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Chen L, Wang XN, Bi HY, Wang GY. Antimicrobial Biosynthetic Potential and Phylogenetic Analysis of Culturable Bacteria Associated with the Sponge Ophlitaspongia sp. from the Yellow Sea, China. Mar Drugs 2022; 20:md20100588. [PMID: 36286412 PMCID: PMC9605435 DOI: 10.3390/md20100588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 09/13/2022] [Accepted: 09/16/2022] [Indexed: 11/25/2022] Open
Abstract
Sponge-derived bacteria are considered to be a promising source of novel drugs, owing to their abundant secondary metabolites that have diverse biological activities. In this study, we explored the antimicrobial biosynthetic potential and phylogenetics of culturable bacteria associated with the sponge Ophlitaspongia sp. from the Yellow Sea, China. Using culture-dependent methods, we obtained 151 bacterial strains, which were then analysed for their antimicrobial activities against seven indicator strains. The results indicate that 94 (62.3%) of the 151 isolated strains exhibited antimicrobial activities and inhibited at least one of the indicator strains. Fifty-two strains were selected for further phylogenetic analysis using 16S rRNA gene sequencing, as well as for the presence of polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) genes. These 52 strains belonged to 20 genera from 18 families in 4 phyla, including Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. Five strains with PKS genes and ten strains with NRPS genes were detected. Among them, two strains contained both PKS and NRPS genes. Notoacmeibacter sp. strain HMA008 (class Alphaproteobacteria) exhibited potent antimicrobial activity; thus, whole genome sequencing methods were used to analyse its secondary metabolite biosynthetic gene clusters. The genome of HMA008 contained 12 biosynthetic gene clusters that potentially encode secondary metabolites belonging to compound classes such as non-ribosomal peptides, prodigiosin, terpene, β-lactones, and siderophore, among others. This study indicates that the sponge Ophlitaspongia sp. harbours diverse bacterial strains with antimicrobial properties and may serve as a potential source of bioactive compounds.
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Affiliation(s)
- Lei Chen
- Department of Bioengineering, School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai 264209, China
- Correspondence: (L.C.); (G.-Y.W.)
| | - Xue-Ning Wang
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hong-Yu Bi
- Department of Bioengineering, School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai 264209, China
| | - Guang-Yu Wang
- Department of Bioengineering, School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai 264209, China
- Correspondence: (L.C.); (G.-Y.W.)
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Chiou WC, Lai WH, Cai YL, Du ML, Lai HM, Chen JC, Huang HC, Liu HK, Huang C. Gut microbiota-directed intervention with high-amylose maize ameliorates metabolic dysfunction in diet-induced obese mice. Food Funct 2022; 13:9481-9495. [PMID: 35993118 DOI: 10.1039/d2fo01211a] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Obesity is a chronic disease that may lead to the development of metabolic diseases, cardiovascular diseases, and cancers and has been predicted to affect one billion adults by 2030. Owing to the pivotal role of the gut microbiota in health, including metabolism and energy homeostasis, dietary fiber, the primary energy resource for the gut microbiota, not only helps reduce appetite and short-term food intake but also modulates the structure of the gut microbiota. In this study, we investigated whether high-amylose maize (HAM), with a particular amount of dietary fiber, improves dysmetabolism and gut microbiota dysbiosis in diet-induced obese mice. Promisingly, the HAM dietary intervention not only reduced body weight gain, adipocyte hypertrophy, and dyslipidemia but also mitigated non-alcoholic fatty liver disease, insulin resistance, impaired glucose tolerance, and inflammation in the liver and epididymal white adipose tissues in high-fat diet (HFD)-fed obese mice. In addition, the HAM dietary intervention ameliorated gut microbiota dysbiosis in HFD-fed mice. Changes in families, genera, and species of gut biota that have a relative abundance of 0.01% in at least one group were scrutinized. At the species level, HAM dietary intervention increased Bifidobacterium pseudolongum, Bifidobacterium animalis, Bifidobacterium bifidum, and Lactobacillus paraplantarum and decreased Streptococcus agalactiae, Mucispirillum schaedleri, and Alistipes indistinctus. This change in the gut microbiota driven by the HAM diet was strongly associated with obesity-related indices, highlighting the nutraceutical potential of HAM for improving overall metabolic health. Taken together, this study demonstrates the potential of the HAM diet for mediating metabolic syndrome and gut microbiota dysbiosis.
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Affiliation(s)
- Wei-Chung Chiou
- Department of Biotechnology and Laboratory Science in Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.
| | - Wei-Han Lai
- Department of Biotechnology and Laboratory Science in Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.
| | - Yu-Lin Cai
- Department of Biotechnology and Laboratory Science in Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.
| | - Meng-Lun Du
- Department of Agricultural Chemistry, National Taiwan University, Taipei, Taiwan
| | - Hsi-Mei Lai
- Department of Agricultural Chemistry, National Taiwan University, Taipei, Taiwan
| | - Jui-Chieh Chen
- Department of Biochemical Science and Technology, National Chiayi University, Chiayi, Taiwan
| | - Hsiu-Chen Huang
- Department of Applied Science, National Tsing Hua University South Campus, Hsinchu, Taiwan.,Center for Teacher Education, National Tsing Hua University, Hsinchu, Taiwan
| | - Hui-Kang Liu
- Division of Basic Chinese Medicine, National Research Institute of Chinese Medicine, Ministry of Health and Welfare, Taipei, Taiwan.,PhD Program for the Clinical Drug Discovery from Herbal Medicine, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Cheng Huang
- Department of Biotechnology and Laboratory Science in Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.
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Grégory D, Chaudet H, Lagier JC, Raoult D. How mass spectrometric approaches applied to bacterial identification have revolutionized the study of human gut microbiota. Expert Rev Proteomics 2018; 15:217-229. [PMID: 29336192 DOI: 10.1080/14789450.2018.1429271] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
INTRODUCTION Describing the human hut gut microbiota is one the most exciting challenges of the 21st century. Currently, high-throughput sequencing methods are considered as the gold standard for this purpose, however, they suffer from several drawbacks, including their inability to detect minority populations. The advent of mass-spectrometric (MS) approaches to identify cultured bacteria in clinical microbiology enabled the creation of the culturomics approach, which aims to establish a comprehensive repertoire of cultured prokaryotes from human specimens using extensive culture conditions. Areas covered: This review first underlines how mass spectrometric approaches have revolutionized clinical microbiology. It then highlights the contribution of MS-based methods to culturomics studies, paying particular attention to the extension of the human gut microbiota repertoire through the discovery of new bacterial species. Expert commentary: MS-based approaches have enabled cultivation methods to be resuscitated to study the human gut microbiota and thus to fill in the blanks left by high-throughput sequencing methods in terms of culturing minority populations. Continued efforts to recover new taxa using culture methods, combined with their rapid implementation in genomic databases, would allow for an exhaustive analysis of the gut microbiota through the use of a comprehensive approach.
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Affiliation(s)
- Dubourg Grégory
- a Aix Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), Assistance Publique - Hôpitaux de Marseille - IHU Méditerranée Infection , Marseille , France
| | - Hervé Chaudet
- a Aix Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), Assistance Publique - Hôpitaux de Marseille - IHU Méditerranée Infection , Marseille , France
| | - Jean-Christophe Lagier
- a Aix Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), Assistance Publique - Hôpitaux de Marseille - IHU Méditerranée Infection , Marseille , France
| | - Didier Raoult
- a Aix Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), Assistance Publique - Hôpitaux de Marseille - IHU Méditerranée Infection , Marseille , France
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Oren A, Garrity GM. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2016; 66:3761-3764. [PMID: 27902176 DOI: 10.1099/ijsem.0.001321] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 91904 Jerusalem, Israel
| | - George M Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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