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Simpson AC, Sengupta P, Zhang F, Hameed A, Parker CW, Singh NK, Miliotis G, Rekha PD, Raman K, Mason CE, Venkateswaran K. Phylogenomics, phenotypic, and functional traits of five novel (Earth-derived) bacterial species isolated from the International Space Station and their prevalence in metagenomes. Sci Rep 2023; 13:19207. [PMID: 37932283 PMCID: PMC10628120 DOI: 10.1038/s41598-023-44172-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 10/04/2023] [Indexed: 11/08/2023] Open
Abstract
With the advent of long-term human habitation in space and on the moon, understanding how the built environment microbiome of space habitats differs from Earth habitats, and how microbes survive, proliferate and spread in space conditions, is becoming more important. The microbial tracking mission series has been monitoring the microbiome of the International Space Station (ISS) for almost a decade. During this mission series, six unique strains of Gram-stain-positive bacteria, including two spore-forming and three non-spore-forming species, were isolated from the environmental surfaces of the ISS. The analysis of their 16S rRNA gene sequences revealed > 99% similarities with previously described bacterial species. To further explore their phylogenetic affiliation, whole genome sequencing was undertaken. For all strains, the gyrB gene exhibited < 93% similarity with closely related species, which proved effective in categorizing these ISS strains as novel species. Average nucleotide identity and digital DNA-DNA hybridization values, when compared to any known bacterial species, were < 94% and <50% respectively for all species described here. Traditional biochemical tests, fatty acid profiling, polar lipid, and cell wall composition analyses were performed to generate phenotypic characterization of these ISS strains. A study of the shotgun metagenomic reads from the ISS samples, from which the novel species were isolated, showed that only 0.1% of the total reads mapped to the novel species, supporting the idea that these novel species are rare in the ISS environments. In-depth annotation of the genomes unveiled a variety of genes linked to amino acid and derivative synthesis, carbohydrate metabolism, cofactors, vitamins, prosthetic groups, pigments, and protein metabolism. Further analysis of these ISS-isolated organisms revealed that, on average, they contain 46 genes associated with virulence, disease, and defense. The main predicted functions of these genes are: conferring resistance to antibiotics and toxic compounds, and enabling invasion and intracellular resistance. After conducting antiSMASH analysis, it was found that there are roughly 16 cluster types across the six strains, including β-lactone and type III polyketide synthase (T3PKS) clusters. Based on these multi-faceted taxonomic methods, it was concluded that these six ISS strains represent five novel species, which we propose to name as follows: Arthrobacter burdickii IIF3SC-B10T (= NRRL B-65660T = DSM 115933T), Leifsonia virtsii F6_8S_P_1AT (= NRRL B-65661T = DSM 115931T), Leifsonia williamsii F6_8S_P_1BT (= NRRL B-65662T = DSM 115932T), Paenibacillus vandeheii F6_3S_P_1CT (= NRRL B-65663T = DSM 115940T), and Sporosarcina highlanderae F6_3S_P_2T (= NRRL B-65664T = DSM 115943T). Identifying and characterizing the genomes and phenotypes of novel microbes found in space habitats, like those explored in this study, is integral for expanding our genomic databases of space-relevant microbes. This approach offers the only reliable method to determine species composition, track microbial dispersion, and anticipate potential threats to human health from monitoring microbes on the surfaces and equipment within space habitats. By unraveling these microbial mysteries, we take a crucial step towards ensuring the safety and success of future space missions.
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Affiliation(s)
- Anna C Simpson
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | - Pratyay Sengupta
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600 036, India
- Center for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology Madras, Chennai, 600 036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology Madras, Chennai, 600 036, India
| | - Flora Zhang
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | - Asif Hameed
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Ceth W Parker
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | - Nitin K Singh
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | - Georgios Miliotis
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland
| | - Punchappady D Rekha
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Karthik Raman
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600 036, India
- Center for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology Madras, Chennai, 600 036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology Madras, Chennai, 600 036, India
| | - Christopher E Mason
- Department of Physiology and Biophysics, and the WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA.
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA.
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Simpson AC, Sengupta P, Zhang F, Hameed A, Parker CW, Singh NK, Miliotis G, Rekha PD, Raman K, Mason CE, Venkateswaran K. Phylogenetic affiliations and genomic characterization of novel bacterial species and their abundance in the International Space Station. RESEARCH SQUARE 2023:rs.3.rs-3126314. [PMID: 37461605 PMCID: PMC10350232 DOI: 10.21203/rs.3.rs-3126314/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Background With the advent of long-term human habitation in space and on the moon, understanding how the built environment microbiome of space habitats differs from Earth habits, and how microbes survive, proliferate and spread in space conditions, is coming more and more important. The Microbial Tracking mission series has been monitoring the microbiome of the International Space Station (ISS) for almost a decade. During this mission series, six unique strains of Gram-positive bacteria, including two spore-forming and three non-spore-forming species, were isolated from the environmental surfaces of the International Space Station (ISS). Results The analysis of their 16S rRNA gene sequences revealed <99% similarities with previously described bacterial species. To further explore their phylogenetic affiliation, whole genome sequencing (WGS) was undertaken. For all strains, the gyrB gene exhibited <93% similarity with closely related species, which proved effective in categorizing these ISS strains as novel species. Average ucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values, when compared to any known bacterial species, were less than <94% and 50% respectively for all species described here. Traditional biochemical tests, fatty acid profiling, polar lipid, and cell wall composition analyses were performed to generate phenotypic characterization of these ISS strains. A study of the shotgun metagenomic reads from the ISS samples, from which the novel species were isolated, showed that only 0.1% of the total reads mapped to the novel species, supporting the idea that these novel species are rare in the ISS environments. In-depth annotation of the genomes unveiled a variety of genes linked to amino acid and derivative synthesis, carbohydrate metabolism, cofactors, vitamins, prosthetic groups, pigments, and protein metabolism. Further analysis of these ISS-isolated organisms revealed that, on average, they contain 46 genes associated with virulence, disease, and defense. The main predicted functions of these genes are: conferring resistance to antibiotics and toxic compounds, and enabling invasion and intracellular resistance. After conducting antiSMASH analysis, it was found that there are roughly 16 cluster types across the six strains, including β-lactone and type III polyketide synthase (T3PKS) clusters. Conclusions Based on these multi-faceted taxonomic methods, it was concluded that these six ISS strains represent five novel species, which we propose to name as follows: Arthrobacter burdickii IIF3SC-B10T (=NRRL B-65660T), Leifsonia virtsii, F6_8S_P_1AT (=NRRL B-65661T), Leifsonia williamsii, F6_8S_P_1BT (=NRRL B- 65662T and DSMZ 115932T), Paenibacillus vandeheii, F6_3S_P_1CT(=NRRL B-65663T and DSMZ 115940T), and Sporosarcina highlanderae F6_3S_P_2 T(=NRRL B-65664T and DSMZ 115943T). Identifying and characterizing the genomes and phenotypes of novel microbes found in space habitats, like those explored in this study, is integral for expanding our genomic databases of space-relevant microbes. This approach offers the only reliable method to determine species composition, track microbial dispersion, and anticipate potential threats to human health from monitoring microbes on the surfaces and equipment within space habitats. By unraveling these microbial mysteries, we take a crucial step towards ensuring the safety and success of future space missions.
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Affiliation(s)
- Anna C. Simpson
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Pratyay Sengupta
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600 036, India
- Center for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology Madras, Chennai, 600 036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology Madras, Chennai, 600 036, India
| | - Flora Zhang
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Asif Hameed
- Yenepoya Research Centre, Yenepoya Deemed to be University, Mangalore 575018, India
| | - Ceth W. Parker
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Nitin K. Singh
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Georgios Miliotis
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland
| | - Punchappady D. Rekha
- Yenepoya Research Centre, Yenepoya Deemed to be University, Mangalore 575018, India
| | - Karthik Raman
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600 036, India
- Center for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology Madras, Chennai, 600 036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology Madras, Chennai, 600 036, India
| | - Christopher E. Mason
- Department of Physiology and Biophysics, and the WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, United States
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
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Khelaifia S, Virginie P, Belkacemi S, Tassery H, Terrer E, Aboudharam G. Culturing the Human Oral Microbiota, Updating Methodologies and Cultivation Techniques. Microorganisms 2023; 11:microorganisms11040836. [PMID: 37110259 PMCID: PMC10143722 DOI: 10.3390/microorganisms11040836] [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: 01/24/2023] [Revised: 03/16/2023] [Accepted: 03/23/2023] [Indexed: 04/29/2023] Open
Abstract
Recent years have been marked by a paradigm shift in the study of the human microbiota, with a re-emergence of culture-dependent approaches. Numerous studies have been devoted to the human microbiota, while studies on the oral microbiota still remain limited. Indeed, various techniques described in the literature may enable an exhaustive study of the microbial composition of a complex ecosystem. In this article, we report different methodologies and culture media described in the literature that can be applied to study the oral microbiota by culture. We report on specific methodologies for targeted culture and specific culture techniques and selection methodologies for cultivating members of the three kingdoms of life commonly found in the human oral cavity, namely, eukaryota, bacteria and archaea. This bibliographic review aims to bring together the various techniques described in the literature, enabling a comprehensive study of the oral microbiota in order to demonstrate its involvement in oral health and diseases.
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Affiliation(s)
- Saber Khelaifia
- Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Univ, IRD, MEPHI, AP-HM, 19-21 Boulevard Jean Moulin, 13385 Marseille CEDEX 05, France
- Ecole de Médecine Dentaire, 27 Boulevard Jean Moulin, 13385 Marseille CEDEX 05, France
| | - Pilliol Virginie
- Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Univ, IRD, MEPHI, AP-HM, 19-21 Boulevard Jean Moulin, 13385 Marseille CEDEX 05, France
- Ecole de Médecine Dentaire, 27 Boulevard Jean Moulin, 13385 Marseille CEDEX 05, France
| | - Souad Belkacemi
- Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Univ, IRD, MEPHI, AP-HM, 19-21 Boulevard Jean Moulin, 13385 Marseille CEDEX 05, France
| | - Herve Tassery
- Ecole de Médecine Dentaire, 27 Boulevard Jean Moulin, 13385 Marseille CEDEX 05, France
| | - Elodie Terrer
- Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Univ, IRD, MEPHI, AP-HM, 19-21 Boulevard Jean Moulin, 13385 Marseille CEDEX 05, France
- Ecole de Médecine Dentaire, 27 Boulevard Jean Moulin, 13385 Marseille CEDEX 05, France
| | - Gérard Aboudharam
- Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Univ, IRD, MEPHI, AP-HM, 19-21 Boulevard Jean Moulin, 13385 Marseille CEDEX 05, France
- Ecole de Médecine Dentaire, 27 Boulevard Jean Moulin, 13385 Marseille CEDEX 05, France
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Choksket S, Jain A, Sharma D, Grover V, Korpole S. Paraclostridium dentum, a novel species with pathogenic features isolated from human dental plaque sample. Anaerobe 2020; 65:102239. [PMID: 32758667 DOI: 10.1016/j.anaerobe.2020.102239] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 07/06/2020] [Accepted: 07/08/2020] [Indexed: 12/21/2022]
Abstract
A strictly anaerobic bacterial strain designated as SKVG24 was isolated from subgingival dental plaque samples of patients suffering from periodontitis. Cells were stained Gram-positive, rod shaped with endospore. The strain showed negative reaction to catalase and oxidase enzymes, but positive for gelatinase activity. Optimal growth was observed at 37 °C temperature and 7.0 pH. The 16S rRNA gene sequence BLAST analysis assigned strain SKVG24 to the genus Paraclostridium as it displayed 99.93% identity with P. benzoelyticum JC272T followed by P. bifermentans ATCC 638T (99.79%). However, average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) of the whole genome sequence showed <97% and <70% identity, respectively, with type strains of all closely related species. The G + C content of the DNA was 28.7 mol%. Total lipids profile showed presence of glycolipids as major lipids. Pathogenic features like hemolysis, gelatin hydrolysis and production of volatile sulfur compounds exhibited by strain SKVG24T were analogous to those observed in the established oral pathogenic strains. Further, whole genome sequence analysis confirmed the presence of genes encoding virulence factors and provided genomic insights on adaptation of the strain in oral environment. Based on the phenotypic and genetic differences with phylogenetic relatives, strain SKVG24T is proposed to represent a new species of the genus Paraclostridium with potential pathogenic ability, for which the name Paraclostridium dentum sp. nov., is suggested. The proposed type strain is SKVG24T (MTCC 12836T; = JCM 32760T).
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Affiliation(s)
- Stanzin Choksket
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, India
| | - Ashish Jain
- Dr. Harvansh Singh Judge Institute of Dental Sciences and Hospital, Panjab University, Chandigarh, India
| | - Deepika Sharma
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, India
| | - Vishakha Grover
- Dr. Harvansh Singh Judge Institute of Dental Sciences and Hospital, Panjab University, Chandigarh, India.
| | - Suresh Korpole
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, India.
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Draft Genome Sequence of Streptococcus halitosis sp. nov., Isolated from the Dorsal Surface of the Tongue of a Patient with Halitosis. Microbiol Resour Announc 2019; 8:MRA01704-18. [PMID: 30701262 PMCID: PMC6346211 DOI: 10.1128/mra.01704-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 01/04/2019] [Indexed: 01/10/2023] Open
Abstract
Here, we report the draft genome of Streptococcus halitosis sp. nov. strain VT-4, a novel bacterium isolated from the dorsal part of the tongue of a patient with halitosis. The genome comprised 1,880,608 bp with a GC content of 41.0%. Here, we report the draft genome of Streptococcus halitosis sp. nov. strain VT-4, a novel bacterium isolated from the dorsal part of the tongue of a patient with halitosis. The genome comprised 1,880,608 bp with a GC content of 41.0%. There were 1,782 predicted protein-coding genes, including those associated with virulence and antibiotic resistance.
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Tetz G, Tetz V. Tetz's theory and law of longevity. Theory Biosci 2018; 137:145-154. [PMID: 29978435 PMCID: PMC6208853 DOI: 10.1007/s12064-018-0267-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 06/29/2018] [Indexed: 11/30/2022]
Abstract
Here, we present new theory and law of longevity intended to evaluate fundamental factors that control lifespan. This theory is based on the fact that genes affecting host organism longevity are represented by subpopulations: genes of host eukaryotic cells, commensal microbiota, and non-living genetic elements. Based on Tetz's theory of longevity, we propose that lifespan and aging are defined by the accumulation of alterations over all genes of macroorganism and microbiome and the non-living genetic elements associated with them. Tetz's law of longevity states that longevity is limited by the accumulation of alterations to the limiting value that is not compatible with life. Based on theory and law, we also propose a novel model to calculate several parameters, including the rate of aging and the remaining lifespan of individuals. We suggest that this theory and model have explanatory and predictive potential to eukaryotic organisms, allowing the influence of diseases, medication, and medical procedures to be re-examined in relation to longevity. Such estimates also provide a framework to evaluate new fundamental aspects that control aging and lifespan.
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Affiliation(s)
- George Tetz
- Human Microbiology Institute, 423 West 127 Street, New York, NY, 10027, USA.
| | - Victor Tetz
- Human Microbiology Institute, 423 West 127 Street, New York, NY, 10027, USA
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Abstract
The last few decades have witnessed an increasing interest in studying the human microbiome and its role in health and disease. The focus of those studies was mainly the characterization of changes in the composition of the microbial communities under different conditions. As a result of those studies, we now know that imbalance in the composition of the microbiome, also referred to as microbial dysbiosis, is directly linked to developing certain conditions. Dysbiosis of the oral microbiome is a prime example of how this imbalance leads to disease in the case of periodontal disease. However, there is considerable overlap in the phylogenetic profiles of microbial communities associated with active and inactive lesions, suggesting that the difference in periodontal status of those sites may not be explained solely by differences in the subgingival microbial composition. These findings suggest that differences in functional activities may be the essential elements that define the dysbiotic process. Researchers have recently begun to study gene expression of the oral microbiome in situ with the goal of identifying changes in functional activities that could explain the transition from health to disease. These initial results suggest that, rather than a specific composition, a better understanding of oral dysbiosis can be obtained from the study of functional activities of the microbial community. In this review, we give a summary of these initial studies, which have opened a new door to our understanding of the dynamics of the oral community during the dysbiotic process in the oral cavity.
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Affiliation(s)
- J Solbiati
- 1 Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA
| | - J Frias-Lopez
- 1 Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA
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Draft Genome Sequence of Tetzosporium hominis VT-49 gen. nov., sp. nov., Isolated from the Dental Decay Plaque of a Patient with Periodontitis. GENOME ANNOUNCEMENTS 2018; 6:6/4/e01541-17. [PMID: 29371362 PMCID: PMC5786688 DOI: 10.1128/genomea.01541-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Here, we report the draft genome sequence of Tetzosporium hominis VT-49 gen. nov., sp. nov., isolated from the dental plaque of a patient with severe periodontal disease. The draft genome sequence was 2,780,751 bp in length with a 43.3% G+C content. We detected 3,001 genes, which are predicted to encode proteins that regulate both virulence and antibiotic resistance.
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Selvaraj GK, Tian Z, Zhang H, Jayaraman M, Yang M, Zhang Y. Culture-based study on the development of antibiotic resistance in a biological wastewater system treating stepwise increasing doses of streptomycin. AMB Express 2018; 8:12. [PMID: 29368072 PMCID: PMC5783987 DOI: 10.1186/s13568-018-0539-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 01/15/2018] [Indexed: 11/10/2022] Open
Abstract
The effects of streptomycin (STM) on the development of antibiotic resistance in an aerobic-biofilm reactor was explored by stepwise increases in STM doses (0-50 mg L-1), over a period of 618 days. Totally 191 bacterial isolates affiliated with 90 different species were harvested from the reactor exposed to six STM exposures. Gammaproteobacteria (20-31.8%), Bacilli (20-35.7%), Betaproteobacteria (4.5-21%) and Actinobacteria (0-18.2%) were dominant, and their diversity was not affected over the whole period. Thirteen dominant isolates from each STM exposures (78 isolates) were applied to determine their resistance prevalence against eight classes of antibiotics. Increased STM resistance (53.8-69.2%) and multi-drug resistance (MDR) (46.2-61.5%) were observed in the STM exposures (0.1-50 mg L-1), compared to exposure without STM (15.3 and 0%, respectively). Based on their variable minimum inhibitory concentration results, 40 differentiated isolates from various STM exposures were selected to check the prevalence of nine aminoglycoside resistance genes (aac(3)-II, aacA4, aadA, aadB, aadE, aphA1, aphA2, strA and strB) and two class I integron genes (3'-CS and IntI). STM resistance genes (aadA, strA and strB), a non-STM resistance gene (aacA4) and integron genes (3'-CS and Int1) were distributed widely in all STM exposures, compared to the exposure without STM. This new culture-based stepwise increasing antibiotic approach reveals that biological systems treating wastewater with lower STM dose (0.1 mg L-1) could lead to notably increased levels of STM resistance, MDR, and resistant gene determinants, which were sustainable even under higher STM doses (> 25 mg L-1).
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Draft Genome Sequence of Chryseobacterium mucoviscidosis sp. nov. Strain VT16-26, Isolated from the Bronchoalveolar Lavage Fluid of a Patient with Cystic Fibrosis. GENOME ANNOUNCEMENTS 2018; 6:6/2/e01473-17. [PMID: 29326226 PMCID: PMC5764950 DOI: 10.1128/genomea.01473-17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report here the draft genome sequence of Chryseobacterium mucoviscidosis VT16-26, a novel bacterium isolated from the lungs of a patient with cystic fibrosis. The genome was composed of 4,403,956 bp and had 36.2% G+C content. We detected 4,048 genes with predicted protein-coding functions, including those associated with antibiotic resistance and virulence.
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Complete Genome Sequence of Kluyvera intestini sp. nov., Isolated from the Stomach of a Patient with Gastric Cancer. GENOME ANNOUNCEMENTS 2017; 5:5/43/e01184-17. [PMID: 29074664 PMCID: PMC5658502 DOI: 10.1128/genomea.01184-17] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
We report here an update to the draft genome sequence of Kluyvera intestini sp. nov. strain GT-16, generated using MinION long-read sequencing technology. The complete genome sequence of the human-derived strain GT-16 measured 5,768,848 bp. An improved high-quality complete genome sequence provides insights into the mobility potential of resistance genes in this species.
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Abstract
Unrelated spore-forming bacteria share unique characteristics stemming from the presence of highly resistant endospores, leading to similar challenges in health and disease. These characteristics are related to the presence of these highly transmissible spores, which are commonly spread within the environment and are implicated in host-to-host transmission. In humans, spore-forming bacteria contribute to a variety of pathological processes that share similar characteristics, including persistence, chronicity, relapses and the maintenance of the resistome. We first outline the necessity of characterizing the totality of the spore-forming bacteria as the sporobiota based on their unique common characteristics. We further propose that the collection of all genes of spore-forming bacteria be known as the sporobiome. Such differentiation is critical for exploring the cross-talk between the sporobiota and other members of the gut microbiota, and will allow for a better understanding of the implications of the sporobiota and sporobiome in a variety of pathologies and the spread of antibiotic resistance.
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Affiliation(s)
- George Tetz
- Human Microbiology Institute, 423 West 127 Street, New York, NY 10027 USA
| | - Victor Tetz
- Human Microbiology Institute, 423 West 127 Street, New York, NY 10027 USA
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Draft Genome Sequence of a Strain of Bacillus intestinalis sp. nov., a New Member of Sporobiota Isolated from the Small Intestine of a Single Patient with Intestinal Cancer. GENOME ANNOUNCEMENTS 2017; 5:5/22/e00489-17. [PMID: 28572333 PMCID: PMC5454216 DOI: 10.1128/genomea.00489-17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report here the draft genome sequence of Bacillus intestinalis strain 1731, a novel spore-forming bacterium isolated from the small intestine of a patient with intestinal cancer. The genome comprised 4,047,276 bp, with 43.9% G+C content. There were 3,913 predicted protein-coding genes, including those associated with antibiotic resistance and virulence.
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Draft Genome Sequence of the Uropathogenic Herbaspirillumfrisingense Strain ureolyticus VT-16-41. GENOME ANNOUNCEMENTS 2017; 5:5/17/e00279-17. [PMID: 28450527 PMCID: PMC5408125 DOI: 10.1128/genomea.00279-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Herbaspirillum frisingense strain ureolyticus VT-16-41 is a clinical cystitis isolate. Here, we report the draft genome sequence of the uropathogenic H. frisingense strain ureolyticus VT-16-41, which contains various antibiotic resistance genes and virulence factors that enable it to colonize and persist in the urinary tract.
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Draft Genome Sequence of Bacillus respiratorii VT-16-64, Isolated from the Bronchiolar Alveolar Lavage Fluid of a Patient with Chronic Obstructive Pulmonary Disease. GENOME ANNOUNCEMENTS 2017; 5:5/17/e00264-17. [PMID: 28450522 PMCID: PMC5408120 DOI: 10.1128/genomea.00264-17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
We report here the draft genome sequence of Bacillus respiratorii VT-16-64, a novel spore-forming bacterium isolated from the bronchiolar alveolar lavage fluid of a patient with chronic obstructive pulmonary disease. The genome was comprised 4,831,386 bp with 4,399 predicted protein-coding genes, including those associated with antibiotic resistance and virulence.
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Draft Genome Sequence of Bacillus obstructivus VT-16-70 Isolated from the Bronchoalveolar Lavage Fluid of a Patient with Chronic Obstructive Pulmonary Disease. GENOME ANNOUNCEMENTS 2017; 5:5/9/e01754-16. [PMID: 28254994 PMCID: PMC5334601 DOI: 10.1128/genomea.01754-16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
We report here the draft genome sequence of Bacillus obstructivus VT-16-70, a novel spore-forming bacterium isolated from the lungs of a patient with chronic obstructive pulmonary disease. The genome comprised 5,220,753 bp, with 35.2% G+C content. There were 4,972 predicted protein-coding genes, including those associated with antibiotic resistance and virulence.
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Complete Genome Sequence of a Novel Bacillus sp. VT 712 Strain Isolated from the Duodenum of a Patient with Intestinal Cancer. GENOME ANNOUNCEMENTS 2016; 4:4/4/e00786-16. [PMID: 27491975 PMCID: PMC4974327 DOI: 10.1128/genomea.00786-16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
We report here the complete genome sequence of the spore-forming Bacillus sp. strain VT 712 isolated from the duodenum of a patient with intestinal cancer. The genome is 3,921,583 bp, with 37.9% G+C content. It contains 3,768 predicted protein-coding genes for multidrug resistance transporters, virulence factors, and daunorubicin resistance.
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