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Liu X, Li J, Zhang Z, He Y, Wang M, Zhao Y, Lin S, Liu T, Liao Y, Zhang N, Yuan K, Ling Y, Liu Z, Chen X, Chen Z, Chen R, Wang X, Gu B. Acetylation of xenogeneic silencer H-NS regulates biofilm development through the nitrogen homeostasis regulator in Shewanella. Nucleic Acids Res 2024; 52:2886-2903. [PMID: 38142446 PMCID: PMC11014242 DOI: 10.1093/nar/gkad1219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 12/08/2023] [Accepted: 12/12/2023] [Indexed: 12/26/2023] Open
Abstract
Adjusting intracellular metabolic pathways and adopting suitable live state such as biofilms, are crucial for bacteria to survive environmental changes. Although substantial progress has been made in understanding how the histone-like nucleoid-structuring (H-NS) protein modulates the expression of the genes involved in biofilm formation, the precise modification that the H-NS protein undergoes to alter its DNA binding activity is still largely uncharacterized. This study revealed that acetylation of H-NS at Lys19 inhibits biofilm development in Shewanella oneidensis MR-1 by downregulating the expression of glutamine synthetase, a critical enzyme in glutamine synthesis. We further found that nitrogen starvation, a likely condition in biofilm development, induces deacetylation of H-NS and the trimerization of nitrogen assimilation regulator GlnB. The acetylated H-NS strain exhibits significantly lower cellular glutamine concentration, emphasizing the requirement of H-NS deacetylation in Shewanella biofilm development. Moreover, we discovered in vivo that the activation of glutamine biosynthesis pathway and the concurrent suppression of the arginine synthesis pathway during both pellicle and attached biofilms development, further suggesting the importance of fine tune nitrogen assimilation by H-NS acetylation in Shewanella. In summary, posttranslational modification of H-NS endows Shewanella with the ability to respond to environmental needs by adjusting the intracellular metabolism pathways.
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Affiliation(s)
- Xiaoxiao Liu
- Laboratory Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510000, China
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China
| | - Jun Li
- Laboratory Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510000, China
| | - Zhixuan Zhang
- Laboratory Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510000, China
- School of Medicine, South China University of Technology, Guangzhou, Guangdong 510080, China
| | - Yizhou He
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China
| | - Mingfang Wang
- Laboratory Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510000, China
| | - Yunhu Zhao
- Laboratory Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510000, China
| | - Shituan Lin
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tianlang Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yiwen Liao
- Laboratory Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510000, China
| | - Ni Zhang
- Laboratory Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510000, China
| | - Kaixuan Yuan
- Laboratory Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510000, China
| | - Yong Ling
- Laboratory Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510000, China
| | - Ziyao Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaozhong Chen
- Laboratory Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510000, China
| | - Zhe Chen
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ran Chen
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China
| | - Xiaoxue Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bing Gu
- Laboratory Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510000, China
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Rao J, Wei Q, Tang L, Wang Y, Liang R, Li K. A design of a nature-like fishway to solve the fractured river connectivity caused by small hydropower based on hydrodynamics and fish behaviors. Environ Sci Pollut Res Int 2024; 31:27883-27896. [PMID: 38523215 DOI: 10.1007/s11356-024-33034-1] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 03/18/2024] [Indexed: 03/26/2024]
Abstract
Achieving a harmonious alignment between the biological characteristics of fish and hydrodynamics patterns is crucial for ensuring the efficacy of fish passage facilities. In this study, based on the hydrodynamic characteristics of the river and the biological characteristics of fish, we evaluated the internal flow field in the nature-like fishway of Congen II hydropower station located along the Chabao river and explored methods to improve the operation efficiency. Based on comprehensive considerations of the flow field, turbulent kinetic energy, and the migration pathways of fish, it is found that the implementation of a continuous oblique bottom slope represents a more cost-effective and operationally convenient solution. The influence of different permutation of bulkheads in the nature-like fishway on operational efficiency was further examined. Our investigation revealed that the nature-like fishway with the continuous slope of 2% and the arrangement of three bulkheads in each row (model 3) exhibited a relatively simple velocity distribution and linear flow line, which poses challenges for fish in locating resting areas. In addition, the distribution of low turbulence kinetic energy area in the mainstream made it less favorable for fish to transition from the mainstream to the rest area within the fishway. The nature-like fishway with the continuous slope of 2% and the arrangement of two or three bulkheads in staggered rows (model 4) demonstrated better performance. Several potential fish migration routes for both model 3 and model 4 were proposed based on the numerical simulation results. In model 3, fish exhibited a continuous sprint through the concentrated high-speed area, which was less favorable for fish to rest and forage. In contrast, model 4 exhibited a diversified flow velocity distribution, enabling fish to make timely changes in their direction during migration. This feather proved to be advantageous in enhancing fish migration within the passage. The design of nature-like fishway in this study provides an important reference and technical support for the construction and optimization of the nature-like fishway for low dams, and is of great significance for restoring river connectivity destroyed by small hydropower construction and improving fish migration.
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Affiliation(s)
- Jianing Rao
- State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065, China
| | - Qi Wei
- Sichuan Water Development Investigation, Design & Research Co., Ltd, Chengdu, 610072, China
| | - Lian Tang
- State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065, China
| | - Yuanming Wang
- State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065, China.
| | - Ruifeng Liang
- State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065, China
| | - Kefeng Li
- State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065, China
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Pan J, Zhang Z, Li Y, Yu J, You Z, Li C, Wang S, Zhu M, Ren F, Zhang X, Sun Y, Wang S. A microbial knowledge graph-based deep learning model for predicting candidate microbes for target hosts. Brief Bioinform 2024; 25:bbae119. [PMID: 38555472 PMCID: PMC10981679 DOI: 10.1093/bib/bbae119] [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] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/23/2024] [Accepted: 03/02/2024] [Indexed: 04/02/2024] Open
Abstract
Predicting interactions between microbes and hosts plays critical roles in microbiome population genetics and microbial ecology and evolution. How to systematically characterize the sophisticated mechanisms and signal interplay between microbes and hosts is a significant challenge for global health risks. Identifying microbe-host interactions (MHIs) can not only provide helpful insights into their fundamental regulatory mechanisms, but also facilitate the development of targeted therapies for microbial infections. In recent years, computational methods have become an appealing alternative due to the high risk and cost of wet-lab experiments. Therefore, in this study, we utilized rich microbial metagenomic information to construct a novel heterogeneous microbial network (HMN)-based model named KGVHI to predict candidate microbes for target hosts. Specifically, KGVHI first built a HMN by integrating human proteins, viruses and pathogenic bacteria with their biological attributes. Then KGVHI adopted a knowledge graph embedding strategy to capture the global topological structure information of the whole network. A natural language processing algorithm is used to extract the local biological attribute information from the nodes in HMN. Finally, we combined the local and global information and fed it into a blended deep neural network (DNN) for training and prediction. Compared to state-of-the-art methods, the comprehensive experimental results show that our model can obtain excellent results on the corresponding three MHI datasets. Furthermore, we also conducted two pathogenic bacteria case studies to further indicate that KGVHI has excellent predictive capabilities for potential MHI pairs.
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Affiliation(s)
- Jie Pan
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology of Shaanxi Province, College of Life Sciences, Northwest University, Xi’an 710069, China
| | - Zhen Zhang
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology of Shaanxi Province, College of Life Sciences, Northwest University, Xi’an 710069, China
| | - Ying Li
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology of Shaanxi Province, College of Life Sciences, Northwest University, Xi’an 710069, China
| | - Jiaoyang Yu
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology of Shaanxi Province, College of Life Sciences, Northwest University, Xi’an 710069, China
| | - Zhuhong You
- School of Computer Science, Northwestern Polytechnical University, Xi’an 710129, China
| | - Chenyu Li
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology of Shaanxi Province, College of Life Sciences, Northwest University, Xi’an 710069, China
| | - Shixu Wang
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology of Shaanxi Province, College of Life Sciences, Northwest University, Xi’an 710069, China
| | - Minghui Zhu
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology of Shaanxi Province, College of Life Sciences, Northwest University, Xi’an 710069, China
| | - Fengzhi Ren
- North China Pharmaceutical Group, Shijiazhuang 050015, Hebei, China
- National Microbial Medicine Engineering & Research Center, Shijiazhuang 050015, Hebei, China
| | - Xuexia Zhang
- North China Pharmaceutical Group, Shijiazhuang 050015, Hebei, China
- National Microbial Medicine Engineering & Research Center, Shijiazhuang 050015, Hebei, China
| | - Yanmei Sun
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology of Shaanxi Province, College of Life Sciences, Northwest University, Xi’an 710069, China
| | - Shiwei Wang
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology of Shaanxi Province, College of Life Sciences, Northwest University, Xi’an 710069, China
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Zhai J, Zhang Z, Yang L, Zhou K. Study of hydrothermal processes in ice-layers subgrade under constant temperature and dynamic loading. Sci Rep 2024; 14:3970. [PMID: 38368438 PMCID: PMC10874452 DOI: 10.1038/s41598-024-54089-7] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 02/08/2024] [Indexed: 02/19/2024] Open
Abstract
The presence of ice-layers in the subgrade soils makes the hydrothermal state of road subgrade built in island permafrost regions more susceptible to external environmental influences. In order to deepen the study of the ice-layers subgrade, a hydrothermal study of subgrade under constant temperature and dynamic loading was carried out. It was found that dynamic loading can change the temperature, moisture and pore water pressure distribution. Under dynamic loading, the hydrothermal and pore water pressure state of the soil in the upper part of the ice layer changed significantly at the beginning of the test. The application of dynamic loads alters the spatial distribution of pore water pressure in the soil, resulting in pressure differences between different areas, which affects the migration of moisture and ultimately leads to the formation of areas with higher moisture content in the area below the load. However, the reduction in soil temperature will weaken the effect of the load, therefore, the temperature of the soil should be controlled for frozen subgrade with ice-layers to prevent the accumulation of moisture in the soil.
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Affiliation(s)
- Jinbang Zhai
- School of Transportation/Ministry of Education Observation and Research Station of Permafrost Geo-Environment System in Northeast China/Permafrost Institute, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Ze Zhang
- School of Civil Engineering/Institute of Cold Regions Science and Engineering/Collaborative Innovation Centre for Permafrost Environment and Road Construction and Maintenance in Northeast China, Northeast Forestry University, Harbin, 150040, People's Republic of China.
| | - Linzhen Yang
- School of Civil Engineering/Institute of Cold Regions Science and Engineering/Collaborative Innovation Centre for Permafrost Environment and Road Construction and Maintenance in Northeast China, Northeast Forestry University, Harbin, 150040, People's Republic of China
- Heilongjiang Provincial Investment Group Co., Ltd., Harbin, 150090, People's Republic of China
- Heilongjiang Transportation Investment Group Co., Ltd., Harbin, 150001, People's Republic of China
| | - Kunchao Zhou
- School of Civil Engineering/Institute of Cold Regions Science and Engineering/Collaborative Innovation Centre for Permafrost Environment and Road Construction and Maintenance in Northeast China, Northeast Forestry University, Harbin, 150040, People's Republic of China
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Gao X, Zhou Z, Breiter K, Mao J, Romer RL, Cook NJ, Holtz F. Magmatic-hydrothermal fluid evolution of the tin-polymetallic metallogenic systems from the Weilasituo ore district, Northeast China. Sci Rep 2024; 14:3006. [PMID: 38321094 PMCID: PMC10847423 DOI: 10.1038/s41598-024-53579-y] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 02/02/2024] [Indexed: 02/08/2024] Open
Abstract
The large Weilasituo Sn-polymetallic deposit is a recent exploration discovery in the southern Great Xing'an Range, northeast China. The ore cluster area shows horizontal mineralization zoning, from the inner granite body outward, consisting of high-T Sn-W-Li mineralization, middle-T Cu-Zn mineralization and peripheral low-T Pb-Zn-Ag mineralization. However, the intrinsic genetic relationship between Sn-W-Li mineralization and peripheral vein-type Pb-Zn-Ag-Cu mineralization, the formation mechanism and the deep geological background are still insufficiently understood. Here, we use fluid inclusions, trace elements concentrations in quartz and sphalerite, and H-O isotope studies to determine the genetic mechanism and establish a metallogenic model. Fluid inclusion microthermometry and Laser Raman spectroscopic analysis results demonstrates that the aqueous ore-forming fluids evolved from low-medium salinity, medium-high temperature to low salinity, low-medium temperature fluids. Laser Raman spectroscopic analysis shows that CH4 is ubiquitous in fluid inclusions of all ore stages. Early ore fluids have δ18OH2O (v-SMOW) values from + 5.5 to + 6.2‰ and δD values of approximately - 67‰, concordant with a magmatic origin. However, the late ore fluids shifted toward lower δ18OH2O (v-SMOW) (as low as 0.3‰) and δD values (~ - 136‰), suggesting mixing between external fluids derived from the wall rocks and a contribution from meteoric water. Ti-in-quartz thermometry indicates a magmatic crystallization temperature of around 700 °C at a pressure of 1.5 kbar for the magmatic ore stage. Cathodoluminescence (CL) imaging and trace element analysis of quartz from a hydrothermal vug highlight at least three growth episodes that relate to different fluid pulses; each episode begins with CL-bright, Al-Li-rich quartz, and ends with CL-dark quartz with low Al and Li contents. Quartz from Episode 1 formed from early Sn-(Zn)-rich fluids which were likely derived from the quartz porphyry. Quartz from episodes 2 and 3 formed from Zn-(Sn)-Cu-rich fluid. The early magmatic fluid is characterized by low fS2. The SO2 produced by magma degassing reacted with heated water to form SO42-, causing the shift from low fS2 to high fS2. The SO42- generated was converted to S2- by mixing with CH4-rich, Fe and Zn-bearing external fluid which led to late-stage alteration and dissolution of micas in vein walls, thus promoting crystallization of pyrrhotite, Fe-rich sphalerite and chalcopyrite and inhibiting the precipitation of anhydrite. This study shows that ore formation encompassed multiple episodes involving steadily evolved fluids, and that the addition of external fluids plays an important role in the formation of the later Cu-Zn and Ag-Pb-Zn mineralization in the Weilasituo ore district.
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Affiliation(s)
- Xu Gao
- MNR Key Laboratory of Metallogeny and Mineral Assessment, Institute of Mineral Resources, Chinese Academy of Geological Sciences, Beijing, 100037, China
- Institut für Mineralogie, Leibniz Universität Hannover, Callinstr. 3, 30167, Hannover, Germany
| | - Zhenhua Zhou
- MNR Key Laboratory of Metallogeny and Mineral Assessment, Institute of Mineral Resources, Chinese Academy of Geological Sciences, Beijing, 100037, China.
- Research School of Earth Sciences, Australian National University, 142 Mills Rd, Canberra, ACT, 2601, Australia.
| | - Karel Breiter
- Institute of Geology of the Czech Academy of Sciences, Rozvojová 269, 16500, Praha 6, Czech Republic
| | - Jingwen Mao
- MNR Key Laboratory of Metallogeny and Mineral Assessment, Institute of Mineral Resources, Chinese Academy of Geological Sciences, Beijing, 100037, China
| | - Rolf L Romer
- GFZ German Research Centre for Geosciences, Telegrafenberg, 14473, Potsdam, Germany
| | - Nigel J Cook
- School of Chemical Engineering, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - François Holtz
- Institut für Mineralogie, Leibniz Universität Hannover, Callinstr. 3, 30167, Hannover, Germany
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Zhang M, Wang C, Bai H, Deng W. A Contribution to the Phylogeny and Taxonomy of Hydnum (Cantharellales, Basidiomycota) from China. J Fungi (Basel) 2024; 10:98. [PMID: 38392770 PMCID: PMC10889965 DOI: 10.3390/jof10020098] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/21/2024] [Accepted: 01/22/2024] [Indexed: 02/24/2024] Open
Abstract
Hydnum is a well-characterized genus in the family Hydnaceae of Cantharellales and is characterized by spinose hymenophores. In this study, an ITS phylogenetic overview and a multilocus (ITS-nrLSU-tef1) phylogenetic tree of Hydnum were carried out. On the basis of morphological characteristics and phylogenetic results, seven species from China were confirmed, described, illustrated, and compared with similar species, including three new species, i.e., H. longipes, H. microcarpum, and H. sinorepandum, and four known species, i.e., H. cremeoalbum, H. melitosarxm, H. orientalbidum, and H. pinicola were recorded for the first time in China. A key to the species of Hydnum in China was provided.
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Affiliation(s)
- Ming Zhang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Chaoqun Wang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Hongfen Bai
- Chuxiong Yi Autonomous Prefecture Forestry and Grassland Science Research Institute, Chuxiong 675000, China
| | - Wangqiu Deng
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
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Pan Z, Li DD, Li P, Geng Y, Jiang Y, Liu Y, Li YZ, Zhang Z. GDPF: a data resource for the distribution of prokaryotic protein families across the global biosphere. Nucleic Acids Res 2024; 52:D724-D731. [PMID: 37823598 PMCID: PMC10767866 DOI: 10.1093/nar/gkad869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/19/2023] [Accepted: 09/26/2023] [Indexed: 10/13/2023] Open
Abstract
Microorganisms encode most of the functions of life on Earth. However, conventional research has primarily focused on specific environments such as humans, soil and oceans, leaving the distribution of functional families throughout the global biosphere poorly comprehended. Here, we present the database of the global distribution of prokaryotic protein families (GDPF, http://bioinfo.qd.sdu.edu.cn/GDPF/), a data resource on the distribution of functional families across the global biosphere. GDPF provides global distribution information for 36 334 protein families, 19 734 superfamilies and 12 089 KEGG (Kyoto Encyclopedia of Genes and Genomes) orthologs from multiple source databases, covering typical environments such as soil, oceans, animals, plants and sediments. Users can browse, search and download the distribution data of each entry in 10 000 global microbial communities, as well as conduct comparative analysis of distribution disparities among multiple entries across various environments. The GDPF data resource contributes to uncovering the geographical distribution patterns, key influencing factors and macroecological principles of microbial functions at a global level, thereby promoting research in Earth ecology and human health.
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Affiliation(s)
- Zhuo Pan
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Dan-dan Li
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Peng Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Yu Geng
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Yiru Jiang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Ya Liu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
- Suzhou Research Institute, Shandong University, Suzhou 215123, China
| | - Yue-zhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Zheng Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
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8
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Li M, Raza M, Song S, Hou L, Zhang ZF, Gao M, Huang JE, Liu F, Cai L. Application of culturomics in fungal isolation from mangrove sediments. Microbiome 2023; 11:272. [PMID: 38082427 PMCID: PMC10712113 DOI: 10.1186/s40168-023-01708-6] [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] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 10/19/2023] [Indexed: 12/18/2023]
Abstract
BACKGROUND Fungi play a crucial role in ecosystems, and they have been widely considered a promising source for natural compounds that are crucial for drug discovery. Fungi have a high diversity, but about 95% of them remain unknown to science. The description rate of fungi is very low, mainly due to the inability of most fungi to grow in artificial media, which could not provide a sufficiently similar environment to their natural habitats. Moreover, many species in nature are in a state of low metabolic activity which cannot readily proliferate without proper resuscitation. Previously developed culturomics techniques are mostly designed and applicable for bacteria, with few attempts for fungal isolation because of their significantly larger cell size and hyphal growth properties. RESULTS This study attempted to isolate previously uncultured and rare fungi from mangrove sediments using newly developed fungal enrichment culture method (FECM) and fungal isolation chips (FiChips). Comparison of fungal community composition at different enrichment stages showed that FECM had great influence on fungal community composition, with rare taxa increased significantly, thus improving the isolation efficiency of previously uncultured fungi. Similarly, in situ cultivation using FiChips has a significant advantage in detecting and culturing rare fungi, as compared to the conventional dilution plate method (DPM). In addition, based on morphological comparisons and phylogenetic analyses, we described and proposed 38 new ascomycetous taxa, including three new families, eight new genera, 25 new species, and two new combinations (presented in additional file 1). CONCLUSIONS Our study demonstrated that mangrove sediments harbor a high diversity of fungi, and our new isolation approaches (FECM and FiChips) presented a high efficiency in isolating hitherto uncultured fungi, which is potentially usable for fungal isolation in other similar environments. Video Abstract.
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Affiliation(s)
- Meng Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mubashar Raza
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- Key Laboratory of Integrated Pest Management On Crops in Northwestern Oasis, Ministry of Agriculture and Rural Affairs, Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, China
| | - Shuang Song
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lingwei Hou
- Key Lab of Space Nutrition and Food Engineering, China Astronaut Research and Training Center, Beijing, 100094, China
| | - Zhi-Feng Zhang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Min Gao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jun-En Huang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fang Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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Wang YW, Wang XH, Zhang J, Du ZJ, Mu DS. Cerina litoralis gen. nov., sp. nov., a novel potential polysaccharide degrading bacterium of the family Flavobacteriaceae, isolated from marine sediment. Antonie Van Leeuwenhoek 2023; 116:1447-1455. [PMID: 37899393 DOI: 10.1007/s10482-023-01888-z] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 09/14/2023] [Indexed: 10/31/2023]
Abstract
The Gram-strain-negative, facultative anaerobic, chemoheterotrophic, short-rod-shaped, non-motile, forming yellow colonies strain, designated F89T, was isolated from marine sediment of Xiaoshi Island, Weihai. Strain F89T grew at 15-37 °C (optimally at 28 °C), at pH 6.0-8.5 (optimally at pH 7.0) and in the presence of 1-5% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain F89T was related to the family Flavobacteriaceae. F89T had highest 16S rRNA gene sequence similarity to Maribacter cobaltidurans MCCC 1K03318T (93.3%). The predominant cellular fatty acids of F89T were iso-C15:0, iso-C15:0 G and Summed Feature 3. The main respiratory quinone of F89T was menaquinone 6 (MK-6), consistent with that observed for all related strains. The polar lipid profile of strain F89T contained phosphatidylethanolamine, two aminolipids and three unidentified polar lipids. The genomic DNA G + C content of strain F89T was 42.7%. Strain F89T encoded 121 glycoside hydrolases and was a potential polysaccharide degrading bacterium. Differential phenotypic and genotypic characteristics of the strain showed that F89T should be classified as a novel genus in Flavobacteriaceae, for which the name Cerina litoralis is proposed. The type strain is F89T (= MCCC 1H00510T = KCTC 92203T).
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Affiliation(s)
- Ya-Wei Wang
- Marine College, Shandong University, Weihai, 264209, Shandong, China
| | - Xin-Hui Wang
- ANU Joint Science College, Shandong University, Weihai, 264209, Shandong, China
| | - Jing Zhang
- Marine College, Shandong University, Weihai, 264209, Shandong, China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, 264209, Shandong, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, Shandong, China
- Weihai Research Institute of Industrial Technology of Shandong University, Weihai, China
| | - Da-Shuai Mu
- Marine College, Shandong University, Weihai, 264209, Shandong, China.
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, Shandong, China.
- Weihai Research Institute of Industrial Technology of Shandong University, Weihai, China.
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10
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Zhang MD, Zhou ZY, Kou YY, Lu DC, Du ZJ. Brumimicrobium oceani sp. nov., isolated from coastal sediment saline lake and environmental adaptability analysis. Antonie Van Leeuwenhoek 2023; 116:1375-1384. [PMID: 37843738 DOI: 10.1007/s10482-023-01892-3] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 09/25/2023] [Indexed: 10/17/2023]
Abstract
A novel Gram-stain-negative, aerobic, non-motile, rod-shaped and orange-colored bacterium, designated as strain C305T, was isolated from marine sediment of the coast area of Weihai, China. Strain C305T growth occurs at 4-40 °C (optimally at 30-33 °C), pH 6.0-9.0 (optimally at pH 8.0) and with 0.5-10.0% (w/v) NaCl (optimum 1.5-3.0%). No growth is observed without NaCl. The major cellular fatty acids of strain C305T were identified as iso-C15:0, iso-C15:1G and iso-C17:0 3-OH. The major respiratory quinone was found to be MK-6, and the DNA G + C content was determined to be 35.5 mol%. The predominant polar lipids were mainly phosphatidylethanolamines (PE), unidentified aminophospholipids (APL), andunidentified lipid (L2). Phylogenetic analysis based on 16S rRNA gene sequences revealed that C305T was a member of the genus Brumimicrobium and had a 16S rRNA gene sequence similarity values of 96.9-98.0% with recognized Brumimicrobium species. On the basis of the phylogenetic and phenotypic evidences, strain C305T represents a novel species of the genus Brumimicrobium, for which the name Brumimicrobium oceani sp. nov. is proposed. The type strain is C305T (= KCTC 62371 T = MCCC 1H00297T).
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Affiliation(s)
- Meng-Di Zhang
- Marine College, Shandong University, Weihai, 264209, Shandong, People's Republic of China
- Joint Science College, Shandong University, Weihai, 264209, Shandong, People's Republic of China
| | - Zi-Yang Zhou
- Marine College, Shandong University, Weihai, 264209, Shandong, People's Republic of China
| | - Yi-Yu Kou
- Marine College, Shandong University, Weihai, 264209, Shandong, People's Republic of China
| | - De-Chen Lu
- Marine College, Shandong University, Weihai, 264209, Shandong, People's Republic of China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, 264209, Shandong, People's Republic of China.
- Weihai Research Institute of Industrial Technology of Shandong University, Weihai, 264209, People's Republic of China.
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11
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Yu S, Zhu Y, He H, Hu Y, Zhu X, Diao W, Li S, Shan G, Chen X. Prevalence and risk factors of oral human papillomavirus infection among 4212 healthy adults in Hebei, China. BMC Infect Dis 2023; 23:773. [PMID: 37940841 PMCID: PMC10634102 DOI: 10.1186/s12879-023-08759-y] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 10/26/2023] [Indexed: 11/10/2023] Open
Abstract
BACKGROUND Human papillomavirus (HPV) infection is an essential cause of oropharyngeal squamous cell carcinoma that is increasing in incidence worldwide. However, little is known about the epidemiology of oral HPV infection among healthy adults in China. METHODS A study in northern China was conducted in 2021 as baseline data of Diverse Life-Course Cohort (DLCC). Residents who aged above 20 were eligible to participate. Oral swab specimens and questionnaires were collected from 4226 participants. HPV DNA in oral exfoliated cells was tested by Nested Polymerase Chain Reaction approach and sequencing. Univariate and multivariate analyses were performed to assess the associations between exposure factors and oral HPV infection. RESULTS Overall prevalence of oral HPV infection was 4.08% (95%CI, 3.69%-4.68%). The most prevalent HPV type detected was HPV-81 (1.35%; 95% CI, 1.00%-1.70%), followed by HPV-16 (0.64%; 95% CI, 0.40%-0.88%). Oral HPV infection presented a bimodal pattern with respect to age in male and female participants. Oral HPV prevalence of male participants was significantly higher than prevalence of female participants (5.0% versus 3.6%, P = 0.041). Prevalence of oral HPV was higher among current smokers (OR = 1.59; 95% CI, 1.11-2.29; P = 0.039) and current drinkers (OR = 1.60; 95% CI, 1.14-2.25; P = 0.023). Current alcohol consumption was independently associated with oral HPV infection (OR = 1.74; 95% CI, 1.22-2.50; P = 0.010). CONCLUSIONS Among healthy adults aged above 20 in Hebei, China, the prevalence of high-risk HPV infection was 1.92% (95%CI, 1.51%-2.34%). Oral HPV prevalence was independently associated with alcohol consumption. More tailored prevention strategies are needed to prevent oral HPV infection through smoking cessation, reduction of alcohol consumption, and HPV vaccination.
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Affiliation(s)
- Shuting Yu
- Department of Otolaryngology-Head and Neck Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Dongcheng District, Beijing, China
| | - Yingying Zhu
- Department of Otolaryngology-Head and Neck Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Dongcheng District, Beijing, China
| | - Huijing He
- Department of Epidemiology and Statistics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, 5 Dongdansantiao, Dongcheng District, Beijing, 100005, China
| | - Yaoda Hu
- Department of Epidemiology and Statistics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, 5 Dongdansantiao, Dongcheng District, Beijing, 100005, China
| | - Xiaoli Zhu
- Department of Otolaryngology-Head and Neck Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Dongcheng District, Beijing, China
| | - Wenwen Diao
- Department of Otolaryngology-Head and Neck Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Dongcheng District, Beijing, China
| | - Shuguang Li
- Department of Music Artificial Intelligence and Music Information Technology, Central Conservatory of Music, 43 Baojiajie, Xicheng District, Beijing, China
| | - Guangliang Shan
- Department of Epidemiology and Statistics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, 5 Dongdansantiao, Dongcheng District, Beijing, 100005, China.
| | - Xingming Chen
- Department of Otolaryngology-Head and Neck Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Dongcheng District, Beijing, China.
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12
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Wang SX, Wang YW, Ma L, An J, Gong Y, Du ZJ. Winogradskyella immobilis sp. nov., an Alginate-Hydrolyzing Bacterium Isolated from the Brown Algae Saccharina japonica. Curr Microbiol 2023; 80:370. [PMID: 37838638 DOI: 10.1007/s00284-023-03474-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 09/04/2023] [Indexed: 10/16/2023]
Abstract
A novel bacterium, designated E313T, was isolated from brown algae Saccharina japonica in Weihai, China. The strain is a Gram-stain-negative, non-flagellated, non-gliding, aerobic, rod-shaped bacterium that grows optimally at 28 °C with pH levels between 7.0 and 7.5 and in the presence of 2-3% (w/v) NaCl. Phylogenetic analyses based on its 16S rRNA gene sequence placed the strain within the monophyletic cluster of the genus Winogradskyella, exhibiting the highest similarity to Winogradskyella wandonensis KCTC 32579T (96.8%). Genome comparison of strain E313T with W. wandonensis KCTC 32579T and W. thalassocola KCTC 12221T revealed average nucleotide identity (ANI) values of 74.2% and 74.8%, and DNA-DNA hybridization (dDDH) values of 19.0% and 19.5%, respectively, lower than prokaryotic species delineation values. The strain E313T could hydrolyze alginate. A total of 123 carbohydrate-active enzymes were annotated according to the CAZy database. Especially, one oligo-alginate lyase and one poly(β-D-mannuronate) lyase were identified in the genome of strain E313T. Strain E313T possessed MK-6 quinone and iso-C15:0, iso-C15:1 G, iso-C17:0 3-OH, and iso-C15:0 3-OH as main fatty acids. Its major polar lipids were phosphatidylethanolamine (PE), one unidentified aminolipid, and two unknown lipids. Thus, based on phylogenetic, physiological, and chemotaxonomic analyses, we propose a novel species of the genus Winogradskyella, named Winogradskyella immobilis sp. nov., with E313T (= MCCC 1H00506T = KCTC 82731T) as the type strain.
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Affiliation(s)
- Shu-Xin Wang
- Marine College, Shandong University, Weihai, 264209, Shandong, China
| | - Ya-Wei Wang
- Marine College, Shandong University, Weihai, 264209, Shandong, China
| | - Lu Ma
- Marine College, Shandong University, Weihai, 264209, Shandong, China
| | - Jing An
- Marine College, Shandong University, Weihai, 264209, Shandong, China
| | - Ya Gong
- Marine College, Shandong University, Weihai, 264209, Shandong, China.
- WeiHai Research Institute of Industrial Technology of Shandong University, Weihai, 264209, Shandong, China.
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, 264209, Shandong, China.
- WeiHai Research Institute of Industrial Technology of Shandong University, Weihai, 264209, Shandong, China.
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13
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Zhang DD, Yue YY, Zhang MD, Du ZJ. Halocynthiibacter halioticoli sp. nov., isolated from the viscera of abalone Haliotis discus hannai. Arch Microbiol 2023; 205:350. [PMID: 37805946 DOI: 10.1007/s00203-023-03686-7] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 09/14/2023] [Accepted: 09/15/2023] [Indexed: 10/10/2023]
Abstract
A Gram-stain-negative, rod-shaped, glide, non-flagellated, and facultatively anaerobic bacterial strain, designated as Z654T, was isolated from the gut of abalone Haliotis discus hannai from Rongcheng, Shandong province, China. Cells are 0.2-0.8 μm in width and 0.7-3.4 μm in length. Cells grew best at 30 °C (range, 15-37 °C), pH 7.0 (range, 6.0-8.5) and NaCl concentration of 2.0% (w/v) (range, 1-10%). According to the phylogenetic analysis of 16S rRNA gene sequence, the strain belongs to the genus Halocynthiibacter and the closest strain is Halocynthiibacter arcticus KCTC 42129 T (97.12%). The genome size of strain Z654T was 3,296,250 bp and the DNA G + C content was 54.2 mol%. The average nucleotide identity (ANI) scores and digital DNA-DNA hybridization (dDDH) scores with H. arcticus KCTC 42129 T were 70% and 14.6-18.2%, respectively. The predominant quinone was Q-10 and the major fatty acids were C18:0, C18:1 ω7c 11-methyl and summed feature 8. The polar lipids consisted of phosphatidylcholine, phosphatidylglycerol, unidentified aminolipid and unidentifed lipids. Based on the phenotypic, phylogenetic and chemotaxonomic data, strain Z654T was considered to represent a novel species of the genus Halocynthiibacter, for which the name Halocynthiibacte halioticoli sp. nov., is proposed. The type strain is Z654T (= MCCC 1H00503T = KCTC 92003 T).
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Affiliation(s)
- Dan-Dan Zhang
- Marine College, Shandong University, Weihai, Shandong, 264209, People's Republic of China
| | - Yu-Yan Yue
- Marine College, Shandong University, Weihai, Shandong, 264209, People's Republic of China
| | - Meng-Di Zhang
- Joint Science College, Shandong University, Weihai, Shandong, 264209, People's Republic of China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, Shandong, 264209, People's Republic of China.
- Weihai Research Institute of Industrial Technology of Shandong University, Weihai, 264209, People's Republic of China.
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14
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Qu Q, Chen T, He P, Geng H, Zeng P, Luan G. Isolation and characterization of a novel lytic bacteriophage vB_Efm_LG62 infecting Enterococcus faecium. Virus Genes 2023; 59:763-774. [PMID: 37422898 DOI: 10.1007/s11262-023-02016-9] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 06/11/2023] [Indexed: 07/11/2023]
Abstract
Enterococcus faecium has been classified as a "high priority" pathogen by the World Health Organization. Enterococcus faecium has rapidly evolved as a global nosocomial pathogen with adaptation to the nosocomial environment and the accumulation of resistance to multiple antibiotics. Phage therapy is considered a promising strategy against difficult-to-treat infections and antimicrobial resistance. In this study, we isolated and characterized a novel virulent bacteriophage, vB_Efm_LG62, that specifically infects multidrug-resistant E. faecium. Morphological observations suggested that the phage has siphovirus morphology, with an optimal multiplicity of infection of 0.001. One-step growth tests revealed that its latent growth was at 20 min, with a burst size of 101 PFU/cell. Phage vB_Efm_LG62 was verified to have a double-stranded genome of 42,236 bp (35.21% GC content), containing 66 predicted coding sequences as determined by whole genomic sequencing. No genes were predicted to have functions associated with virulence factors or antibiotic resistance, indicating that the phage vB_Efm_LG62 has good therapeutic potential. Our isolation and characterization of this highly efficient phage aids in expanding our knowledge of E. faecium-targeting phages, and provides additional options for phage cocktail therapy.
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Affiliation(s)
- Qianyu Qu
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Tao Chen
- Medical Laboratory, Xindu District People's Hospital of Chengdu, Chengdu, China
| | - Penggang He
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Huaixin Geng
- Non-Coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, China
| | - Peibin Zeng
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China.
| | - Guangxin Luan
- Non-Coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, China.
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15
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Dai M, He SL, Chen B, Li TJ. Phylogeny of Rhynchium and Its Related Genera (Hymenoptera: Eumeninae) Based on Universal Single-Copy Orthologs and Ultraconserved Elements. Insects 2023; 14:775. [PMID: 37754743 PMCID: PMC10532281 DOI: 10.3390/insects14090775] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 09/15/2023] [Accepted: 09/18/2023] [Indexed: 09/28/2023]
Abstract
The subfamily Eumeninae is a large group of fierce predatory insects that prey mainly on the larvae of Lepidoptera pests. Because of the highly similar morphologies of the genus Rhynchium and its related genera in the subfamily, including Rhynchium Spinola, Allorhynchium van der Vecht, Anterhynchium de Saussure, Pararrhynchium de Saussure, it is essential to delineate their relationships. A previous phylogenetic analysis based on mitochondrial genomes suggested the inconsistent relationships of these genera under traditional classification based on morphological characters. In this study, we first used single-copy orthologs [USCO] and ultraconserved elements [UCE] extracted from 10 newly sequenced low-coverage whole genomes to resolve the phylogenetic relationships of the above genera. The newly sequenced genomes are 152.99 Mb to 211.49 Mb in size with high completeness (BUSCO complete: 91.5-95.6%) and G + C content (36.31-38.76%). Based on extracted 5811 USCOs and 2312 UCEs, the phylogenetic relationships of Rhynchium and its related genera were: ((Allorhynchium + Lissodynerus) + (Pararrhynchium + (Anterhynchium + (Dirhynchium + Rhynchium)))), which was consistent with the mitochondrial genome results. The results supported the genus Rhynchium as monophyletic, whereas Anterhynchium was recovered as paraphyletic, with Anterhynchium (Dirhynchium) as a sister to Rhynchium and hence deserving generic status; In addition, in the genus Pararrhynchium, P. septemfasciatus feanus and P. venkataramani were separated, not clustered on a branch, just as P. septemfasciatus feanus was not together with P. striatum based on mitochondrial genomes. Since Lissodynerus septemfasciatus, the type species of the genus Lissodynerus, was transferred to Pararrhynchium, it is considered that the genus Lissodynerus should be restituted as a valid genus, not a synonym of Pararrhynchium.
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Affiliation(s)
| | | | | | - Ting-Jing Li
- Chongqing Key Laboratory of Vector Insects, Institute of Entomology and Molecular Biology, College of Life Science, Chongqing Normal University, Chongqing 401331, China; (M.D.); (S.-L.H.); (B.C.)
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16
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Xiang C, Li Y, Jing S, Han S, He H. Trichomonas gallinae Kills Host Cells Using Trogocytosis. Pathogens 2023; 12:1008. [PMID: 37623968 PMCID: PMC10459183 DOI: 10.3390/pathogens12081008] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/18/2023] [Accepted: 07/18/2023] [Indexed: 08/26/2023] Open
Abstract
Trichomonas gallinae (T. gallinae) is an infectious parasite that is prevalent worldwide in poultry and can cause death in both poultry and wild birds. Although studies have shown that T. gallinae damages host cells through direct contact, the mechanism is still unclear. In this study, we found that T. gallinae can kill host cells by ingesting fragments of the host cells, that is, by trogocytosis. Moreover, we found that the PI3K inhibitor wortmannin and the cysteine protease inhibitor E-64D prevented T. gallinae from destroying host cells. To the best of our knowledge, our study has demonstrated for the first time that T. gallinae uses trogocytosis to kill host cells. Understanding this mechanism is crucial for the prevention and control of avian trichomoniasis and will contribute to the development of vaccines and drugs for the prevention and control of avian trichomoniasis.
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Affiliation(s)
- Chen Xiang
- National Research Center for Wildlife-Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (C.X.); (S.H.)
- University of Chinese Academy of Sciences, Beijing 100101, China
| | - Yi Li
- College of Veterinary Medicine, Hebei Agricultural University, Baoding 071000, China; (Y.L.); (S.J.)
| | - Shengfan Jing
- College of Veterinary Medicine, Hebei Agricultural University, Baoding 071000, China; (Y.L.); (S.J.)
| | - Shuyi Han
- National Research Center for Wildlife-Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (C.X.); (S.H.)
- University of Chinese Academy of Sciences, Beijing 100101, China
| | - Hongxuan He
- National Research Center for Wildlife-Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (C.X.); (S.H.)
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17
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Wu Z, Tian X, Liu X, Zhou J, Yu W, Qi X, Peng J, Hsiang T, Wang Q, Wu N, Jiang Y. Complete genome sequence of a novel chrysovirus infecting Aspergillus terreus. Arch Virol 2023; 168:209. [PMID: 37474811 DOI: 10.1007/s00705-023-05839-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 06/16/2023] [Indexed: 07/22/2023]
Abstract
A double-stranded RNA (dsRNA) mycovirus was obtained from Aspergillus terreus strain HJ3-26 and designated "Aspergillus terreus chrysovirus 1" (AtCV1). It consists of four dsRNA segments (dsRNA1-4) with lengths of 3612 bp, 3132 bp, 3153 bp, and 3144 bp, respectively. Sequence analysis showed that dsRNA1 encodes an RNA-dependent RNA polymerase (RdRp), dsRNA2 encodes a capsid protein, and both dsRNA3 and dsRNA4 encode hypothetical proteins. Phylogenetic analysis of the RdRp suggested that AtCV1 is a member of a new species of the genus Alphachrysovirus in the family Chrysoviridae. This is the first chrysovirus obtained from A. terreus.
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Affiliation(s)
- Zunqiu Wu
- Key Laboratory of Endemic and Ethnic Diseases, Guizhou Medical University, Ministry of Education, 550004, Guiyang, China
- Key Laboratory of Medical Molecular Biology, Guizhou Medical University), 550004, Guiyang, Guizhou Province, China
- National experimental demonstration center of basic medicine (Guizhou Medical University, 550025, Guiyang, Guizhou Province, China
| | - Xun Tian
- Key Laboratory of Endemic and Ethnic Diseases, Guizhou Medical University, Ministry of Education, 550004, Guiyang, China
- Key Laboratory of Medical Molecular Biology, Guizhou Medical University), 550004, Guiyang, Guizhou Province, China
| | - Xiang Liu
- Key Laboratory of Endemic and Ethnic Diseases, Guizhou Medical University, Ministry of Education, 550004, Guiyang, China
- Key Laboratory of Medical Molecular Biology, Guizhou Medical University), 550004, Guiyang, Guizhou Province, China
| | - Jianhong Zhou
- Key Laboratory of Endemic and Ethnic Diseases, Guizhou Medical University, Ministry of Education, 550004, Guiyang, China
- Key Laboratory of Medical Molecular Biology, Guizhou Medical University), 550004, Guiyang, Guizhou Province, China
| | - Wenfeng Yu
- Key Laboratory of Endemic and Ethnic Diseases, Guizhou Medical University, Ministry of Education, 550004, Guiyang, China
- Key Laboratory of Medical Molecular Biology, Guizhou Medical University), 550004, Guiyang, Guizhou Province, China
| | - Xiaolan Qi
- Key Laboratory of Endemic and Ethnic Diseases, Guizhou Medical University, Ministry of Education, 550004, Guiyang, China
- Key Laboratory of Medical Molecular Biology, Guizhou Medical University), 550004, Guiyang, Guizhou Province, China
| | - Jian Peng
- Key Laboratory of Infectious Immune and Antibody Engineering of Guizhou Province, School of Biology and Engineering, Guizhou Medical University), 550004, Guiyang, Guizhou Province, China
| | - Tom Hsiang
- School of Environmental Sciences, University of Guelph), N1G 2W1, Guelph, ON, Canada
| | - Qinrong Wang
- Key Laboratory of Endemic and Ethnic Diseases, Guizhou Medical University, Ministry of Education, 550004, Guiyang, China
- Key Laboratory of Medical Molecular Biology, Guizhou Medical University), 550004, Guiyang, Guizhou Province, China
| | - Ning Wu
- Key Laboratory of Endemic and Ethnic Diseases, Guizhou Medical University, Ministry of Education, 550004, Guiyang, China.
- Key Laboratory of Medical Molecular Biology, Guizhou Medical University), 550004, Guiyang, Guizhou Province, China.
- National experimental demonstration center of basic medicine (Guizhou Medical University, 550025, Guiyang, Guizhou Province, China.
| | - Yinhui Jiang
- Key Laboratory of Endemic and Ethnic Diseases, Guizhou Medical University, Ministry of Education, 550004, Guiyang, China.
- Key Laboratory of Medical Molecular Biology, Guizhou Medical University), 550004, Guiyang, Guizhou Province, China.
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18
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Yu S, Chen J, Zhao Y, Yan F, Fan Y, Xia X, Shan G, Zhang P, Chen X. Oral-microbiome-derived signatures enable non-invasive diagnosis of laryngeal cancers. J Transl Med 2023; 21:438. [PMID: 37408030 DOI: 10.1186/s12967-023-04285-2] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 06/17/2023] [Indexed: 07/07/2023] Open
Abstract
BACKGROUND Recent studies have uncovered that the microbiota in patients with head and neck cancers is significantly altered and may drive cancer development. However, there is limited data to explore the unique microbiota of laryngeal squamous cell carcinoma (LSCC), and little is known regarding whether the oral microbiota can be utilized as an early diagnostic biomarker. METHODS Using 16S rRNA gene sequencing, we characterized the microbiome of oral rinse and tissue samples from 77 patients with LSCC and 76 control patients with vocal polyps, and then performed bioinformatic analyses to identify taxonomic groups associated with clinicopathologic features. RESULTS Multiple bacterial genera exhibited significant differences in relative abundance when stratifying by histologic and tissue type. By exploiting the distinct microbial abundance and identifying the tumor-associated microbiota taxa between patients of LSCC and vocal polyps, we developed a predictive classifier by using rinse microbiota as key features for the diagnosis of LSCC with 85.7% accuracy. CONCLUSION This is the first evidence of taxonomical features based on the oral rinse microbiome that could diagnose LSCC. Our results revealed the oral rinse microbiome is an understudied source of clinical variation and represents a potential non-evasive biomarker of LSCC.
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Affiliation(s)
- Shuting Yu
- Department of Otolaryngology-Head and Neck Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Shuaifuyuan, Dongcheng District, Beijing, China
| | - Junru Chen
- Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao, China
| | - Yan Zhao
- Department of Otolaryngology Head and Neck Surgery, Beijing TongRen Hospital, Capital Medical University, Beijing, China
| | - Fangxu Yan
- Department of Otolaryngology-Head and Neck Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Shuaifuyuan, Dongcheng District, Beijing, China
| | - Yue Fan
- Department of Otolaryngology-Head and Neck Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Shuaifuyuan, Dongcheng District, Beijing, China
| | - Xin Xia
- Department of Otolaryngology-Head and Neck Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Shuaifuyuan, Dongcheng District, Beijing, China
| | - Guangliang Shan
- Department of Epidemiology and Statistics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Peng Zhang
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, MOE Key Laboratory of Major Diseases in Children, Rare Disease Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China.
| | - Xingming Chen
- Department of Otolaryngology-Head and Neck Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Shuaifuyuan, Dongcheng District, Beijing, China.
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19
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Zhang Z, Zhang J, Li D, Xia J, Zhang X. Morphological and Phylogenetic Analyses Reveal Three New Species of Pestalotiopsis ( Sporocadaceae, Amphisphaeriales) from Hainan, China. Microorganisms 2023; 11:1627. [PMID: 37512800 PMCID: PMC10385101 DOI: 10.3390/microorganisms11071627] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/20/2023] [Accepted: 06/20/2023] [Indexed: 07/30/2023] Open
Abstract
Species of Pestalotiopsis were mainly introduced as endophytes, plant pathogens or saprobes from various hosts. In this study, ten strains were isolated from Ficus macrocarpa, Phoebe zhennan and Spatholobus suberectus in China. Based on multilocus phylogenies from the internal transcribed spacer (ITS), the partial translation elongation factor 1-alpha gene (tef1α) and the partial beta-tubulin gene (tub2), in conjunction with morphological characteristics, we describe three new species, viz., Pestalotiopsis ficicola sp. nov., P. phoebes sp. nov. and P. spatholobi sp. nov.
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Affiliation(s)
- Zhaoxue Zhang
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian 271018, China
| | - Jie Zhang
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian 271018, China
| | - Duhua Li
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian 271018, China
| | - Jiwen Xia
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian 271018, China
| | - Xiuguo Zhang
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian 271018, China
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20
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Liu M, Hu M, Zhou H, Dong Z, Chen X. High-level production of Aspergillus niger prolyl endopeptidase from agricultural residue and its application in beer brewing. Microb Cell Fact 2023; 22:93. [PMID: 37143012 PMCID: PMC10161650 DOI: 10.1186/s12934-023-02087-1] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 04/10/2023] [Indexed: 05/06/2023] Open
Abstract
BACKGROUND Prolyl endopeptidase from Aspergillus niger (AN-PEP) is a prominent serine proteinase with various potential applications in the food and pharmaceutical industries. However, the availability of efficient and low-cost AN-PEP remains a challenge owing to its low yield and high fermentation cost. RESULTS Here, AN-PEP was recombinantly expressed in Trichoderma reesei (rAN-PEP) under the control of the cbh1 promoter and its secretion signal. After 4 days of shaking flask cultivation with the model cellulose Avicel PH101 as the sole carbon source, the extracellular prolyl endopeptidase activity reached up to 16.148 U/mL, which is the highest titer reported to date and the secretion of the enzyme is faster in T. reesei than in other eukaryotic expression systems including A. niger and Komagataella phaffii. Most importantly, when cultivated on the low-cost agricultural residue corn cob, the recombinant strain was found to secret a remarkable amount of rAN-PEP (37.125 U/mL) that is twice the activity under the pure cellulose condition. Furthermore, treatment with rAN-PEP during beer brewing lowered the content of gluten below the ELISA kit detection limit (< 10 mg/kg) and thereby, reduced turbidity, which would be beneficial for improving the non-biological stability of beer. CONCLUSION Our research provides a promising approach for industrial production of AN-PEP and other enzymes (proteins) from renewable lignocellulosic biomass, which provides a new idea with relevant researchers for the utilization of agricultural residues.
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Affiliation(s)
- Minglu Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Meng Hu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hui Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhiyang Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Xiuzhen Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
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21
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Li Y, Guo S, Dang H, Zhang L, Xu J, Li S. Oncomelania hupensis Distribution and Schistosomiasis Transmission Risk in Different Environments under Field Conditions. Trop Med Infect Dis 2023; 8:tropicalmed8050242. [PMID: 37235290 DOI: 10.3390/tropicalmed8050242] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/15/2023] [Accepted: 04/16/2023] [Indexed: 05/28/2023] Open
Abstract
The goal of schistosomiasis prevention and control in China is shifting from transmission interruption to elimination. However, the area inhabited by the intermediate host, the snail Oncomelania hupensis, has not changed much in recent years. Different environmental types have different impacts on snail breeding, and understanding these differences is conducive to improving the efficiency of snail monitoring and control and to saving resources. Based on previous epidemiological data, we selected 199 villages in 2020 and 269 villages in 2021 from transmission control, transmission interruption, and elimination areas of snail breeding. Snail surveys were conducted in selected villages using systematic sampling and/or environmental sampling methods in six types of snail-breeding environments (canals, ponds, paddy fields, dry lands, bottomlands, and undefined environments). All live snails collected from the field were evaluated for Schistosoma japonicum infection using the microscopic dissection method, and a subsample of snails was subjected to loop-mediated isothermal amplification (LAMP) to assess the presence of S. japonicum infection. Snail distribution data and infection rate and nucleic acid positive rate of schistosomes in snails were calculated and analyzed. The 2-year survey covered 29,493 ha of the environment, in which 12,313 ha of snail habitats were detected. In total, 51.16 ha of new snail habitats and 107.76 ha of re-emergent snail habitats were identified during the survey. The occurrence rate of snails in canals (10.04%, 95% CI: 9.88-10.20%) and undefined environments (20.66%, 95% CI: 19.64-21.67%) was relatively high in 2020, and the density of snails in bottomlands (0.39, 95% CI: 0.28-0.50) and undefined environments (0.43, 95% CI: 0.14-1.60) was relatively high in 2021. Of the 227,355 live snails collected in this study, none were S. japonicum-positive as determined by microscopy. Of the 20,131 pooled samples, however, 5 were S. japonicum-positive based on LAMP analysis, and they were distributed in three environmental types: 3 in bottomland, 1 in dry land, and 1 in a canal. The bottomland environment has a high risk of schistosomiasis transmission because it contains a large area of newly emerging and re-emerging snail habitats, and it also had the most breeding snails infected with S. japonicum. Thus, this habitat type should be the key target for snail monitoring and early warning and for the prevention and control of schistosomiasis.
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Affiliation(s)
- Yinlong Li
- National Institute of Parasitic Disease, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Disease Research), NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Center for Tropical Disease, National Center for International Research on Tropical Disease, Shanghai 200025, China
| | - Suying Guo
- National Institute of Parasitic Disease, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Disease Research), NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Center for Tropical Disease, National Center for International Research on Tropical Disease, Shanghai 200025, China
| | - Hui Dang
- National Institute of Parasitic Disease, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Disease Research), NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Center for Tropical Disease, National Center for International Research on Tropical Disease, Shanghai 200025, China
| | - Lijuan Zhang
- National Institute of Parasitic Disease, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Disease Research), NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Center for Tropical Disease, National Center for International Research on Tropical Disease, Shanghai 200025, China
| | - Jing Xu
- National Institute of Parasitic Disease, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Disease Research), NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Center for Tropical Disease, National Center for International Research on Tropical Disease, Shanghai 200025, China
| | - Shizhu Li
- National Institute of Parasitic Disease, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Disease Research), NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Center for Tropical Disease, National Center for International Research on Tropical Disease, Shanghai 200025, China
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Li G, Wang Q, Zhang M, Hu B, Han S, Xiang C, Yuan G, He H. Male-Biased Parasitism of Brandt's Voles ( Lasiopodomys brandtii) in Inner Mongolia, China. Animals (Basel) 2023; 13:ani13081290. [PMID: 37106853 PMCID: PMC10135223 DOI: 10.3390/ani13081290] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/03/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
The abundance and prevalence of parasitic infection often vary in different host sexes, and this phenomenon has been named sex-biased parasitism. Brandt's voles are the dominant rodent species in typical steppe habitat and are widely distributed in Inner Mongolia, China, but the prevalence of parasites in Brandt's voles are poorly reported. In this study, we investigated the prevalence of six intestinal parasites in Brandt's voles in May, June, July, and August 2022 around the Xilingol Grassland in Inner Mongolia, China. The results showed that Syphacia obvelata, Aspiculuris tetraptera, and Trichostrongylidae family were the dominant intestinal parasites in Brandt's voles that we captured in this study, and the infection rates of the three parasites were significantly higher in males than females, which showed obvious male-biased parasitism. Season and human activities such as grazing had no significant effect on the infection rates for different parasites, while the parasite reproduction level was higher when the ambient temperature was around 18 °C. Sexual size dimorphism was ubiquitous in Brandt's voles, and it was mainly manifested by the differences in body weight and length between males and females. Simple linear regression analysis showed a significant positive correlation between bodyweight and parasite infection rates, so the sex-biased parasitism in Brandt's voles could be explained by the body size hypothesis, as a larger body could provide more ecological niches for parasitic infection.
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Affiliation(s)
- Gaojian Li
- National Research Center for Wildlife-Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100101, China
| | - Qinghe Wang
- Nanyang Wild Animals and Plants Protection Station, Nanyang 473000, China
| | - Min Zhang
- National Research Center for Wildlife-Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Bin Hu
- National Research Center for Wildlife-Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100101, China
| | - Shuyi Han
- National Research Center for Wildlife-Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100101, China
| | - Chen Xiang
- National Research Center for Wildlife-Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100101, China
| | - Guohui Yuan
- National Research Center for Wildlife-Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hongxuan He
- National Research Center for Wildlife-Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
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Zhang TT, Liu D, Zhang XY, Wang JC, Du ZJ. Spiribacter salilacus sp. nov., a novel moderately halophilic bacterium isolated from a saline lake in China. Arch Microbiol 2023; 205:166. [PMID: 37014519 DOI: 10.1007/s00203-023-03511-1] [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] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/19/2023] [Accepted: 03/22/2023] [Indexed: 04/05/2023]
Abstract
A Gram-staining-negative, non-motile, rod-shaped or curved rod-shaped, moderately halophilic bacterium, designated C176T, was isolated from Yuncheng Salt Lake in Shanxi Province, P.R. China. The optimal temperature, salinity and pH for growth of strain C176T was 37 °C, 6% (w/v) NaCl and 7.5. Phylogenetic analysis using 16S rRNA gene sequences indicated strain C176T has the highest similarity with Spiribacter salinus LMG 27464 T (97.7%), following by the S. halobius E85T (97.6%), S. curvatus DSM 28542 T (97.2%), S. roseus CECT 9117 T (97.0%) and S. vilamensis DSM 21056 T (96.9%). The ANI and dDDH values between strain C176T and S. salinus LMG 27464 T were 69.8 and 17.7%, respectively. The DNA G + C content of genome for strain C176T was 54.1%. Summed feature 8 (C18:1 ω7c and/or C18:1 ω6c) and C16:0 were detected as its major fatty acids, with content of 38.7 and 28.6% respectively, while Q-8 was the predominant ubiquinone. The major polar lipids of strain C176T contained phospholipid, phosphatidylglycerol and phosphoglycolipid. In accordance with results of polyphasic taxonomy, strain C176T is considered as a novel species of the genus Spiribacter, for which the name Spiribacter salilacus sp. nov. is proposed. The type strain is C176T (= MCCC 1H00417T = KCTC 72692 T).
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Affiliation(s)
- Tong-Tong Zhang
- SDU-ANU Joint Science College, Shandong University, Weihai, 264209, Shandong, China
| | - Dun Liu
- SDU-ANU Joint Science College, Shandong University, Weihai, 264209, Shandong, China
| | - Xiao-Yu Zhang
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, Guangdong, China
| | - Jia-Cheng Wang
- University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, 264209, Shandong, China.
- Weihai Research Institute of Industrial Technology, Shandong University, Weihai, 264209, Shandong, China.
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