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Xie F, Pathom-aree W. Actinobacteria From Desert: Diversity and Biotechnological Applications. Front Microbiol 2021; 12:765531. [PMID: 34956128 PMCID: PMC8696123 DOI: 10.3389/fmicb.2021.765531] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 11/08/2021] [Indexed: 12/25/2022] Open
Abstract
Deserts, as an unexplored extreme ecosystem, are known to harbor diverse actinobacteria with biotechnological potential. Both multidrug-resistant (MDR) pathogens and environmental issues have sharply raised the emerging demand for functional actinobacteria. From 2000 to 2021, 129 new species have been continuously reported from 35 deserts worldwide. The two largest numbers are of the members of the genera Streptomyces and Geodermatophilus, followed by other functional extremophilic strains such as alkaliphiles, halotolerant species, thermophiles, and psychrotolerant species. Improved isolation strategies for the recovery of culturable and unculturable desert actinobacteria are crucial for the exploration of their diversity and offer a better understanding of their survival mechanisms under extreme environmental stresses. The main bioprospecting processes involve isolation of target actinobacteria on selective media and incubation and selection of representatives from isolation plates for further investigations. Bioactive compounds obtained from desert actinobacteria are being continuously explored for their biotechnological potential, especially in medicine. To date, there are more than 50 novel compounds discovered from these gifted actinobacteria with potential antimicrobial activities, including anti-MDR pathogens and anti-inflammatory, antivirus, antifungal, antiallergic, antibacterial, antitumor, and cytotoxic activities. A range of plant growth-promoting abilities of the desert actinobacteria inspired great interest in their agricultural potential. In addition, several degradative, oxidative, and other functional enzymes from desert strains can be applied in the industry and the environment. This review aims to provide a comprehensive overview of desert environments as a remarkable source of diverse actinobacteria while such rich diversity offers an underexplored resource for biotechnological exploitations.
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Affiliation(s)
- Feiyang Xie
- Doctor of Philosophy Program in Applied Microbiology (International Program), Faculty of Science, Chiang Mai University, under the CMU Presidential Scholarship, Chiang Mai, Thailand
| | - Wasu Pathom-aree
- Research Center of Microbial Diversity and Sustainable Utilization, Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
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Microbiome Studies from Saudi Arabia over the Last 10 Years: Achievements, Gaps, and Future Directions. Microorganisms 2021; 9:microorganisms9102021. [PMID: 34683342 PMCID: PMC8537179 DOI: 10.3390/microorganisms9102021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 11/17/2022] Open
Abstract
In the past ten years, microbiome studies have shown tremendous potentiality for implementation of understanding microbiome structures and functions of various biomes and application of this knowledge for human betterment. Saudi Arabia is full of geographical, ecological, ethnical, and industrial diversities and scientific capacities. Therefore, there is a great potential in Saudi Arabia to conduct and implement microbiome-based research and applications. However, there is no review available on where Saudi Arabia stands with respect to global microbiome research trends. This review highlights the metagenome-assisted microbiome research from Saudi Arabia compared to the global focuses on microbiome research. Further, it also highlights the gaps and areas that should be focused on by Saudi microbiome researchers and the possible initiatives to be taken by Saudi government and universities. This literature review shows that the global trends of microbiome research cover a broad spectrum of human and animal health conditions and diseases, environmental and antimicrobial resistance surveillance, surveillance of food and food processing, production of novel industrial enzymes and bioactive pharmaceutical products, and space applications. However, Saudi microbiome studies are mostly confined to very few aspects of health (human and animal) and environment/ecology in last ten years, without much application. Therefore, Saudi Arabia should focus more on applied microbiome research through government, academic, and industry initiatives and global cooperation to match the global trends.
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Zheng X, Wang H, Yan Q, Zhang G, Chen C. Simultaneous nitrogen removal and methane production from Taihu blue algae against ammonia inhibition using integrated bioelectrochemical system (BES). THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 777:146144. [PMID: 33684748 DOI: 10.1016/j.scitotenv.2021.146144] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/22/2021] [Accepted: 02/22/2021] [Indexed: 06/12/2023]
Abstract
Simultaneous nitrogen removal and methane production using an integrated bioelectrochemical system (BES) during the anaerobic digestion (AD) process of Taihu blue algae were investigated. Upon an applied voltage of 0.4 V and total solids (TS) ratio of blue algae to anaerobic sludge as 1:1, the highest methanogenesis potential as 69.12 mL/g VS could be obtained, attaining 18.7 times of the TS ratio group of 3:1. Moreover, methane production of the integrated BES group reached 3.18 times of the AD group using conical flask, even with the same TS ratio (1:1) and initial ammonia nitrogen concentration (1000 mg NH4+-N/L). Apart from the bettered electrochemical performance, bio-augmented microbial genus responsible for acetoclastic methanogenesis, power generation, resisting to hostile circumstance, co-existence with hydrogenotrophic methanogens could all be enriched. Therefore, integrated BES with appropriate TS ratio under applied voltage might help offset both the ammonia and electrical stress, thereby to maintain enhanced biomethanation performance.
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Affiliation(s)
- Xiaoxiao Zheng
- School of Environmental and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Han Wang
- School of Environmental and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Qun Yan
- School of Environmental and Civil Engineering, Jiangnan University, Wuxi 214122, China; Jiangsu Key Laboratory of Anaerobic Biotechnology, Wuxi 214122, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou 215011, China..
| | - Guangsheng Zhang
- School of Environmental and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Chongjun Chen
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China
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Salam N, Xian WD, Asem MD, Xiao M, Li WJ. From ecophysiology to cultivation methodology: filling the knowledge gap between uncultured and cultured microbes. MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:132-147. [PMID: 37073336 PMCID: PMC10077289 DOI: 10.1007/s42995-020-00064-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 07/22/2020] [Indexed: 05/03/2023]
Abstract
Earth is dominated by a myriad of microbial communities, but the majority fails to grow under in situ laboratory conditions. The basic cause of unculturability is that bacteria dominantly occur as biofilms in natural environments. Earlier improvements in the culture techniques are mostly done by optimizing media components. However, with technological advancement particularly in the field of genome sequencing and cell imagining techniques, new tools have become available to understand the ecophysiology of microbial communities. Hence, it becomes easier to mimic environmental conditions in the culture plate. Other methods include co-culturing, emendation of growth factors, and cultivation after physical cell sorting. Most recently, techniques have been proposed for bacterial cultivation by employing genomic data to understand either microbial interactions (network-directed targeted bacterial isolation) or ecosystem engineering (reverse genomics). Hopefully, these techniques may be applied to almost all environmental samples, and help fill the gaps between the cultured and uncultured microbial communities.
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Affiliation(s)
- Nimaichand Salam
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Science and School of Ecology, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Wen-Dong Xian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Science and School of Ecology, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Mipeshwaree Devi Asem
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Science and School of Ecology, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Min Xiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Science and School of Ecology, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Science and School of Ecology, Sun Yat-Sen University, Guangzhou, 510275 China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011 China
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Wang X, Yang J, Huang Y, Wu X, Wang L, Han L, Li S, Li H, Fu X, Chen H, Zhu X. Georgenia faecalis sp. nov. isolated from the faeces of Tibetan antelope. J Microbiol 2020; 58:734-740. [PMID: 32710298 DOI: 10.1007/s12275-020-0060-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 06/11/2020] [Accepted: 06/16/2020] [Indexed: 11/26/2022]
Abstract
Two aerobic, Gram-stain-positive, non-motile, non-sporulating coccoid strains, designated ZLJ0423T and ZLJ0321, were isolated from the faeces of Tibetan antelope (Pantholops hodgsonii). Their optimal temperature, NaCl concentration and pH for growth were 28°C, 0.5% (w/v) NaCl and pH 7.5, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains ZLJ0423T and ZLJ0321 were very similar to each other (99.8%) and had a sequence similarity of 97.0% with Georgenia satyanarayanai NBRC 107612T and Georgenia subflava CGMCC 1.12782T. Phylogenomic analysis based on 688 core genes indicated that these strains formed a clade with G. satyanarayanai NBRC 107612T and Georgenia wutianyii Z294. The predominant cellular fatty acids were anteiso-C15:0, anteiso-C15:1A and C16:0. The major menaquinone was MK-8(H4). The cell-wall amino acids consisted of alanine, lysine, glycine and aspartic acid, with lysine as the diagnostic diamino acid. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides and two unidentified lipids formed the polar lipid profile. The DNA G + C content of both isolates was 73.9 mol%. The digital DNA-DNA hybridization value between strains ZLJ0423T and ZLJ0321 was 91.2%, but their values with closely related species and other available type strains of the genus Georgenia were lower than the 70% threshold. On the basis of polyphasic taxonomic data, strains ZLJ0423T and ZLJ0321 represent a novel species within the genus Georgenia, for which the name Georgenia faecalis sp. nov. is proposed. The type strain is ZLJ0423T (= CGMCC 1.13681T = JCM 33470T).
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Affiliation(s)
- Xiaoxia Wang
- Central & Clinical Laboratory of Sanya People's Hospital, Sanya, Hainan, 572000, P. R. China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, 102206, P. R. China
| | - Jing Yang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, 102206, P. R. China
- Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai, 201508, P. R. China
- Research Units of Discovery of Unknown Bacteria and function, Chinese Academy of Medical Sciences, Beijing, 100730, P. R. China
| | - Yuyuan Huang
- Guangxi Key Laboratory of AIDS Prevention and Treatment & Guangxi Collaborative Innovation Center for Biomedicine, School of Public Health, Guangxi Medical University, Nanning, Guangxi, 530021, P. R. China
| | - Xiaomin Wu
- Shaanxi Institute of Zoology, Xi'an, 710032, P. R. China
| | - Licheng Wang
- Central & Clinical Laboratory of Sanya People's Hospital, Sanya, Hainan, 572000, P. R. China
| | - Limei Han
- Central & Clinical Laboratory of Sanya People's Hospital, Sanya, Hainan, 572000, P. R. China
| | - Sha Li
- Central & Clinical Laboratory of Sanya People's Hospital, Sanya, Hainan, 572000, P. R. China
| | - Huan Li
- Central & Clinical Laboratory of Sanya People's Hospital, Sanya, Hainan, 572000, P. R. China
| | - Xiaoying Fu
- Central & Clinical Laboratory of Sanya People's Hospital, Sanya, Hainan, 572000, P. R. China
| | - Hai Chen
- Central & Clinical Laboratory of Sanya People's Hospital, Sanya, Hainan, 572000, P. R. China
| | - Xiong Zhu
- Central & Clinical Laboratory of Sanya People's Hospital, Sanya, Hainan, 572000, P. R. China.
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Tian Z, Zhang D, Lu S, Jin D, Yang J, Pu J, Lai XH, Huang Y, Lei W, Zhang S, Li J, Dong K, Wang S, Xu J. Georgenia wutianyii sp. nov. and Georgenia yuyongxinii sp. nov. isolated from plateau pika ( Ochotona curzoniae) on the Qinghai-Tibet plateau of China. Int J Syst Evol Microbiol 2020; 70:2318-2324. [PMID: 32195648 DOI: 10.1099/ijsem.0.004042] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Four novel bacterial strains, designated Z294T, Z311, Z443T and Z446, were isolated from the intestinal contents of plateau pika (Ochotona curzoniae) on the Qinghai-Tibet Plateau of China. Cells were Gram-stain-positive, catalase-positive, oxidase-negative, aerobic, non-motile and short-rod shaped. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the four isolates belong to the genus Georgenia, but clearly separate from the currently recognized species. Both type strains (Z294T and Z443T) shared low 16S rRNA gene sequence similarity, digital DNA-DNA hybridization relatedness and average nucleotide identity values with Georginia satyanarayanai NBRC 107612T, G. subflava JCM 19765T, G. ruanii JCM 15130T and G. thermotolerans DSM 21501T and against each other. The genomic DNA G+C contents of strains Z294T and Z443T were 73.3 and 70 %, respectively. The major cellular fatty acids of strain Z294T were anteiso-C15 : 0, anteiso-C15 : 1 A and C16 : 0, in contrast to anteiso-C15 : 0 and anteiso-C15 : 1 A for strain Z443T. Both type strains (Z294T and Z443T) shared the following common features: glucose, rhamnose and ribose as cell-wall sugars; MK-8(H4) as major menaquinone; alanine, glutamic acid and lysine as cell-wall amino acids; and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside and one unidentified phosphoglycolipid as polar lipids. Comparing the phenotypic and phylogenetic features among the four strains and their related organisms, strains Z294T and Z443T represent two novel species within the genus Georgenia, for which the names Georgenia wutianyii sp. nov. (type strain Z294T=CGMCC 1.16428T=DSM 106344T) and Georgenia yuyongxinii sp. nov. (type strain Z443T=CGMCC 1.16435T=DSM 106174T) are proposed.
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Affiliation(s)
- Zhi Tian
- Department of Epidemiology, Shanxi Medical University School of Public Health, Taiyuan, Shanxi 030001, PR China
| | - Dezhu Zhang
- Guizhou Provincial Center for Disease Control and Prevention, Guiyang, Guizhou, 550004, PR China
| | - Shan Lu
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, PR China.,Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai 201508, PR China.,State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Dong Jin
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, PR China.,Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai 201508, PR China.,State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Jing Yang
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, PR China.,Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai 201508, PR China.,State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Xin-He Lai
- School of Biology and Food Sciences, Shangqiu Normal University, Shangqiu, Henan 476000, PR China
| | - Ying Huang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Wenjing Lei
- Department of Epidemiology, Shanxi Medical University School of Public Health, Taiyuan, Shanxi 030001, PR China
| | - Sihui Zhang
- Department of Epidemiology, Shanxi Medical University School of Public Health, Taiyuan, Shanxi 030001, PR China
| | - Junqin Li
- Department of Epidemiology, Shanxi Medical University School of Public Health, Taiyuan, Shanxi 030001, PR China
| | - Kui Dong
- Department of Epidemiology, Shanxi Medical University School of Public Health, Taiyuan, Shanxi 030001, PR China
| | - Suping Wang
- Department of Epidemiology, Shanxi Medical University School of Public Health, Taiyuan, Shanxi 030001, PR China
| | - Jianguo Xu
- Department of Epidemiology, Shanxi Medical University School of Public Health, Taiyuan, Shanxi 030001, PR China.,State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China.,Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai 201508, PR China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, PR China
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Oren A, Garrity GM. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2019; 69:1247-1250. [PMID: 31066659 DOI: 10.1099/ijsem.0.003357] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Aharon Oren
- 1The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George M Garrity
- 2Department of Microbiology and Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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