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Huang HJ, Zhang X, Sun XW, Chen B, Li XT, Zhou N, Abdugheni R, Cheng QY, Zhang TJ, Liu Y, Jiang Y, Deng Y, Liu SJ, Jiang CY. Xiashengella succiniciproducens gen. nov., sp. nov., a succinate-producing bacterium isolated from an anaerobic digestion tank in the family Marinilabiliaceae of the order Bacteroidales. Arch Microbiol 2024; 206:141. [PMID: 38441685 DOI: 10.1007/s00203-024-03909-5] [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: 09/08/2023] [Revised: 01/26/2024] [Accepted: 02/24/2024] [Indexed: 03/07/2024]
Abstract
A strictly anaerobic, motile bacterium, designated as strain Ai-910T, was isolated from the sludge of an anaerobic digestion tank in China. Cells were Gram-stain-negative rods. Optimal growth was observed at 38 °C (growth range 25-42 °C), pH 8.5 (growth range 5.5-10.5), and under a NaCl concentration of 0.06% (w/v) (range 0-2.0%). Major cellular fatty acids were iso-C15 : 0 and anteiso-C15 : 0. The respiratory quinone was MK-7. Using xylose as the growth substrate, succinate was produced as the fermentation product. Phylogenetic analysis based on the 16 S rRNA gene sequences indicated that strain Ai-910T formed a distinct phylogenetic lineage that reflects a new genus in the family Marinilabiliaceae, sharing high similarities to Alkaliflexus imshenetskii Z-7010T (92.78%), Alkalitalea saponilacus SC/BZ-SP2T (92.51%), and Geofilum rubicundum JAM-BA0501T (92.36%). Genomic similarity (average nucleotide identity and digital DNA-DNA hybridization) values between strain Ai-910T and its phylogenetic neighbors were below 65.27 and 16.90%, respectively, indicating that strain Ai-910T represented a novel species. The average amino acid identity between strain Ai-910T and other related members of the family Marinilabiliaceae were below 69.41%, supporting that strain Ai-910T was a member of a new genus within the family Marinilabiliaceae. Phylogenetic, genomic, and phenotypic analysis revealed that strain Ai-910T was distinguished from other phylogenetic relatives within the family Marinilabiliaceae. The genome size was 3.10 Mbp, and the DNA G + C content of the isolate was 42.8 mol%. Collectively, differences of the phenotypic and phylogenetic features of strain Ai-910T from its close relatives suggest that strain Ai-910T represented a novel species in a new genus of the family Marinilabiliaceae, for which the name Xiashengella succiniciproducens gen. nov., sp. nov. was proposed. The type strain of Xiashengella succiniciproducens is Ai-910T (= CGMCC 1.17893T = KCTC 25,304T).
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Affiliation(s)
- Hao-Jie Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266000, China
| | - Xi Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xin-Wei Sun
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266000, China
| | - Biao Chen
- Xuzhou Medical University, Xuzhou, 221004, China
| | - Xiu-Tong Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Nan Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Rashidin Abdugheni
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiu-Yin Cheng
- Beijing Drainage Group Co., Ltd, Beijing, 100044, China
| | - Tie-Jun Zhang
- Beijing Drainage Group Co., Ltd, Beijing, 100044, China
| | - Yao Liu
- Beijing Drainage Group Co., Ltd, Beijing, 100044, China
| | - Yong Jiang
- Beijing Drainage Group Co., Ltd, Beijing, 100044, China
| | - Ye Deng
- IMCAS-RCEES Joint Lab at CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China.
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266000, China.
- IMCAS-RCEES Joint Lab at CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
| | - Cheng-Ying Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China.
- IMCAS-RCEES Joint Lab at CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
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La Cono V, Messina E, Reva O, Smedile F, La Spada G, Crisafi F, Marturano L, Miguez N, Ferrer M, Selivanova EA, Golyshina OV, Golyshin PN, Rohde M, Krupovic M, Merkel AY, Sorokin DY, Hallsworth JE, Yakimov MM. Nanohaloarchaea as beneficiaries of xylan degradation by haloarchaea. Microb Biotechnol 2023; 16:1803-1822. [PMID: 37317055 PMCID: PMC10443357 DOI: 10.1111/1751-7915.14272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/18/2023] [Accepted: 04/28/2023] [Indexed: 06/16/2023] Open
Abstract
Climate change, desertification, salinisation of soils and the changing hydrology of the Earth are creating or modifying microbial habitats at all scales including the oceans, saline groundwaters and brine lakes. In environments that are saline or hypersaline, the biodegradation of recalcitrant plant and animal polysaccharides can be inhibited by salt-induced microbial stress and/or by limitation of the metabolic capabilities of halophilic microbes. We recently demonstrated that the chitinolytic haloarchaeon Halomicrobium can serve as the host for an ectosymbiont, nanohaloarchaeon 'Candidatus Nanohalobium constans'. Here, we consider whether nanohaloarchaea can benefit from the haloarchaea-mediated degradation of xylan, a major hemicellulose component of wood. Using samples of natural evaporitic brines and anthropogenic solar salterns, we describe genome-inferred trophic relations in two extremely halophilic xylan-degrading three-member consortia. We succeeded in genome assembly and closure for all members of both xylan-degrading cultures and elucidated the respective food chains within these consortia. We provide evidence that ectosymbiontic nanohaloarchaea is an active ecophysiological component of extremely halophilic xylan-degrading communities (although by proxy) in hypersaline environments. In each consortium, nanohaloarchaea occur as ectosymbionts of Haloferax, which in turn act as scavenger of oligosaccharides produced by xylan-hydrolysing Halorhabdus. We further obtained and characterised the nanohaloarchaea-host associations using microscopy, multi-omics and cultivation approaches. The current study also doubled culturable nanohaloarchaeal symbionts and demonstrated that these enigmatic nano-sized archaea can be readily isolated in binary co-cultures using an appropriate enrichment strategy. We discuss the implications of xylan degradation by halophiles in biotechnology and for the United Nation's Sustainable Development Goals.
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Affiliation(s)
| | | | - Oleg Reva
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, Centre for Bioinformatics and Computational BiologyUniversity of PretoriaPretoriaSouth Africa
| | | | | | | | | | - Noa Miguez
- Instituto de Catalisis y Petroleoquimica (ICP), CSICMadridSpain
| | - Manuel Ferrer
- Instituto de Catalisis y Petroleoquimica (ICP), CSICMadridSpain
| | - Elena A. Selivanova
- Institute for Cellular and Intracellular SymbiosisUral Branch, Russian Academy of SciencesOrenburgRussia
| | | | | | - Manfred Rohde
- Central Facility for MicrobiologyHelmholtz Centre for Infection ResearchBraunschweigGermany
| | - Mart Krupovic
- Institut PasteurUniversité Paris Cité, Archaeal Virology UnitParisFrance
| | - Alexander Y. Merkel
- Winogradsky Institute of MicrobiologyResearch Centre of Biotechnology, Russian Academy of SciencesMoscowRussia
| | - Dimitry Y. Sorokin
- Winogradsky Institute of MicrobiologyResearch Centre of Biotechnology, Russian Academy of SciencesMoscowRussia
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
| | - John E. Hallsworth
- Institute for Global Food Security, School of Biological SciencesQueen's University BelfastNorthern IrelandUK
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Suleiman M, Kounosu A, Murcott B, Dayi M, Pawluk R, Yoshida A, Viney M, Kikuchi T, Hunt VL. piRNA-like small RNAs target transposable elements in a Clade IV parasitic nematode. Sci Rep 2022; 12:10156. [PMID: 35710810 PMCID: PMC9203780 DOI: 10.1038/s41598-022-14247-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 06/03/2022] [Indexed: 12/02/2022] Open
Abstract
The small RNA (sRNA) pathways identified in the model organism Caenorhabditis elegans are not widely conserved across nematodes. For example, the PIWI pathway and PIWI-interacting RNAs (piRNAs) are involved in regulating and silencing transposable elements (TE) in most animals but have been lost in nematodes outside of the C. elegans group (Clade V), and little is known about how nematodes regulate TEs in the absence of the PIWI pathway. Here, we investigated the role of sRNAs in the Clade IV parasitic nematode Strongyloides ratti by comparing two genetically identical adult stages (the parasitic female and free-living female). We identified putative small-interfering RNAs, microRNAs and tRNA-derived sRNA fragments that are differentially expressed between the two adult stages. Two classes of sRNAs were predicted to regulate TE activity including (i) a parasite-associated class of 21-22 nt long sRNAs with a 5' uridine (21-22Us) and a 5' monophosphate, and (ii) 27 nt long sRNAs with a 5' guanine/adenine (27GAs) and a 5' modification. The 21-22Us show striking resemblance to the 21U PIWI-interacting RNAs found in C. elegans, including an AT rich upstream sequence, overlapping loci and physical clustering in the genome. Overall, we have shown that an alternative class of sRNAs compensate for the loss of piRNAs and regulate TE activity in nematodes outside of Clade V.
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Affiliation(s)
- Mona Suleiman
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
| | - Asuka Kounosu
- Parasitology, Department of Infectious Dieses, Faculty of Medicine, University of Miyazaki, Miyazaki, 889-1692, Japan
| | - Ben Murcott
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
| | - Mehmet Dayi
- Parasitology, Department of Infectious Dieses, Faculty of Medicine, University of Miyazaki, Miyazaki, 889-1692, Japan
- Forestry Vocational School, Duzce University, 81620, Duzce, Turkey
| | - Rebecca Pawluk
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
| | - Akemi Yoshida
- Laboratory of Genomics, Frontier Science Research Center, University of Miyazaki, Miyazaki, 889-1692, Japan
| | - Mark Viney
- Department of Evolution, Ecology and Behaviour, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Taisei Kikuchi
- Parasitology, Department of Infectious Dieses, Faculty of Medicine, University of Miyazaki, Miyazaki, 889-1692, Japan.
| | - Vicky L Hunt
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK.
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Solano-Aguilar GI, Lakshman S, Jang S, Gupta R, Molokin A, Schroeder SG, Gillevet PM, Urban JF. The Effects of Consuming White Button Mushroom Agaricus bisporus on the Brain and Liver Metabolome Using a Targeted Metabolomic Analysis. Metabolites 2021; 11:metabo11110779. [PMID: 34822437 PMCID: PMC8625434 DOI: 10.3390/metabo11110779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/29/2021] [Accepted: 11/11/2021] [Indexed: 11/21/2022] Open
Abstract
A targeted metabolomic analysis was performed on tissues derived from pigs fed diets supplemented with white button mushrooms (WBM) to determine the effect on the liver and brain metabolome. Thirty-one pigs were fed a grower diet alone or supplemented with either three or six servings of freeze-dried WBM for six weeks. Tissue metabolomes were analyzed using targeted liquid chromatography-mass spectrometry (LC-MS) combined with chemical similarity enrichment analysis (ChemRICH) and correlated to WBM-induced changes in fecal microbiome composition. Results indicated that WBM can differentially modulate metabolites in liver, brain cortex and hippocampus of healthy pigs. Within the glycero-phospholipids, there was an increase in alkyl-acyl-phosphatidyl-cholines (PC-O 40:3) in the hippocampus of pigs fed six servings of WBM. A broader change in glycerophospholipids and sphingolipids was detected in the liver with a reduction in several lipid species in pigs fed both WBM diets but with an increase in amino acids known as precursors of neurotransmitters in the cortex of pigs fed six servings of WBM. Metabolomic changes were positively correlated with increased abundance of Cryomorphaceae, Lachnospiraceae, Flammeovirgaceae and Ruminococcaceae in the microbiome suggesting that WBM can also positively impact tissue metabolite composition.
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Affiliation(s)
- Gloria I. Solano-Aguilar
- Diet Genomics and Immunology Laboratory, Beltsville Human Nutrition Research Center, Agricultural Research Service, U.S. Department of Agriculture Northeast Area, Beltsville, MD 20705, USA; (S.L.); (S.J.); (A.M.); (J.F.U.J.)
- Correspondence: ; Tel.: +1-301-504-8068
| | - Sukla Lakshman
- Diet Genomics and Immunology Laboratory, Beltsville Human Nutrition Research Center, Agricultural Research Service, U.S. Department of Agriculture Northeast Area, Beltsville, MD 20705, USA; (S.L.); (S.J.); (A.M.); (J.F.U.J.)
| | - Saebyeol Jang
- Diet Genomics and Immunology Laboratory, Beltsville Human Nutrition Research Center, Agricultural Research Service, U.S. Department of Agriculture Northeast Area, Beltsville, MD 20705, USA; (S.L.); (S.J.); (A.M.); (J.F.U.J.)
| | - Richi Gupta
- Microbiome Analysis Center, George Mason University, Science & Technology Campus, Manassas, VA 20108, USA; (R.G.); (P.M.G.)
| | - Aleksey Molokin
- Diet Genomics and Immunology Laboratory, Beltsville Human Nutrition Research Center, Agricultural Research Service, U.S. Department of Agriculture Northeast Area, Beltsville, MD 20705, USA; (S.L.); (S.J.); (A.M.); (J.F.U.J.)
| | - Steven G. Schroeder
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture Northeast Area, Beltsville, MD 20705, USA;
| | - Patrick M. Gillevet
- Microbiome Analysis Center, George Mason University, Science & Technology Campus, Manassas, VA 20108, USA; (R.G.); (P.M.G.)
| | - Joseph F. Urban
- Diet Genomics and Immunology Laboratory, Beltsville Human Nutrition Research Center, Agricultural Research Service, U.S. Department of Agriculture Northeast Area, Beltsville, MD 20705, USA; (S.L.); (S.J.); (A.M.); (J.F.U.J.)
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Qian Y, Gao Z, Wang J, Wang C, Li G, Fu F, Guo J, Shan Y. Safety Evaluation and Whole Genome Sequencing of Aspergillus japonicas PJ01 Reveal Its Potential to Degrade Citrus Segments in Juice Processing. Foods 2021; 10:foods10081736. [PMID: 34441514 PMCID: PMC8391945 DOI: 10.3390/foods10081736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/23/2021] [Accepted: 07/23/2021] [Indexed: 11/20/2022] Open
Abstract
Aspergillus japonicas PJ01 (A. japonicas PJ01) is a strain isolated from the rotten branches. In previ-ous studies, it was shown that it can produce complex enzymes to degrade polysaccharide com-ponents. In this study, we evaluated the safety of its crude enzyme solution. Acute oral toxicity, subchronic toxicity, micronucleus and sperm malformation tests all validated the high biologi-cal safety for the crude enzymes. Secondly, we carried out the citrus segment degradation ex-periment of crude enzyme solution. Compared with the control group, the crude enzyme solu-tion of A. japonicas PJ01 can completely degrade the segments in 50 min, which provides the basis for enzymatic peeling during juice processing. The whole genome sequencing showed that the genome of A. japonicus PJ01 has a GC content of 51.37% with a size of 36204647 bp, and encoded 10070 genes. GO, COG, KEGG and CAZy databases were used in gene annotation analyses. Pathway enrichment showed many genes related to carbohydrate metabolism, rich in genes re-lated to pectinase, xylanase and carboxylcellulase. Therefore, the complex enzyme produced by A. japonicus PJ01 can be used in gizzard juice processing to achieve efficient enzymatic decapsu-lation.
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Affiliation(s)
- Yujiao Qian
- Longping Branch, Graduate School of Hunan University, Changsha 410125, China; (Y.Q.); (J.W.); (C.W.); (G.L.); (F.F.)
- International Joint Lab on Fruits & Vegetables Processing, Quality and Safety, Hunan Key Lab of Fruits & Vegetables Storage, Processing, Quality and Safety, Hunan Agriculture Product Processing Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Zhipeng Gao
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China;
| | - Jieyi Wang
- Longping Branch, Graduate School of Hunan University, Changsha 410125, China; (Y.Q.); (J.W.); (C.W.); (G.L.); (F.F.)
| | - Chen Wang
- Longping Branch, Graduate School of Hunan University, Changsha 410125, China; (Y.Q.); (J.W.); (C.W.); (G.L.); (F.F.)
| | - Gaoyang Li
- Longping Branch, Graduate School of Hunan University, Changsha 410125, China; (Y.Q.); (J.W.); (C.W.); (G.L.); (F.F.)
- International Joint Lab on Fruits & Vegetables Processing, Quality and Safety, Hunan Key Lab of Fruits & Vegetables Storage, Processing, Quality and Safety, Hunan Agriculture Product Processing Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Fuhua Fu
- Longping Branch, Graduate School of Hunan University, Changsha 410125, China; (Y.Q.); (J.W.); (C.W.); (G.L.); (F.F.)
- International Joint Lab on Fruits & Vegetables Processing, Quality and Safety, Hunan Key Lab of Fruits & Vegetables Storage, Processing, Quality and Safety, Hunan Agriculture Product Processing Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Jiajing Guo
- Longping Branch, Graduate School of Hunan University, Changsha 410125, China; (Y.Q.); (J.W.); (C.W.); (G.L.); (F.F.)
- International Joint Lab on Fruits & Vegetables Processing, Quality and Safety, Hunan Key Lab of Fruits & Vegetables Storage, Processing, Quality and Safety, Hunan Agriculture Product Processing Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
- Correspondence: (Y.S.); (J.G.)
| | - Yang Shan
- Longping Branch, Graduate School of Hunan University, Changsha 410125, China; (Y.Q.); (J.W.); (C.W.); (G.L.); (F.F.)
- International Joint Lab on Fruits & Vegetables Processing, Quality and Safety, Hunan Key Lab of Fruits & Vegetables Storage, Processing, Quality and Safety, Hunan Agriculture Product Processing Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
- Correspondence: (Y.S.); (J.G.)
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Wan H, Wei Q, Ji Q, Lan H, Dai X, Chen W, Dong Y, Zeng C. The karyotype, genome survey, and assembly of Mud artemisia (Artemisia selengensis). Mol Biol Rep 2021; 48:5897-5904. [PMID: 34297325 DOI: 10.1007/s11033-021-06584-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 07/20/2021] [Indexed: 11/30/2022]
Abstract
BACKGROUND Artemisia selengensis is traditional Chinese medicine and phytochemical analysis indicated that A. selengensis contains essential oils, fatty acids and phenolic acids. The lack of reference genomic information may lead to tardiness in molecular biology research of A. selengensis. METHOD AND RESULTS Karyotype analysis, genome survey, and genome assembly was employed to acquire information on the genome structure of A. selengensis. The chromosome number is 2n = 2x = 36, karyotype formula is 28 m + 8Sm, karyotype asymmetry coefficient is 58.8%, and karyotypes were symmetric to Stebbins' type 2A. Besides, the flow cytometry findings reported that the mean peak value of fluorescent intensity is 1,170,677, 2C DNA content is 12 pg and the genome size was estimated to be approximately 5.87 Gb. Furthermore, the genome survey generates 341,478,078 clean reads, unfortunately, after K-mer analysis, no significant peak can be observed, the heterozygosity, repetitive rate and genome size was unable to estimated. It is speculated that this phenomenon might be due to the complexity of genome structure. 37,266 contigs are preliminary assembled with Oxford Nanopore Technology (ONT) sequencing, totaling 804 Mb and GC content was 34.08%. The total length is 804,475,881 bp, N50 is 29,624 bp, and the largest contig length is 239,792 bp. CONCLUSION This study reveals the preliminary information of genome size of A. selengensis. These findings may provide supportive information for sequencing and assembly of whole-genome sequencing and encourage the progress of functional gene discovery, genetic improvement, evolutionary study, and structural studies of A. selengensis.
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Affiliation(s)
- Heping Wan
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River BasinSchool of Life Science, Jianghan University, Wuhan, 430056, China
| | - Qingying Wei
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River BasinSchool of Life Science, Jianghan University, Wuhan, 430056, China
| | - Qiangqiang Ji
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River BasinSchool of Life Science, Jianghan University, Wuhan, 430056, China
| | - Hong Lan
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River BasinSchool of Life Science, Jianghan University, Wuhan, 430056, China
| | - Xigang Dai
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River BasinSchool of Life Science, Jianghan University, Wuhan, 430056, China
| | - Weida Chen
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River BasinSchool of Life Science, Jianghan University, Wuhan, 430056, China
| | - Yuanhuo Dong
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River BasinSchool of Life Science, Jianghan University, Wuhan, 430056, China
| | - Changli Zeng
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River BasinSchool of Life Science, Jianghan University, Wuhan, 430056, China.
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Garali I, Sahbatou M, Daunay A, Baudrin LG, Renault V, Bouyacoub Y, Deleuze JF, How-Kit A. Improvements and inter-laboratory implementation and optimization of blood-based single-locus age prediction models using DNA methylation of the ELOVL2 promoter. Sci Rep 2020; 10:15652. [PMID: 32973211 PMCID: PMC7515898 DOI: 10.1038/s41598-020-72567-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 09/02/2020] [Indexed: 01/21/2023] Open
Abstract
Several blood-based age prediction models have been developed using less than a dozen to more than a hundred DNA methylation biomarkers. Only one model (Z-P1) based on pyrosequencing has been developed using DNA methylation of a single locus located in the ELOVL2 promoter, which is considered as one of the best age-prediction biomarker. Although multi-locus models generally present better performances compared to the single-locus model, they require more DNA and present more inter-laboratory variations impacting the predictions. Here we developed 17,018 single-locus age prediction models based on DNA methylation of the ELOVL2 promoter from pooled data of four different studies (training set of 1,028 individuals aged from 0 and 91 years) using six different statistical approaches and testing every combination of the 7 CpGs, aiming to improve the prediction performances and reduce the effects of inter-laboratory variations. Compared to Z-P1 model, three statistical models with the optimal combinations of CpGs presented improved performances (MAD of 4.41–4.77 in the testing set of 385 individuals) and no age-dependent bias. In an independent testing set of 100 individuals (19–65 years), we showed that the prediction accuracy could be further improved by using different CpG combinations and increasing the number of technical replicates (MAD of 4.17).
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Affiliation(s)
- Imene Garali
- Laboratory for Bioinformatics, Foundation Jean Dausset-CEPH, Paris, France.,Laboratory of Excellence GenMed, Paris, France
| | - Mourad Sahbatou
- Laboratory for Human Genetics, Foundation Jean Dausset-CEPH, Paris, France
| | - Antoine Daunay
- Laboratory for Genomics, Foundation Jean Dausset-CEPH, 75010, Paris, France
| | - Laura G Baudrin
- Laboratory of Excellence GenMed, Paris, France.,Laboratory for Genomics, Foundation Jean Dausset-CEPH, 75010, Paris, France
| | - Victor Renault
- Laboratory for Bioinformatics, Foundation Jean Dausset-CEPH, Paris, France
| | - Yosra Bouyacoub
- Laboratory of Excellence GenMed, Paris, France.,Laboratory for Genomics, Foundation Jean Dausset-CEPH, 75010, Paris, France
| | - Jean-François Deleuze
- Laboratory for Bioinformatics, Foundation Jean Dausset-CEPH, Paris, France.,Laboratory of Excellence GenMed, Paris, France.,Laboratory for Human Genetics, Foundation Jean Dausset-CEPH, Paris, France.,Laboratory for Genomics, Foundation Jean Dausset-CEPH, 75010, Paris, France.,Centre National de Recherche en Génomique Humaine, CEA, Institut François Jacob, Evry, France
| | - Alexandre How-Kit
- Laboratory for Genomics, Foundation Jean Dausset-CEPH, 75010, Paris, France.
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8
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Montalvo-Rodríguez R, Maupin-Furlow JA. Insights through Genetics of Halophilic Microorganisms and Their Viruses. Genes (Basel) 2020; 11:genes11040388. [PMID: 32252451 PMCID: PMC7230515 DOI: 10.3390/genes11040388] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 04/01/2020] [Indexed: 12/14/2022] Open
Abstract
Halophilic microorganisms are found in all domains of life and thrive in hypersaline (high salt content) environments. These unusual microbes have been a subject of study for many years due to their interesting properties and physiology. Study of the genetics of halophilic microorganisms (from gene expression and regulation to genomics) has provided understanding into mechanisms of how life can occur at high salinity levels. Here we highlight recent studies that advance knowledge of biological function through study of the genetics of halophilic microorganisms and their viruses.
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Affiliation(s)
- Rafael Montalvo-Rodríguez
- Department of Biology, University of Puerto Rico, Box 9000, Mayagüez, PR 00681, USA
- Correspondence: (R.M.-R.); (J.A.M.-F.)
| | - Julie A. Maupin-Furlow
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA
- Correspondence: (R.M.-R.); (J.A.M.-F.)
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Goh KM, Shahar S, Chan KG, Chong CS, Amran SI, Sani MH, Zakaria II, Kahar UM. Current Status and Potential Applications of Underexplored Prokaryotes. Microorganisms 2019; 7:E468. [PMID: 31635256 PMCID: PMC6843859 DOI: 10.3390/microorganisms7100468] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 10/05/2019] [Accepted: 10/08/2019] [Indexed: 12/20/2022] Open
Abstract
Thousands of prokaryotic genera have been published, but methodological bias in the study of prokaryotes is noted. Prokaryotes that are relatively easy to isolate have been well-studied from multiple aspects. Massive quantities of experimental findings and knowledge generated from the well-known prokaryotic strains are inundating scientific publications. However, researchers may neglect or pay little attention to the uncommon prokaryotes and hard-to-cultivate microorganisms. In this review, we provide a systematic update on the discovery of underexplored culturable and unculturable prokaryotes and discuss the insights accumulated from various research efforts. Examining these neglected prokaryotes may elucidate their novelties and functions and pave the way for their industrial applications. In addition, we hope that this review will prompt the scientific community to reconsider these untapped pragmatic resources.
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Affiliation(s)
- Kian Mau Goh
- Faculty of Science, Universiti Teknologi Malaysia, Skudai 81310, Johor, Malaysia.
| | - Saleha Shahar
- Faculty of Science, Universiti Teknologi Malaysia, Skudai 81310, Johor, Malaysia.
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Science, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia.
- International Genome Centre, Jiangsu University, ZhenJiang 212013, China.
| | - Chun Shiong Chong
- Faculty of Science, Universiti Teknologi Malaysia, Skudai 81310, Johor, Malaysia.
| | - Syazwani Itri Amran
- Faculty of Science, Universiti Teknologi Malaysia, Skudai 81310, Johor, Malaysia.
| | - Mohd Helmi Sani
- Faculty of Science, Universiti Teknologi Malaysia, Skudai 81310, Johor, Malaysia.
| | - Iffah Izzati Zakaria
- Malaysia Genome Institute, National Institutes of Biotechnology Malaysia, Jalan Bangi, Kajang 43000, Selangor, Malaysia.
| | - Ummirul Mukminin Kahar
- Malaysia Genome Institute, National Institutes of Biotechnology Malaysia, Jalan Bangi, Kajang 43000, Selangor, Malaysia.
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