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Maghembe R, Moto E, Makaranga A, Mdoe F, Mpemba J, Magulye MAK, Mark D, Mtewa A. Complete genome sequence of Bacillus subtilis strain MARUCo01 isolated from marine sediments of the Indian Ocean in Bagamoyo, Tanzania. Microbiol Resour Announc 2023; 12:e0047323. [PMID: 37606380 PMCID: PMC10508113 DOI: 10.1128/mra.00473-23] [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: 06/02/2023] [Accepted: 07/19/2023] [Indexed: 08/23/2023] Open
Abstract
Bacillus subtilis has emerged as a species with potential for versatile nonribosomal peptides and polyketides of therapeutic importance, including antibiotics. From our molecular bioprospecting project, we report a full genome of Bacillus subtilis strain MARUCo01 locally isolated from sediments of the Indian Ocean along the coast of Bagamoyo in Tanzania.
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Affiliation(s)
- Reuben Maghembe
- Biological and Marine Sciences Unit, Faculty of Natural and Applied Sciences, Marian University College, Bagamoyo, Tanzania
- Department of Biological Sciences, Faculty of Science, University of Botswana, Gaborone, Botswana
- Department of Microbiology and Immunology, Faculty of Biomedical Sciences, Kampala International University Western Campus, Kampala, Uganda
| | - Edward Moto
- Department of Biology, College of Natural and Mathematics Sciences, University of Dodoma, Dodoma, Tanzania
| | - Abdalah Makaranga
- Biological and Marine Sciences Unit, Faculty of Natural and Applied Sciences, Marian University College, Bagamoyo, Tanzania
| | - France Mdoe
- Biological and Marine Sciences Unit, Faculty of Natural and Applied Sciences, Marian University College, Bagamoyo, Tanzania
| | - James Mpemba
- Department of Biochemistry and Physiology, St. Francis University College of Health and Allied Sciences, Ifakara, Tanzania
| | - Maximilian A. K. Magulye
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University, Kampala, Uganda
| | - Deogratius Mark
- Department of Disease Control, Tanzania Agricultural Research Institute (TARI), Dar es Salaam, Tanzania
| | - Andrew Mtewa
- Chemistry Section, Department of Applied Sciences, Malawi Institute of Technology, Malawi University of Science and Technology, Limbe, Malawi
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Maghembe RS, Mdoe FP, Makaranga A, Mpemba JA, Mark D, Mlay C, Moto EA, Mtewa AG. Complete genome sequence data of Priestia megaterium strain MARUCO02 isolated from marine mangrove-inhabited sediments of the Indian Ocean in the Bagamoyo Coast. Data Brief 2023. [DOI: 10.1016/j.dib.2023.109119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023] Open
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dos Santos Melo-Nascimento AO, Mota Moitinho Sant´Anna B, Gonçalves CC, Santos G, Noronha E, Parachin N, de Abreu Roque MR, Bruce T. Complete genome reveals genetic repertoire and potential metabolic strategies involved in lignin degradation by environmental ligninolytic Klebsiella variicola P1CD1. PLoS One 2020; 15:e0243739. [PMID: 33351813 PMCID: PMC7755216 DOI: 10.1371/journal.pone.0243739] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 11/30/2020] [Indexed: 11/23/2022] Open
Abstract
Lignin is a recalcitrant macromolecule formed by three alcohols (monolignols) predominantly connected by β-aryl ether linkages and is one of the most abundant organic macromolecules in the biosphere. However, the role played by environmental bacteria in lignin degradation is still not entirely understood. In this study, we identified an environmental Klebsiella strain isolated from sediment collected from an altitudinal region in a unique Brazilian biome called Caatinga. This organism can also grow in the presence of kraft lignin as a sole source of carbon and aromatic compounds. We performed whole-genome sequencing and conducted an extensive genome-based metabolic reconstruction to reveal the potential mechanisms used by the bacterium Klebsiella variicola P1CD1 for lignin utilization as a carbon source. We identified 262 genes associated with lignin-modifying enzymes (LMEs) and lignin-degrading auxiliary enzymes (LDAs) required for lignin and aromatic compound degradation. The presence of one DyP (Dye-decolorizing Peroxidase) gene suggests the ability of P1CD1 strain to access phenolic and nonphenolic structures of lignin molecules, resulting in the production of catechol and protocatechuate (via vanillin or syringate) along the peripheral pathways of lignin degradation. K. variicola P1CD1 uses aldehyde-alcohol dehydrogenase to perform direct conversion of vanillin to protocatechol. The upper funneling pathways are linked to the central pathways of the protocatechuate/catechol catabolic branches via β-ketoadipate pathways, connecting the more abundant catabolized aromatic compounds with essential cellular functions, such as energy cellular and biomass production (i.e., via acetyl-CoA formation). The combination of phenotypic and genomic approaches revealed the potential dissimilatory and assimilatory ability of K. variicola P1CD1 to perform base-catalyzed lignin degradation, acting on high- and low-molecular-weight lignin fragments. These findings will be relevant for developing metabolic models to predict the ligninolytic mechanism used by environmental bacteria and shedding light on the flux of carbon in the soil.
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Affiliation(s)
| | | | - Carolyne Caetano Gonçalves
- Departamento de Biologia Celular, Instituto de Biologia, Laboratório de Engenharia de Biocatalizadores, Universidade de Brasília, Brasília, Brazil
| | - Giovanna Santos
- Departamento de Biologia Celular, Instituto de Biologia, Laboratório de Engenharia de Biocatalizadores, Universidade de Brasília, Brasília, Brazil
| | - Eliane Noronha
- Departamento de Biologia Celular, Instituto de Biologia, Laboratório de Engenharia de Biocatalizadores, Universidade de Brasília, Brasília, Brazil
| | - Nádia Parachin
- Departamento de Biologia Celular, Instituto de Biologia, Universidade de Brasília, Brasília, Brazil
| | - Milton Ricardo de Abreu Roque
- Departamento de Microbiologia, Instituto de Biologia, Grupo de Biotecnologia Ambiental, Universidade Federal da Bahia, Salvador, Brazil
- Instituto de Ciências da Saúde, Laboratório de Bioprospecção, Universidade Federal da Bahia, Salvador, Brazil
| | - Thiago Bruce
- Departamento de Microbiologia, Instituto de Biologia, Grupo de Biotecnologia Ambiental, Universidade Federal da Bahia, Salvador, Brazil
- Departamento de Biologia Celular, Instituto de Biologia, Universidade de Brasília, Brasília, Brazil
- * E-mail:
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Crawley AB, Barrangou R. Conserved Genome Organization and Core Transcriptome of the Lactobacillus acidophilus Complex. Front Microbiol 2018; 9:1834. [PMID: 30150974 PMCID: PMC6099100 DOI: 10.3389/fmicb.2018.01834] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 07/23/2018] [Indexed: 01/08/2023] Open
Abstract
The Lactobacillus genus encompasses a genetically and functionally diverse group of species, and contains many strains widely formulated in the human food supply chain as probiotics and starter cultures. Within this genetically expansive group, there are several distinct clades that have high levels of homology, one of which is the Lactobacillus acidophilus group. Of the uniting features, small genomes, low GC content, adaptation to dairy environments, and fastidious growth requirements, are some of the most defining characteristics of this group. To better understand what truly links and defines this clade, we sought to characterize the genomic organization and content of the genomes of several members of this group. Through core genome analysis we explored the synteny and intrinsic genetic underpinnings of the L. acidophilus clade, and observed key features related to the evolution and adaptation of these organisms. While genetic content is able to provide a large map of the potential of each organism, it does not always reflect their functionality. Through transcriptomic data we inferred the core transcriptome of the L. acidophilus complex to better define the true metabolic capabilities that unite this clade. Using this approach we have identified seven small ORFs that are both highly conserved and transcribed in diverse members of this clade and could be potential novel small peptide or untranslated RNA regulators. Overall, our results reveal the core features of the L. acidophilus complex and open new avenues for the enhancement and formulation and of next generation probiotics and starter cultures.
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Affiliation(s)
- Alexandra B Crawley
- Genomic Sciences Program, NC State University, Raleigh, NC, United States.,Department of Food, Bioprocessing and Nutrition Sciences, NC State University, Raleigh, NC, United States
| | - Rodolphe Barrangou
- Genomic Sciences Program, NC State University, Raleigh, NC, United States.,Department of Food, Bioprocessing and Nutrition Sciences, NC State University, Raleigh, NC, United States
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Dantur KI, Chalfoun NR, Claps MP, Tórtora ML, Silva C, Jure Á, Porcel N, Bianco MI, Vojnov A, Castagnaro AP, Welin B. The Endophytic Strain Klebsiella michiganensis Kd70 Lacks Pathogenic Island-Like Regions in Its Genome and Is Incapable of Infecting the Urinary Tract in Mice. Front Microbiol 2018; 9:1548. [PMID: 30061870 PMCID: PMC6054940 DOI: 10.3389/fmicb.2018.01548] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 06/21/2018] [Indexed: 01/14/2023] Open
Abstract
Klebsiella spp. have been isolated from many different environmental habitats but have mainly been associated with nosocomial acquired diseases in humans. Although there are many recently published sequenced genomes of members of this genus, there are very few studies on whole genome comparisons between clinical and non-clinical isolates, and it is therefore still an open question if a strain found in nature is capable of infecting humans/animals. Klebsiella michiganensis Kd70 was isolated from the intestine of larvae of Diatraea saccharalis but genome analysis revealed multiple genes associated with colonization and growth promotion in plants suggesting an endophytic lifestyle. Kd70 cells labeled with gfp confirmed capability of root colonization and soil application of Kd70 promoted growth in greenhouse grown sugarcane. Further genomic analysis showed that the Kd70 genome harbored fewer mammalian virulence factors and no pathogen island-like regions when compared to clinical isolates of this species, suggesting attenuated animal/human pathogenicity. This postulation was corroborated by in vivo experiments in which it was demonstrated that Kd70 was unable to infect the mouse urinary tract. This is to the best of our knowledge the first experimental example of a member of a pathogenic Klebsiella spp. unable to infect a mammalian organism. A proteomic comparison deduced from the genomic sequence between Kd70 and several other K. michiganensis strains showed a high similarity with isolates from many different environments including clinical strains, and demonstrated the existence of conserved genetic lineages within this species harboring members from different ecological niches and geographical locations. Furthermore, most genetic differences were found to be associated with genomic islands of clinical isolates, suggesting that evolutionary adaptation of animal pathogenicity to a large extent has depended on horizontal gene transfer. In conclusion our results demonstrate the importance of conducting thorough in vivo pathogenicity studies before presupposing animal/human virulence of non-clinical bacterial isolates.
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Affiliation(s)
- Karina I. Dantur
- Instituto de Tecnología Agroindustrial del Noroeste Argentino, Estación Experimental Agroindustrial Obispo Colombres – Consejo Nacional de Investigaciones Científicas y Técnicas, Las Talitas, Argentina
| | - Nadia R. Chalfoun
- Instituto de Tecnología Agroindustrial del Noroeste Argentino, Estación Experimental Agroindustrial Obispo Colombres – Consejo Nacional de Investigaciones Científicas y Técnicas, Las Talitas, Argentina
| | - Maria P. Claps
- Instituto de Tecnología Agroindustrial del Noroeste Argentino, Estación Experimental Agroindustrial Obispo Colombres – Consejo Nacional de Investigaciones Científicas y Técnicas, Las Talitas, Argentina
| | - Maria L. Tórtora
- Instituto de Tecnología Agroindustrial del Noroeste Argentino, Estación Experimental Agroindustrial Obispo Colombres – Consejo Nacional de Investigaciones Científicas y Técnicas, Las Talitas, Argentina
| | - Clara Silva
- Instituto de Microbiología, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Tucumán, Argentina
| | - Ángela Jure
- Instituto de Microbiología, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Tucumán, Argentina
| | - Norma Porcel
- Instituto de Microbiología, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Tucumán, Argentina
| | - Maria I. Bianco
- Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará – Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Adrián Vojnov
- Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará – Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Atilio P. Castagnaro
- Instituto de Tecnología Agroindustrial del Noroeste Argentino, Estación Experimental Agroindustrial Obispo Colombres – Consejo Nacional de Investigaciones Científicas y Técnicas, Las Talitas, Argentina
| | - Björn Welin
- Instituto de Tecnología Agroindustrial del Noroeste Argentino, Estación Experimental Agroindustrial Obispo Colombres – Consejo Nacional de Investigaciones Científicas y Técnicas, Las Talitas, Argentina
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Knudsen PK, Gammelsrud KW, Alfsnes K, Steinbakk M, Abrahamsen TG, Müller F, Bohlin J. Transfer of a bla CTX-M-1-carrying plasmid between different Escherichia coli strains within the human gut explored by whole genome sequencing analyses. Sci Rep 2018; 8:280. [PMID: 29321570 PMCID: PMC5762863 DOI: 10.1038/s41598-017-18659-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 12/14/2017] [Indexed: 01/08/2023] Open
Abstract
Horizontal transfer of antibiotic resistance determinants contributes to dissemination of antibiotic resistance. Such transfer of resistance genes within the human gut has been documented in some in vivo studies. The present study investigated seven bla CTX-M-1-carrying Escherichia coli isolates from three consecutive faecal samples collected from one cystic fibrosis patient in a nine-months period, by analysing whole genome sequencing data. The analyses showed that the seven E. coli isolates represented three genetically diverse strains. All isolates contained bla CTX-M-1-carrying Incl1 plasmids that shared a common 101 kb backbone differing by only four SNPs. The plasmids harboured by the three different E. coli strains varied within limited regions suggestive of recombination events, according to the phylogenetic topology of the genomes of the isolates harbouring them. The findings strongly suggest that horizontal transfer of a bla CTX-M-1-carrying plasmid had occurred within the patient´s gut. The study illustrates the within-host diversity of faecally carried resistant E. coli isolates and highlights the value of collecting multiple bacterial colonies from longitudinally collected samples to assess faecal carriage of resistant enterobacteria. The clustering of the plasmids with the corresponding E. coli strains carrying them indicates that the plasmids appear to have adapted to their respective E. coli hosts.
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Affiliation(s)
- Per Kristian Knudsen
- Department of Paediatric Medicine, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, PB 4956 Nydalen, 0424, Oslo, Norway. .,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, PB 1171 Blindern, 0318, Oslo, Norway.
| | - Karianne Wiger Gammelsrud
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, PB 1171 Blindern, 0318, Oslo, Norway.,Department of Microbiology, Division of Laboratory Medicine, Oslo University Hospital, PB 4956 Nydalen, 0424, Oslo, Norway
| | - Kristian Alfsnes
- Department of Molecular Biology, Domain of Infection Control and Environmental Health, Norwegian Institute of Public Health, PB 4404 Nydalen, 0403, Oslo, Norway
| | - Martin Steinbakk
- Department of Antibiotic Resistance and Infection Prevention, Domain of Infection Control and Environmental Health, Norwegian Institute of Public Health, PB 4404 Nydalen, 0403, Oslo, Norway
| | - Tore G Abrahamsen
- Department of Paediatric Medicine, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, PB 4956 Nydalen, 0424, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, PB 1171 Blindern, 0318, Oslo, Norway
| | - Fredrik Müller
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, PB 1171 Blindern, 0318, Oslo, Norway.,Department of Microbiology, Division of Laboratory Medicine, Oslo University Hospital, PB 4956 Nydalen, 0424, Oslo, Norway
| | - Jon Bohlin
- Department of Methodology Research and Analysis, Domain of Infection Control and Environmental Health, Norwegian Institute of Public Health, PB 4404 Nydalen, 0403, Oslo, Norway
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Genome Sequence of a Gram-Positive Diazotroph, Paenibacillus durus Type Strain ATCC 35681. GENOME ANNOUNCEMENTS 2016; 4:4/1/e00005-16. [PMID: 26893411 PMCID: PMC4759058 DOI: 10.1128/genomea.00005-16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Here, we report the complete genome sequence of Paenibacillus durus type strain ATCC 35681, which can fix atmospheric nitrogen even in the presence of nitrate.
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