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Lim TW, Choo KY, Lim RLH, Pui LP, Tan CP, Ho CW. The indigenous microbial diversity involved in the spontaneous fermentation of red dragon fruit ( Hylocereus polyrhizus) identified by means of molecular tools. Heliyon 2023; 9:e21940. [PMID: 38027851 PMCID: PMC10658323 DOI: 10.1016/j.heliyon.2023.e21940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 10/31/2023] [Accepted: 10/31/2023] [Indexed: 12/01/2023] Open
Abstract
Red dragon fruit (RDF) is well-known for its high nutritional content, especially the red pigment betacyanins that possess high antioxidant activity. Natural fermentation is an ancient yet outstanding technique that relies on the autochthonous microbiota from fruits and vegetables surfaces to preserve and improve the nutritional values and quality of the food product. The present study was to evaluate and identify the indigenous microbial community (bacteria and fungi) that are involved in the natural fermentation of RDF. Results revealed a total of twenty bacterial pure cultures and nine fungal pure cultures were successfully isolated from fermented red dragon fruit drink (FRDFD). For the first time, the PCR amplification of 16S rRNA and ITS regions and sequence analysis suggested nine genera of bacteria and three genera of fungi (Aureobasidium pullulans, Clavispora opuntiae, and Talaromyces aurantiacus) present in the FRDFD. Four dominant (≥10 % isolates) bacteria species identified from FRDFD were Klebsiella pneumonia, Brevibacillus parabrevis, Bacillus tequilensis and Bacillus subtilis. The carbohydrate fermentation test showed that all the indigenous microbes identified were able to serve as useful starter culture by fermenting sucrose and glucose, thereby producing acid to lower the pH of FRDFD to around pH 4 for better betacyanins stability. The present study provides a more comprehensive understanding of the indigenous microbial community that serves as the starter culture in the fermentation of RDF. Besides, this study provides a useful guide for future research to be conducted on studying the rare bacterial strains (such as B. tequilensis) identified from the FRDFD for their potential bioactivities and applications in medical treatment and functional foods industries.
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Affiliation(s)
- Teck Wei Lim
- Department of Biotechnology, Faculty of Applied Sciences, UCSI University, No. 1, Jalan Menara Gading, UCSI Heights, 56000, Cheras, Kuala Lumpur, Malaysia
- Department of Food Science and Nutrition, Faculty of Applied Sciences, UCSI University, No. 1, Jalan Menara Gading, UCSI Heights, 56000, Cheras, Kuala Lumpur, Malaysia
| | - Kah Yee Choo
- Department of Food Science and Nutrition, Faculty of Applied Sciences, UCSI University, No. 1, Jalan Menara Gading, UCSI Heights, 56000, Cheras, Kuala Lumpur, Malaysia
| | - Renee Lay Hong Lim
- Department of Biotechnology, Faculty of Applied Sciences, UCSI University, No. 1, Jalan Menara Gading, UCSI Heights, 56000, Cheras, Kuala Lumpur, Malaysia
| | - Liew Phing Pui
- Department of Food Science and Nutrition, Faculty of Applied Sciences, UCSI University, No. 1, Jalan Menara Gading, UCSI Heights, 56000, Cheras, Kuala Lumpur, Malaysia
| | - Chin Ping Tan
- Department of Food Technology, Faculty of Food Science and Technology, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia
| | - Chun Wai Ho
- Department of Food Science and Nutrition, Faculty of Applied Sciences, UCSI University, No. 1, Jalan Menara Gading, UCSI Heights, 56000, Cheras, Kuala Lumpur, Malaysia
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Zhao Y, Ye Q, Feng Y, Chen Y, Tan L, Ouyang Z, Zhao J, Hu J, Chen N, Su X, Dusenge MA, Feng Y, Guo Y. Prevotella genus and its related NOD-like receptor signaling pathway in young males with stage III periodontitis. Front Microbiol 2022; 13:1049525. [PMID: 36569059 PMCID: PMC9772451 DOI: 10.3389/fmicb.2022.1049525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 10/31/2022] [Indexed: 12/14/2022] Open
Abstract
Background As periodontitis progresses, the oral microbiota community changes dynamically. In this study, we evaluated the dominant bacteria and their roles in the potential pathway in young males with stage III periodontitis. Methods 16S rRNA sequencing was performed to evaluate variations in the composition of oral bacteria between males with stage I and III periodontitis and identify the dominant bacteria of each group. Function prediction was obtained based on 16S rRNA sequencing data. The inhibitor of the predominant pathway for stage III periodontitis was used to investigate the role of the dominant bacteria in periodontitis in vivo and in vitro. Results Chao1 index, Observed Species and Phylogenetic Diversity (PD) whole tree values were significantly higher in the stage III periodontitis group. β-diversity suggested that samples could be divided according to the stages of periodontitis. The dominant bacteria in stage III periodontitis were Prevotella, Prevotella_7, and Dialister, whereas that in stage I periodontitis was Cardiobacterium. KEGG analysis predicted that variations in the oral microbiome may be related to the NOD-like receptor signaling pathway. The inhibitor of this pathway, NOD-IN-1, decreased P. intermedia -induced Tnf-α mRNA expression and increased P. intermedia -induced Il-6 mRNA expression, consistent with the ELISA results. Immunohistochemistry confirmed the down-regulation of TNF-α and IL-6 expressions by NOD-IN-1 in P. intermedia-induced periodontitis. Conclusion The composition of the oral bacteria in young males varied according to the stage of periodontitis. The species richness of oral microtia was greater in young males with stage III periodontitis than those with stage I periodontitis. Prevotella was the dominant bacteria in young males with stage III periodontitis, and inhibition of the NOD-like receptor signaling pathway can decrease the periodontal inflammation induced by P. intermedia.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Yue Guo
- *Correspondence: Yunzhi Feng, ; Yue Guo,
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Tang J, Zhao JY, Li LL, Ding ZG, Ye SQ, Ling C, Zhang MY, Liang SG, Li JY, Yang PW, Xiong J, Feng LY, Shi ZF, Li MG, Tang SK. Cohnella mopanensis sp. nov., a new Gram-negative bacterium isolated from soil in Xinping Mountain National Forest Park. Arch Microbiol 2022; 204:492. [PMID: 35841443 DOI: 10.1007/s00203-022-03050-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 06/03/2022] [Indexed: 11/02/2022]
Abstract
A Gram-stain-negative, aerobic, rod-shaped bacteria strain, named YIM B01951T, was isolated from a forest soil sample collected from Mopan Mountain National Forest Park, Xinping City, Yunnan Province, southwest PR China (101°58'06" N, 23°03'02" E). Growth occurred at 15-40 °C (optimum, 30 °C), pH 5.0-8.0 (optimum, pH 6.5) and with up to ≤ 3.0% (w/v) NaCl on Nutrient Agar plates. The results of 16S rRNA gene sequence similarity analysis showed that strain YIM B01951T was closely related to the type strain of Cohnella arctica M9-62T (96.5%) and Cohnella lupini RLAHU4BT (96.3%). YIM B01951T contains anteiso-C15:0 and iso-C16:0 as the major cellular fatty acids; the main polar lipids are diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), lysylphosphatidylglycerol (PGL) and five aminophospholipids (APL). The MK-7 is the major respiratory quinone and the DNA G + C content is 49.2 mol%. Based on these phenotypic, chemotaxonomic and phylogenetic analyses, strain YIM B01951T is considered to be a novel species of the genus Cohnella, and named Cohnella mopanensis sp. nov. The type strain is YIM B01951T (= NBRC 115331T = KCTC 43370T).
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Huang YA, Huang ZA, Li JQ, You ZH, Wang L, Yi HC, Yu CQ. GBDR: a Bayesian model for precise prediction of pathogenic microorganisms using 16S rRNA gene sequences. BMC Genomics 2022; 22:916. [PMID: 35296232 PMCID: PMC8925046 DOI: 10.1186/s12864-022-08423-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 02/25/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Recent evidences have suggested that human microorganisms participate in important biological activities in the human body. The dysfunction of host-microbiota interactions could lead to complex human disorders. The knowledge on host-microbiota interactions can provide valuable insights into understanding the pathological mechanism of diseases. However, it is time-consuming and costly to identify the disorder-specific microbes from the biological "haystack" merely by routine wet-lab experiments. With the developments in next-generation sequencing and omics-based trials, it is imperative to develop computational prediction models for predicting microbe-disease associations on a large scale. RESULTS Based on the known microbe-disease associations derived from the Human Microbe-Disease Association Database (HMDAD), the proposed model shows reliable performance with high values of the area under ROC curve (AUC) of 0.9456 and 0.8866 in leave-one-out cross validations and five-fold cross validations, respectively. In case studies of colorectal carcinoma, 80% out of the top-20 predicted microbes have been experimentally confirmed via published literatures. CONCLUSION Based on the assumption that functionally similar microbes tend to share the similar interaction patterns with human diseases, we here propose a group based computational model of Bayesian disease-oriented ranking to prioritize the most potential microbes associating with various human diseases. Based on the sequence information of genes, two computational approaches (BLAST+ and MEGA 7) are leveraged to measure the microbe-microbe similarity from different perspectives. The disease-disease similarity is calculated by capturing the hierarchy information from the Medical Subject Headings (MeSH) data. The experimental results illustrate the accuracy and effectiveness of the proposed model. This work is expected to facilitate the characterization and identification of promising microbial biomarkers.
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Affiliation(s)
- Yu-An Huang
- Department of Information Engineering, Xijing University, Xi'an, 710123, China.
| | - Zhi-An Huang
- Center for Computer Science and Information Technology, City University of Hong Kong Dongguan Research Institute, Dongguan, China
| | - Jian-Qiang Li
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, 518000, China.
| | - Zhu-Hong You
- Department of Information Engineering, Xijing University, Xi'an, 710123, China
| | - Lei Wang
- Guangxi Academy of Science, Nanning, 530000, China
| | - Hai-Cheng Yi
- Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Ürümqi, 830000, China
| | - Chang-Qing Yu
- Department of Information Engineering, Xijing University, Xi'an, 710123, China
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Geng Y, Zhao JY, Yuan HR, Li LL, Wen ML, Li MG, Tang SK. Aestuariimicrobium ganziense sp. nov., a new Gram-positive bacterium isolated from soil in the Ganzi Tibetan autonomous prefecture, China. Arch Microbiol 2021; 203:2653-2658. [PMID: 33710378 DOI: 10.1007/s00203-021-02261-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/19/2021] [Accepted: 02/22/2021] [Indexed: 11/25/2022]
Abstract
A novel Gram-stain positive, oval-shaped, and non-flagellated bacterium, designated YIM S02566T, was isolated from alpine soil in Shadui Towns, Ganzi County, Ganzi Tibetan Autonomous Prefecture, Sichuan Province, PR China. Growth occurred at 23-35 °C (optimum, 30 °C) in the presence of 0.5-4% (w/v) NaCl (optimum, 1%) and at pH 7.0-8.0 (optimum, pH 7.0). The phylogenetic analysis based on 16S rRNA gene sequence revealed that strain YIM S02566T was most closely related to the genus Aestuariimicrobium, with Aestuariimicrobium kwangyangense R27T and Aestuariimicrobium soli D6T as its closest relative (sequence similarities were 96.3% and 95.4%, respectively). YIM S02566T contained LL-diaminopimelic acid in the cell wall. MK-9(H4) was the predominant menaquinone. The major fatty acid patterns were anteiso-C15:0 (60.0%). The major polar lipid was DPG. The genome size of strain YIM S02566T was 3.1 Mb, comprising 3078 predicted genes with a DNA G + C content of 69.0 mol%. Based on these genotypic, chemotaxonomic and phenotypic evidences, strain YIM S02566T was identified as a novel species in the genus Aestuariimicrobium, for which the name Aestuariimicrobium ganziense sp. nov. is proposed. The type strain is YIM S02566T (= CGMCC 1.18751 T = KCTC 49,477 T).
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Affiliation(s)
- Yu Geng
- Key Laboratory for Conservation and Utilization of Bio-Resource, and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China
| | - Jiang-Yuan Zhao
- Key Laboratory for Conservation and Utilization of Bio-Resource, and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China
| | - Hui-Ren Yuan
- Key Laboratory for Conservation and Utilization of Bio-Resource, and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China
| | - Le-Le Li
- Key Laboratory for Conservation and Utilization of Bio-Resource, and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China
| | - Meng-Liang Wen
- Key Laboratory for Conservation and Utilization of Bio-Resource, and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China
| | - Ming-Gang Li
- Key Laboratory for Conservation and Utilization of Bio-Resource, and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China.
| | - Shu-Kun Tang
- Key Laboratory for Conservation and Utilization of Bio-Resource, and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China.
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Sarkar P, Malik S, Laha S, Das S, Bunk S, Ray JG, Chatterjee R, Saha A. Dysbiosis of Oral Microbiota During Oral Squamous Cell Carcinoma Development. Front Oncol 2021; 11:614448. [PMID: 33708627 PMCID: PMC7940518 DOI: 10.3389/fonc.2021.614448] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 01/05/2021] [Indexed: 12/24/2022] Open
Abstract
Infection with specific pathogens and alterations in tissue commensal microbial composition are intricately associated with the development of many human cancers. Likewise, dysbiosis of oral microbiome was also shown to play critical role in the initiation as well as progression of oral cancer. However, there are no reports portraying changes in oral microbial community in the patients of Indian subcontinent, which has the highest incidence of oral cancer per year, globally. To establish the association of bacterial dysbiosis and oral squamous cell carcinoma (OSCC) among the Indian population, malignant lesions and anatomically matched adjacent normal tissues were obtained from fifty well-differentiated OSCC patients and analyzed using 16S rRNA V3-V4 amplicon based sequencing on the MiSeq platform. Interestingly, in contrast to the previous studies, a significantly lower bacterial diversity was observed in the malignant samples as compared to the normal counterpart. Overall our study identified Prevotella, Corynebacterium, Pseudomonas, Deinococcus and Noviherbaspirillum as significantly enriched genera, whereas genera including Actinomyces, Sutterella, Stenotrophomonas, Anoxybacillus, and Serratia were notably decreased in the OSCC lesions. Moreover, we demonstrated HPV-16 but not HPV-18 was significantly associated with the OSCC development. In future, with additional validation, this panel could directly be applied into clinical diagnostic and prognostic workflows for OSCC in Indian scenario.
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Affiliation(s)
- Purandar Sarkar
- School of Biotechnology, Presidency University, Kolkata, India
| | - Samaresh Malik
- School of Biotechnology, Presidency University, Kolkata, India
| | - Sayantan Laha
- Human Genetics Unit, Indian Statistical Institute, Kolkata, India
| | - Shantanab Das
- Human Genetics Unit, Indian Statistical Institute, Kolkata, India
| | - Soumya Bunk
- Department of Life Sciences, Presidency University, Kolkata, India
| | - Jay Gopal Ray
- Department of Oral Pathology, Dr. R Ahmed Dental College and Hospital, Kolkata, India
| | | | - Abhik Saha
- School of Biotechnology, Presidency University, Kolkata, India.,Department of Life Sciences, Presidency University, Kolkata, India
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Koizumi Y, Ohno T, Takada T, Sakanashi D, Nakamura A, Yamada A, Asai N, Shiota A, Hagihara M, Yamagishi Y, Suematsu H, Deie M, Mikamo H. An unexpected case of Cardiobacterium valvarum prosthetic arthritis without cardiac lesions: Case report and literature review. J Infect Chemother 2021; 27:747-50. [PMID: 33402300 DOI: 10.1016/j.jiac.2020.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 11/07/2020] [Accepted: 12/11/2020] [Indexed: 11/22/2022]
Abstract
We report a case of prosthetic arthritis caused by Cardiobacterium valvarum, which has been exclusively reported to cause intravascular infections. A 81-year-old Japanese female complained prosthetic knee joint pain. Arthrocentesis cultured no pathogen, and surgical replacement of the implant surface was performed. Modified Levinthal medium culture and 16S rRNA sequencing has finally led to diagnosis of C. valvarum prosthetic knee arthritis without cardiac lesions. Fastidious bacteria such as C. valvarum can be candidate pathogens of orthopedic infections whose causative agents are sometimes unidentified. Further development of molecular diagnostics is expected, but also the importance of conventional methods should be noted.
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Yang L, Huang HW, Wang Y, Kou YR, Yin M, Li Y, Wang XQ, Zhao GF, Zhu WY, Tang SK. Paenibacillus turpanensis sp. nov., isolated from a salt lake of Turpan city in Xinjiang province, north-west China. Arch Microbiol 2020; 203:77-83. [PMID: 32748000 DOI: 10.1007/s00203-020-02003-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 07/04/2020] [Accepted: 07/24/2020] [Indexed: 11/30/2022]
Abstract
Strain YIM B00363T, a Gram-positive, aerobic, non-motile, rod-shaped, spore-forming bacterium, was isolated from saline soil samples collected from a salt lake in Xinjiang province, north-west China, and was characterized using a polyphasic approach. The optimum growth temperature was 37 °C and the optimum pH was 7.5-8.0. The major menaquinone was MK-7; anteiso-C15:0 (53.52%), iso-C15:0 (15.04%) and C16:0 (12.76%) were the predominant cellular fatty acids. The diagnostic diamino acid of the cell wall peptidoglycan was meso-diaminopimelic acid. The phospholipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, unidentified phospholipids, unidentified glycolipids and unknown lipids. The DNA G + C content of the type strain was 50.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain YIM B00363T belonged to a cluster comprising species of the genus Paenibacillus. The nearest relatives were P. residui MC-246T and P. senegalensis JC66T, with 93.2% and 92.8% gene sequence similarities, respectively. On the basis of its phenotypic characteristics and phylogenetic distinctivenes, strain YIM B00363T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus turpanensis sp. nov. is proposed. The type strain is YIM B00363T (= CGMCC 1.17507T = KCTC 43184T).
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Affiliation(s)
- Li Yang
- Key Laboratory for Conservation and Utilization of Bio-resource, and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan Institute of MicrobiologySchool of Life SciencesYunnan University, Kunming, 650091, People's Republic of China
| | - Hua-Wei Huang
- Key Laboratory for Conservation and Utilization of Bio-resource, and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan Institute of MicrobiologySchool of Life SciencesYunnan University, Kunming, 650091, People's Republic of China
| | - Yun Wang
- Life Science and Technology School, Lingnan Normal University, Zhanjiang, 524048, People's Republic of China
| | - Ya-Rong Kou
- Walvax Biotechnology Co., Ltd, Kunming, 650106, People's Republic of China
| | - Min Yin
- School of Medicine, Yunnan University, Kunming, 650091, People's Republic of China
| | - Yu Li
- Key Laboratory for Conservation and Utilization of Bio-resource, and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan Institute of MicrobiologySchool of Life SciencesYunnan University, Kunming, 650091, People's Republic of China
| | - Xue-Qian Wang
- Key Laboratory for Conservation and Utilization of Bio-resource, and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan Institute of MicrobiologySchool of Life SciencesYunnan University, Kunming, 650091, People's Republic of China
| | - Gui-Fang Zhao
- Key Laboratory for Conservation and Utilization of Bio-resource, and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan Institute of MicrobiologySchool of Life SciencesYunnan University, Kunming, 650091, People's Republic of China
| | - Wen-Yong Zhu
- Key Laboratory for Conservation and Utilization of Bio-resource, and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan Institute of MicrobiologySchool of Life SciencesYunnan University, Kunming, 650091, People's Republic of China. .,Yunnan Key Laboratory of Vaccine Research and Development on Severe Infections Diseases, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650118, People's Republic of China.
| | - Shu-Kun Tang
- Key Laboratory for Conservation and Utilization of Bio-resource, and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan Institute of MicrobiologySchool of Life SciencesYunnan University, Kunming, 650091, People's Republic of China.
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Oztas Gulmus E, Gormez A. Characterization and biotechnological application of protease from thermophilic Thermomonas haemolytica. Arch Microbiol 2019; 202:153-159. [PMID: 31541265 DOI: 10.1007/s00203-019-01728-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 09/04/2019] [Accepted: 09/11/2019] [Indexed: 01/25/2023]
Abstract
In this study, it was aimed to determine the ability to produce protease enzyme of Thermomonas haemolytica isolated from geothermal Nenehatun hot spring in Turkey and utilization of this enzyme in the detergent industry to remove protein stains. The protease-producing strains were screened from hot springs, and a potential strain was identified as T. haemolytica according to morphological, physiological and biochemical characteristics and sequence of 16S rRNA gene. Maximum protease activity was observed at 55 °C and pH 9.0 at 72 h of incubation. Activity was very stable between 50 and 65 °C and pH 8.0-10.0, respectively. The enzyme activity was significantly inhibited by PMSF and partly inhibited by EDTA, EGTA, SDS, and urea. Some divalent metal ions such as Ca2+, Mg2+, and Mn2+ increased the enzyme activity, while Zn2+ and Cu2+ decreased. Michaelis-Menten constant (Km) and maximum velocity (Vmax) values were calculated by Lineweaver-Burk plot as 125 EU/ml and 1262 mg/ml, respectively. The biochemical characterization of the protease obtained from T. haemolytica was performed and applied on the blood and grass-stained fabrics with detergent to evaluate the stain removal performance of the enzyme. It was observed that the application of detergent with enzyme was more effective than the detergent without enzyme to clean up the stained fabrics. This is the first report of characterization of the protease of T. haemolytica. According to results obtained from this study, this new strain is a promising candidate for industrial applications in production of detergent.
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Affiliation(s)
- Ebru Oztas Gulmus
- Department of Molecular Biology and Genetics, Faculty of Science, Erzurum Technical University, Erzurum, Turkey
| | - Arzu Gormez
- Department of Molecular Biology and Genetics, Faculty of Science, Erzurum Technical University, Erzurum, Turkey.
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Ekermans P, de Gama R, Kock C, Hoosien E, Slavik T, Marshall T, Corcoran C, van Ingen J. An unusual case of abdominal mycobacterial infection: Case report and literature review. South Afr J HIV Med 2019; 20:993. [PMID: 31534791 PMCID: PMC6739527 DOI: 10.4102/sajhivmed.v20i1.993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 07/13/2019] [Indexed: 11/30/2022] Open
Abstract
This article presents a case of an HIV-infected paediatric patient with an unusual Mycobacterium genavense infection with predominantly abdominal organ involvement.
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Affiliation(s)
- Pieter Ekermans
- Department of Microbiology, National Reference Laboratory, AMPATH Laboratories, Centurion, South Africa
| | - Rene de Gama
- Department of Paediatrics, Netcare Unitas Hospital, Centurion, South Africa
| | - Celeste Kock
- Department of Paediatrics, Mediclinic Midstream Hospital, Midstream, South Africa
| | - Ebrahim Hoosien
- Department of Microbiology, National Reference Laboratory, AMPATH Laboratories, Centurion, South Africa
| | - Tomas Slavik
- Department of Histology, AMPATH Laboratories, Pretoria, South Africa
| | - Terry Marshall
- Department of Molecular Medicine, National Reference Laboratory, AMPATH Laboratories, Centurion, South Africa
| | - Craig Corcoran
- Department of Molecular Medicine, National Reference Laboratory, AMPATH Laboratories, Centurion, South Africa
| | - Jakko van Ingen
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands
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Naz I, Bano A, Mirza MS. Assessment of microbial diversity in the rhizosphere of Pinus roxburghii (Sarg.) and bio-inoculant potential of selected pine bacterial isolates for wheat varieties based on cultureindependent and culture-dependent techniques. Plant Biol (Stuttg) 2018; 20:143-150. [PMID: 29032584 DOI: 10.1111/plb.12648] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Accepted: 10/09/2017] [Indexed: 06/07/2023]
Abstract
Evidence is lacking regarding compatibility of pine bacteria as bio-inoculants for crops. The diversity and abundance of rhizosphere bacteria of Pinus roxburghii has never been investigated with simultaneous application of culture-dependent and culture-independent techniques. The present study was aimed to isolate, characterise, check the bio-inoculant potential of pine bacteria and assess rhizosphere bacterial diversity using culture-independent advanced approaches. Forty bacteria isolated from the rhizoplane of P. roxburghii growing in a cold climate at high altitude in Murree, were morphologically characterised; nine were identified by 16S rRNA sequence analyses and used in experiments. Diversity and abundance of the 16S rRNA gene and nifH gene in the rhizosphere was assessed by cloning, RFLP analysis, 454-amplicon pyrosequencing and qPCR. The bacterial isolates significantly improved dry weight of shoot, root, root area, IAA and GA3 content, number of grains plant-1 , weight of grains plant-1 in wheat varieties Chakwal-50 and Fareed-06 under axenic and field conditions. The number of 16S rRNA sequences (2979) identified by pyrosequencing shared similarity with 13 phyla of bacteria and archaea. The results confirm the existence of diverse bacteria of agricultural and industrial importance in the rhizosphere and compatibility of rhizoplane bacteria as bio-inoculants for wheat varieties.
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Affiliation(s)
- I Naz
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - A Bano
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
- Department of BioSciences, University of Wah, Wah Cantt, Pakistan
| | - M S Mirza
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology & Genetic Engineering (NIBGE), Faisalabad, Pakistan
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Chitra MA, Jayalakshmi K, Ponnusamy P, Manickam R, Ronald BSM. Dermatophilus congolensis infection in sheep and goats in Delta region of Tamil Nadu. Vet World 2017; 10:1314-1318. [PMID: 29263591 PMCID: PMC5732335 DOI: 10.14202/vetworld.2017.1314-1318] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 10/11/2017] [Indexed: 11/16/2022] Open
Abstract
Aim The study was conducted to isolate and identify Dermatophilus congolensis (DC) using conventional and molecular diagnostic techniques in scab materials collected from skin infections of sheep and goats in the Delta region of Tamil Nadu. Materials and Methods A total of 20 scab samples collected from 18 goats and 2 sheep from Nagapattinam, Thanjavur, and Tiruvarur districts of Tamil Nadu. Smears were made from softened scab materials and stained by either Gram's or Giemsa staining. Isolation was attempted on blood agar plates, and colonies were stained by Gram's staining for morphological identification. Identification was also done by biochemical tests and confirmed by 16S rRNA polymerase chain reaction (PCR), followed by sequencing and phylogenetic analysis of the amplified product. Results The peculiar laddering arrangement of coccoid forms in stained smears prepared from scab materials revealed the presence of DC. Isolated colonies from scab materials of sheep and goats on bovine blood agar plate were small, hemolytic, rough, adherent, and bright orange-yellow in color, but some colonies were white to cream color. Gram-staining of cultured organisms revealed Gram-positive branching filaments with various disintegration stages of organisms. 16S rRNA PCR yielded 500 bp amplicon specific for DC. Sequence analysis of a sheep DC isolate showed 99-100% sequence homology with other DC isolates available in NCBI database, and phylogenetic tree showed a close cluster with DC isolates of Congo, Nigeria, and Angola of Africa. Genes for virulence factors such as serine protease and alkaline ceramidase could not be detected by PCR in any of the DC strains isolated of this study. Conclusion The presence of dermatophilosis in Tamil Nadu was established from this study.
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Affiliation(s)
- M Ananda Chitra
- Department of Veterinary Microbiology, Veterinary College and Research Institute, Tamil Nadu Veterinary and Animal Sciences University, Orathanadu - 614 625, Thanjavur, Tamil Nadu, India
| | - K Jayalakshmi
- Department of Veterinary Medicine, Veterinary College and Research Institute, Tamil Nadu Veterinary and Animal Sciences University, Orathanadu - 614 625, Thanjavur, Tamil Nadu, India
| | - P Ponnusamy
- Department of Veterinary Microbiology, Veterinary College and Research Institute, Tamil Nadu Veterinary and Animal Sciences University, Orathanadu - 614 625, Thanjavur, Tamil Nadu, India
| | - R Manickam
- Department of Veterinary Microbiology, Veterinary College and Research Institute, Tamil Nadu Veterinary and Animal Sciences University, Orathanadu - 614 625, Thanjavur, Tamil Nadu, India
| | - B S M Ronald
- Department of Veterinary Microbiology, Veterinary College and Research Institute, Tamil Nadu Veterinary and Animal Sciences University, Orathanadu - 614 625, Thanjavur, Tamil Nadu, India
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Subba Reddy Gangireddygari V, Kanderi D, Golla R, Bangeppagari M, Anand Kumar Babu Gundi V, Ntushelo K, Reddy Bontha R. Biodegradation of Quinalphos by a Soil Bacterium-Bacillus subtilis. Pak J Biol Sci 2017; 20:410-422. [PMID: 29023062 DOI: 10.3923/pjbs.2017.410.422] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND AND OBJECTIVE A widely used pesticide quinalphos (O, O-diethyl O-quinoxalin-2-yl phosphorothioate) may be an undesirable and persistent pollutant to non-target environments like rivers and other ecosystems. The objective of this study was to isolate a potential degradant bacterium of quinalphos from polluted soils and test its fitness under various culture conditions. MATERIALS AND METHODS A soil bacterium strain, capable of utilizing quinalphos as its sole source of carbon and energy was isolated from soil by enrichment method on a minimal salts medium (MSM). On the basis of morphological, biochemical and 16S rRNA gene sequence analysis the bacterium is a species of the genus Bacillus and it was closely related to Bacillus subtilis. Quinalphos degrading capabilities of this bacterium were assessed under different culture conditions. Quinalphos degradation data were analysed byusing a two-way ANOVA analysis with the Statistica v.10. RESULTS Bacillus subtilis grew on quinalphos with a generation time of 32.34 min or 0.54 h in the logarithmic phase. Maximum degradation of quinalphos was observed with an inoculum of 1.0 optical density, around pH-7.5 and at an optimum temperature of 35-37°C. Among the additional carbon and nitrogen sources, carbon source-glucose and nitrogen source-yeast extract marginally improved the rate of degradation of quinalphos. Gas chromatography-mass spectrometry (GC-MS) analysis of the culture of B. subtilis grown on quinalphos indicated the formation of one main metabolite-quinoxaline. CONCLUSION The B. subtilis strain discovered in this study has a unique combination of abilities to degrade quinalphos and it is therefore suitable candidate bioremediator of quinalphos polluted environments.
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Affiliation(s)
| | - DileepKumar Kanderi
- Department of Microbiology, Sri Krishnadevaraya University, 515 003 Anantapuramu, Andhra Pradesh, India
| | - Ramanjaneyulu Golla
- Department of Microbiology, Sri Krishnadevaraya University, 515 003 Anantapuramu, Andhra Pradesh, India
| | - Manjunatha Bangeppagari
- Center for Biofluid and Biomimic Research,Pohang University of Science and Technology (POSTECH), 790-784 Pohang, South Korea
| | | | - Khayalethu Ntushelo
- Department of Agriculture and Animal Health, College of Agriculture and Environmental Sciences, Florida Science Campus, Corner Christiaan De Wet and Pioneer Avenue, Florida, University of South Africa, 1710 Johannesburg, Gauteng, South Africa
| | - Rajasekhar Reddy Bontha
- Department of Microbiology, Sri Krishnadevaraya University, 515 003 Anantapuramu, Andhra Pradesh, India
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14
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Yano R, Shimoda T, Watanabe R, Kuroki Y, Okubo T, Nakamura S, Matsuo J, Yoshimura S, Yamaguchi H. Diversity changes of microbial communities into hospital surface environments. J Infect Chemother 2017; 23:439-445. [PMID: 28431935 DOI: 10.1016/j.jiac.2017.03.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 03/21/2017] [Accepted: 03/22/2017] [Indexed: 01/23/2023]
Abstract
Previous works have demonstrated considerable variability in hospital cleanliness in Japan, suggesting that contamination is driven by factors that are currently poorly controlled. We undertook 16S rRNA sequence analysis to study population structures of hospital environmental microbiomes to see which factor(s) impacted contamination. One hundred forty-four samples were collected from surfaces of three hospitals with distinct sizes ("A": >500 beds, "B": 100-500 beds, "C": <100 beds). Sample locations of two ward types (Surgical and Internal) included patient room bed table (multiple) (4BT), patient overbed table (multiple) (4OT), patient room sink (multiple) (4S), patient room bed table (single) (SBT), patient overbed table (single) (SOT), patient room sink (single) (SS), nurse desk (ND), and nurse wagon (NW). Total DNA was extracted from each sample, and the 50 samples that yielded sufficient DNA were used for further 16S rRNA sequencing of hospital microbiome populations with cluster analysis. The number of assigned bacterial OTU populations was significantly decreased in hospital "C" compared to the other hospitals. Cluster analysis of sampling locations revealed that the population structure in almost all locations of hospital "C" and some locations in the other hospitals was very similar and unusually skewed with a family, Enterobacteriaceae. Interestingly, locations included patient area (4OT, 4BT, SBT) and nurse area (ND), with a device (NW) bridging the two and a place (4S and SS) shared between patients or visitors. We demonstrated diversity changes of hospital environmental microbiomes with a skewed population, presumably by medical staff pushing NWs or sinks shared by patients or visitors.
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Affiliation(s)
- Rika Yano
- Department of Fundamental Nursing, Faculty of Health Sciences, Hokkaido University, Sapporo, Japan.
| | - Tomoko Shimoda
- Department of Fundamental Nursing, Faculty of Health Sciences, Hokkaido University, Sapporo, Japan.
| | - Reina Watanabe
- Department of Fundamental Nursing, Faculty of Health Sciences, Hokkaido University, Sapporo, Japan.
| | - Yasutoshi Kuroki
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Sapporo, Japan.
| | - Torahiko Okubo
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Sapporo, Japan.
| | - Shinji Nakamura
- Laboratory of Morphology and Image Analysis, Biomedical Research Center, Juntendo University Graduate School of Medicine, Tokyo, Japan.
| | - Junji Matsuo
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Sapporo, Japan.
| | - Sadako Yoshimura
- Department of Fundamental Nursing, Faculty of Health Sciences, Hokkaido University, Sapporo, Japan.
| | - Hiroyuki Yamaguchi
- Department of Fundamental Nursing, Faculty of Health Sciences, Hokkaido University, Sapporo, Japan.
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15
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Subba Reddy GV, Rafi MM, Rubesh Kumar S, Khayalethu N, Muralidhara Rao D, Manjunatha B, Philip GH, Reddy BR. Optimization study of 2-hydroxyquinoxaline (2-HQ) biodegradation by Ochrobactrum sp. HQ1. 3 Biotech 2016; 6:51. [PMID: 28330121 PMCID: PMC4746200 DOI: 10.1007/s13205-015-0358-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 08/17/2015] [Indexed: 11/22/2022] Open
Abstract
A novel aerobic gram-negative bacterial strain capable of utilizing 2-hydroxyquinoxaline (2-HQ) as sole source of carbon and energy was isolated from Indian agricultural soil and named as HQ1. Strain HQ1 was identified as Ochrobactrum sp. on the basis of morphology, physico-biochemical characteristics and 16S rRNA sequence analysis. The generation time of Ochrobactrum sp. HQ1 on 2-HQ at log phase is 0.71 h or 42.6 min. The degradation of 2-HQ by HQ1 under various physico-chemical parameters was analysed by HPLC and observed to be optimum with a high inoculum density (1.0 OD) at pH 7–8, temperatures 37–40°C and a high concentration of 2-HQ (500 ppm). Degradation of 2-HQ was also improved when additional nitrogen sources were used and this was attributed to the enhanced growth of the bacterium on the readily available nitrogen sources. Analysis of 2-HQ degradation by GC–MS resulted in elucidation of the degradation pathway for HQ1, a novel observation for aerobic Gram-negative bacteria. These findings are a possible indication of the application of HQ1 in the bioremediation of pesticide/metabolite contamination.
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Reddy GVS, Reddy BR, Tlou MG. Biodegradation of 2-hydroxyquinoxaline (2-HQ) by Bacillus sp. J Hazard Mater 2014; 278:100-107. [PMID: 24953941 DOI: 10.1016/j.jhazmat.2014.05.080] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 05/16/2014] [Accepted: 05/28/2014] [Indexed: 06/03/2023]
Abstract
An aerobic Gram +ve bacterial strain capable of utilizing 2-Hydroxyquinoxaline (2-HQ) as sole source of carbon and energy was isolated from Chrysanthemum indicum Indian agricultural soil and named as HQ2. On the basis of morphology, physico-biochemical characteristics and 16S rRNA sequence analysis, strain HQ2 was identified as Bacillus sp. The generation time of Bacillus sp. in log phase during growth on 2-HQ is 0.79 h or 47.4 min. The optimal conditions for 2-HQ degradation by Bacillus sp. were inoculum density of 1.0 OD, pH of 6-8, temperature of 37-45 °C and 2-HQ concentration of 500 ppm. Among the additional carbon and nitrogen sources, carbon sources did not influence the degradation rate of 2-HQ, but nitrogen sources-yeast extract marginally enhanced the rate of degradation of 2-HQ. GC-MS analysis of the culture Bacillus sp. grown on 2-HQ indicated the formation of dimers from 2 molecules of 2-hydroxyquinoxaline. The formation of dimer for degradation of 2-HQ by the culture appears to be the first report to our scientific knowledge.
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Affiliation(s)
- G V Subba Reddy
- Department of Microbiology, Sri Krishnadevaraya University, Anantapuram - 515 003, A.P., India; Faculty of Science, Department of Biochemistry, University of Johannesburg, PO Box-524, APK Campus, Johannesburg 2006, South Africa.
| | - B R Reddy
- Department of Microbiology, Sri Krishnadevaraya University, Anantapuram - 515 003, A.P., India
| | - M G Tlou
- Faculty of Science, Department of Biochemistry, University of Johannesburg, PO Box-524, APK Campus, Johannesburg 2006, South Africa
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