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Chuandong Z, Hu J, Li J, Wu Y, Wu C, Lai G, Shen H, Wu F, Tao C, Liu S, Zhang W, Shao H. Distribution and roles of Ligilactobacillus murinus in hosts. Microbiol Res 2024; 282:127648. [PMID: 38367479 DOI: 10.1016/j.micres.2024.127648] [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: 08/30/2023] [Revised: 10/26/2023] [Accepted: 02/10/2024] [Indexed: 02/19/2024]
Abstract
Ligilactobacillus murinus, a member of the Ligilactobacillus genus, holds significant potential as a probiotic. While research on Ligilactobacillus murinus has been relatively limited compared to well-studied probiotic lactic acid bacteria such as Limosilactobacillus reuteri and Lactobacillus gasseri, a mounting body of evidence highlights its extensive involvement in host intestinal metabolism and immune activities. Moreover, its abundance exhibits a close correlation with intestinal health. Notably, beyond the intestinal context, Ligilactobacillus murinus is gaining recognition for its contributions to metabolism and regulation in the oral cavity, lungs, and vagina. As such, Ligilactobacillus murinus emerges as a potential probiotic candidate with a pivotal role in supporting host well-being. This review delves into studies elucidating the multifaceted roles of Ligilactobacillus murinus. It also examines its medicinal potential and associated challenges, underscoring the imperative to delve deeper into unraveling the mechanisms of its actions and exploring its health applications.
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Affiliation(s)
- Zhou Chuandong
- School of Life Science and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong, PR China
| | - Jicong Hu
- School of Life Science and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong, PR China
| | - Jiawen Li
- School of Life Science and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong, PR China
| | - Yuting Wu
- School of Clinical Medicine, Guangdong Pharmaceutical University, Guangzhou, Guangdong, PR China
| | - Chan Wu
- School of Clinical Medicine, Guangdong Pharmaceutical University, Guangzhou, Guangdong, PR China
| | - Guanxi Lai
- School of Clinical Pharmacy, Guangdong Pharmaceutical University, Guangzhou, Guangdong, PR China
| | - Han Shen
- School of Life Science and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong, PR China
| | - Fenglin Wu
- School of Life Science and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong, PR China
| | - Changli Tao
- School of Life Science and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong, PR China
| | - Song Liu
- School of Clinical Pharmacy, Guangdong Pharmaceutical University, Guangzhou, Guangdong, PR China
| | - Wenfeng Zhang
- School of Life Science and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong, PR China.
| | - Hongwei Shao
- School of Life Science and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong, PR China.
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Hu R, Li F, Chen Y, Liu C, Li J, Ma Z, Wang Y, Cui C, Luo C, Zhou P, Ni W, Yang QY, Hu S. AnimalMetaOmics: a multi-omics data resources for exploring animal microbial genomes and microbiomes. Nucleic Acids Res 2024; 52:D690-D700. [PMID: 37897361 PMCID: PMC10768125 DOI: 10.1093/nar/gkad931] [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: 08/12/2023] [Revised: 09/19/2023] [Accepted: 10/12/2023] [Indexed: 10/30/2023] Open
Abstract
The Animal Meta-omics landscape database (AnimalMetaOmics, https://yanglab.hzau.edu.cn/animalmetaomics#/) is a comprehensive and freely available resource that includes metagenomic, metatranscriptomic, and metaproteomic data from various non-human animal species and provides abundant information on animal microbiomes, including cluster analysis of microbial cognate genes, functional gene annotations, active microbiota composition, gene expression abundance, and microbial protein identification. In this work, 55 898 microbial genomes were annotated from 581 animal species, including 42 924 bacterial genomes, 12 336 virus genomes, 496 archaea genomes and 142 fungi genomes. Moreover, 321 metatranscriptomic datasets were analyzed from 31 animal species and 326 metaproteomic datasets from four animal species, as well as the pan-genomic dynamics and compositional characteristics of 679 bacterial species and 13 archaea species from animal hosts. Researchers can efficiently access and acquire the information of cross-host microbiota through a user-friendly interface, such as species, genomes, activity levels, expressed protein sequences and functions, and pan-genome composition. These valuable resources provide an important reference for better exploring the classification, functional diversity, biological process diversity and functional genes of animal microbiota.
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Affiliation(s)
- Ruirui Hu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Fulin Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Yifan Chen
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Xinjiang 832003, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Chuyang Liu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Jiawei Li
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Xinjiang 832003, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhongchen Ma
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Yue Wang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Chaowen Cui
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Chengfang Luo
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Xinjiang 832003, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Ping Zhou
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Xinjiang 832003, China
| | - Wei Ni
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Qing-Yong Yang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Xinjiang 832003, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Shengwei Hu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
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Meng D, Ai S, Spanos M, Shi X, Li G, Cretoiu D, Zhou Q, Xiao J. Exercise and microbiome: From big data to therapy. Comput Struct Biotechnol J 2023; 21:5434-5445. [PMID: 38022690 PMCID: PMC10665598 DOI: 10.1016/j.csbj.2023.10.034] [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: 06/13/2023] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
Exercise is a vital component in maintaining optimal health and serves as a prospective therapeutic intervention for various diseases. The human microbiome, comprised of trillions of microorganisms, plays a crucial role in overall health. Given the advancements in microbiome research, substantial databases have been created to decipher the functionality and mechanisms of the microbiome in health and disease contexts. This review presents an initial overview of microbiomics development and related databases, followed by an in-depth description of the multi-omics technologies for microbiome. It subsequently synthesizes the research pertaining to exercise-induced modifications of the microbiome and diseases that impact the microbiome. Finally, it highlights the potential therapeutic implications of an exercise-modulated microbiome in intestinal disease, obesity and diabetes, cardiovascular disease, and immune/inflammation-related diseases.
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Affiliation(s)
- Danni Meng
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People’s Hospital of Nantong), School of Medicine, Shanghai University, Nantong 226011, China
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai 200444, China
| | - Songwei Ai
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People’s Hospital of Nantong), School of Medicine, Shanghai University, Nantong 226011, China
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai 200444, China
| | - Michail Spanos
- Cardiovascular Division of the Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Xiaohui Shi
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People’s Hospital of Nantong), School of Medicine, Shanghai University, Nantong 226011, China
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai 200444, China
| | - Guoping Li
- Cardiovascular Division of the Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Dragos Cretoiu
- Department of Medical Genetics, Carol Davila University of Medicine and Pharmacy, Bucharest 020031, Romania
- Materno-Fetal Assistance Excellence Unit, Alessandrescu-Rusescu National Institute for Mother and Child Health, Bucharest 011062, Romania
| | - Qiulian Zhou
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People’s Hospital of Nantong), School of Medicine, Shanghai University, Nantong 226011, China
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai 200444, China
| | - Junjie Xiao
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People’s Hospital of Nantong), School of Medicine, Shanghai University, Nantong 226011, China
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai 200444, China
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Sengupta P, Sivabalan SKM, Mahesh A, Palanikumar I, Kuppa Baskaran DK, Raman K. Big Data for a Small World: A Review on Databases and Resources for Studying Microbiomes. J Indian Inst Sci 2023; 103:1-17. [PMID: 37362854 PMCID: PMC10073628 DOI: 10.1007/s41745-023-00370-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 03/05/2023] [Indexed: 06/28/2023]
Abstract
Microorganisms are ubiquitous in nature and form complex community networks to survive in various environments. This community structure depends on numerous factors like nutrient availability, abiotic factors like temperature and pH as well as microbial composition. Categorising accessible biomes according to their habitats would help in understanding the complexity of the environment-specific communities. Owing to the recent improvements in sequencing facilities, researchers have started to explore diverse microbiomes rapidly and attempts have been made to study microbial crosstalk. However, different metagenomics sampling, preprocessing, and annotation methods make it difficult to compare multiple studies and hinder the recycling of data. Huge datasets originating from these experiments demand systematic computational methods to extract biological information beyond microbial compositions. Further exploration of microbial co-occurring patterns across the biomes could help us in designing cross-biome experiments. In this review, we catalogue databases with system-specific microbiomes, discussing publicly available common databases as well as specialised databases for a range of microbiomes. If the new datasets generated in the future could maintain at least biome-specific annotation, then researchers could use those contemporary tools for relevant and bias-free analysis of complex metagenomics data.
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Affiliation(s)
- Pratyay Sengupta
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu 600036 India
- Centre for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu 600036 India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu 600036 India
| | | | - Amrita Mahesh
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu 600036 India
- Centre for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu 600036 India
| | - Indumathi Palanikumar
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu 600036 India
- Centre for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu 600036 India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu 600036 India
| | - Dinesh Kumar Kuppa Baskaran
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu 600036 India
- Centre for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu 600036 India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu 600036 India
| | - Karthik Raman
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu 600036 India
- Centre for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu 600036 India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu 600036 India
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Rigden DJ, Fernández XM. The 2023 Nucleic Acids Research Database Issue and the online molecular biology database collection. Nucleic Acids Res 2023; 51:D1-D8. [PMID: 36624667 PMCID: PMC9825711 DOI: 10.1093/nar/gkac1186] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The 2023 Nucleic Acids Research Database Issue contains 178 papers ranging across biology and related fields. There are 90 papers reporting on new databases and 82 updates from resources previously published in the Issue. Six more papers are updates from databases most recently published elsewhere. Major nucleic acid databases reporting updates include Genbank, ENA, ChIPBase, JASPAR, mirDIP and the Issue's first Breakthrough Article, NACDDB for Circular Dichroism data. Updates from BMRB and RCSB cover experimental protein structural data while AlphaFold 2 computational structure predictions feature widely. STRING and REBASE are stand-out updates in the signalling and enzymes section. Immunology-related databases include CEDAR, the second Breakthrough Article, for cancer epitopes and receptors alongside returning IPD-IMGT/HLA and the new PGG.MHC. Genomics-related resources include Ensembl, GWAS Central and UCSC Genome Browser. Major returning databases for drugs and their targets include Open Targets, DrugCentral, CTD and Pubchem. The EMPIAR image archive appears in the Issue for the first time. The entire database Issue is freely available online on the Nucleic Acids Research website (https://academic.oup.com/nar). The NAR online Molecular Biology Database Collection has been updated, revisiting 463 entries, adding 92 new resources and eliminating 96 discontinued URLs so bringing the current total to 1764 databases. It is available at http://www.oxfordjournals.org/nar/database/c/.
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