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Achache W, Mege JL, Fellag M, Drancourt M. The Enterococcus secretome inhibits the growth of Mycobacterium tuberculosis complex mycobacteria. Access Microbiol 2023; 5:acmi000471.v3. [PMID: 37424563 PMCID: PMC10323786 DOI: 10.1099/acmi.0.000471.v3] [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: 07/18/2022] [Accepted: 04/03/2023] [Indexed: 07/11/2023] Open
Abstract
Enterococcus mundtii , a commensal intestinal bacterium, was demonstrated to inhibit the growth of some Mycobacterium tuberculosis complex (MTC) species that cause tuberculosis in humans and mammals. To further explore this preliminary observation, we cross-investigated five E. mundtii strains and seven MTC strains representative of four MTC species using a standardized quantitative agar well diffusion assay. All five E. mundtii strains, calibrated at 10 MacFarland, inhibited the growth of all M. tuberculosis strains with various susceptibility profiles, but no inhibition was observed with lower inoculums. Further, eight E. mundtii freeze-dried cell-free culture supernatants (CFCS) inhibited the growth of M. tuberculosis , Mycobacterium africanum, Mycobacterium bovis and Mycobacterium canettii, the most susceptible MTC species (inhibition diameter 25±1 mm), proportionally to CFCS protein concentrations. The data reported here indicate that the E. mundtii secretome inhibited growth of all MTC species of medical interest, which broadens previously reported data. In the gut, the E. mundtii secretome may modulate the expression of tuberculosis, exhibiting an anti-tuberculosis effect, with some protective roles in human and animal health.
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Affiliation(s)
- Wafaa Achache
- Aix-Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Jean Louis Mege
- Aix-Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Mustapha Fellag
- Aix-Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Michel Drancourt
- Aix-Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
- IHU Méditerranée Infection, Marseille, France
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2
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Sinpoo C, In-on A, Noirungsee N, Attasopa K, Chantawannakul P, Chaimanee V, Phokasem P, Ling TC, Purahong W, Disayathanoowat T. Microbial community profiling and culturing reveal functional groups of bacteria associated with Thai commercial stingless worker bees (Tetragonula pagdeni). PLoS One 2023; 18:e0280075. [PMID: 36857385 PMCID: PMC9977063 DOI: 10.1371/journal.pone.0280075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 12/20/2022] [Indexed: 03/02/2023] Open
Abstract
Stingless bees play a crucial role in the environment and agriculture as they are effective pollinators. Furthermore, they can produce various products that can be exploited economically, such as propolis and honey. Despite their economic value, the knowledge of microbial community of stingless bees, and their roles on the bees' health, especially in Thailand, are in its infancy. This study aimed to investigate the composition and the functions of bacterial community associated with Tetragonula pagdeni stingless bees using culture-independent and culture-dependent approaches with emphasis on lactic acid bacteria. The culture-independent results showed that the dominant bacterial phyla were Firmicutes, Proteobacteria and Actinobacteria. The most abundant families were Lactobacillaceae and Halomonadaceae. Functional prediction indicated that the prevalent functions of bacterial communities were chemoheterotrophy and fermentation. In addition, the bacterial community might be able to biosynthesize amino acid and antimicrobial compounds. Further isolation and characterization resulted in isolates that belonged to the dominant taxa of the community and possessed potentially beneficial metabolic activity. This suggested that they are parts of the nutrient acquisition and host defense bacterial functional groups in Thai commercial stingless bees.
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Affiliation(s)
- Chainarong Sinpoo
- Bee Protection Laboratory, Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Ammarin In-on
- Bioinformatics & Systems Biology Program, King Mongkut’s University of Technology Thonburi (Bang Khun Thian Campus), Bang Khun Thian, Bangkok, Thailand
| | - Nuttapol Noirungsee
- Bee Protection Laboratory, Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Korrawat Attasopa
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai, Thailand
| | - Panuwan Chantawannakul
- Bee Protection Laboratory, Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Veeranan Chaimanee
- Department of Agro-Industrial Biotechnology, Maejo University Phrae Campus, Rong Kwang, Phrae, Thailand
| | - Patcharin Phokasem
- Bee Protection Laboratory, Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Tial Cung Ling
- Bee Protection Laboratory, Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Witoon Purahong
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle (Saale), Germany
- * E-mail: (WP); (TD)
| | - Terd Disayathanoowat
- Bee Protection Laboratory, Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- * E-mail: (WP); (TD)
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3
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Regulation of Resistance in Vancomycin-Resistant Enterococci: The VanRS Two-Component System. Microorganisms 2021; 9:microorganisms9102026. [PMID: 34683347 PMCID: PMC8541618 DOI: 10.3390/microorganisms9102026] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 01/20/2023] Open
Abstract
Vancomycin-resistant enterococci (VRE) are a serious threat to human health, with few treatment options being available. New therapeutics are urgently needed to relieve the health and economic burdens presented by VRE. A potential target for new therapeutics is the VanRS two-component system, which regulates the expression of vancomycin resistance in VRE. VanS is a sensor histidine kinase that detects vancomycin and in turn activates VanR; VanR is a response regulator that, when activated, directs expression of vancomycin-resistance genes. This review of VanRS examines how the expression of vancomycin resistance is regulated, and provides an update on one of the field’s most pressing questions: How does VanS sense vancomycin?
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4
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Transcriptomics Reveal the Survival Strategies of Enterococcus mundtii in the Gut of Spodoptera littoralis. J Chem Ecol 2021; 47:227-241. [PMID: 33459999 DOI: 10.1007/s10886-021-01246-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 12/22/2020] [Accepted: 01/04/2021] [Indexed: 12/25/2022]
Abstract
The complex interaction between a higher organism and its resident gut flora is a subject of immense interest in the field of symbiosis. Many insects harbor a complex community of microorganisms in their gut. Larvae of Spodoptera littoralis, a lepidopteran pest, house a bacterial community that varies both spatially (along the length of the gut) and temporally (during the insect's life cycle). To monitor the rapid adaptation of microbes to conditions in the gut, a GFP-tagged reporter strain of E. mundtii, a major player in the gut community, was constructed. After early-instar S. littoralis larvae were fed with the tagged microbes, these were recovered from the larval fore- and hindgut by flow cytometry. The fluorescent reporter confirmed the persistence of E. mundtii in the gut. RNA-sequencing of the sorted bacteria highlighted various strategies of the symbiont's survival, including upregulated pathways for tolerating alkaline stress, forming biofilms and two-component signaling systems for quorum sensing, and resisting oxidative stress. Although these symbionts depend on the host for amino acid and fatty acids, differential regulation among various metabolic pathways points to an enriched lysine synthesis pathway of E. mundtii in the hindgut of the larvae.
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5
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Transcriptome profile of carbon catabolite repression in an efficient l-(+)-lactic acid-producing bacterium Enterococcus mundtii QU25 grown in media with combinations of cellobiose, xylose, and glucose. PLoS One 2020; 15:e0242070. [PMID: 33201910 PMCID: PMC7671544 DOI: 10.1371/journal.pone.0242070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 10/26/2020] [Indexed: 11/19/2022] Open
Abstract
Enterococcus mundtii QU25, a non-dairy lactic acid bacterium of the phylum Firmicutes, is capable of simultaneously fermenting cellobiose and xylose, and is described as a promising strain for the industrial production of optically pure l-lactic acid (≥ 99.9%) via homo-fermentation of lignocellulosic hydrolysates. Generally, Firmicutes bacteria show preferential consumption of sugar (usually glucose), termed carbon catabolite repression (CCR), while hampering the catabolism of other sugars. In our previous study, QU25 exhibited apparent CCR in a glucose-xylose mixture phenotypically, and transcriptional repression of the xylose operon encoding initial xylose metabolism genes, likely occurred in a CcpA-dependent manner. QU25 did not exhibit CCR phenotypically in a cellobiose-xylose mixture. The aim of the current study is to elucidate the transcriptional change associated with the simultaneous utilization of cellobiose and xylose. To this end, we performed RNA-seq analysis in the exponential growth phase of E. mundtii QU25 cells grown in glucose, cellobiose, and/or xylose as either sole or co-carbon sources. Our transcriptomic data showed that the xylose operon was weakly repressed in cells grown in a cellobiose-xylose mixture compared with that in cells grown in a glucose-xylose mixture. Furthermore, the gene expression of talC, the sole gene encoding transaldolase, is expected to be repressed by CcpA-mediated CCR. QU25 metabolized xylose without using transaldolase, which is necessary for homolactic fermentation from pentoses using the pentose-phosphate pathway. Hence, the metabolism of xylose in the presence of cellobiose by QU25 may have been due to 1) sufficient amounts of proteins encoded by the xylose operon genes for xylose metabolism despite of the slight repression of the operon, and 2) bypassing of the pentose-phosphate pathway without the TalC activity. Accordingly, we have determined the targets of genetic modification in QU25 to metabolize cellobiose, xylose and glucose simultaneously for application of the lactic fermentation from lignocellulosic hydrolysates.
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Nabeta K, Watanabe S, Chibazakura T, Zendo T, Sonomoto K, Shimizu-Kadota M, Yoshikawa H. Constitutive expression of phosphoketolase, a key enzyme for metabolic shift from homo- to heterolactic fermentation in Enterococcus mundtii QU 25. BIOSCIENCE OF MICROBIOTA FOOD AND HEALTH 2019; 38:111-114. [PMID: 31384523 PMCID: PMC6663511 DOI: 10.12938/bmfh.18-030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 04/15/2019] [Indexed: 11/05/2022]
Abstract
Phosphoketolase (PK) is responsible for heterolactic fermentation; however, the PK gene of Enterococcus mundtii QU 25, xfpA, is transcribed constitutively, even under homolactic fermentation conditions. In order to deduce the regulatory mechanisms of PK activity in QU 25, XfpA levels in QU 25 cells under hetero- and homolactic fermentation conditions were tested using western blotting. The results showed that the XfpA protein expression was similar under both conditions and that the expression products formed complexes, most likely homodimers, indicating that the regulation of PK activity is downstream of translation.
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Affiliation(s)
- Keisuke Nabeta
- Department of Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Satoru Watanabe
- Department of Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Taku Chibazakura
- Department of Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Takeshi Zendo
- Laboratory of Microbial Technology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Kenji Sonomoto
- Laboratory of Microbial Technology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Mariko Shimizu-Kadota
- Department of Environmental Systems Sciences, Musashino University, 3-3-3 Ariake, Koto-ku, Tokyo 135-8181, Japan.,Department of Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Hirofumi Yoshikawa
- Department of Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan.,NODAI Genome Research Center, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
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7
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Complete Genome Sequence of Enterococcus faecium QU50, a Thermophilic Lactic Acid Bacterium Capable of Metabolizing Xylose. Microbiol Resour Announc 2019; 8:8/21/e00413-19. [PMID: 31123015 PMCID: PMC6533385 DOI: 10.1128/mra.00413-19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Herein, we report the complete genome sequence of Enterococcus faecium QU50, isolated from Egyptian soil and exhibiting intermediate susceptibility to vancomycin. The genome contains a 2,535,796-bp circular chromosome and two plasmids of 196,595 bp and 17,267 bp. Herein, we report the complete genome sequence of Enterococcus faecium QU50, isolated from Egyptian soil and exhibiting intermediate susceptibility to vancomycin. The genome contains a 2,535,796-bp circular chromosome and two plasmids of 196,595 bp and 17,267 bp. IS1062-like sequences were not found.
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8
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Draft Genome Sequences of Enterococcus mundtii Strains Isolated from Beef Slaughterhouses in Kenya. GENOME ANNOUNCEMENTS 2018; 6:6/21/e00446-18. [PMID: 29798926 PMCID: PMC5968732 DOI: 10.1128/genomea.00446-18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present here draft genome sequences of Enterococcus mundtii strains K7-EM, P2-EM, C11-EM, and H18-EM, which were isolated from slaughterhouse equipment, carcasses, and personnel of small- and medium-sized beef slaughterhouses in Kenya.
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9
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Liang X, Sun C, Chen B, Du K, Yu T, Luang-In V, Lu X, Shao Y. Insect symbionts as valuable grist for the biotechnological mill: an alkaliphilic silkworm gut bacterium for efficient lactic acid production. Appl Microbiol Biotechnol 2018; 102:4951-4962. [DOI: 10.1007/s00253-018-8953-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 02/12/2018] [Accepted: 03/14/2018] [Indexed: 11/29/2022]
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10
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Genome Sequence of Enterococcus mundtii EM01, Isolated from Bombyx mori Midgut and Responsible for Flacherie Disease in Silkworms Reared on an Artificial Diet. GENOME ANNOUNCEMENTS 2018; 6:6/3/e01495-17. [PMID: 29348354 PMCID: PMC5773739 DOI: 10.1128/genomea.01495-17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The whole genome sequence of Enterococcus mundtii strain EM01 is reported here. The isolate proved to be the cause of flacherie in Bombyx mori. To date, the genomes of 11 other E. mundtii strains have been sequenced. EM01 is the only strain that displayed active pathological effects on its associated animal species.
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11
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Draft Genome Sequence of Enterococcus mundtii QAUEM2808, Isolated from Dahi, a Fermented Milk Product. GENOME ANNOUNCEMENTS 2016; 4:4/5/e00995-16. [PMID: 27635009 PMCID: PMC5026449 DOI: 10.1128/genomea.00995-16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Enterococcus mundtii QAUEM2808 has been isolated from dahi, an indigenous fermented milk product of Pakistan. Here, we report the draft genome sequence for this strain, which consists of 160 contigs corresponding to 2,957,514 bp and a G+C content of 38.5%.
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12
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Gatto V, Tabanelli G, Montanari C, Prodomi V, Bargossi E, Torriani S, Gardini F. Tyrosine decarboxylase activity of Enterococcus mundtii: new insights into phenotypic and genetic aspects. Microb Biotechnol 2016; 9:801-813. [PMID: 27624853 PMCID: PMC5072196 DOI: 10.1111/1751-7915.12402] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 06/15/2016] [Indexed: 01/24/2023] Open
Abstract
Few information is available about the tyraminogenic potential of the species Enterococcus mundtii. In this study, two plant‐derived strains of E. mundtii were selected and investigated to better understand the phenotypic behaviour and the genetic mechanisms involved in tyramine accumulation. Both the strains accumulated tyramine from the beginning of exponential phase of growth, independently on the addition of tyrosine to the medium. The strains accumulated also 2‐phenylethylamine, although with lower efficiency and in greater extent when tyrosine was not added. Accordingly, the tyrosine decarboxylase (tyrDC) gene expression level increased during the exponential phase with tyrosine added, while it remained constant and high without precursor. The genetic organization as well as sequence identity levels of tyrDC and tyrosine permease (tyrP) genes indicated a correlation with those of phylogenetically closer enterococcal species, such as E. faecium, E. hirae and E. durans; however, the gene Na+/H+ antiporter (nhaC) that usually follow tyrP is missing. In addition, BLAST analysis revealed the presence of additional genes encoding for decarboxylase and permease in the genome of several E. mundtii strains. It is speculated the occurrence of a duplication event and the acquisition of different specificity for these enzymes that deserves further investigations.
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Affiliation(s)
- Veronica Gatto
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Giulia Tabanelli
- Department of Agricultural and Food Sciences, University of Bologna, Cesena, Italy
| | - Chiara Montanari
- Interdepartmental Center for Industrial Agri-food Research, University of Bologna, Cesena, Italy
| | | | - Eleonora Bargossi
- Department of Agricultural and Food Sciences, University of Bologna, Cesena, Italy
| | - Sandra Torriani
- Department of Biotechnology, University of Verona, Verona, Italy.
| | - Fausto Gardini
- Department of Agricultural and Food Sciences, University of Bologna, Cesena, Italy.,Interdepartmental Center for Industrial Agri-food Research, University of Bologna, Cesena, Italy
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The Plasmidome of Firmicutes: Impact on the Emergence and the Spread of Resistance to Antimicrobials. Microbiol Spectr 2016; 3:PLAS-0039-2014. [PMID: 26104702 DOI: 10.1128/microbiolspec.plas-0039-2014] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The phylum Firmicutes is one of the most abundant groups of prokaryotes in the microbiota of humans and animals and includes genera of outstanding relevance in biomedicine, health care, and industry. Antimicrobial drug resistance is now considered a global health security challenge of the 21st century, and this heterogeneous group of microorganisms represents a significant part of this public health issue.The presence of the same resistant genes in unrelated bacterial genera indicates a complex history of genetic interactions. Plasmids have largely contributed to the spread of resistance genes among Staphylococcus, Enterococcus, and Streptococcus species, also influencing the selection and ecological variation of specific populations. However, this information is fragmented and often omits species outside these genera. To date, the antimicrobial resistance problem has been analyzed under a "single centric" perspective ("gene tracking" or "vehicle centric" in "single host-single pathogen" systems) that has greatly delayed the understanding of gene and plasmid dynamics and their role in the evolution of bacterial communities.This work analyzes the dynamics of antimicrobial resistance genes using gene exchange networks; the role of plasmids in the emergence, dissemination, and maintenance of genes encoding resistance to antimicrobials (antibiotics, heavy metals, and biocides); and their influence on the genomic diversity of the main Gram-positive opportunistic pathogens under the light of evolutionary ecology. A revision of the approaches to categorize plasmids in this group of microorganisms is given using the 1,326 fully sequenced plasmids of Gram-positive bacteria available in the GenBank database at the time the article was written.
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14
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Abdel-Rahman MA, Tashiro Y, Zendo T, Sakai K, Sonomoto K. Highly efficient l-lactic acid production from xylose in cell recycle continuous fermentation using Enterococcus mundtii QU 25. RSC Adv 2016. [DOI: 10.1039/c5ra27579b] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
We report an effective cell recycling continuous fermentation of xylose to l-lactic acid with high concentration, productivity, and yield using strain QU 25. pH was found to affect the yield and corn steep liquor as feeding medium enhanced the yield.
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Affiliation(s)
- Mohamed Ali Abdel-Rahman
- Laboratory of Microbial Technology
- Division of Systems Bioengineering
- Department of Bioscience and Biotechnology
- Faculty of Agriculture
- Graduate School
| | - Yukihiro Tashiro
- Laboratory of Soil and Environmental Microbiology
- Division of Systems Bioengineering
- Department of Bioscience and Biotechnology
- Faculty of Agriculture
- Graduate School
| | - Takeshi Zendo
- Laboratory of Microbial Technology
- Division of Systems Bioengineering
- Department of Bioscience and Biotechnology
- Faculty of Agriculture
- Graduate School
| | - Kenji Sakai
- Laboratory of Soil and Environmental Microbiology
- Division of Systems Bioengineering
- Department of Bioscience and Biotechnology
- Faculty of Agriculture
- Graduate School
| | - Kenji Sonomoto
- Laboratory of Microbial Technology
- Division of Systems Bioengineering
- Department of Bioscience and Biotechnology
- Faculty of Agriculture
- Graduate School
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15
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Lyons C, Raustad N, Bustos MA, Shiaris M. Incidence of Type II CRISPR1-Cas Systems in Enterococcus Is Species-Dependent. PLoS One 2015; 10:e0143544. [PMID: 26600384 PMCID: PMC4658022 DOI: 10.1371/journal.pone.0143544] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 11/05/2015] [Indexed: 12/19/2022] Open
Abstract
CRISPR-Cas systems, which obstruct both viral infection and incorporation of mobile genetic elements by horizontal transfer, are a specific immune response common to prokaryotes. Antiviral protection by CRISPR-Cas comes at a cost, as horizontally-acquired genes may increase fitness and provide rapid adaptation to habitat change. To date, investigations into the prevalence of CRISPR have primarily focused on pathogenic and clinical bacteria, while less is known about CRISPR dynamics in commensal and environmental species. We designed PCR primers and coupled these with DNA sequencing of products to detect and characterize the presence of cas1, a universal CRISPR-associated gene and proxy for the Type II CRISPR1-Cas system, in environmental and non-clinical Enterococcus isolates. CRISPR1-cas1 was detected in approximately 33% of the 275 strains examined, and differences in CRISPR1 carriage between species was significant. Incidence of cas1 in E. hirae was 73%, nearly three times that of E. faecalis (23.6%) and 10 times more frequent than in E. durans (7.1%). Also, this is the first report of CRISPR1 presence in E. durans, as well as in the plant-associated species E. casseliflavus and E. sulfureus. Significant differences in CRISPR1-cas1 incidence among Enterococcus species support the hypothesis that there is a tradeoff between protection and adaptability. The differences in the habitats of enterococcal species may exert varying selective pressure that results in a species-dependent distribution of CRISPR-Cas systems.
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Affiliation(s)
- Casandra Lyons
- Biology Department, University of Massachusetts Boston, Boston, Massachusetts, United States of America
| | - Nicole Raustad
- Biology Department, University of Massachusetts Boston, Boston, Massachusetts, United States of America
| | - Mario A. Bustos
- Biology Department, University of Massachusetts Boston, Boston, Massachusetts, United States of America
| | - Michael Shiaris
- Biology Department, University of Massachusetts Boston, Boston, Massachusetts, United States of America
- * E-mail:
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16
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Yanase H, Araya-Kojima T, Shiwa Y, Watanabe S, Zendo T, Chibazakura T, Shimizu-Kadota M, Sonomoto K, Yoshikawa H. Transcriptional regulation of xylose utilization in Enterococcus mundtii QU 25. RSC Adv 2015. [DOI: 10.1039/c5ra15028k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In the xylose and/or glucose utilization by QU 25,the transcriptional regulation of related genes is involved in the catabolite repression,not in the metabolic shift between homo- and hetero-lactic fermentations.
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Affiliation(s)
- Hiroaki Yanase
- Department of Bioscience
- Tokyo University of Agriculture
- Tokyo 156-8502
- Japan
| | | | - Yuh Shiwa
- Genome Research Center
- NODAI Research Institute
- Tokyo University of Agriculture
- Tokyo 156-8502
- Japan
| | - Satoru Watanabe
- Department of Bioscience
- Tokyo University of Agriculture
- Tokyo 156-8502
- Japan
| | - Takeshi Zendo
- Laboratory of Microbial Technology
- Division of Systems Bioengineering
- Department of Bioscience and Biotechnology
- Faculty of Agriculture
- Graduate School
| | - Taku Chibazakura
- Department of Bioscience
- Tokyo University of Agriculture
- Tokyo 156-8502
- Japan
| | - Mariko Shimizu-Kadota
- Department of Environmental Sciences
- Musashino University
- Tokyo 135-8181
- Japan
- Department of Bioscience
| | - Kenji Sonomoto
- Laboratory of Microbial Technology
- Division of Systems Bioengineering
- Department of Bioscience and Biotechnology
- Faculty of Agriculture
- Graduate School
| | - Hirofumi Yoshikawa
- Department of Bioscience
- Tokyo University of Agriculture
- Tokyo 156-8502
- Japan
- Genome Research Center
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17
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Microbial taxonomy in the post-genomic era: rebuilding from scratch? Arch Microbiol 2014; 197:359-70. [PMID: 25533848 DOI: 10.1007/s00203-014-1071-2] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Revised: 12/04/2014] [Accepted: 12/05/2014] [Indexed: 12/20/2022]
Abstract
Microbial taxonomy should provide adequate descriptions of bacterial, archaeal, and eukaryotic microbial diversity in ecological, clinical, and industrial environments. Its cornerstone, the prokaryote species has been re-evaluated twice. It is time to revisit polyphasic taxonomy, its principles, and its practice, including its underlying pragmatic species concept. Ultimately, we will be able to realize an old dream of our predecessor taxonomists and build a genomic-based microbial taxonomy, using standardized and automated curation of high-quality complete genome sequences as the new gold standard.
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