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Ren M, Qin Y, Zhang L, Zhao Y, Zhang R, Shi H. Effects of fermentation chamber temperature on microbes and quality of cigar wrapper tobacco leaves. Appl Microbiol Biotechnol 2023; 107:6469-6485. [PMID: 37665370 DOI: 10.1007/s00253-023-12750-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 08/13/2023] [Accepted: 08/26/2023] [Indexed: 09/05/2023]
Abstract
The natural fermentation of cigar tobacco leaves usually utilizes natural temperature and humidity for fermentation. Cigars produced in China are often fermented in winter, and the low environmental temperatures can lead to slow heating of the tobacco stack, affecting the cigar tobacco leaves quality. This study aimed to determine the minimum chamber temperature required to initiate the process of fermentation for cigar tobacco leaves and to explore the impact of temperature on the microbial community of tobacco leaves. Here, the cigar variety "Dexue 1" were subjected to stacking fermentation under three temperature parameters (20 ℃, 27 ℃, 34 ℃). With an increase in environmental temperature, the temperature inside the stack of cigar leaves increased significantly, the protein, total sugar, starch, and total alkaloid content in fermented tobacco leaves decreased, and the aroma components and amino acid content increased. Microbial richness and community diversity associated with fermented tobacco were highest at chamber temperatures of above 27 ℃. The relative abundance of Chryseobacterium and Rhodococcus was significantly negatively correlated with protein, alkaloids, total sugar, and starch, and positively correlated with amino acids and aroma components. Chryseobacterium and Rhodococcus may be responsible for the degradation of macromolecular substances and the conversion of favorable aromatic substances, thus improving the tobacco leaves quality. This study demonstrated that increasing the fermentation chamber temperature above 27 ℃ was conductive to raising the inner-stack temperature, increased microbial diversity and aromatic quality, reduced the strength and irritation, and extremely enhanced the overall quality of fermented cigar tobacco leaves. KEY POINTS: • The environmental temperature of the fermentation chamber has a significant impact on the quality of tobacco • Temperature > 27 ℃ can initiate the process of cigar tobacco leaves fermentation and increase inner-stack temperature and microbial diversity and abundance • Chryseobacterium and Rhodococcus may be related to the degradation of macromolecular substances and the transformation of aromatic substances, thereby improving the quality of tobacco leaves.
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Affiliation(s)
- Mengjuan Ren
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450046, Henan Province, China
| | - Yanqing Qin
- Sichuan Provincial Tobacco Company, Chengdu, 600041, Sichuan Province, China
| | - Lanyue Zhang
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450046, Henan Province, China
| | - Yuanyuan Zhao
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450046, Henan Province, China
| | - Ruina Zhang
- Deyang Branch of Sichuan Provincial Tobacco Company, Deyang, 618400, Sichuan Province, China
| | - Hongzhi Shi
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450046, Henan Province, China.
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Kokwe L, Nnolim NE, Ezeogu LI, Sithole B, Nwodo UU. Thermoactive metallo-keratinase from Bacillus sp. NFH5: Characterization, structural elucidation, and potential application as detergent additive. Heliyon 2023; 9:e13635. [PMID: 36852054 PMCID: PMC9957710 DOI: 10.1016/j.heliyon.2023.e13635] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 02/15/2023] Open
Abstract
In recent times, robust green technological developments have advanced the goal of a circular economy by minimizing waste generation. The study was undertaken to explore the keratinolytic activity of chicken feather-degrading bacteria from South African soil. Isolates coded as SSN-01 and HSN-01 were identified as Bacillus sp. NFH5 and Bacillus sp. FHNM and their sequences were deposited in GenBank, with accession numbers MW165830.1 and MW165831.1, respectively. Extracellular enzyme production and thiol group generation by Bacillus sp. NFH5 peaked at 120 h with 1879.09 ± 88.70 U/mL and 9.49 ± 0.78 mM, respectively. Glutamic acid (4.44%), aspartic acid (3.50%), arginine (3.23%), glycine (2.61%), serine (2.08%), and proline (2.08%) were relatively higher in concentration. Keratinase (KerBAN) activity was highest at pH 8.0 and 90 °C but was inhibited by both EDTA and 1,10-phenanthroline. In addition, the keratinase-encoding gene (kerBAN) accessioned OK033360 had 362 amino acid residues, with molecular weight and theoretical isoelectric point of 39 kDa and 8.81, respectively. Findings from this study highlight the significance of Bacillus sp. NFH5 in the bio-recycling of recalcitrant keratinous wastes to protein hydrolysates - potential dietary supplements for livestock feeds. The properties of KerBAN underscore its application potential in green biotechnological processes.
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Affiliation(s)
- Lupho Kokwe
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, Private Bag X1314, 5700, South Africa.,Applied and Environmental Microbiology Research Group (AEMREG), Department of Biochemistry and Microbiology, University of Fort Hare, Alice, 5700, South Africa
| | - Nonso E Nnolim
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, Private Bag X1314, 5700, South Africa.,Applied and Environmental Microbiology Research Group (AEMREG), Department of Biochemistry and Microbiology, University of Fort Hare, Alice, 5700, South Africa
| | - Lewis I Ezeogu
- Department of Microbiology, Faculty of Biological Sciences, University of Nigeria, Nsukka, Nigeria
| | - Bruce Sithole
- The Biorefinery Industry Development Facility, Chemicals Cluster, Council for Scientific and Industrial Research, 359 Mazisi Kunene Road, 4001, Glenwood, Durban, South Africa
| | - Uchechukwu U Nwodo
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, Private Bag X1314, 5700, South Africa.,Applied and Environmental Microbiology Research Group (AEMREG), Department of Biochemistry and Microbiology, University of Fort Hare, Alice, 5700, South Africa
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Damas MSF, Ferreira RL, Campanini EB, Soares GG, Campos LC, Laprega PM, Soares da Costa A, Freire CCDM, Pitondo-Silva A, Cerdeira LT, da Cunha AF, Pranchevicius MCDS. Whole genome sequencing of the multidrug-resistant Chryseobacterium indologenes isolated from a patient in Brazil. Front Med (Lausanne) 2022; 9:931379. [PMID: 35966843 PMCID: PMC9366087 DOI: 10.3389/fmed.2022.931379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 06/30/2022] [Indexed: 12/03/2022] Open
Abstract
Chryseobacterium indologenes is a non-glucose-fermenting Gram-negative bacillus. This emerging multidrug resistant opportunistic nosocomial pathogen can cause severe infections in neonates and immunocompromised patients. This study aimed to present the first detailed draft genome sequence of a multidrug-resistant C. indologenes strain isolated from the cerebrospinal fluid of an infant hospitalized at the Neonatal Intensive Care Unit of Brazilian Tertiary Hospital. We first analyzed the susceptibility of C. indologenes strain to different antibiotics using the VITEK 2 system. The strain demonstrated an outstanding resistance to all the antibiotic classes tested, including β-lactams, aminoglycosides, glycylcycline, and polymyxin. Next, C. indologenes was whole-genome-sequenced, annotated using Prokka and Rapid Annotation using Subsystems Technology (RAST), and screened for orthologous groups (EggNOG), gene ontology (GO), resistance genes, virulence genes, and mobile genetic elements using different software tools. The draft genome contained one circular chromosome of 4,836,765 bp with 37.32% GC content. The genomic features of the chromosome present numerous genes related to cellular processes that are essential to bacteria. The MDR C. indologenes revealed the presence of genes that corresponded to the resistance phenotypes, including genes to β-lactamases (blaIND–13, blaCIA–3, blaTEM–116, blaOXA–209, blaVEB–15), quinolone (mcbG), tigecycline (tet(X6)), and genes encoding efflux pumps which confer resistance to aminoglycosides (RanA/RanB), and colistin (HlyD/TolC). Amino acid substitutions related to quinolone resistance were observed in GyrA (S83Y) and GyrB (L425I and K473R). A mutation that may play a role in the development of colistin resistance was detected in lpxA (G68D). Chryseobacterium indologenes isolate harbored 19 virulence factors, most of which were involved in infection pathways. We identified 13 Genomic Islands (GIs) and some elements associated with one integrative and conjugative element (ICEs). Other elements linked to mobile genetic elements (MGEs), such as insertion sequence (ISEIsp1), transposon (Tn5393), and integron (In31), were also present in the C. indologenes genome. Although plasmids were not detected, a ColRNAI replicon type and the most resistance genes detected in singletons were identified in unaligned scaffolds. We provided a wide range of information toward the understanding of the genomic diversity of C. indologenes, which can contribute to controlling the evolution and dissemination of this pathogen in healthcare settings.
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Affiliation(s)
| | - Roumayne Lopes Ferreira
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - Emeline Boni Campanini
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | | | | | - Pedro Mendes Laprega
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - Andrea Soares da Costa
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | | | - André Pitondo-Silva
- Programa de Pós-graduação em Odontologia e Tecnologia Ambiental, Universidade de Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | | | | | - Maria-Cristina da Silva Pranchevicius
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
- Centro de Ciências Biológicas e da Saúde, Biodiversidade Tropical - BIOTROP, Universidade Federal de São Carlos, São Carlos, Brazil
- *Correspondence: Maria-Cristina da Silva Pranchevicius,
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Clark CM, Hernandez A, Mullowney MW, Fitz-Henley J, Li E, Romanowski SB, Pronzato R, Manconi R, Sanchez LM, Murphy BT. Relationship between bacterial phylotype and specialized metabolite production in the culturable microbiome of two freshwater sponges. ISME COMMUNICATIONS 2022; 2:22. [PMID: 37938725 PMCID: PMC9723699 DOI: 10.1038/s43705-022-00105-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 02/08/2022] [Accepted: 02/10/2022] [Indexed: 11/09/2023]
Abstract
Microbial drug discovery programs rely heavily on accessing bacterial diversity from the environment to acquire new specialized metabolite (SM) lead compounds for the therapeutic pipeline. Therefore, knowledge of how commonly culturable bacterial taxa are distributed in nature, in addition to the degree of variation of SM production within those taxa, is critical to informing these front-end discovery efforts and making the overall sample collection and bacterial library creation process more efficient. In the current study, we employed MALDI-TOF mass spectrometry and the bioinformatics pipeline IDBac to analyze diversity within phylotype groupings and SM profiles of hundreds of bacterial isolates from two Eunapius fragilis freshwater sponges, collected 1.5 km apart. We demonstrated that within two sponge samples of the same species, the culturable bacterial populations contained significant overlap in approximate genus-level phylotypes but mostly nonoverlapping populations of isolates when grouped lower than the level of genus. Further, correlations between bacterial phylotype and SM production varied at the species level and below, suggesting SM distribution within bacterial taxa must be analyzed on a case-by-case basis. Our results suggest that two E. fragilis freshwater sponges collected in similar environments can exhibit large culturable diversity on a species-level scale, thus researchers should scrutinize the isolates with analyses that take both phylogeny and SM production into account to optimize the chemical space entering into a downstream bacterial library.
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Affiliation(s)
- Chase M Clark
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Antonio Hernandez
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Michael W Mullowney
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Jhewelle Fitz-Henley
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Emma Li
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Sean B Romanowski
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Roberto Pronzato
- Dipartimento di Scienze della Terra, dell'Ambiente e della Vita, Università di Genova, Genova, Italy
| | - Renata Manconi
- Dipartimento Medicina Veterinaria, Università di Sassari, Sassari, Italy
| | - Laura M Sanchez
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Brian T Murphy
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA.
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Park H, Seo SI, Lim JH, Song J, Seo JH, Kim PI. Screening of Carbofuran-Degrading Bacteria Chryseobacterium sp. BSC2-3 and Unveiling the Change in Metabolome during Carbofuran Degradation. Metabolites 2022; 12:metabo12030219. [PMID: 35323662 PMCID: PMC8950912 DOI: 10.3390/metabo12030219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 12/20/2021] [Accepted: 12/29/2021] [Indexed: 02/01/2023] Open
Abstract
Carbofuran is one of the most commonly used N-methylcarbamate-based pesticides and is excellent for controlling pests; however, carbofuran also causes soil and water pollution. Although various studies have been conducted on the bioremediation of pesticide-contaminated soil, the changes occurring in the metabolome during the bioremediation of carbofuran are not fully understood. In this study, the intracellular and extracellular metabolites of the Chryseobacterium sp. BSC2-3 strain were analysed during carbofuran degradation by using a liquid chromatography–mass spectrometry-based metabolomics approach. We found that the BSC2-3 strain extracellularly transformed carbofuran into 3-hydroxycarbofuran. Intracellular metabolite analysis revealed that carbofuran mainly affected aminobenzoate degradation, ubiquinone and terpenoid-quinone biosynthesis, and arginine and proline metabolism. Carbofuran especially affected the metabolic pathway for the degradation of naphthalene and aminobenzoate. Metabolomics additionally revealed that the strain produces disease resistance inducers and plant growth regulators. We also identified the genes involved in the production of indole-3-acetic acid, which is one of the most active auxins. Overall, we identified the metabolic changes induced in carbofuran-degrading bacteria and the genes predicted to be responsible for the degradation of carbofuran.
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Affiliation(s)
- Haeseong Park
- Center for Industrialization of Agricultural and Livestock Microorganisms, 241 Cheomdangwahak-ro, Jeongeup-si 56212, Korea; (H.P.); (S.I.S.); (J.-H.L.)
| | - Sun Il Seo
- Center for Industrialization of Agricultural and Livestock Microorganisms, 241 Cheomdangwahak-ro, Jeongeup-si 56212, Korea; (H.P.); (S.I.S.); (J.-H.L.)
| | - Ji-Hwan Lim
- Center for Industrialization of Agricultural and Livestock Microorganisms, 241 Cheomdangwahak-ro, Jeongeup-si 56212, Korea; (H.P.); (S.I.S.); (J.-H.L.)
| | - Jaekyeong Song
- Division of Agricultural Microbiology, National Academy of Agricultural Science, 166 Nongsaengmyeong-ro, Wanju-gun 55365, Korea;
| | - Joo-Hyun Seo
- Department of Bio and Fermentation Convergence Technology, Kookmin University, Seoul 02707, Korea
- Correspondence: (J.-H.S.); (P.I.K.); Tel.: +82-63-536-6001 (P.I.K.)
| | - Pyoung Il Kim
- Center for Industrialization of Agricultural and Livestock Microorganisms, 241 Cheomdangwahak-ro, Jeongeup-si 56212, Korea; (H.P.); (S.I.S.); (J.-H.L.)
- Correspondence: (J.-H.S.); (P.I.K.); Tel.: +82-63-536-6001 (P.I.K.)
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Concha C, Miranda CD, Santander J, Roberts MC. Genetic Characterization of the Tetracycline-Resistance Gene tet(X) Carried by Two Epilithonimonas Strains Isolated from Farmed Diseased Rainbow Trout, Oncorhynchus mykiss in Chile. Antibiotics (Basel) 2021; 10:antibiotics10091051. [PMID: 34572633 PMCID: PMC8464911 DOI: 10.3390/antibiotics10091051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/12/2021] [Accepted: 08/13/2021] [Indexed: 11/17/2022] Open
Abstract
The main objective of this study was to characterize the tet(X) genes, which encode a monooxygenase that catalyzes the degradation of tetracycline antibiotics, carried by the resistant strains FP105 and FP233-J200, using whole-genome sequencing analysis. The isolates were recovered from fin lesion and kidney samples of diseased rainbow trout Oncorhynchus mykiss, during two Flavobacteriosis outbreaks occurring in freshwater farms located in Southern Chile. The strains were identified as Epilithonimonas spp. by using biochemical tests and by genome comparison analysis using the PATRIC bioinformatics platform and exhibited a minimum inhibitory concentration (MIC) of oxytetracycline of 128 µg/mL. The tet(X) genes were located on small contigs of the FP105 and FP233-J200 genomes. The sequences obtained for the tet(X) genes and their genetic environment were compared with the genomes available in the GenBank database of strains of the Chryseobacterium clade belonging to the Flavobacterium family, isolated from fish and carrying the tet(X) gene. The Tet(X) proteins synthesized by the Chilean Epilithonimonas strains showed a high amino acid similarity (range from 84% to 100%), with the available sequences found in strains belonging to the genus Chryseobacterium and Flavobacterium isolated from fish. An identical neighborhood of tet(X) genes from both Chilean strains was observed. The genetic environment of tet(X) observed in the two strains of Epilithonimonas studied was characterized by the upstream location of a sequence encoding a hypothetical protein and a downstream located alpha/beta hydrolase-encoding gene, similar to the observed in some of the tet(X) genes carried by Chryseobacterium and Flavobacterium strains isolated from fish, but the produced proteins exhibited a low amino acid identity (25–27%) when compared to these synthesized by the Chilean strains. This study reports for the first time the carriage of the tet(X) gene by the Epilithonimonas genus and their detection in fish pathogenic bacteria isolated from farmed salmonids in Chile, thus limiting the use of therapies based on oxytetracycline, the antimicrobial most widely used in Chilean freshwater salmonid farming. This results suggest that pathogenic strains of the Chryseobacterium clade occurring in Chilean salmonid farms may serve as important reservoirs of tet(X) genes.
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Affiliation(s)
- Christopher Concha
- Laboratorio de Patobiología Acuática, Departamento de Acuicultura, Universidad Católica del Norte, Coquimbo 1780000, Chile;
| | - Claudio D. Miranda
- Laboratorio de Patobiología Acuática, Departamento de Acuicultura, Universidad Católica del Norte, Coquimbo 1780000, Chile;
- Centro AquaPacífico, Coquimbo 1780000, Chile
- Correspondence: ; Tel.: +56-512209762
| | - Javier Santander
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, NL A1C 5S7, Canada;
| | - Marilyn C. Roberts
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, 4225 Roosevelt Way NE, Suit #100, Seattle, WA 98105, USA;
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