genome stability, virulence factors, bacteriocin production, and antimicrobial resistance genes of the HN9 strain, as well as to ensure its safety as a potential starter culture in food applications. A 2,034,522 bp circular chromosome and two circular plasmids, designated pHN9-1 (42,239-bp) and pHN9-2 (30,711-bp), were detected, and used for pan-genome analysis, as well as for identification of bacteriocin-encoding genes in 129 strains belonging to all Pediococcus species. Two CRISPR regions were identified in P. acidilactici HN9, including type II-A CRISPR/CRISPR-associated (Cas). This study provides an in-depth analysis on P. acidilactici HN9, facilitating a better understanding of its adaptability to different environments and its mechanism to maintain genome stability over time.
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Affiliation(s)
- Komwit Surachat
- Division of Computational Science, Faculty of Science, Prince of Songkla University, Hatyai, Songkhla 90110, Thailand
- Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Hatyai, Songkhla 90110, Thailand
- Correspondence:
| | - Duangporn Kantachote
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hatyai, Songkhla 90110, Thailand; (D.K.); (P.D.); (M.W.)
| | - Panchalika Deachamag
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hatyai, Songkhla 90110, Thailand; (D.K.); (P.D.); (M.W.)
| | - Monwadee Wonglapsuwan
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hatyai, Songkhla 90110, Thailand; (D.K.); (P.D.); (M.W.)
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