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Isaac SL, Abdul Malek AZ, Hazif NS, Roslan FS, Mohd Hashim A, Song AAL, Abdul Rahim R, Wan Nur Ismah WAK. Genome mining of Lactiplantibacillus plantarum PA21: insights into its antimicrobial potential. BMC Genomics 2024; 25:571. [PMID: 38844835 PMCID: PMC11157852 DOI: 10.1186/s12864-024-10451-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 05/24/2024] [Indexed: 06/09/2024] Open
Abstract
BACKGROUND The dramatic increase of antimicrobial resistance in the healthcare realm has become inexorably linked to the abuse of antibiotics over the years. Therefore, this study seeks to identify potential postbiotic metabolites derived from lactic acid bacteria such as Lactiplantibacillus plantarum that could exhibit antimicrobial properties against multi-drug resistant pathogens. RESULTS In the present work, the genome sequence of Lactiplantibacillus plantarum PA21 consisting of three contigs was assembled to a size of 3,218,706 bp. Phylogenomic analysis and average nucleotide identity (ANI) revealed L. plantarum PA21 is closely related to genomes isolated from diverse niches such as dairy products, food, and animals. Genome mining through the BAGEL4 and antiSMASH database revealed four bacteriocins in a single cluster and four regions of biosynthetic gene clusters responsible for the production of bioactive compounds. The potential probiotic genes indirectly responsible for postbiotic metabolites production were also identified. Additionally, in vitro studies showed that the L. plantarum PA21 cell-free supernatant exhibited antimicrobial activity against all nine methicillin-resistant Staphylococcus aureus (MRSA) and three out of 13 Klebsiella pneumoniae clinical isolates tested. CONCLUSION Results in this study demonstrates that L. plantarum PA21 postbiotic metabolites is a prolific source of antimicrobials against multi-drug resistant pathogens with potential antimicrobial properties.
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Affiliation(s)
- Sharleen Livina Isaac
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), Serdang, 43400, Selangor, Malaysia
| | - Ahmad Zuhairi Abdul Malek
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), Serdang, 43400, Selangor, Malaysia
- Halal Products Research Institute, Universiti Putra Malaysia (UPM), Serdang, 43400, Selangor, Malaysia
| | - Nurul Syafika Hazif
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), Serdang, 43400, Selangor, Malaysia
| | - Farah Syahrain Roslan
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), Serdang, 43400, Selangor, Malaysia
| | - Amalia Mohd Hashim
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), Serdang, 43400, Selangor, Malaysia
- Halal Products Research Institute, Universiti Putra Malaysia (UPM), Serdang, 43400, Selangor, Malaysia
| | - Adelene Ai-Lian Song
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), Serdang, 43400, Selangor, Malaysia
| | - Raha Abdul Rahim
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), Serdang, 43400, Selangor, Malaysia
- National Institutes of Biotechnology Malaysia (NIBM), Serdang, 43400, Selangor, Malaysia
| | - Wan Ahmad Kamil Wan Nur Ismah
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), Serdang, 43400, Selangor, Malaysia.
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Prema P, Ali D, Nguyen VH, Pradeep BV, Veeramanikandan V, Daglia M, Arciola CR, Balaji P. A Response Surface Methodological Approach for Large-Scale Production of Antibacterials from Lactiplantibacillus plantarum with Potential Utility against Foodborne and Orthopedic Infections. Antibiotics (Basel) 2024; 13:437. [PMID: 38786166 PMCID: PMC11118495 DOI: 10.3390/antibiotics13050437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 05/06/2024] [Accepted: 05/09/2024] [Indexed: 05/25/2024] Open
Abstract
A variety of bacteria, including beneficial probiotic lactobacilli, produce antibacterials to kill competing bacteria. Lactobacilli secrete antimicrobial peptides (AMPs) called bacteriocins and organic acids. In the food industry, bacteriocins, but even whole cell-free supernatants, are becoming more and more important as bio-preservatives, while, in orthopedics, bacteriocins are introducing new perspectives in biomaterials technologies for anti-infective surfaces. Studies are focusing on Lactiplantibacillus plantarum (previously known as Lactobacillus plantarum). L. plantarum exhibits great phenotypic versatility, which enhances the chances for its industrial exploitation. Importantly, more than other lactobacilli, it relies on AMPs for its antibacterial activity. In this study, Response Surface Methodology (RSM) through a Box-Behnken experimental design was used to estimate the optimal conditions for the production of antibacterials by L. plantarum. A temperature of 35 °C, pH 6.5, and an incubation time of 48 h provided the highest concentration of antibacterials. The initial pH was the main factor influencing the production of antibacterials, at 95% confidence level. Thanks to RSM, the titer of antibacterials increased more than 10-fold, this result being markedly higher than those obtained in the very few studies that have so far used similar statistical methodologies. The Box-Behnken design turned out to be a valid model to satisfactorily plan a large-scale production of antibacterials from L. plantarum.
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Affiliation(s)
- Paulpandian Prema
- Department of Zoology, VHN Senthikumar Nadar College, Virudhunagar 626001, TN, India;
| | - Daoud Ali
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia;
| | - Van-Huy Nguyen
- Centre for Herbal Pharmacology and Environmental Sustainability, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam 603103, TN, India;
| | - Bhathini Vaikuntavasan Pradeep
- Centre for Microbial Technology, Department of Microbiology, Karpagam Academy of Higher Education, Coimbatore 641021, TN, India; (B.V.P.); (V.V.)
| | - Veeramani Veeramanikandan
- Centre for Microbial Technology, Department of Microbiology, Karpagam Academy of Higher Education, Coimbatore 641021, TN, India; (B.V.P.); (V.V.)
| | - Maria Daglia
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy;
- International Research Center for Food Nutrition and Safety, Jiangsu University, Zhenjiang 212013, China
| | - Carla Renata Arciola
- Laboratory of Immunorheumatology and Tissue Regeneration, Laboratory of Pathology of Implant Infections, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano 1/10, 40136 Bologna, Italy
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Via San Giacomo 14, 40126 Bologna, Italy
| | - Paulraj Balaji
- PG and Research Centre in Biotechnology, MGR College, Hosur 635130, TN, India
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3
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Montecillo JAV. Comparative genomics of the genus Halioglobus reveals the genetic basis for the reclassification of Halioglobus pacificus as Parahalioglobus pacificus gen. nov. comb. nov. Int Microbiol 2024:10.1007/s10123-024-00516-8. [PMID: 38558270 DOI: 10.1007/s10123-024-00516-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/13/2024] [Accepted: 03/22/2024] [Indexed: 04/04/2024]
Abstract
The genus Halioglobus is one of the environmentally relevant members of the family Halieaceae, class Gammaproteobacteria. At present, the genus is composed of three validly published species. However, in the recent study of the family Halieaceae, the species Halioglobus pacificus was observed to branch outside of the main clade formed by the members of Halioglobus, suggesting its distinct taxonomic placement within the family. In the present study, the taxonomic placement of H. pacificus was reassessed using comparative genomics. Phylogenomic analysis revealed the paraphyletic relationship of H. pacificus with the type species of the genus Halioglobus, and further demonstrated its genus-level placement. This phylogenetic relationship was reinforced by the average nucleotide and amino acid identity values shared by H. pacificus with the members of the family Halieaceae. Moreover, the results of the pan-genome analysis, together with the phenotype data, further supported the exclusion of H. pacificus from the genus Halioglobus. Based on these findings, the species H. pacificus is thereby assigned to a new genus Parahalioglobus gen. nov. as Parahalioglobus pacificus comb. nov.
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Affiliation(s)
- Jake Adolf V Montecillo
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk, 38541, Republic of Korea.
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4
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Sato K, Ikagawa Y, Niwa R, Nishioka H, Horie M, Iwahashi H. Genome Sequencing Unveils Nomadic Traits of Lactiplantibacillus plantarum in Japanese Post-Fermented Tea. Curr Microbiol 2023; 81:52. [PMID: 38155273 DOI: 10.1007/s00284-023-03566-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 11/17/2023] [Indexed: 12/30/2023]
Abstract
Post-fermented tea production involving microbial fermentation is limited to a few regions, such as Southeast Asia and Japan, with Japan's Shikoku island being particularly prominent. Lactiplantibacillus plantarum was the dominant species found in tea leaves after anaerobic fermentation of Awa-bancha in Miyoshi City, Tokushima, and Ishizuchi-kurocha in Ehime. Although the draft genome of L. plantarum from Japanese post-fermented tea has been previously reported, its genetic diversity requires further exploration. In this study, whole-genome sequencing was conducted on four L. plantarum strains isolated from Japanese post-fermented tea using nanopore sequencing. These isolates were then compared with other sources to examine their genetic diversity revealing that L. plantarum isolated from Japanese post-fermented tea contained several highly variable gene regions associated with sugar metabolism and transportation. However, no source-specific genes or clusters were identified within accessory or core gene regions. This study indicates that L. plantarum possesses high genetic diversity and that the unique environment of Japanese post-fermented tea does not appear to exert selective pressure on L. plantarum growth.
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Affiliation(s)
- Kyoka Sato
- Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, Gifu University, Gifu, 501-1193, Japan.
| | - Yuichiro Ikagawa
- Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, Gifu University, Gifu, 501-1193, Japan
| | - Ryo Niwa
- Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan
| | - Hiroki Nishioka
- Food and Biotechnology Division, Tokushima Prefectural Industrial Technology Center, Tokushima, 770-8021, Japan
| | - Masanori Horie
- Health and Medical Research Institute (HMRI), National Institute of Advanced Industrial Science and Technology (AIST), Kagawa, 761-0395, Japan
| | - Hitoshi Iwahashi
- Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, Gifu University, Gifu, 501-1193, Japan.
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5
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Dias RS, Kremer FS, da Costa de Avila LF. In silico prospection of Lactobacillus acidophilus strains with potential probiotic activity. Braz J Microbiol 2023; 54:2733-2743. [PMID: 37801223 PMCID: PMC10689588 DOI: 10.1007/s42770-023-01139-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 09/26/2023] [Indexed: 10/07/2023] Open
Abstract
Lactic acid bacteria (LAB) are fermentative microorganisms and perform different roles in biotechnological processes, mainly in the food and pharmaceutical industries. Among the LAB, Lactobacillus acidophilus is a species that deserves to be highlighted for being used both in prophylaxis and in the treatment of pathologies. Most of the metabolites produced by this species are linked to the inhibition of pathogens. In this study, we utilized a pangenomic and metabolic annotation analysis using Roary and BlastKOALA, ML-based probiotic activity prediction with iProbiotic and whole-genome similarity using ANI to identify strains of L. acidophilus with potential probiotic activity. According to the results in BlastKOALA and iProbiotics, L. acidophilus NCTC 13721 had the greatest potential among the 64 strains tested, both in terms of its ability to be a Lactobacillus spp. probiotic, when in the amount of genes involved in the metabolism of organic acids and quorum sensing. In addition, DSM 20079 proved to be promising for prospecting new probiotic Lactobacillus from BlastKOALA analyses, as they presented similar results in the number of genes involved in the production of lactic acid, acetic acid, hydrogen peroxide, except for quorum sensing where the NCTC 13721 strain had 14 more genes. L. acidophilus NCTC 13721 and L. acidophilus La-5 strains showed greater ability to be Lactobacillus spp. probiotic capacity, showing 84.8% and 51.9% capacity in the iProbiotics tool, respectively. When analyzed in ANI, none of the evaluated strains showed genomic similarity with NCTC 13721. In contrast, the DSM 20079 strain showed genomic similarity with all evaluated strains except NCTC 13721. Furthermore, eight strains with characteristics with approximately 100% genomic similarity to La-5 were listed: S20_1, LA-5, FSI4, APC2845, LA-G80-111, DS1_1A, LA1, and BCRC 14065. Therefore, according to the findings in iProbiotics and BlastKoala, among the 64 strains evaluated, NCTC 13721 is the most promising strain to be used for future in vitro studies.
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Affiliation(s)
- Rafaella Sinnott Dias
- Post-Graduate Program in Health Sciences, Universidade Federal do Rio Grande - FURG, Faculty of Medicine, Academic Area of the University Hospital, Rio Grande, RS, Brazil.
| | - Frederico Schmitt Kremer
- Bioinformatics Laboratory, Technological Development Center, Federal University of Pelotas, Capão do Leão, Rio Grande do Sul, Brazil
| | - Luciana Farias da Costa de Avila
- Post-Graduate Program in Health Sciences, Universidade Federal do Rio Grande - FURG, Faculty of Medicine, Academic Area of the University Hospital, Rio Grande, RS, Brazil
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6
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Aziz G, Zaidi A, Sullivan DJO'. Insights from metagenome-assembled genomes on the genetic stability and safety of over-the-counter probiotic products. Curr Genet 2023; 69:213-234. [PMID: 37237157 DOI: 10.1007/s00294-023-01271-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 04/04/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023]
Abstract
The demand for and acceptance of probiotics is determined by their quality and safety. Illumina NGS sequencing and analytics were used to examine eight marketed probiotics. Up to the species level, sequenced DNA was taxonomically identified, and relative abundances were determined using Kaiju. The genomes were constructed using GTDB and validated through PATRICK and TYGS. A FastTree 2 phylogenetic tree was constructed using several type strain sequences from relevant species. Bacteriocin and ribosomally synthesized polypeptide (RiPP) genes were discovered, and a safety check was performed to test for toxins, antibiotic resistance, and genetic drift genes. Except for two products with unclaimed species, the labeling was taxonomically correct. In three product formulations, Lactobacillus acidophilus, Limosilactobacillus reuteri, Lacticaseibacillus paracasei, and Bifidobacterium animalis exhibited two to three genomic alterations, while Streptococcus equinus was found in one. TYGS and GDTB discovered E. faecium and L. paracasei in distinctly different ways. All the bacteria tested had the genetic repertoire to tolerate GIT transit, although some exhibited antibiotic resistance, and one strain had two virulence genes. Except for Bifidobacterium strains, the others revealed a variety of bacteriocins and ribosomally synthesized polypeptides (RiPP), 92% of which were unique and non-homologous to known ones. Plasmids and mobile genetic elements are present in strains of L. reuteri (NPLps01.et_L.r and NPLps02.uf_L.r), Lactobacillus delbrueckii (NPLps01.et_L.d), Streptococcus thermophilus (NPLps06.ab_S.t), and E. faecium (NPLps07.nf_E.f). Our findings support the use of metagenomics to build better and efficient production and post-production practices for probiotic quality and safety assessment.
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Affiliation(s)
- Ghazal Aziz
- National Probiotic Laboratory, National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Punjab, 38000, Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, 45650, Islamabad (ICT), Pakistan
- Department of Food Science and Nutrition, Center for Microbial and Plant Genomics, University of Minnesota, 1500 Gortner Ave, St. Paul, MN, 55108, USA
| | - Arsalan Zaidi
- National Probiotic Laboratory, National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Punjab, 38000, Faisalabad, Pakistan.
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, 45650, Islamabad (ICT), Pakistan.
| | - Daniel J O ' Sullivan
- Department of Food Science and Nutrition, Center for Microbial and Plant Genomics, University of Minnesota, 1500 Gortner Ave, St. Paul, MN, 55108, USA
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7
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Raza S, Koh Y, Yoon SS, Woo SY, Ahn KS, Kim HL, Kim HN. Identification of novel Carnobacterium maltaromaticum strains in bone marrow samples of patients with acute myeloid leukemia using a metagenomic binning approach. Int Microbiol 2023; 26:1033-1040. [PMID: 37087535 DOI: 10.1007/s10123-023-00360-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 04/12/2023] [Accepted: 04/15/2023] [Indexed: 04/24/2023]
Abstract
The aim of this study aimed to examine the existence of a bacterial metagenome in the bone marrow of patients with acute myeloid leukemia (AML). We re-examined whole-genome sequencing data from the bone marrow samples of seven patients with AML, four of whom were remitted after treatment, for metagenomic analysis. After the removal of human reads, unmapped reads were used to profile the species-level composition. We used the metagenomic binning approach to confirm whether the identified taxon was a complete genome of known or novel strains. We observed a unique and novel microbial signature in which Carnobacterium maltaromaticum was the most abundant species in five patients with AML or remission. The complete genome of C. maltaromaticum "BMAML_KR01," which was observed in all samples, was 100% complete with 8.5% contamination and closely clustered with C. maltaromaticum strains DSM20730 and SF668 based on single nucleotide polymorphism variations. We identified five unique proteins that could contribute to cancer progression and 104 virulent factor proteins in the BMAML_KR01 genome. To our knowledge, this is the first report of a new strain of C. maltaromaticum in patients with AML. The presence of C. maltaromaticum and its new strain in patients indicates an urgent need to validate the existence of this bacterium and evaluate its pathophysiological role.
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Affiliation(s)
- Shahbaz Raza
- Department of Clinical Research Design and Evaluation, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul, Republic of Korea
| | - Youngil Koh
- Cancer Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
- Department of Internal Medicine, Seoul National University, College of Medicine, Seoul, Republic of Korea
| | - Sung-Soo Yoon
- Cancer Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
- Department of Internal Medicine, Seoul National University, College of Medicine, Seoul, Republic of Korea
| | - So-Youn Woo
- Department of Microbiology, Ewha Medical Research Institute, School of Medicine, Ewha Woman University, Seoul, Republic of Korea
| | - Kwang-Sung Ahn
- Functional Genome Institute, PDXen Biosystems Inc., Daejeon, Republic of Korea
| | - Hyung-Lae Kim
- Functional Genome Institute, PDXen Biosystems Inc., Daejeon, Republic of Korea
- Department of Biochemistry, College of Medicine, Ewha Womans University, Seoul, Republic of Korea
| | - Han-Na Kim
- Department of Clinical Research Design and Evaluation, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul, Republic of Korea.
- Biomedical Statistics Center, Research Institute for Future Medicine, Samsung Medical Center, Seoul, Republic of Korea.
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8
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Abramov VM, Kosarev IV, Machulin AV, Deryusheva EI, Priputnevich TV, Panin AN, Chikileva IO, Abashina TN, Manoyan AM, Ahmetzyanova AA, Ivanova OE, Papazyan TT, Nikonov IN, Suzina NE, Melnikov VG, Khlebnikov VS, Sakulin VK, Samoilenko VA, Gordeev AB, Sukhikh GT, Uversky VN. Ligilactobacillus salivarius 7247 Strain: Probiotic Properties and Anti- Salmonella Effect with Prebiotics. Antibiotics (Basel) 2023; 12:1535. [PMID: 37887236 PMCID: PMC10604316 DOI: 10.3390/antibiotics12101535] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 09/28/2023] [Accepted: 10/02/2023] [Indexed: 10/28/2023] Open
Abstract
The Ligilactobacillus salivarius 7247 (LS7247) strain, originally isolated from a healthy woman's intestines and reproductive system, has been studied for its probiotic potential, particularly against Salmonella Enteritidis (SE) and Salmonella Typhimurium (ST) as well as its potential use in synbiotics. LS7247 showed high tolerance to gastric and intestinal stress and effectively adhered to human and animal enterocyte monolayers, essential for realizing its probiotic properties. LS7247 showed high anti-Salmonella activity. Additionally, the cell-free culture supernatant (CFS) of LS7247 exhibited anti-Salmonella activity, with a partial reduction upon neutralization with NaOH (p < 0.05), suggesting the presence of anti-Salmonella factors such as lactic acid (LA) and bacteriocins. LS7247 produced a high concentration of LA, reaching 124.0 ± 2.5 mM after 48 h of cultivation. Unique gene clusters in the genome of LS7247 contribute to the production of Enterolysin A and metalloendopeptidase. Notably, LS7247 carries a plasmid with a gene cluster identical to human intestinal strain L. salivarius UCC118, responsible for class IIb bacteriocin synthesis, and a gene cluster identical to porcine strain L. salivarius P1ACE3, responsible for nisin S synthesis. Co-cultivation of LS7247 with SE and ST pathogens reduced their viability by 1.0-1.5 log, attributed to cell wall damage and ATP leakage caused by the CFS. For the first time, the CFS of LS7247 has been shown to inhibit adhesion of SE and ST to human and animal enterocytes (p < 0.01). The combination of Actigen prebiotic and the CFS of LS7247 demonstrated a significant combined effect in inhibiting the adhesion of SE and ST to human and animal enterocytes (p < 0.001). These findings highlight the potential of using the LS7247 as a preventive strategy and employing probiotics and synbiotics to combat the prevalence of salmonellosis in animals and humans caused by multidrug resistant (MDR) strains of SE and ST pathogens.
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Affiliation(s)
- Vyacheslav M. Abramov
- Federal Service for Veterinary and Phytosanitary Surveillance (Rosselkhoznadzor) Federal State Budgetary Institution “The Russian State Center for Animal Feed and Drug Standardization and Quality” (FGBU VGNKI), 123022 Moscow, Russia; (I.V.K.)
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Health, 117997 Moscow, Russia
| | - Igor V. Kosarev
- Federal Service for Veterinary and Phytosanitary Surveillance (Rosselkhoznadzor) Federal State Budgetary Institution “The Russian State Center for Animal Feed and Drug Standardization and Quality” (FGBU VGNKI), 123022 Moscow, Russia; (I.V.K.)
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Health, 117997 Moscow, Russia
| | - Andrey V. Machulin
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Science”, Russian Academy of Science, 142290 Pushchino, Russia
| | - Evgenia I. Deryusheva
- Institute for Biological Instrumentation, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Science”, Russian Academy of Science, 142290 Pushchino, Russia
| | - Tatiana V. Priputnevich
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Health, 117997 Moscow, Russia
| | - Alexander N. Panin
- Federal Service for Veterinary and Phytosanitary Surveillance (Rosselkhoznadzor) Federal State Budgetary Institution “The Russian State Center for Animal Feed and Drug Standardization and Quality” (FGBU VGNKI), 123022 Moscow, Russia; (I.V.K.)
| | - Irina O. Chikileva
- Laboratory of Cell Immunity, Blokhin National Research Center of Oncology, Ministry of Health RF, 115478 Moscow, Russia;
| | - Tatiana N. Abashina
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Science”, Russian Academy of Science, 142290 Pushchino, Russia
| | - Ashot M. Manoyan
- Federal Service for Veterinary and Phytosanitary Surveillance (Rosselkhoznadzor) Federal State Budgetary Institution “The Russian State Center for Animal Feed and Drug Standardization and Quality” (FGBU VGNKI), 123022 Moscow, Russia; (I.V.K.)
| | - Anna A. Ahmetzyanova
- Federal Service for Veterinary and Phytosanitary Surveillance (Rosselkhoznadzor) Federal State Budgetary Institution “The Russian State Center for Animal Feed and Drug Standardization and Quality” (FGBU VGNKI), 123022 Moscow, Russia; (I.V.K.)
| | - Olga E. Ivanova
- Federal Service for Veterinary and Phytosanitary Surveillance (Rosselkhoznadzor) Federal State Budgetary Institution “The Russian State Center for Animal Feed and Drug Standardization and Quality” (FGBU VGNKI), 123022 Moscow, Russia; (I.V.K.)
| | | | - Ilia N. Nikonov
- Federal State Educational Institution of Higher Professional Education Moscow State Academy of Veterinary Medicine and Biotechnology Named after K.I. Skryabin, 109472 Moscow, Russia
| | - Nataliya E. Suzina
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Science”, Russian Academy of Science, 142290 Pushchino, Russia
| | - Vyacheslav G. Melnikov
- Gabrichevsky Research Institute for Epidemiology and Microbiology, 125212 Moscow, Russia
| | | | - Vadim K. Sakulin
- Institute of Immunological Engineering, 142380 Lyubuchany, Russia
| | - Vladimir A. Samoilenko
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Science”, Russian Academy of Science, 142290 Pushchino, Russia
| | - Alexey B. Gordeev
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Health, 117997 Moscow, Russia
| | - Gennady T. Sukhikh
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Health, 117997 Moscow, Russia
| | - Vladimir N. Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA;
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9
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Rajput A, Chauhan SM, Mohite OS, Hyun JC, Ardalani O, Jahn LJ, Sommer MO, Palsson BO. Pangenome analysis reveals the genetic basis for taxonomic classification of the Lactobacillaceae family. Food Microbiol 2023; 115:104334. [PMID: 37567624 DOI: 10.1016/j.fm.2023.104334] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 06/29/2023] [Accepted: 07/05/2023] [Indexed: 08/13/2023]
Abstract
Lactobacillaceae represent a large family of important microbes that are foundational to the food industry. Many genome sequences of Lactobacillaceae strains are now available, enabling us to conduct a comprehensive pangenome analysis of this family. We collected 3591 high-quality genomes from public sources and found that: 1) they contained enough genomes for 26 species to perform a pangenomic analysis, 2) the normalized Heap's coefficient λ (a measure of pangenome openness) was found to have an average value of 0.27 (ranging from 0.07 to 0.37), 3) the pangenome openness was correlated with the abundance and genomic location of transposons and mobilomes, 4) the pangenome for each species was divided into core, accessory, and rare genomes, that highlight the species-specific properties (such as motility and restriction-modification systems), 5) the pangenome of Lactiplantibacillus plantarum (which contained the highest number of genomes found amongst the 26 species studied) contained nine distinct phylogroups, and 6) genome mining revealed a richness of detected biosynthetic gene clusters, with functions ranging from antimicrobial and probiotic to food preservation, but ∼93% were of unknown function. This study provides the first in-depth comparative pangenomics analysis of the Lactobacillaceae family.
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Affiliation(s)
- Akanksha Rajput
- Department of Bioengineering, University of California, San Diego, La Jolla, USA
| | - Siddharth M Chauhan
- Department of Bioengineering, University of California, San Diego, La Jolla, USA
| | - Omkar S Mohite
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens, Lyngby, Denmark
| | - Jason C Hyun
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, USA
| | - Omid Ardalani
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens, Lyngby, Denmark
| | - Leonie J Jahn
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens, Lyngby, Denmark
| | - Morten Oa Sommer
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens, Lyngby, Denmark
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, USA; Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens, Lyngby, Denmark.
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10
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Mollova D, Gozmanova M, Apostolova E, Yahubyan G, Iliev I, Baev V. Illuminating the Genomic Landscape of Lactiplantibacillus plantarum PU3-A Novel Probiotic Strain Isolated from Human Breast Milk, Explored through Nanopore Sequencing. Microorganisms 2023; 11:2440. [PMID: 37894099 PMCID: PMC10609609 DOI: 10.3390/microorganisms11102440] [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: 08/17/2023] [Revised: 09/11/2023] [Accepted: 09/25/2023] [Indexed: 10/29/2023] Open
Abstract
Lactiplantibacillus plantarum stands out as a remarkably diverse species of lactic acid bacteria, occupying a myriad of ecological niches. Particularly noteworthy is its presence in human breast milk, which can serve as a reservoir of probiotic bacteria, contributing significantly to the establishment and constitution of infant gut microbiota. In light of this, our study attempted to conduct an initial investigation encompassing both genomic and phenotypic aspects of the L. plantarum PU3 strain, that holds potential as a probiotic agent. By employing the cutting-edge third-generation Nanopore sequencing technology, L. plantarum PU3 revealed a circular chromosome of 3,180,940 bp and nine plasmids of various lengths. The L. plantarum PU3 genome has a total of 2962 protein-coding and non-coding genes. Our in-depth investigations revealed more than 150 probiotic gene markers that unfold the genetic determinants for acid tolerance, bile resistance, adhesion, and oxidative and osmotic stress. The in vivo analysis showed the strain's proficiency in utilizing various carbohydrates as growth substrates, complementing the in silico analysis of the genes involved in metabolic pathways. Notably, the strain demonstrated a pronounced affinity for D-sorbitol, D-mannitol, and D-Gluconic acid, among other carbohydrate sources. The in vitro experimental verification of acid, osmotic and bile tolerance validated the robustness of the strain in challenging environments. Encouragingly, no virulence factors were detected in the genome of PU3, suggesting its safety profile. In search of beneficial properties, we found potential bacteriocin biosynthesis clusters, suggesting its capability for antimicrobial activity. The characteristics exhibited by L. plantarum PU3 pave the way for promising strain potential, warranting further investigations to unlock its full capacity and contributions to probiotic and therapeutic avenues.
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Affiliation(s)
- Daniela Mollova
- Faculty of Biology, Department of Biochemistry and Microbiology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria; (D.M.); (I.I.)
| | - Mariyana Gozmanova
- Faculty of Biology, Department of Plant Physiology and Molecular Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria; (M.G.); (E.A.); (G.Y.)
| | - Elena Apostolova
- Faculty of Biology, Department of Plant Physiology and Molecular Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria; (M.G.); (E.A.); (G.Y.)
| | - Galina Yahubyan
- Faculty of Biology, Department of Plant Physiology and Molecular Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria; (M.G.); (E.A.); (G.Y.)
| | - Ilia Iliev
- Faculty of Biology, Department of Biochemistry and Microbiology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria; (D.M.); (I.I.)
| | - Vesselin Baev
- Faculty of Biology, Department of Plant Physiology and Molecular Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria; (M.G.); (E.A.); (G.Y.)
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11
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Zhang G, Yang N, Liu Z, Chen X, Li M, Fu T, Zhang D, Zhao C. Genome-Assisted Probiotic Characterization and Application of Lactiplantibacillus plantarum 18 as a Candidate Probiotic for Laying Hen Production. Microorganisms 2023; 11:2373. [PMID: 37894031 PMCID: PMC10609342 DOI: 10.3390/microorganisms11102373] [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: 08/23/2023] [Revised: 09/19/2023] [Accepted: 09/19/2023] [Indexed: 10/29/2023] Open
Abstract
Probiotics gained significant attention for their potential to improve gut health and enhance productivity in animals, including poultry. This comprehensive study focused on the genetic analysis of Lactiplantibacillus plantarum 18 (LP18) to understand its survival and colonization characteristics in the gastrointestinal tract. LP18 was supplemented in the late-stage diet of laying hens to investigate its impact on growth performance, egg quality, and lipid metabolism. The complete genome sequence of LP18 was determined, consisting of 3,275,044 base pairs with a GC content of 44.42% and two circular plasmids. Genomic analysis revealed genes associated with adaptability, adhesion, and gastrointestinal safety. LP18 supplementation significantly improved the daily laying rate (p < 0.05) during the late-production phase and showed noteworthy advancements in egg quality, including egg shape index (p < 0.05), egg albumen height (p < 0.01), Haugh unit (p < 0.01), and eggshell strength (p < 0.05), with notable improvements in eggshell ultrastructure. Additionally, LP18 supplementation resulted in a significant reduction in serum lipid content, including LDL (p < 0.01), FFA (p < 0.05), and Gly (p < 0.05). These findings provide valuable insights into the genomic characteristics of LP18 and the genes that support its survival and colonization in the gastrointestinal tract. Importantly, this study highlights the potential of LP18 as a probiotic candidate to enhance productivity, optimize egg quality, and modulate lipid metabolism in poultry production.
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Affiliation(s)
| | | | | | | | | | | | | | - Cuiqing Zhao
- College of Animal Science and Technology, Jilin Agricultural Science and Technology University, Jilin 132101, China; (G.Z.)
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12
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Umanets A, Surono IS, Venema K. I am better than I look: genome based safety assessment of the probiotic Lactiplantibacillus plantarum IS-10506. BMC Genomics 2023; 24:518. [PMID: 37667166 PMCID: PMC10478331 DOI: 10.1186/s12864-023-09495-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 06/30/2023] [Indexed: 09/06/2023] Open
Abstract
BACKGROUND Safety of probiotic strains that are used in human and animal trials is a prerequisite. Genome based safety assessment of probiotics has gained popularity due its cost efficiency and speed, and even became a part of national regulation on foods containing probiotics in Indonesia. However, reliability of the safety assessment based only on a full genome sequence is not clear. Here, for the first time, we sequenced, assembled, and analysed the genome of the probiotic strain Lactiplantibacillus plantarum IS-10506, that was isolated from dadih, a traditional fermented buffalo milk. The strain has already been used as a probiotic for more than a decade, and in several clinical trials proven to be completely safe. METHODS The genome of the probiotic strain L. plantarum IS-10506 was sequenced using Nanopore sequencing technology, assembled, annotated and screened for potential harmful (PH) and beneficial genomic features. The presence of the PH features was assessed from general annotation, as well as with the use of specialised tools. In addition, PH regions in the genome were compared to all other probiotic and non-probiotic L. plantarum strains available in the NCBI RefSeq database. RESULTS For the first time, a high-quality complete genome of L. plantarum IS-10506 was obtained, and an extensive search for PH and a beneficial signature was performed. We discovered a number of PH features within the genome of L. plantarum IS-10506 based on the general annotation, including various antibiotic resistant genes (AMR); however, with a few exceptions, bioinformatics tools specifically developed for AMR detection did not confirm their presence. We further demonstrated the presence of the detected PH genes across multiple L. plantarum strains, including probiotics, and overall high genetic similarities between strains. CONCLUSION The genome of L. plantarum IS-10506 is predicted to have several PH features. However, the strain has been utilized as a probiotic for over a decade in several clinical trials without any adverse effects, even in immunocompromised children with HIV infection and undernourished children. This implies the presence of PH feature signatures within the probiotic genome does not necessarily indicate their manifestation during administration. Importantly, specialized tools for the search of PH features were found more robust and should be preferred over manual searches in a general annotation.
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Affiliation(s)
- Alexander Umanets
- Centre for Healthy Eating & Food Innovation (HEFI), Maastricht University - campus Venlo, Villafloraweg 1, Venlo, 5928 SZ, the Netherlands
- Chair Group Youth Food and Health, Faculty of Science and Engineering, Maastricht University - campus Venlo, Villafloraweg 1, Venlo, 5928 SZ, the Netherlands
| | - Ingrid S Surono
- Food Technology Department, Faculty of Engineering, Bina Nusantara University, Jakarta, 11480, Indonesia
| | - Koen Venema
- Centre for Healthy Eating & Food Innovation (HEFI), Maastricht University - campus Venlo, Villafloraweg 1, Venlo, 5928 SZ, the Netherlands.
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Bae WY, Lee YJ, Jung WH, Shin SL, Kim TR, Sohn M. Draft genome sequence and probiotic functional property analysis of Lactobacillus gasseri LM1065 for food industry applications. Sci Rep 2023; 13:12212. [PMID: 37500806 PMCID: PMC10374649 DOI: 10.1038/s41598-023-39454-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 07/25/2023] [Indexed: 07/29/2023] Open
Abstract
Probiotics are defined as live organisms in the host that contribute to health benefits. Lactobacillus gasseri LM1065, isolated from human breast milk, was investigated for its probiotic properties based on its genome. Draft genome map and de novo assembly were performed using the PacBio RS II system and hierarchical genome assembly process (HGAP). Probiotic properties were determined by the resistance to gastric conditions, adherence ability, enzyme production, safety assessment and mobile genetic elements. The fungistatic effect and inhibition of hyphae transition were studied using the cell-free supernatant (CFS). L. gasseri LM1065 showed high gastric pepsin tolerance and mild tolerance to bile salts. Auto-aggregation and hydrophobicity were measured to be 61.21% and 61.55%, respectively. The adherence to the human intestinal epithelial cells was measured to be 2.02%. Antibiotic-resistance genes and putative virulence genes were not predicted in the genomic analysis, and antibiotic susceptibility was satisfied by the criteria of the European Food Safety Authority. CFS showed a fungistatic effect and suppressed the tricarboxylic acid cycle in Candida albicans (29.02%). CFS also inhibited the transition to true hyphae and damaged the blastoconidia. This study demonstrates the essential properties of this novel probiotic, L. gasseri LM1065, and potential to inhibit vaginal C. albicans infection.
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Affiliation(s)
- Won-Young Bae
- Microbiome R&D Center, Lactomason, Seoul, 06620, Republic of Korea.
| | - Young Jin Lee
- Microbiome R&D Center, Lactomason, Seoul, 06620, Republic of Korea
| | - Woo-Hyun Jung
- Microbiome R&D Center, Lactomason, Seoul, 06620, Republic of Korea
| | - So Lim Shin
- Microbiome R&D Center, Lactomason, Seoul, 06620, Republic of Korea
| | - Tae-Rahk Kim
- Microbiome R&D Center, Lactomason, Seoul, 06620, Republic of Korea
| | - Minn Sohn
- Microbiome R&D Center, Lactomason, Seoul, 06620, Republic of Korea
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Emergence and Evolution of OXA-23-Producing ST46 Pas-ST462 Oxf-KL28-OCL1 Carbapenem-Resistant Acinetobacter baumannii Mediated by a Novel IS Aba1-Based Tn 7534 Transposon. Antibiotics (Basel) 2023; 12:antibiotics12020396. [PMID: 36830307 PMCID: PMC9951949 DOI: 10.3390/antibiotics12020396] [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: 11/30/2022] [Revised: 01/23/2023] [Accepted: 02/14/2023] [Indexed: 02/18/2023] Open
Abstract
Carbapenem-resistant Acinetobacter baumannii (CRAB) isolates of global clone 1 (GC1) and global clone 2 (GC2) have been widely reported. Nevertheless, non-GC1 and non-GC2 CRAB strains have been studied less. In particular, no reports concerning sequence type 46 (ST46Pas) CRAB strains have been described thus far. In this work, the genomic features and possible evolution mechanism of ST46Pas OXA-23-producing CRAB isolates from clinical specimens are reported for the first time. Antimicrobial susceptibility testing of three ST46Pas strains revealed identical resistance profiles (resistance to imipenem, meropenem, ciprofloxacin and the combination of cefoperazone/sulbactam at a 2:1 ratio). They were found to belong to ST46Pas and ST462Oxf with capsular polysaccharide 28 (KL28) and lipooligosaccharide 1 (OCL1), respectively. Whole-genome sequencing (WGS) revealed that all contained one copy of chromosomal blaOXA-23, which was located in a novel ISAba1-based Tn7534 composite transposon. In particular, another copy of the Tn7534 composite transposon was identified in an Hgz_103-type plasmid with 9 bp target site duplications (TSDs, ACAACATGC) in the A. baumannii ZHOU strain. As the strains originated from two neighboring intensive care units (ICUs), ST46Pas OXA-23-producing CRAB strains may have evolved via transposition events or a pdif module. Based on the GenBank database, ST46Pas strains were collected from various sources; however, most were collected in Hangzhou (China) from 2014 to 2021. Pan-genome analysis revealed 3276 core genes, 0 soft-core genes, 768 shell genes and 443 cloud genes shared among all ST46Pas strains. In conclusion, the emergence of ST46Pas CRAB strains might present a new threat to healthcare settings; therefore, effective surveillance is required to prevent further dissemination.
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Davray D, Bawane H, Kulkarni R. Non-redundant nature of Lactiplantibacillus plantarum plasmidome revealed by comparative genomic analysis of 105 strains. Food Microbiol 2023; 109:104153. [DOI: 10.1016/j.fm.2022.104153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 09/09/2022] [Accepted: 09/21/2022] [Indexed: 11/16/2022]
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Aziz T, Naveed M, Jabeen K, Shabbir MA, Sarwar A, Zhennai Y, Alharbi M, Alshammari A, Alasmari AF. Integrated genome based evaluation of safety and probiotic characteristics of Lactiplantibacillus plantarum YW11 isolated from Tibetan kefir. Front Microbiol 2023; 14:1157615. [PMID: 37152722 PMCID: PMC10158936 DOI: 10.3389/fmicb.2023.1157615] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 03/22/2023] [Indexed: 05/09/2023] Open
Abstract
The comparative genomic analysis of Lactiplantibacillus plantarum YW11 (L. plantarum YW11) isolated from Tibetan kefir involves comparison of the complete genome sequences of the isolated strain with other closely related L. plantarum strains. This type of analysis can be used to identify the genetic diversity among strains and to explore the genetic characteristics of the YW11 strain. The genome of L. plantarum YW11 was found to be composed of a circular single chromosome of 4,597,470 bp with a G + C content of 43.2%. A total of 4,278 open reading frames (ORFs) were identified in the genome and the coding density was found to be 87.8%. A comparative genomic analysis was conducted using two other L. plantarum strains, L. plantarum C11 and L. plantarum LMG21703. Genomic comparison revealed that L. plantarum YW11 shared 72.7 and 75.2% of gene content with L. plantarum C11 and L. plantarum LMG21703, respectively. Most of the genes shared between the three L. plantarum strains were involved in carbohydrate metabolism, energy production and conversion, amino acid metabolism, and transcription. In this analysis, 10 previously sequenced entire genomes of the species were compared using an in-silico technique to discover genomic divergence in genes linked with carbohydrate intake and their potential adaptations to distinct human intestinal environments. The subspecies pan-genome was open, which correlated with its extraordinary capacity to colonize several environments. Phylogenetic analysis revealed that the novel genomes were homogenously grouped among subspecies of l Lactiplantibacillus. L. plantarum was resistant to cefoxitin, erythromycin, and metronidazole, inhibited pathogens including Listeria monocytogenes, Clostridium difficile, Vibrio cholera, and others, and had excellent aerotolerance, which is useful for industrial operations. The comparative genomic analysis of L. plantarum YW11 isolated from Tibetan kefir can provide insights into the genetic characteristics of the strain, which can be used to further understand its role in the production of kefir.
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Affiliation(s)
- Tariq Aziz
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing, China
- Department of Agriculture, University of Ioannina, Ioannina, Greece
| | - Muhammad Naveed
- Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Khizra Jabeen
- Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Muhammad Aqib Shabbir
- Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Abid Sarwar
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing, China
| | - Yang Zhennai
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing, China
- *Correspondence: Yang Zhennai,
| | - Metab Alharbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Abdulrahman Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Abdullah F. Alasmari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
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Phenotypic and Safety Assessment of the Cheese Strain Lactiplantibacillus plantarum LL441, and Sequence Analysis of its Complete Genome and Plasmidome. Int J Mol Sci 2022; 24:ijms24010605. [PMID: 36614048 PMCID: PMC9820265 DOI: 10.3390/ijms24010605] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/20/2022] [Accepted: 12/27/2022] [Indexed: 12/31/2022] Open
Abstract
This work describes the phenotypic typing and complete genome analysis of LL441, a dairy Lactiplantibacillus plantarum strain. LL441 utilized a large range of carbohydrates and showed strong activity of some carbohydrate-degrading enzymes. The strain grew slowly in milk and produced acids and ketones along with other volatile compounds. The genome of LL441 included eight circular molecules, the bacterial chromosome, and seven plasmids (pLL441-1 through pLL441-7), ranging in size from 8.7 to 53.3 kbp. Genome analysis revealed vast arrays of genes involved in carbohydrate utilization and flavor formation in milk, as well as genes providing acid and bile resistance. No genes coding for virulence traits or pathogenicity factors were detected. Chromosome and plasmids were packed with insertion sequence (IS) elements. Plasmids were also abundant in genes encoding heavy metal resistance traits and plasmid maintenance functions. Technologically relevant phenotypes linked to plasmids, such as the production of plantaricin C (pLL441-1), lactose utilization (pLL441-2), and bacteriophage resistance (pLL441-4), were also identified. The absence of acquired antibiotic resistance and of phenotypes and genes of concern suggests L. plantarum LL441 be safe. The strain might therefore have a use as a starter or starter component in dairy and other food fermentations or as a probiotic.
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Pan-Genome Analysis of Staphylococcus aureus Reveals Key Factors Influencing Genomic Plasticity. Microbiol Spectr 2022; 10:e0311722. [PMID: 36318042 PMCID: PMC9769869 DOI: 10.1128/spectrum.03117-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The massive quantities of bacterial genomic data being generated have facilitated in-depth analyses of bacteria for pan-genomic studies. However, the pan-genome compositions of one species differed significantly between different studies, so we used Staphylococcus aureus as a model organism to explore the influences driving bacterial pan-genome composition. We selected a series of diverse strains for pan-genomic analysis to explore the pan-genomic composition of S. aureus at the species level and the actual contribution of influencing factors (sequence type [ST], source of isolation, country of isolation, and date of collection) to pan-genome composition. We found that the distribution of core genes in bacterial populations restrained under different conditions differed significantly and showed "local core gene regions" in the same ST. Therefore, we propose that ST may be a key factor driving the dynamic distribution of bacterial genomes and that phylogenetic analyses using whole-genome alignment are no longer appropriate in populations containing multiple ST strains. Pan-genomic analysis showed that some of the housekeeping genes of multilocus sequence typing (MLST) are carried at less than 60% in S. aureus strains. Consequently, we propose a new set of marker genes for the classification of S. aureus, which provides a reference for finding a new set of housekeeping genes to apply to MLST. In this study, we explored the role of driving factors influencing pan-genome composition, providing new insights into the study of bacterial pan-genomes. IMPORTANCE We sought to explore the impact of driving factors influencing pan-genome composition using Staphylococcus aureus as a model organism to provide new insights for the study of bacterial pan-genomes. We believe that the sequence type (ST) of the strains under consideration plays a significant role in the dynamic distribution of bacterial genes. Our findings indicate that there are a certain number of essential genes in Staphylococcus aureus; however, the number of core genes is not as high as previously thought. The new classification method proposed herein suggests that a new set of housekeeping genes more suitable for Staphylococcus aureus must be identified to improve the current classification status of this species.
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Lactiplantibacillus plantarum LOC1 Isolated from Fresh Tea Leaves Modulates Macrophage Response to TLR4 Activation. Foods 2022. [DOI: 10.3390/foods11203257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Previously, we demonstrated that Lactiplantibacillus plantarum LOC1, originally isolated from fresh tea leaves, was able to improve epithelial barrier integrity in in vitro models, suggesting that this strain is an interesting probiotic candidate. In this work, we aimed to continue characterizing the potential probiotic properties of the LOC1 strain, focusing on its immunomodulatory properties in the context of innate immunity triggered by Toll-like receptor 4 (TLR4) activation. These studies were complemented by comparative and functional genomics analysis to characterize the bacterial genes involved in the immunomodulatory capacity. We carried out a transcriptomic study to evaluate the effect of L. plantarum LOC1 on the response of murine macrophages (RAW264.7 cells) to the activation of TLR4. We demonstrated that L. plantarum LOC1 exerts a modulatory effect on lipopolysaccharide (LPS)-induced inflammation, resulting in a differential regulation of immune factor expression in macrophages. The LOC1 strain markedly reduced the LPS-induced expression of some inflammatory cytokines (IL-1β, IL-12, and CSF2) and chemokines (CCL17, CCL28, CXCL3, CXCL13, CXCL1, and CX3CL1), while it significantly increased the expression of other cytokines (TNF-α, IL-6, IL-18, IFN-β, IFN-γ, and CSF3), chemokines (IL-15 and CXCL9), and activation markers (H2-k1, H2-M3, CD80, and CD86) in RAW macrophages. Our results show that L. plantarum LOC1 would enhance the intrinsic functions of macrophages, promoting their protective effects mediated by the stimulation of the Th1 response without affecting the regulatory mechanisms that help control inflammation. In addition, we sequenced the LOC1 genome and performed a genomic characterization. Genomic comparative analysis with the well-known immunomodulatory strains WCSF1 and CRL1506 demonstrated that L. plantarum LOC1 possess a set of adhesion factors and genes involved in the biosynthesis of teichoic acids and lipoproteins that could be involved in its immunomodulatory capacity. The results of this work can contribute to the development of immune-related functional foods containing L. plantarum LOC1.
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Yang T, Gao F. High-quality pan-genome of Escherichia coli generated by excluding confounding and highly similar strains reveals an association between unique gene clusters and genomic islands. Brief Bioinform 2022; 23:6638794. [PMID: 35809555 DOI: 10.1093/bib/bbac283] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 06/17/2022] [Accepted: 06/20/2022] [Indexed: 01/24/2023] Open
Abstract
The pan-genome analysis of bacteria provides detailed insight into the diversity and evolution of a bacterial population. However, the genomes involved in the pan-genome analysis should be checked carefully, as the inclusion of confounding strains would have unfavorable effects on the identification of core genes, and the highly similar strains could bias the results of the pan-genome state (open versus closed). In this study, we found that the inclusion of highly similar strains also affects the results of unique genes in pan-genome analysis, which leads to a significant underestimation of the number of unique genes in the pan-genome. Therefore, these strains should be excluded from pan-genome analysis at the early stage of data processing. Currently, tens of thousands of genomes have been sequenced for Escherichia coli, which provides an unprecedented opportunity as well as a challenge for pan-genome analysis of this classical model organism. Using the proposed strategies, a high-quality E. coli pan-genome was obtained, and the unique genes was extracted and analyzed, revealing an association between the unique gene clusters and genomic islands from a pan-genome perspective, which may facilitate the identification of genomic islands.
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Affiliation(s)
- Tong Yang
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China
| | - Feng Gao
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
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A Comparative Genomic and Safety Assessment of Six Lactiplantibacillus plantarum subsp. argentoratensis Strains Isolated from Spontaneously Fermented Greek Wheat Sourdoughs for Potential Biotechnological Application. Int J Mol Sci 2022; 23:ijms23052487. [PMID: 35269627 PMCID: PMC8910486 DOI: 10.3390/ijms23052487] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/18/2022] [Accepted: 02/21/2022] [Indexed: 02/05/2023] Open
Abstract
The comparative genome analysis of six Lactiplantibacillus plantarum subsp. argentoratensis strains previously isolated from spontaneously fermented Greek wheat sourdoughs is presented. Genomic attributes related to food safety have been studied according to the European Food Safety Authority (EFSA) suggestions for the use of lactic acid bacteria (LAB) in the production of foods. Bioinformatic analysis revealed a complete set of genes for maltose, sucrose, glucose, and fructose fermentation; conversion of fructose to mannitol; folate and riboflavin biosynthesis; acetoin production; conversion of citrate to oxaloacetate; and the ability to produce antimicrobial compounds (plantaricins). Pathogenic factors were absent but some antibiotic resistance genes were detected. CRISPR and cas genes were present as well as various mobile genetic elements (MGEs) such as plasmids, prophages, and insertion sequences. The production of biogenic amines by these strains was not possible due to the absence of key genes in their genome except lysine decarboxylase associated with cadaverine; however, potential degradation of these substances was identified due to the presence of a blue copper oxidase precursor and a multicopper oxidase protein family. Finally, comparative genomics and pan-genome analysis showed genetic differences between the strains (e.g., variable pln locus), and it facilitated the identification of various phenotypic and probiotic-related properties.
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