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Qian M, Zhou X, Xu T, Li M, Yang Z, Han X. Evaluation of Potential Probiotic Properties of Limosilactobacillus fermentum Derived from Piglet Feces and Influence on the Healthy and E. coli-Challenged Porcine Intestine. Microorganisms 2023; 11:microorganisms11041055. [PMID: 37110478 PMCID: PMC10142273 DOI: 10.3390/microorganisms11041055] [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: 03/06/2023] [Revised: 03/31/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
In this work, we evaluated the probiotic properties of Limosilactobacillus fermentum strains (FL1, FL2, FL3, FL4) isolated from feces of healthy piglets. The in vitro auto-aggregation, hydrophobicity, biofilm-forming capacity, survival in the gastrointestinal tract, antimicrobial activity and anti-oxidation capacity were evaluated. Four strains were resistant to simulated gastrointestinal conditions, including low pH, pepsin, trypsin and bile salts. They also maintained strong self-aggregation and cell surface hydrophobicity. Limosilactobacillus fermentum FL4, which had the strongest adhesion ability and antimicrobial effect on Enterotoxigenic Escherichia coli K88 (ETEC K88), was then tested in porcine intestinal organoid models. The in vitro experiments in basal-out and apical-out organoids demonstrated that L. fermentum FL4 adhered to the apical surfaces more efficiently than basolateral surfaces, had the ability to activate the Wnt/β-catenin pathway to protect the mucosal barrier integrity, stimulated the proliferation and differentiation of the intestinal epithelium, and repaired ETEC K88-induced damage. Moreover, L. fermentum FL4 inhibited inflammatory responses induced by ETEC K88 through the reduced expression of pro-inflammatory cytokines (TNF-α, IL-1β and IFN-γ) and higher levels of anti-inflammatory cytokines (TGF-β and IL-10). These results show that L. fermentum FL4 isolated from feces of healthy Tunchang piglets has the potential to be used as an anti-inflammatory probiotic and for mitigation of intestinal damage in piglets.
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Affiliation(s)
- Mengqi Qian
- Hainan Institute, Zhejiang University, Yazhou Bay Sci-Tech City, Sanya 572000, China
- College of Animal Science, Zhejiang University, Hangzhou 310058, China
| | - Xinchen Zhou
- Hainan Institute, Zhejiang University, Yazhou Bay Sci-Tech City, Sanya 572000, China
- College of Animal Science, Zhejiang University, Hangzhou 310058, China
| | - Tingting Xu
- College of Animal Science, Zhejiang University, Hangzhou 310058, China
| | - Meng Li
- Hainan Institute, Zhejiang University, Yazhou Bay Sci-Tech City, Sanya 572000, China
- College of Animal Science, Zhejiang University, Hangzhou 310058, China
| | - Zhiren Yang
- Hainan Institute, Zhejiang University, Yazhou Bay Sci-Tech City, Sanya 572000, China
- College of Animal Science, Zhejiang University, Hangzhou 310058, China
| | - Xinyan Han
- Hainan Institute, Zhejiang University, Yazhou Bay Sci-Tech City, Sanya 572000, China
- College of Animal Science, Zhejiang University, Hangzhou 310058, China
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Myers BK, Shin GY, Agarwal G, Stice SP, Gitaitis RD, Kvitko BH, Dutta B. Genome-wide association and dissociation studies in Pantoea ananatis reveal potential virulence factors affecting Allium porrum and Allium fistulosum × Allium cepa hybrid. Front Microbiol 2023; 13:1094155. [PMID: 36817114 PMCID: PMC9933511 DOI: 10.3389/fmicb.2022.1094155] [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: 11/09/2022] [Accepted: 12/30/2022] [Indexed: 02/05/2023] Open
Abstract
Pantoea ananatis is a member of a Pantoea species complex that causes center rot of bulb onions (A. cepa) and also infects other Allium crops like leeks (Allium porrum), chives (Allium schoenoprasum), bunching onion or Welsh onion (Allium fistulosum), and garlic (Allium sativum). This pathogen relies on a chromosomal phosphonate biosynthetic gene cluster (HiVir) and a plasmid-borne thiosulfinate tolerance cluster (alt) for onion pathogenicity and virulence, respectively. However, pathogenicity and virulence factors associated with other Allium species remain unknown. We used phenotype-dependent genome-wide association (GWAS) and phenotype-independent gene-pair coincidence (GPC) analyses on a panel of diverse 92 P. ananatis strains, which were inoculated on A. porrum and A. fistulosum × A. cepa under greenhouse conditions. Phenotypic assays showed that, in general, these strains were more aggressive on A. fistulosum × A. cepa as opposed to A. porrum. Of the 92 strains, only six showed highly aggressive foliar lesions on A. porrum compared to A. fistulosum × A. cepa. Conversely, nine strains showed highly aggressive foliar lesions on A. fistulosum × A. cepa compared to A. porrum. These results indicate that there are underlying genetic components in P. ananatis that may drive pathogenicity in these two Allium spp. Based on GWAS for foliar pathogenicity, 835 genes were associated with P. ananatis' pathogenicity on A. fistulosum × A. cepa whereas 243 genes were associated with bacterial pathogenicity on A. porrum. The Hivir as well as the alt gene clusters were identified among these genes. Besides the 'HiVir' and the alt gene clusters that are known to contribute to pathogenicity and virulence from previous studies, genes annotated with functions related to stress responses, a potential toxin-antitoxin system, flagellar-motility, quorum sensing, and a previously described phosphonoglycan biosynthesis (pgb) cluster were identified. The GPC analysis resulted in the identification of 165 individual genes sorted into 39 significant gene-pair association components and 255 genes sorted into 50 significant gene-pair dissociation components. Within the coincident gene clusters, several genes that occurred on the GWAS outputs were associated with each other but dissociated with genes that did not appear in their respective GWAS output. To focus on candidate genes that could explain the difference in virulence between hosts, a comparative genomics analysis was performed on five P. ananatis strains that were differentially pathogenic on A. porrum or A. fistulosum × A. cepa. Here, we found a putative type III secretion system, and several other genes that occurred on both GWAS outputs of both Allium hosts. Further, we also demonstrated utilizing mutational analysis that the pepM gene in the HiVir cluster is important than the pepM gene in the pgb cluster for P. ananatis pathogenicity in A. fistulosum × A. cepa and A. porrum. Overall, our results support that P. ananatis may utilize a common set of genes or gene clusters to induce symptoms on A. fistulosum × A. cepa foliar tissue as well as A. cepa but implicates additional genes for infection on A. porrum.
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Affiliation(s)
- Brendon K. Myers
- Department of Plant Pathology, The University of Georgia, Tifton, GA, United States
| | - Gi Yoon Shin
- Department of Plant Pathology, The University of Georgia, Athens, GA, United States
| | - Gaurav Agarwal
- Department of Plant Pathology, The University of Georgia, Tifton, GA, United States
| | - Shaun P. Stice
- Department of Plant Pathology, The University of Georgia, Athens, GA, United States
| | - Ronald D. Gitaitis
- Department of Plant Pathology, The University of Georgia, Tifton, GA, United States
| | - Brian H. Kvitko
- Department of Plant Pathology, The University of Georgia, Athens, GA, United States
| | - Bhabesh Dutta
- Department of Plant Pathology, The University of Georgia, Tifton, GA, United States,*Correspondence: Bhabesh Dutta, ✉
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Srivastava A, Pati S, Kaushik H, Singh S, Garg LC. Toxin-antitoxin systems and their medical applications: current status and future perspective. Appl Microbiol Biotechnol 2021; 105:1803-1821. [PMID: 33582835 DOI: 10.1007/s00253-021-11134-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 01/13/2021] [Accepted: 01/20/2021] [Indexed: 12/11/2022]
Abstract
Almost all bacteria synthesize two types of toxins-one for its survival by regulating different cellular processes and another as a strategy to interact with host cells for pathogenesis. Usually, "bacterial toxins" are contemplated as virulence factors that harm the host organism. However, toxins produced by bacteria, as a survival strategy against the host, also hamper its cellular processes. To overcome this, the bacteria have evolved with the production of a molecule, referred to as antitoxin, to negate the deleterious effect of the toxin against itself. The toxin and antitoxins are encoded by a two-component toxin-antitoxin (TA) system. The antitoxin, a protein or RNA, sequesters the toxins of the TA system for neutralization within the bacterial cell. In this review, we have described different TA systems of bacteria and their potential medical and biotechnological applications. It is of interest to note that while bacterial toxin-antitoxin systems have been well studied, the TA system in unicellular eukaryotes, though predicted by the investigators, have never been paid the desired attention. In the present review, we have also touched upon the TA system of eukaryotes identified to date. KEY POINTS: Bacterial toxins harm the host and also affect the bacterial cellular processes. The antitoxin produced by bacteria protect it from the toxin's harmful effects. The toxin-antitoxin systems can be targeted for various medical applications.
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Affiliation(s)
- Akriti Srivastava
- Department of Life Sciences, Shiv Nadar University, Gautam Buddha Nagar, Greater Noida, Uttar Pradesh, 201314, India
| | - Soumya Pati
- Department of Life Sciences, Shiv Nadar University, Gautam Buddha Nagar, Greater Noida, Uttar Pradesh, 201314, India
| | - Himani Kaushik
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi, 110067, India
| | - Shailja Singh
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, 110067, India.
| | - Lalit C Garg
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi, 110067, India.
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Klimina KM, Voroshilova VN, Poluektova EU, Veselovsky VA, Yunes RA, Kovtun AS, Kudryavtseva AV, Kasianov AS, Danilenko VN. Toxin-Antitoxin Systems: A Tool for Taxonomic Analysis of Human Intestinal Microbiota. Toxins (Basel) 2020; 12:toxins12060388. [PMID: 32545455 PMCID: PMC7354421 DOI: 10.3390/toxins12060388] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/08/2020] [Accepted: 06/10/2020] [Indexed: 01/14/2023] Open
Abstract
The human gastrointestinal microbiota (HGM) is known for its rich diversity of bacterial species and strains. Yet many studies stop at characterizing the HGM at the family level. This is mainly due to lack of adequate methods for a high-resolution profiling of the HGM. One way to characterize the strain diversity of the HGM is to look for strain-specific functional markers. Here, we propose using type II toxin-antitoxin systems (TAS). To identify TAS systems in the HGM, we previously developed the software TAGMA. This software was designed to detect the TAS systems, MazEF and RelBE, in lactobacilli and bifidobacteria. In this study, we updated the gene catalog created previously and used it to test our software anew on 1346 strains of bacteria, which belonged to 489 species and 49 genera. We also sequenced the genomes of 20 fecal samples and analyzed the results with TAGMA. Although some differences were detected at the strain level, the results showed no particular difference in the bacterial species between our method and other classic analysis software. These results support the use of the updated catalog of genes encoding type II TAS as a useful tool for computer-assisted species and strain characterization of the HGM.
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Affiliation(s)
- Ksenia M. Klimina
- Vavilov Institute of General Genetics Russian Academy of Sciences, 119991 Moscow, Russia; (V.N.V.); (E.U.P.); (R.A.Y.); (A.S.K.); (A.S.K.); (V.N.D.)
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia;
- Correspondence:
| | - Viktoriya N. Voroshilova
- Vavilov Institute of General Genetics Russian Academy of Sciences, 119991 Moscow, Russia; (V.N.V.); (E.U.P.); (R.A.Y.); (A.S.K.); (A.S.K.); (V.N.D.)
- Moscow Institute of Physics and Technology, Dolgoprudny, 141701 Moscow, Russia
| | - Elena U. Poluektova
- Vavilov Institute of General Genetics Russian Academy of Sciences, 119991 Moscow, Russia; (V.N.V.); (E.U.P.); (R.A.Y.); (A.S.K.); (A.S.K.); (V.N.D.)
| | - Vladimir A. Veselovsky
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia;
| | - Roman A. Yunes
- Vavilov Institute of General Genetics Russian Academy of Sciences, 119991 Moscow, Russia; (V.N.V.); (E.U.P.); (R.A.Y.); (A.S.K.); (A.S.K.); (V.N.D.)
| | - Aleksey S. Kovtun
- Vavilov Institute of General Genetics Russian Academy of Sciences, 119991 Moscow, Russia; (V.N.V.); (E.U.P.); (R.A.Y.); (A.S.K.); (A.S.K.); (V.N.D.)
- Moscow Institute of Physics and Technology, Dolgoprudny, 141701 Moscow, Russia
| | - Anna V. Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia;
| | - Artem S. Kasianov
- Vavilov Institute of General Genetics Russian Academy of Sciences, 119991 Moscow, Russia; (V.N.V.); (E.U.P.); (R.A.Y.); (A.S.K.); (A.S.K.); (V.N.D.)
- Moscow Institute of Physics and Technology, Dolgoprudny, 141701 Moscow, Russia
| | - Valery N. Danilenko
- Vavilov Institute of General Genetics Russian Academy of Sciences, 119991 Moscow, Russia; (V.N.V.); (E.U.P.); (R.A.Y.); (A.S.K.); (A.S.K.); (V.N.D.)
- Faculty of Ecology, International Institute for Strategic Development of Sectoral Economics, Peoples’ Friendship University of Russia (RUDN University), 117198 Moscow, Russia
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Terán LC, Cuozzo SA, Aristimuño Ficoseco MC, Fadda S, Chaillou S, Champomier-Vergès MC, Zagorec M, Hébert EM, Raya RR. Nucleotide sequence and analysis of pRC12 and pRC18, two theta-replicating plasmids harbored by Lactobacillus curvatus CRL 705. PLoS One 2020; 15:e0230857. [PMID: 32240216 PMCID: PMC7117683 DOI: 10.1371/journal.pone.0230857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 03/10/2020] [Indexed: 11/19/2022] Open
Abstract
The nucleotide sequences of plasmids pRC12 (12,342 bp; GC 43.99%) and pRC18 (18,664 bp; GC 34.33%), harbored by the bacteriocin-producer Lactobacillus curvatus CRL 705, were determined and analyzed. Plasmids pRC12 and pRC18 share a region with high DNA identity (> 83% identity between RepA, a Type II toxin-antitoxin system and a tyrosine integrase genes) and are stably maintained in their natural host L. curvatus CRL 705. Both plasmids are low copy number and belong to the theta-type replicating group. While pRC12 is a pUCL287-like plasmid that possesses iterons and the repA and repB genes for replication, pRC18 harbors a 168 amino acid replication protein affiliated to RepB, which was named RepB'. Plasmid pRC18 also possesses a pUCL287-like repA gene but it was disrupted by an 11 kb insertion element that contains RepB', several transposases/IS elements, and the lactocin Lac705 operon. An Escherichia coli / Lactobacillus shuttle vector, named plasmid p3B1, carrying the pRC18 replicon (i.e. repB' and replication origin), a chloramphenicol resistance gene and a pBluescript backbone, was constructed and used to define the host range of RepB'. Chloramphenicol-resistant transformants were obtained after electroporation of Lactobacillus plantarum CRL 691, Lactobacillus sakei 23K and a plasmid-cured derivative of L. curvatus CRL 705, but not of L. curvatus DSM 20019 or Lactococcus lactis NZ9000. Depending on the host, transformation efficiency ranged from 102 to 107 per μg of DNA; in the new hosts, the plasmid was relatively stable as 29-53% of recombinants kept it after cell growth for 100 generations in the absence of selective pressure. Plasmid p3B1 could therefore be used for cloning and functional studies in several Lactobacillus species.
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Affiliation(s)
- Lucrecia C. Terán
- Centro de Referencia para Lactobacilos (CERELA)-CONICET, Tucumán, Argentina
| | - Sergio A. Cuozzo
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI)-CONICET, Tucumán, Argentina
| | | | - Silvina Fadda
- Centro de Referencia para Lactobacilos (CERELA)-CONICET, Tucumán, Argentina
| | - Stéphane Chaillou
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | | | | | - Elvira M. Hébert
- Centro de Referencia para Lactobacilos (CERELA)-CONICET, Tucumán, Argentina
| | - Raúl R. Raya
- Centro de Referencia para Lactobacilos (CERELA)-CONICET, Tucumán, Argentina
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Klimina KM, Kasianov AS, Poluektova EU, Emelyanov KV, Voroshilova VN, Zakharevich NV, Kudryavtseva AV, Makeev VJ, Danilenko VN. Employing toxin-antitoxin genome markers for identification of Bifidobacterium and Lactobacillus strains in human metagenomes. PeerJ 2019; 7:e6554. [PMID: 30863681 PMCID: PMC6404652 DOI: 10.7717/peerj.6554] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 02/02/2019] [Indexed: 01/22/2023] Open
Abstract
Recent research has indicated that in addition to the unique genotype each individual may also have a unique microbiota composition. Difference in microbiota composition may emerge from both its species and strain constituents. It is important to know the precise composition especially for the gut microbiota (GM), since it can contribute to the health assessment, personalized treatment, and disease prevention for individuals and groups (cohorts). The existing methods for species and strain composition in microbiota are not always precise and usually not so easy to use. Probiotic bacteria of the genus Bifidobacterium and Lactobacillus make an essential component of human GM. Previously we have shown that in certain Bifidobacterium and Lactobacillus species the RelBE and MazEF superfamily of toxin-antitoxin (TA) systems may be used as functional biomarkers to differentiate these groups of bacteria at the species and strain levels. We have composed a database of TA genes of these superfamily specific for all lactobacilli and bifidobacteria species with complete genome sequence and confirmed that in all Lactobacillus and Bifidobacterium species TA gene composition is species and strain specific. To analyze composition of species and strains of two bacteria genera, Bifidobacterium and Lactobacillus, in human GM we developed TAGMA (toxin antitoxin genes for metagenomes analyses) software based on polymorphism in TA genes. TAGMA was tested on gut metagenomic samples. The results of our analysis have shown that TAGMA can be used to characterize species and strains of Lactobacillus and Bifidobacterium in metagenomes.
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Affiliation(s)
- Ksenia M Klimina
- Vavilov Institute of General Genetics Russian Academy of Sciences, Moscow, Russia.,Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Artem S Kasianov
- Vavilov Institute of General Genetics Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Elena U Poluektova
- Vavilov Institute of General Genetics Russian Academy of Sciences, Moscow, Russia
| | | | | | | | - Anna V Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Vsevolod J Makeev
- Vavilov Institute of General Genetics Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Valery N Danilenko
- Vavilov Institute of General Genetics Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny, Russia
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Huang CH, Huang L. Rapid species- and subspecies-specific level classification and identification of Lactobacillus casei group members using MALDI Biotyper combined with ClinProTools. J Dairy Sci 2018; 101:979-991. [DOI: 10.3168/jds.2017-13642] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 09/30/2017] [Indexed: 12/16/2022]
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Klimina KM, Poluektova EU, Danilenko VN. Bacterial toxin–antitoxin systems: Properties, functional significance, and possibility of use (Review). APPL BIOCHEM MICRO+ 2017. [DOI: 10.1134/s0003683817050076] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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