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Du Y, Guo HL, Su X, Guo M, Li B, Wang H, Gao X, Yuan Q, Teng Y, Wang T, Zheng B. Surface nanocoating-based universal platform for programmed delivery of microorganisms in complicated digestive tract. J Colloid Interface Sci 2024; 673:765-780. [PMID: 38905998 DOI: 10.1016/j.jcis.2024.06.093] [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: 04/17/2024] [Revised: 06/04/2024] [Accepted: 06/11/2024] [Indexed: 06/23/2024]
Abstract
Microbial therapies have promising applications in the treatment of a broad range of diseases. However, effective colonization of the target region by therapeutic microorganisms remains a significant challenge owing to the complexity of the intestinal system. Here, we developed surface nanocoating-based universal platform (SNUP), which enabled the manipulation of controlled release and targeted colonization of therapeutic microbes in the digestive tract without the utilization of any targeting molecules. The system controlled the decomposition time of SNUP in the gut by regulating different modification layers and modification sequences on the microorganism's surface, so that the microorganism was released at a predetermined time and space. With the SNUP nanomodification technology, we could effectively deliver therapeutic microorganisms to specific complex intestinal regions such as the small intestine and colon, and protect the bioactivity of therapeutic microorganisms from destruction by both strong acids and digestive enzymes. In this study, we found that two layers SNUP-encapsulated Liiliilactobacillus salivarius (LS@CCMC) could efficiently colonize the small intestine and significantly improve the symptoms of a mouse model of Parkinson's disease through sustained secretion of γ-aminobutyric acid (GABA). This surface nanocoating-based universal platform system does not require the design of specific targeting molecules, providing a simple and universal method for colonized microbial therapy, target theranostics, precision medicine, and personalized medicine.
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Affiliation(s)
- Yajing Du
- School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Hao Lin Guo
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 102401, China
| | - Xin Su
- School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Mingming Guo
- Academy of Medical Engineering and Translational Medicine, Tianjin Key Laboratory of Brain Science and Neural Engineering, Tianjin University, Tianjin 300072, China
| | - Bowen Li
- Academy of Medical Engineering and Translational Medicine, Tianjin Key Laboratory of Brain Science and Neural Engineering, Tianjin University, Tianjin 300072, China
| | - Hua Wang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Xiaoning Gao
- School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Qing Yuan
- Department of Urology, The Third Medical Center, Chinese People's Liberation Army (PLA), General Hospital, Beijing 721399, China
| | - Yue Teng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China.
| | - Tao Wang
- School of Life Sciences, Tianjin University, Tianjin 300072, China.
| | - Bin Zheng
- Academy of Medical Engineering and Translational Medicine, Tianjin Key Laboratory of Brain Science and Neural Engineering, Tianjin University, Tianjin 300072, China.
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2
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Lichtenegger AS, Posadas-Cantera S, Badr MT, Häcker G. Comparison of the diversity of anaerobic-cultured gut bacterial communities on different culture media using 16S rDNA sequencing. J Microbiol Methods 2024; 224:106988. [PMID: 38977080 DOI: 10.1016/j.mimet.2024.106988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 07/03/2024] [Accepted: 07/03/2024] [Indexed: 07/10/2024]
Abstract
The gut microbiome is a dense and diverse community of different microorganisms that deeply influence human physiology and that have important interactions with pathogens. For the correct antibiotic treatment of infections, with its twin goals of effective inhibition of the pathogen and limitation of collateral damage to the microbiome, the identification of infectious organisms is key. Microbiological culturing is still the mainstay of pathogen identification, and anaerobic species are among the most demanding bacterial communities to culture. This study aimed to evaluate the impact of growth media on the culture of an-aerobic bacteria from human stool samples. Stool samples from eight human subjects were cultured each on a yeast extract cysteine blood agar (HCB) and a modified peptone-yeast extract-glucose (MPYG) plate and subjected to Illumina NGS analysis after DNA extraction and amplification. The results showed tight clustering of sequencing samples belonging to the same human subject. Various differences in bacterial richness and evenness could be observed between the two media, with HCB plates supporting the growth of a more diverse microbial community, and MPYG plates improving the growth rates of certain taxa. No statistical significance was observed between the groups. This study highlights the importance of choosing the appropriate growth media for anaerobic bacterial culture and adjusting culture conditions to target specific pathological conditions. HCB plates are suitable for standard microbiological diagnostics, while MPYG plates may be more appropriate for targeting specific conditions. This work emphasizes the role of next-generation sequencing in supporting future research in clinical microbiology.
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Affiliation(s)
- Anne Sophie Lichtenegger
- Institute of Medical Microbiology and Hygiene, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany.
| | - Sara Posadas-Cantera
- Institute of Medical Microbiology and Hygiene, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Mohamed Tarek Badr
- Institute of Medical Microbiology and Hygiene, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Georg Häcker
- Institute of Medical Microbiology and Hygiene, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signaling Studies, University of Freiburg, 79104 Freiburg, Germany
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3
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Jiang MZ, Liu C, Xu C, Jiang H, Wang Y, Liu SJ. Gut microbial interactions based on network construction and bacterial pairwise cultivation. SCIENCE CHINA. LIFE SCIENCES 2024; 67:1751-1762. [PMID: 38600293 DOI: 10.1007/s11427-023-2537-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 01/27/2024] [Indexed: 04/12/2024]
Abstract
Association networks are widely applied for the prediction of bacterial interactions in studies of human gut microbiomes. However, the experimental validation of the predicted interactions is challenging due to the complexity of gut microbiomes and the limited number of cultivated bacteria. In this study, we addressed this challenge by integrating in vitro time series network (TSN) associations and co-cultivation of TSN taxon pairs. Fecal samples were collected and used for cultivation and enrichment of gut microbiome on YCFA agar plates for 13 days. Enriched cells were harvested for DNA extraction and metagenomic sequencing. A total of 198 metagenome-assembled genomes (MAGs) were recovered. Temporal dynamics of bacteria growing on the YCFA agar were used to infer microbial association networks. To experimentally validate the interactions of taxon pairs in networks, we selected 24 and 19 bacterial strains from this study and from the previously established human gut microbial biobank, respectively, for pairwise co-cultures. The co-culture experiments revealed that most of the interactions between taxa in networks were identified as neutralism (51.67%), followed by commensalism (21.67%), amensalism (18.33%), competition (5%) and exploitation (3.33%). Genome-centric analysis further revealed that the commensal gut bacteria (helpers and beneficiaries) might interact with each other via the exchanges of amino acids with high biosynthetic costs, short-chain fatty acids, and/or vitamins. We also validated 12 beneficiaries by adding 16 additives into the basic YCFA medium and found that the growth of 66.7% of these strains was significantly promoted. This approach provides new insights into the gut microbiome complexity and microbial interactions in association networks. Our work highlights that the positive relationships in gut microbial communities tend to be overestimated, and that amino acids, short-chain fatty acids, and vitamins are contributed to the positive relationships.
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Affiliation(s)
- Min-Zhi Jiang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266000, China
| | - Chang Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266000, China
| | - Chang Xu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266000, China
| | - He Jiang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266000, China
| | - Yulin Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266000, China.
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266000, China.
- State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center (EMRC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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4
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Dong Y, Chen WH, Zhao XM. VirRep: a hybrid language representation learning framework for identifying viruses from human gut metagenomes. Genome Biol 2024; 25:177. [PMID: 38965579 PMCID: PMC11229495 DOI: 10.1186/s13059-024-03320-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 06/24/2024] [Indexed: 07/06/2024] Open
Abstract
Identifying viruses from metagenomes is a common step to explore the virus composition in the human gut. Here, we introduce VirRep, a hybrid language representation learning framework, for identifying viruses from human gut metagenomes. VirRep combines a context-aware encoder and an evolution-aware encoder to improve sequence representation by incorporating k-mer patterns and sequence homologies. Benchmarking on both simulated and real datasets with varying viral proportions demonstrates that VirRep outperforms state-of-the-art methods. When applied to fecal metagenomes from a colorectal cancer cohort, VirRep identifies 39 high-quality viral species associated with the disease, many of which cannot be detected by existing methods.
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Affiliation(s)
- Yanqi Dong
- Department of Neurology, Zhongshan Hospital and Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, 200433, China
| | - Wei-Hua Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular Imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China.
- Institution of Medical Artificial Intelligence, Binzhou Medical University, Yantai, 264003, China.
| | - Xing-Ming Zhao
- Department of Neurology, Zhongshan Hospital and Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, 200433, China.
- State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Fudan University, Shanghai, China.
- MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China.
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5
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Valdezate S, Medina-Pascual MJ, Villalón P, Garrido N, Monzón S, Cuesta I, Cobo F. Co-occurrence of the cephalosporinase cepA and carbapenemase cfiA genes in a Bacteroides fragilis division II strain, an unexpected finding. J Antimicrob Chemother 2024; 79:1683-1687. [PMID: 38814812 DOI: 10.1093/jac/dkae166] [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: 03/08/2024] [Accepted: 05/07/2024] [Indexed: 06/01/2024] Open
Abstract
BACKGROUND Bacteroides fragilis, an anaerobic gut bacterium and opportunistic pathogen, comprises two genetically divergent groups (or divisions) at the species level. Differences exist both in the core and accessory genomes and the beta-lactamase genes, with the cephalosporinase gene cepA represented only in division I and the carbapenemase gene cfiA only in division II. METHODS Multidrug resistance in a clinical B. fragilis strain was examined by whole-genome sequencing. RESULTS Strain CNM20200260 carried the antimicrobial resistance genes cepA, cfiA2, ant(6'), erm(F), mef(En2), est(T), tet(Q) and cat(A), along with 82-Phe mutation in gyrA (together with 47 amino acid changes in gyrA/B and parC/parE). bexA/B and other efflux pump genes were also observed. None of the detected insertion sequences was located upstream of cfiA2. The genome-based taxonomy coefficients (average nucleotide identity, DNA-DNA hybridization similarity and difference in genomic G + C%) with respect to genomes of the strains of B. fragilis division II and the novel species Bacteroides hominis (both cfiA-positive) met the criteria for CNM20200260 to belong to either species (>95%, >70% and <1%, respectively). No such similarity was seen with type strain NCTC 9343 or the representative genome FDAARGOS 1225 of B. fragilis (division I, cfiA-negative). Strain CNM20200260 harboured four out of nine Kyoto Encyclopedia of Genes and Genomes orthologues defined for division I and one of two defined for division II. CONCLUSIONS This is the first description of the co-occurrence of cepA and cfiA in a Bacteroides strain, confirming the complexity of the taxonomy of this species.
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Affiliation(s)
- S Valdezate
- Reference and Research Laboratory for Taxonomy, National Centre of Microbiology, Instituto de Salud Carlos III, Majadahonda, Carretera Pozuelo-Majadahonda km 2.2, 28220, Madrid, Spain
| | - M J Medina-Pascual
- Reference and Research Laboratory for Taxonomy, National Centre of Microbiology, Instituto de Salud Carlos III, Majadahonda, Carretera Pozuelo-Majadahonda km 2.2, 28220, Madrid, Spain
| | - P Villalón
- Reference and Research Laboratory for Taxonomy, National Centre of Microbiology, Instituto de Salud Carlos III, Majadahonda, Carretera Pozuelo-Majadahonda km 2.2, 28220, Madrid, Spain
| | - N Garrido
- Reference and Research Laboratory for Taxonomy, National Centre of Microbiology, Instituto de Salud Carlos III, Majadahonda, Carretera Pozuelo-Majadahonda km 2.2, 28220, Madrid, Spain
| | - S Monzón
- Bioinformatics Unit, Applied Services, Training and Research, Instituto de Salud Carlos III, Majadahonda, Carretera Pozuelo-Majadahonda km 2.2, 28220, Madrid, Spain
| | - I Cuesta
- Bioinformatics Unit, Applied Services, Training and Research, Instituto de Salud Carlos III, Majadahonda, Carretera Pozuelo-Majadahonda km 2.2, 28220, Madrid, Spain
| | - F Cobo
- Department of Microbiology and Instituto Biosanitario de Granada, University Hospital of Virgen de las Nieves, Avda. Fuerzas Armadas s/n, 18014 Granada, Spain
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He JH, Wang CY, Abdugheni R, Ni X, Liu C, Bi MX, Liu SJ. Acutalibacter caecimuris sp. nov., Acutalibacter intestini sp. nov. and Neglectibacter caecimuris sp. nov. , three novel species of the family Oscillospiraceae isolated from caecal contents of C57BL/6J mice. Int J Syst Evol Microbiol 2024; 74:006449. [PMID: 38995185 PMCID: PMC11316587 DOI: 10.1099/ijsem.0.006449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 06/27/2024] [Indexed: 07/13/2024] Open
Abstract
The intestines of mice are colonized by diverse, as-yet-uncultivated bacteria. In this report, we describe the isolation, culture, genotypic and phenotypic characterization, as well as taxonomic classification of three novel anaerobic bacterial strains derived from the caecal contents of C57BL/6J male mice. According to the phenotypic and genotype-based polyphasic taxonomy, we propose three novel species within the family Oscillospiraceae. They are Acutalibacter caecimuris sp. nov. (type strain M00118T=CGMCC 1.18042T=KCTC 25739T), Acutalibacter intestini sp. nov. (type strain M00204T=CGMCC 1.18044T=KCTC 25741T) and Neglectibacter caecimuris sp. nov. (type strain M00184T=CGMCC 1.18043T=KCTC 25740T).
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Affiliation(s)
- Jia-Hui He
- College of Veterinary Medicine, Shanxi Agricultural University (Shanxi Academy of Agricultural Sciences), Jinzhong 030801, PR China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Chang-Yu Wang
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, PR China
| | - Rashidin Abdugheni
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China
| | - Xue Ni
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Chang Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Ming-Xia Bi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
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7
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Yan Z, Hao T, Yan Y, Zhao Y, Wu Y, Tan Y, Bi Y, Cui Y, Yang R, Zhao Y. Quantitative and dynamic profiling of human gut core microbiota by real-time PCR. Appl Microbiol Biotechnol 2024; 108:396. [PMID: 38922447 PMCID: PMC11208268 DOI: 10.1007/s00253-024-13204-4] [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: 08/09/2023] [Revised: 05/05/2024] [Accepted: 05/27/2024] [Indexed: 06/27/2024]
Abstract
The human gut microbiota refers to a diverse community of microorganisms that symbiotically exist in the human intestinal system. Altered microbial communities have been linked to many human pathologies. However, there is a lack of rapid and efficient methods to assess gut microbiota signatures in practice. To address this, we established an appraisal system containing 45 quantitative real-time polymerase chain reaction (qPCR) assays targeting gut core microbes with high prevalence and/or abundance in the population. Through comparative genomic analysis, we selected novel species-specific genetic markers and primers for 31 of the 45 core microbes with no previously reported specific primers or whose primers needed improvement in specificity. We comprehensively evaluated the performance of the qPCR assays and demonstrated that they showed good sensitivity, selectivity, and quantitative linearity for each target. The limit of detection ranged from 0.1 to 1.0 pg/µL for the genomic DNA of these targets. We also demonstrated the high consistency (Pearson's r = 0.8688, P < 0.0001) between the qPCR method and metagenomics next-generation sequencing (mNGS) method in analyzing the abundance of selected bacteria in 22 human fecal samples. Moreover, we quantified the dynamic changes (over 8 weeks) of these core microbes in 14 individuals using qPCR, and considerable stability was demonstrated in most participants, albeit with significant individual differences. Overall, this study enables the simple and rapid quantification of 45 core microbes in the human gut, providing a promising tool to understand the role of gut core microbiota in human health and disease. KEY POINTS: • A panel of original qPCR assays was developed to quantify human gut core microbes. • The qPCR assays were evaluated and compared with mNGS using real fecal samples. • This method was used to dynamically profile the gut core microbiota in individuals.
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Affiliation(s)
- Ziheng Yan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Tongyu Hao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Yanfeng Yan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Yanting Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Yarong Wu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Yafang Tan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Yujing Bi
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Yujun Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.
- Beijing Key Laboratory of POCT for Bioemergency and Clinic, Beijing, 100071, China.
| | - Yong Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.
- Beijing Key Laboratory of POCT for Bioemergency and Clinic, Beijing, 100071, China.
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8
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Huang P, Dong Q, Wang Y, Tian Y, Wang S, Zhang C, Yu L, Tian F, Gao X, Guo H, Yi S, Li M, Liu Y, Zhang Q, Lu W, Wang G, Yang B, Cui S, Hua D, Wang X, Jiao Y, Liu L, Deng Q, Ma B, Wu T, Zou H, Shi J, Zhang H, Fan D, Sheng Y, Zhao J, Tang L, Zhang H, Sun W, Chen W, Kong X, Chen L, Zhai Q. Gut microbial genomes with paired isolates from China illustrate probiotic and cardiometabolic effects. CELL GENOMICS 2024; 4:100559. [PMID: 38740021 PMCID: PMC11228888 DOI: 10.1016/j.xgen.2024.100559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 02/04/2024] [Accepted: 04/15/2024] [Indexed: 05/16/2024]
Abstract
The gut microbiome displays genetic differences among populations, and characterization of the genomic landscape of the gut microbiome in China remains limited. Here, we present the Chinese Gut Microbial Reference (CGMR) set, comprising 101,060 high-quality metagenomic assembled genomes (MAGs) of 3,707 nonredundant species from 3,234 fecal samples across primarily rural Chinese locations, 1,376 live isolates mainly from lactic acid bacteria, and 987 novel species relative to worldwide databases. We observed region-specific coexisting MAGs and MAGs with probiotic and cardiometabolic functionalities. Preliminary mouse experiments suggest a probiotic effect of two Faecalibacillus intestinalis isolates in alleviating constipation, cardiometabolic influences of three Bacteroides fragilis_A isolates in obesity, and isolates from the genera Parabacteroides and Lactobacillus in host lipid metabolism. Our study expands the current microbial genomes with paired isolates and demonstrates potential host effects, contributing to the mechanistic understanding of host-microbe interactions.
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Affiliation(s)
- Pan Huang
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Quanbin Dong
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China; Department of Gastroenterology, Changzhou Medical Center, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Nanjing Medical University, Changzhou, China
| | - Yifeng Wang
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China; Cardiovascular Research Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Yunfan Tian
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China
| | - Shunhe Wang
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Chengcheng Zhang
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Leilei Yu
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Fengwei Tian
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Xiaoxiang Gao
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Hang Guo
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Shanrong Yi
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Mingyang Li
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Yang Liu
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Qingsong Zhang
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Wenwei Lu
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Gang Wang
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Bo Yang
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Shumao Cui
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Dongxu Hua
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China
| | - Xiuchao Wang
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China
| | - Yuwen Jiao
- Department of Gastroenterology, Changzhou Medical Center, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Nanjing Medical University, Changzhou, China
| | - Lu Liu
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China
| | - Qiufeng Deng
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China
| | - Beining Ma
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China
| | - Tingting Wu
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China
| | - Huayiyang Zou
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China
| | - Jing Shi
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China
| | - Haifeng Zhang
- Cardiovascular Research Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Daming Fan
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Yanhui Sheng
- Cardiovascular Research Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Liming Tang
- Department of Gastroenterology, Changzhou Medical Center, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Nanjing Medical University, Changzhou, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Wei Sun
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China
| | - Wei Chen
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Xiangqing Kong
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China; Cardiovascular Research Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China.
| | - Lianmin Chen
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China; Department of Gastroenterology, Changzhou Medical Center, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Nanjing Medical University, Changzhou, China.
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China.
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Xu MQ, Pan F, Peng LH, Yang YS. Advances in the isolation, cultivation, and identification of gut microbes. Mil Med Res 2024; 11:34. [PMID: 38831462 PMCID: PMC11145792 DOI: 10.1186/s40779-024-00534-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 04/17/2024] [Indexed: 06/05/2024] Open
Abstract
The gut microbiome is closely associated with human health and the development of diseases. Isolating, characterizing, and identifying gut microbes are crucial for research on the gut microbiome and essential for advancing our understanding and utilization of it. Although culture-independent approaches have been developed, a pure culture is required for in-depth analysis of disease mechanisms and the development of biotherapy strategies. Currently, microbiome research faces the challenge of expanding the existing database of culturable gut microbiota and rapidly isolating target microorganisms. This review examines the advancements in gut microbe isolation and cultivation techniques, such as culturomics, droplet microfluidics, phenotypic and genomics selection, and membrane diffusion. Furthermore, we evaluate the progress made in technology for identifying gut microbes considering both non-targeted and targeted strategies. The focus of future research in gut microbial culturomics is expected to be on high-throughput, automation, and integration. Advancements in this field may facilitate strain-level investigation into the mechanisms underlying diseases related to gut microbiota.
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Affiliation(s)
- Meng-Qi Xu
- Department of Gastroenterology and Hepatology, the First Medical Center of Chinese, PLA General Hospital, Beijing, 100853, China
- Medical School of Chinese PLA, Beijing, 100853, China
| | - Fei Pan
- Department of Gastroenterology and Hepatology, the First Medical Center of Chinese, PLA General Hospital, Beijing, 100853, China
| | - Li-Hua Peng
- Department of Gastroenterology and Hepatology, the First Medical Center of Chinese, PLA General Hospital, Beijing, 100853, China
| | - Yun-Sheng Yang
- Department of Gastroenterology and Hepatology, the First Medical Center of Chinese, PLA General Hospital, Beijing, 100853, China.
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10
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Heng YC, Kittelmann S. Proposal for reclassification of the species Hungatella xylanolytica as Lacrimispora xylanisolvens nom. nov. and transfer of the genus Hungatella to the family Lachnospiraceae. Int J Syst Evol Microbiol 2024; 74. [PMID: 38869948 DOI: 10.1099/ijsem.0.006417] [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] [Indexed: 06/14/2024] Open
Abstract
Hungatella xylanolytica X5-1T is an anaerobic, xylan-fermenting bacterium first isolated from methane-producing cattle manure. Initially identified as Bacteroides xylanolyticus, this species was later reclassified as H. xylanolytica in 2019. Although this reclassification found support through Genome blast Distance Phylogeny analysis which placed H. xylanolytica X5-1T into the same clade as Hungatella effluvii DSM 24995T, it was contradicted by 16S rRNA gene phylogenetic analysis, which associated it with a set of misnamed Clostridium species later reassigned into the genus Lacrimispora. To ascertain its taxonomic position, comparative analyses were performed to re-examine the relationship between H. xylanolytica X5-1T and all species of the genera Hungatella and Lacrimispora. The ranges of 16S rRNA gene sequence similarity, average amino acid identity, and percentage of conserved protein prediction values were higher between H. xylanolytica X5-1T and species of the genus Lacrimispora than Hungatella. In addition, H. xylanolytica X5-1T was found to harbour genes and pathways conserved and exclusive to species within the genus Lacrimispora but not Hungatella. Essentially, in both the 16S rRNA gene phylogenetic tree and the core-genome phylogenomic tree, H. xylanolytica X5-1T clustered into the same clade as species of the genus Lacrimispora, distinct from species of the genus Hungatella. It is thus clear that H. xylanolytica X5-1T represents a species within the genus Lacrimispora, which we propose to reclassify as Lacrimispora xylanisolvens nom. nov. Finally, based on the results from the phylogenetic and comparative analyses, the genus Hungatella was transferred to the family Lachnospiraceae.
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Affiliation(s)
- Yu Chyuan Heng
- Wilmar International Limited, WIL@NUS Corporate Laboratory, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore
| | - Sandra Kittelmann
- Wilmar International Limited, WIL@NUS Corporate Laboratory, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore
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11
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Guan Y, Zhu Z, Peng Q, Li M, Li X, Yang JW, Lu YH, Wang M, Xie BB. Genomic and Metagenomic Insights into the Distribution of Nicotine-degrading Enzymes in Human Microbiota. Curr Genomics 2024; 25:226-235. [PMID: 39086996 PMCID: PMC11288164 DOI: 10.2174/0113892029302230240319042208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/03/2024] [Accepted: 03/10/2024] [Indexed: 08/02/2024] Open
Abstract
Introduction Nicotine degradation is a new strategy to block nicotine-induced pathology. The potential of human microbiota to degrade nicotine has not been explored. Aims This study aimed to uncover the genomic potentials of human microbiota to degrade nicotine. Methods To address this issue, we performed a systematic annotation of Nicotine-Degrading Enzymes (NDEs) from genomes and metagenomes of human microbiota. A total of 26,295 genomes and 1,596 metagenomes for human microbiota were downloaded from public databases and five types of NDEs were annotated with a custom pipeline. We found 959 NdhB, 785 NdhL, 987 NicX, three NicA1, and three NicA2 homologs. Results Genomic classification revealed that six phylum-level taxa, including Proteobacteria, Firmicutes, Firmicutes_A, Bacteroidota, Actinobacteriota, and Chloroflexota, can produce NDEs, with Proteobacteria encoding all five types of NDEs studied. Analysis of NicX prevalence revealed differences among body sites. NicX homologs were found in gut and oral samples with a high prevalence but not found in lung samples. NicX was found in samples from both smokers and non-smokers, though the prevalence might be different. Conclusion This study represents the first systematic investigation of NDEs from the human microbiota, providing new insights into the physiology and ecological functions of human microbiota and shedding new light on the development of nicotine-degrading probiotics for the treatment of smoking-related diseases.
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Affiliation(s)
- Ying Guan
- Joint Institute of Tobacco and Health, Kunming, 650106, Yunnan, China
| | - Zhouhai Zhu
- Joint Institute of Tobacco and Health, Kunming, 650106, Yunnan, China
| | - Qiyuan Peng
- Joint Institute of Tobacco and Health, Kunming, 650106, Yunnan, China
| | - Meng Li
- Joint Institute of Tobacco and Health, Kunming, 650106, Yunnan, China
| | - Xuan Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Jia-Wei Yang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Yan-Hong Lu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Meng Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Bin-Bin Xie
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
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12
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Fu J, Hao Z. The causality between gut microbiota and non-Hodgkin lymphoma: a two-sample bidirectional Mendelian randomization study. Front Microbiol 2024; 15:1403825. [PMID: 38860220 PMCID: PMC11163074 DOI: 10.3389/fmicb.2024.1403825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 05/10/2024] [Indexed: 06/12/2024] Open
Abstract
Background Studies have indicated an association between gut microbiota (GM) and non-Hodgkin lymphoma (NHL). However, the causality between GM and NHL remains unclear. This study aims to investigate the causality between GM and NHL using Mendelian randomization (MR). Methods Data on GM is sourced from the MiBioGen consortium, while data on NHL and its subtypes is sourced from the FinnGen consortium R10 version. Inverse variance weighted (IVW) was employed for the primary MR analysis method, with methods such as Bayesian weighted Mendelian randomisation (BWMR) as an adjunct. Sensitivity analyses were conducted using Cochran's Q test, MR-Egger regression, MR-PRESSO, and the "Leave-one-out" method. Results The MR results showed that there is a causality between 27 GMs and NHL. Among them, 20 were negatively associated (OR < 1), and 7 were positively associated (OR > 1) with the corresponding diseases. All 27 MR results passed sensitivity tests, and there was no reverse causal association. Conclusion By demonstrating a causal link between GM and NHL, this research offers novel ideas to prevent, monitor, and cure NHL later.
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Affiliation(s)
- Jinjie Fu
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- College of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Zheng Hao
- College of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Tianjin Key Laboratory of Modern Chinese Medicine Theory of Innovation and Application, Tianjin, China
- Guo Aichun Institute of Medical History and Literature, Tianjin University of Traditional Chinese Medicine, Tianjin, China
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13
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Nie Q, Luo X, Wang K, Ding Y, Jia S, Zhao Q, Li M, Zhang J, Zhuo Y, Lin J, Guo C, Zhang Z, Liu H, Zeng G, You J, Sun L, Lu H, Ma M, Jia Y, Zheng MH, Pang Y, Qiao J, Jiang C. Gut symbionts alleviate MASH through a secondary bile acid biosynthetic pathway. Cell 2024; 187:2717-2734.e33. [PMID: 38653239 DOI: 10.1016/j.cell.2024.03.034] [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: 07/16/2023] [Revised: 02/05/2024] [Accepted: 03/23/2024] [Indexed: 04/25/2024]
Abstract
The gut microbiota has been found to play an important role in the progression of metabolic dysfunction-associated steatohepatitis (MASH), but the mechanisms have not been established. Here, by developing a click-chemistry-based enrichment strategy, we identified several microbial-derived bile acids, including the previously uncharacterized 3-succinylated cholic acid (3-sucCA), which is negatively correlated with liver damage in patients with liver-tissue-biopsy-proven metabolic dysfunction-associated fatty liver disease (MAFLD). By screening human bacterial isolates, we identified Bacteroides uniformis strains as effective producers of 3-sucCA both in vitro and in vivo. By activity-based protein purification and identification, we identified an enzyme annotated as β-lactamase in B. uniformis responsible for 3-sucCA biosynthesis. Furthermore, we found that 3-sucCA is a lumen-restricted metabolite and alleviates MASH by promoting the growth of Akkermansia muciniphila. Together, our data offer new insights into the gut microbiota-liver axis that may be leveraged to augment the management of MASH.
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Affiliation(s)
- Qixing Nie
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China; Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China; State Key Laboratory of Food Science and Resources, Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, Nanchang, China
| | - Xi Luo
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China; Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
| | - Kai Wang
- Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China; Department of Immunology, School of Basic Medical Sciences, NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China
| | - Yong Ding
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China; Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
| | - Shumi Jia
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences and Chemical Biology Center, Peking University, Beijing 100191, China
| | - Qixiang Zhao
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China; Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
| | - Meng Li
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China; Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
| | - Jinxin Zhang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China; Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
| | - Yingying Zhuo
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China; Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
| | - Jun Lin
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China; Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
| | - Chenghao Guo
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China; Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
| | - Zhiwei Zhang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China; Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
| | - Huiying Liu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China; Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
| | - Guangyi Zeng
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China; Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
| | - Jie You
- Department of Thyroid Surgery, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Lulu Sun
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China; Department of Endocrinology and Metabolism, Peking University Third Hospital, Beijing 100191, China
| | - Hua Lu
- Beijing National Laboratory for Molecular Sciences, Center for Soft Matter Science and Engineering, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People's Republic of China
| | - Ming Ma
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences and Chemical Biology Center, Peking University, Beijing 100191, China
| | - Yanxing Jia
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences and Chemical Biology Center, Peking University, Beijing 100191, China.
| | - Ming-Hua Zheng
- MAFLD Research Center, Department of Hepatology, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China; Key Laboratory of Diagnosis and Treatment for the Development of Chronic Liver Disease in Zhejiang Province, Wenzhou, China; Translational Medicine Laboratory, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325035, China.
| | - Yanli Pang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China; Institute of Advanced Clinical Medicine, Peking University, Beijing 100191, China; National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China.
| | - Jie Qiao
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China; Institute of Advanced Clinical Medicine, Peking University, Beijing 100191, China; National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China.
| | - Changtao Jiang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China; Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China; Department of Immunology, School of Basic Medical Sciences, NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China; Center of Basic Medical Research, Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China.
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14
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Láng L, McArthur S, Lazar AS, Pourtau L, Gaudout D, Pontifex MG, Müller M, Vauzour D. Dietary (Poly)phenols and the Gut-Brain Axis in Ageing. Nutrients 2024; 16:1500. [PMID: 38794738 PMCID: PMC11124177 DOI: 10.3390/nu16101500] [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: 04/03/2024] [Revised: 05/07/2024] [Accepted: 05/12/2024] [Indexed: 05/26/2024] Open
Abstract
As the population ages, the incidence of age-related neurodegenerative diseases is rapidly increasing, and novel approaches to mitigate this soaring prevalence are sorely needed. Recent studies have highlighted the importance of gut microbial homeostasis and its impact on brain functions, commonly referred to as the gut-brain axis, in maintaining overall health and wellbeing. Nonetheless, the mechanisms by which this system acts remains poorly defined. In this review, we will explore how (poly)phenols, a class of natural compounds found in many plant-based foods and beverages, can modulate the gut-brain axis, and thereby promote neural health. While evidence indicates a beneficial role of (poly)phenol consumption as part of a balanced diet, human studies are scarce and mechanistic insight is still lacking. In this regard, we make the case that dietary (poly)phenols should be further explored to establish their therapeutic efficacy on brain health through modulation of the gut-brain axis, with much greater emphasis on carefully designed human interventions.
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Affiliation(s)
- Léonie Láng
- Norwich Medical School, Biomedical Research Centre, University of East Anglia, Norwich NR4 7TJ, UK; (L.L.); (M.M.)
| | - Simon McArthur
- Faculty of Medicine & Dentistry, Queen Mary, University of London, Blizard Institute, London E1 2AT, UK;
| | - Alpar S. Lazar
- Faculty of Medicine and Health Sciences, The Queen’s Building, University of East Anglia, Norwich NR4 7TJ, UK; (A.S.L.); (M.G.P.)
| | - Line Pourtau
- Activ’Inside, 33750 Beychac et Caillau, France; (L.P.); (D.G.)
| | - David Gaudout
- Activ’Inside, 33750 Beychac et Caillau, France; (L.P.); (D.G.)
| | - Matthew G. Pontifex
- Faculty of Medicine and Health Sciences, The Queen’s Building, University of East Anglia, Norwich NR4 7TJ, UK; (A.S.L.); (M.G.P.)
| | - Michael Müller
- Norwich Medical School, Biomedical Research Centre, University of East Anglia, Norwich NR4 7TJ, UK; (L.L.); (M.M.)
| | - David Vauzour
- Norwich Medical School, Biomedical Research Centre, University of East Anglia, Norwich NR4 7TJ, UK; (L.L.); (M.M.)
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15
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Liu FL, Abdugheni R, Ran CG, Zhou N, Liu SJ. Eubacterium album sp. nov., a butyrate-producing bacterium isolated from faeces of a healthy human. Int J Syst Evol Microbiol 2024; 74. [PMID: 38739685 DOI: 10.1099/ijsem.0.006380] [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] [Indexed: 05/16/2024] Open
Abstract
An oval to rod-shaped, Gram-stain-positive, strictly anaerobic bacterium, designated LFL-14T, was isolated from the faeces of a healthy Chinese woman. Cells of the strain were non-spore-forming, grew optimally at 37 °C (growth range 30-45 °C) and pH 7.0 (growth range 6.0-9.0) under anaerobic conditions in the liquid modified Gifu anaerobic medium (mGAM). The result of 16S rRNA gene-based analysis indicated that LFL-14T shared an identity of 94.7 0% with Eubacterium ventriosum ATCC 27560T, indicating LFL-14T represented a novel taxon. The results of genome-based analysis revealed that the average nucleotide identity (ANI), the digital DNA-DNA hybridisation (dDDH) and average amino acid identity (AAI) between LFL-14T and its phylogenetically closest neighbour, Eubacterium ventriosum ATCC 27560T, were 77.0 %, 24.6 and 70.9 %, respectively, indicating that LFL-14T represents a novel species of the genus Eubacterium. The genome size of LFL-14T was 2.92 Mbp and the DNA G+C content was 33.14 mol%. We analysed the distribution of the genome of LFL-14T in cohorts of healthy individuals, type 2 diabetes patients (T2D) and patients with non-alcoholic fatty liver disease (NAFLD). We found that its abundance was higher in the T2D cohort, but it had a low average abundance of less than 0.2 % in all three cohorts. The percentages of frequency of occurrence in the T2D, healthy and NAFLD cohorts were 48.87 %, 16.72 % and 13.10 % respectively. The major cellular fatty acids of LFL-14T were C16 : 0 (34.4 %), C17 : 0 2-OH (21.4 %) and C14 : 0 (11.7 %). Additionally, the strain contained diphosphatidylglycerol (DPG) and phosphatidylethanolamine (PE), as well as unidentified phospholipids and unidentified glycolipids. The glucose fermentation products of LFL-14T were acetate and butyrate. In summary, On the basis of its chemotaxonomic, phenotypic, phylogenetic and phylogenomic properties, strain LFL-14T (= CGMCC 1.18005T = KCTC 25580T) is identified as representing a novel species of the genus Eubacterium, for which the name Eubacterium album sp. nov. is proposed.
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Affiliation(s)
- Feng-Lan Liu
- College of Life Sciences, Hebei University, Baoding, 071000, PR China
| | - Rashidin Abdugheni
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, PR China
| | - Cong-Guo Ran
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
- University of the Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Nan Zhou
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
- University of the Chinese Academy of Sciences, Beijing, 100049, PR China
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16
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Song HS, Kim YB, Kim JY, Roh SW, Whon TW. Advances in Culturomics Research on the Human Gut Microbiome: Optimizing Medium Composition and Culture Techniques for Enhanced Microbial Discovery. J Microbiol Biotechnol 2024; 34:757-764. [PMID: 38379289 DOI: 10.4014/jmb.2311.11024] [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: 11/17/2023] [Revised: 01/29/2024] [Accepted: 02/03/2024] [Indexed: 02/22/2024]
Abstract
Despite considerable advancements achieved using next-generation sequencing technologies in exploring microbial diversity, several species of the gut microbiome remain unknown. In this transformative era, culturomics has risen to prominence as a pivotal approach in unveiling realms of microbial diversity that were previously deemed inaccessible. Utilizing innovative strategies to optimize growth and culture medium composition, scientists have successfully cultured hard-to-cultivate microbes. This progress has fostered the discovery and understanding of elusive microbial entities, highlighting their essential role in human health and disease paradigms. In this review, we emphasize the importance of culturomics research on the gut microbiome and provide new theories and insights for expanding microbial diversity via the optimization of cultivation conditions.
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Affiliation(s)
- Hye Seon Song
- Division of Environmental Materials, Honam National Institute of Biological Resource (HNIBR), Mokpo 58762, Republic of Korea
| | - Yeon Bee Kim
- Kimchi Functionality Research Group, World Institute of Kimchi, Gwangju 61755, Republic of Korea
| | - Joon Yong Kim
- Microbiome Research Institute, LISCure Biosciences Inc., Gyeonggi-do 13486, Republic of Korea
| | - Seong Woon Roh
- Microbiome Research Institute, LISCure Biosciences Inc., Gyeonggi-do 13486, Republic of Korea
| | - Tae Woong Whon
- Kimchi Functionality Research Group, World Institute of Kimchi, Gwangju 61755, Republic of Korea
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17
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Qin X, Pu H, Fang X, Shang Q, Li J, Zhao Q, Wang X, Gu W. Microbial communities of Schisandra sphenanthera Rehd. et Wils. and the correlations between microbial community and the active secondary metabolites. PeerJ 2024; 12:e17240. [PMID: 38685939 PMCID: PMC11057425 DOI: 10.7717/peerj.17240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 03/25/2024] [Indexed: 05/02/2024] Open
Abstract
Background Schisandra sphenanthera Rehd. et Wils. is a plant used in traditional Chinese medicine (TCM). However, great differences exist in the content of active secondary metabolites in various parts of S. sphenanthera. Do microorganisms critically influence the accumulation of active components in different parts of S. sphenanthera? Methods In this study, 16S/ITS amplicon sequencing analysis was applied to unravel microbial communities in rhizospheric soil and different parts of wild S. sphenanthera. At the same time, the active secondary metabolites in different parts were detected, and the correlation between the secondary metabolites and microorganisms was analyzed. Results The major components identified in the essential oils were sesquiterpene and oxygenated sesquiterpenes. The contents of essential oil components in fruit were much higher than that in stem and leaf, and the dominant essential oil components were different in these parts. The dominant components of the three parts were γ-muurolene, δ-cadinol, and trans farnesol (stem); α-cadinol and neoisolongifolene-8-ol (leaf); isosapathulenol, α-santalol, cedrenol, and longiverbenone (fruit). The microbial amplicon sequences were taxonomically grouped into eight (bacteria) and seven (fungi) different phyla. Community diversity and composition analyses showed that different parts of S. sphenanthera had similar and unique microbial communities, and functional prediction analysis showed that the main functions of microorganisms were related to metabolism. Moreover, the accumulation of secondary metabolites in S. sphenanthera was closely related to the microbial community composition, especially bacteria. In endophytic bacteria, Staphylococcus and Hypomicrobium had negative effects on five secondary metabolites, among which γ-muurolene and trans farnesol were the dominant components in the stem. That is, the dominant components in stems were greatly affected by microorganisms. Our results provided a new opportunity to further understand the effects of microorganisms on the active secondary metabolites and provided a basis for further research on the sustainable utilization of S. sphenanthera.
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Affiliation(s)
- Xiaolu Qin
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi’an, Shaanxi, China
| | - Han Pu
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi’an, Shaanxi, China
| | - Xilin Fang
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi’an, Shaanxi, China
| | - Qianqian Shang
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi’an, Shaanxi, China
| | - Jianhua Li
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi’an, Shaanxi, China
| | - Qiaozhu Zhao
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi’an, Shaanxi, China
| | - Xiaorui Wang
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi’an, Shaanxi, China
| | - Wei Gu
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi’an, Shaanxi, China
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Kolzhetsov N, Markelova N, Frolova M, Alikina O, Glazunova O, Safonova L, Kalashnikova I, Yudin V, Makarov V, Keskinov A, Yudin S, Troshina D, Rechkina V, Shcherbakova V, Shavkunov K, Ozoline O. Enterotype-Dependent Probiotic-Mediated Changes in the Male Rat Intestinal Microbiome In Vivo and In Vitro. Int J Mol Sci 2024; 25:4558. [PMID: 38674145 PMCID: PMC11049970 DOI: 10.3390/ijms25084558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/08/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024] Open
Abstract
Beneficial properties of lactic acid bacteria have been known long ago, but particular interest in probiotics has arisen in the last two decades due to the understanding of the important role of intestinal microflora in human life. Thus, the ability of probiotics to support healthy homeostasis of gut microbiomes has received particular attention. Here, we evaluated the effect of a probiotic consisting of Bifidobacterium longum and Lacticaseibacillus paracasei on the gut microbiome of male rats, assessed their persistence in the fecal biota, and compared probiotic-mediated changes in vitro and in vivo. As expected, microbiomes of two enterotypes were identified in the feces of 21 animals, and it turned out that even a single dose of the probiotic altered the microbial composition. Upon repeated administration, the E1 biota temporarily acquired properties of the E2 type. Being highly sensitive to the intervention of probiotic bacteria at the phylum and genus levels, the fecal microbiomes retained the identity of their enterotypes when transferred to a medium optimized for gut bacteria. For the E2 biota, even similarities between probiotic-mediated reactions in vitro and in vivo were detected. Therefore, fecal-derived microbial communities are proposed as model consortia to optimize the response of resident bacteria to various agents.
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Affiliation(s)
- Nikolay Kolzhetsov
- Laboratory of Functional Genomics of Prokaryotes, Institute of Cell Biophysics of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Russia; (N.K.); (N.M.); (M.F.); (O.A.); (O.G.); (K.S.)
| | - Natalia Markelova
- Laboratory of Functional Genomics of Prokaryotes, Institute of Cell Biophysics of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Russia; (N.K.); (N.M.); (M.F.); (O.A.); (O.G.); (K.S.)
| | - Maria Frolova
- Laboratory of Functional Genomics of Prokaryotes, Institute of Cell Biophysics of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Russia; (N.K.); (N.M.); (M.F.); (O.A.); (O.G.); (K.S.)
| | - Olga Alikina
- Laboratory of Functional Genomics of Prokaryotes, Institute of Cell Biophysics of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Russia; (N.K.); (N.M.); (M.F.); (O.A.); (O.G.); (K.S.)
| | - Olga Glazunova
- Laboratory of Functional Genomics of Prokaryotes, Institute of Cell Biophysics of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Russia; (N.K.); (N.M.); (M.F.); (O.A.); (O.G.); (K.S.)
| | - Lubov Safonova
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical and Biological Agency, 119121 Moscow, Russia; (L.S.); (I.K.); (V.Y.); (V.M.); (A.K.); (S.Y.)
| | - Irina Kalashnikova
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical and Biological Agency, 119121 Moscow, Russia; (L.S.); (I.K.); (V.Y.); (V.M.); (A.K.); (S.Y.)
| | - Vladimir Yudin
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical and Biological Agency, 119121 Moscow, Russia; (L.S.); (I.K.); (V.Y.); (V.M.); (A.K.); (S.Y.)
| | - Valentin Makarov
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical and Biological Agency, 119121 Moscow, Russia; (L.S.); (I.K.); (V.Y.); (V.M.); (A.K.); (S.Y.)
| | - Anton Keskinov
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical and Biological Agency, 119121 Moscow, Russia; (L.S.); (I.K.); (V.Y.); (V.M.); (A.K.); (S.Y.)
| | - Sergey Yudin
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical and Biological Agency, 119121 Moscow, Russia; (L.S.); (I.K.); (V.Y.); (V.M.); (A.K.); (S.Y.)
| | - Daria Troshina
- Faculty of Biotechnology, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Viktoria Rechkina
- Laboratory of Anaerobic Microorganisms, Institute of Biochemistry and Physiology of Microorganisms of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Russia; (V.R.); (V.S.)
| | - Viktoria Shcherbakova
- Laboratory of Anaerobic Microorganisms, Institute of Biochemistry and Physiology of Microorganisms of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Russia; (V.R.); (V.S.)
| | - Konstantin Shavkunov
- Laboratory of Functional Genomics of Prokaryotes, Institute of Cell Biophysics of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Russia; (N.K.); (N.M.); (M.F.); (O.A.); (O.G.); (K.S.)
| | - Olga Ozoline
- Laboratory of Functional Genomics of Prokaryotes, Institute of Cell Biophysics of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Russia; (N.K.); (N.M.); (M.F.); (O.A.); (O.G.); (K.S.)
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Deryabin D, Lazebnik C, Vlasenko L, Karimov I, Kosyan D, Zatevalov A, Duskaev G. Broiler Chicken Cecal Microbiome and Poultry Farming Productivity: A Meta-Analysis. Microorganisms 2024; 12:747. [PMID: 38674691 PMCID: PMC11052200 DOI: 10.3390/microorganisms12040747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 03/31/2024] [Accepted: 04/03/2024] [Indexed: 04/28/2024] Open
Abstract
The cecal microbial community plays an important role in chicken growth and development via effective feed conversion and essential metabolite production. The aim of this study was to define the microbial community's variants in chickens' ceca and to explore the most significant association between the microbiome compositions and poultry farming productivity. The meta-analysis included original data from 8 control broiler chicken groups fed with a standard basic diet and 32 experimental groups supplemented with various feed additives. Standard Illumina 16S-RNA gene sequencing technology was used to characterize the chicken cecal microbiome. Zootechnical data sets integrated with the European Production Effectiveness Factor (EPEF) were collected. Analysis of the bacterial taxa abundance and co-occurrence in chicken cecal microbiomes revealed two alternative patterns: Bacteroidota-dominated with decreased alpha biodiversity; and Bacillota-enriched, which included the Actinomycetota, Cyanobacteriota and Thermodesulfobacteriota phyla members, with increased biodiversity indices. Bacillota-enriched microbiome groups showed elevated total feed intake (especially due to the starter feed intake) and final body weight, and high EPEF values, while Bacteroidota-dominated microbiomes were negatively associated with poultry farming productivity. The meta-analysis results lay the basis for the development of chicken growth-promoting feed supplementations, aimed at the stimulation of beneficial and inhibition of harmful bacterial patterns, where relevant metagenomic data can be a tool for their control and selection.
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Affiliation(s)
- Dmitry Deryabin
- Federal Research Centre of Biological Systems and Agrotechnologies of the Russian Academy of Sciences, January 9 Street, 29, 460000 Orenburg, Russia; (C.L.); (L.V.); (D.K.); (G.D.)
| | - Christina Lazebnik
- Federal Research Centre of Biological Systems and Agrotechnologies of the Russian Academy of Sciences, January 9 Street, 29, 460000 Orenburg, Russia; (C.L.); (L.V.); (D.K.); (G.D.)
| | - Ludmila Vlasenko
- Federal Research Centre of Biological Systems and Agrotechnologies of the Russian Academy of Sciences, January 9 Street, 29, 460000 Orenburg, Russia; (C.L.); (L.V.); (D.K.); (G.D.)
| | - Ilshat Karimov
- Orenburg State Medical University of the Ministry of Health of Russia, Sovetskaya Street, 6, 460014 Orenburg, Russia;
| | - Dianna Kosyan
- Federal Research Centre of Biological Systems and Agrotechnologies of the Russian Academy of Sciences, January 9 Street, 29, 460000 Orenburg, Russia; (C.L.); (L.V.); (D.K.); (G.D.)
| | - Alexander Zatevalov
- G.N. Gabrichevsky Research Institute for Epidemiology and Microbiology, Admiral Makarov Street, 10, 125212 Moscow, Russia;
| | - Galimzhan Duskaev
- Federal Research Centre of Biological Systems and Agrotechnologies of the Russian Academy of Sciences, January 9 Street, 29, 460000 Orenburg, Russia; (C.L.); (L.V.); (D.K.); (G.D.)
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20
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Yan Y, Zhao QH, Xu C, Wei RQ, Jiang H, Liu SJ. Anaerolentibacter hominis gen. nov. sp. nov., Diplocloster hominis sp. nov. and Pilosibacter fragilis gen. nov. sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2024; 74. [PMID: 38687183 DOI: 10.1099/ijsem.0.006359] [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] [Indexed: 05/02/2024] Open
Abstract
Three Gram-positive, obligately anaerobic bacterial strains, namely CSJ-1T, CSJ-3T, and CSJ-4T, were isolated from faeces of healthy persons. They were characterized through a combination of whole-genome sequencing, phenotypic traits, and metabolomic analysis. The genome sizes of CSJ-1T, CSJ-4T, and CSJ-3T were 3.3, 3.8, and 6.1 Mbp, with DNA G+C contents of 47.2, 48.3, and 48.8 mol%, respectively. Strain CSJ-3T was identified as representing a novel species, Diplocloster hominis (type strain CSJ-3T=CGMCC 1.18033T=JCM 36512T) of the genus Diplocloster. The 16S rRNA gene sequence similarity and whole genome average nucleotide identity (gANI) of CSJ-4T to its closest related species, Diplocloster modestus ASD 4241T, were 98.3 and 91.4 %, respectively. Comparative analysis of 16S rRNA gene sequences showed 91.6 % similarity between CSJ-1T and its closest phylogenetic neighbour, Catenibacillus scindens DSM 106146T, and 93.3 % similarity between CSJ-4T and its closest relative strain, Clostridium fessum SNUG30386T. Based on the polyphasic taxonomic results, we proposed two novel genera and three novel species. Strain CSJ-1T was identified as representing a novel species of novel genus, Anaerolentibacter hominis gen. nov. sp. nov. (type strain CSJ-1T=CGMCC 1.18046T=JCM 36511T) of the family Lachnospiraceae, and strain CSJ-4T was identified as representing a novel species of novel genus Pilosibacter fragilis gen. nov. sp. nov. (type strain CSJ-4T=CGMCC 1.18026T= JCM 36513T) of the family Clostridiaceae.
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Affiliation(s)
- Yang Yan
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Qing-Hua Zhao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Chang Xu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Rui-Qi Wei
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - He Jiang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
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21
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Jimonet P, Druart C, Blanquet-Diot S, Boucinha L, Kourula S, Le Vacon F, Maubant S, Rabot S, Van de Wiele T, Schuren F, Thomas V, Walther B, Zimmermann M. Gut Microbiome Integration in Drug Discovery and Development of Small Molecules. Drug Metab Dispos 2024; 52:274-287. [PMID: 38307852 DOI: 10.1124/dmd.123.001605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 02/04/2024] Open
Abstract
Human microbiomes, particularly in the gut, could have a major impact on the efficacy and toxicity of drugs. However, gut microbial metabolism is often neglected in the drug discovery and development process. Medicen, a Paris-based human health innovation cluster, has gathered more than 30 international leading experts from pharma, academia, biotech, clinical research organizations, and regulatory science to develop proposals to facilitate the integration of microbiome science into drug discovery and development. Seven subteams were formed to cover the complementary expertise areas of 1) pharma experience and case studies, 2) in silico microbiome-drug interaction, 3) in vitro microbial stability screening, 4) gut fermentation models, 5) animal models, 6) microbiome integration in clinical and regulatory aspects, and 7) microbiome ecosystems and models. Each expert team produced a state-of-the-art report of their respective field highlighting existing microbiome-related tools at every stage of drug discovery and development. The most critical limitations are the growing, but still limited, drug-microbiome interaction data to produce predictive models and the lack of agreed-upon standards despite recent progress. In this paper we will report on and share proposals covering 1) how microbiome tools can support moving a compound from drug discovery to clinical proof-of-concept studies and alert early on potential undesired properties stemming from microbiome-induced drug metabolism and 2) how microbiome data can be generated and integrated in pharmacokinetic models that are predictive of the human situation. Examples of drugs metabolized by the microbiome will be discussed in detail to support recommendations from the working group. SIGNIFICANCE STATEMENT: Gut microbial metabolism is often neglected in the drug discovery and development process despite growing evidence of drugs' efficacy and safety impacted by their interaction with the microbiome. This paper will detail existing microbiome-related tools covering every stage of drug discovery and development, current progress, and limitations, as well as recommendations to integrate them into the drug discovery and development process.
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Affiliation(s)
- Patrick Jimonet
- Medicen Paris Région, Paris, France (P.J.); Pharmabiotic Research Institute, Narbonne, France (C.D.); UMR 454 MEDIS, Université Clermont Auvergne, Clermont-Ferrand, France (S.B.D.); Global Bioinformatics, Evotec ID, Lyon, France (L.B.); Preclinical Sciences & Translational Safety, JNJ Innovative Medicine, Beerse, Belgium (S.K.); Biofortis, Saint-Herblain, France (F.L.V.); Translational Pharmacology Department, Oncodesign Services, Dijon, France (S.M.); Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France (S.R.); Center of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium (T.V.W.); TNO, Leiden, The Netherlands (F.S.); Lallemand Health Solutions, Blagnac, France (V.T.); Servier, Saclay, France (B.W.); and Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany (M.Z.)
| | - Céline Druart
- Medicen Paris Région, Paris, France (P.J.); Pharmabiotic Research Institute, Narbonne, France (C.D.); UMR 454 MEDIS, Université Clermont Auvergne, Clermont-Ferrand, France (S.B.D.); Global Bioinformatics, Evotec ID, Lyon, France (L.B.); Preclinical Sciences & Translational Safety, JNJ Innovative Medicine, Beerse, Belgium (S.K.); Biofortis, Saint-Herblain, France (F.L.V.); Translational Pharmacology Department, Oncodesign Services, Dijon, France (S.M.); Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France (S.R.); Center of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium (T.V.W.); TNO, Leiden, The Netherlands (F.S.); Lallemand Health Solutions, Blagnac, France (V.T.); Servier, Saclay, France (B.W.); and Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany (M.Z.)
| | - Stéphanie Blanquet-Diot
- Medicen Paris Région, Paris, France (P.J.); Pharmabiotic Research Institute, Narbonne, France (C.D.); UMR 454 MEDIS, Université Clermont Auvergne, Clermont-Ferrand, France (S.B.D.); Global Bioinformatics, Evotec ID, Lyon, France (L.B.); Preclinical Sciences & Translational Safety, JNJ Innovative Medicine, Beerse, Belgium (S.K.); Biofortis, Saint-Herblain, France (F.L.V.); Translational Pharmacology Department, Oncodesign Services, Dijon, France (S.M.); Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France (S.R.); Center of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium (T.V.W.); TNO, Leiden, The Netherlands (F.S.); Lallemand Health Solutions, Blagnac, France (V.T.); Servier, Saclay, France (B.W.); and Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany (M.Z.)
| | - Lilia Boucinha
- Medicen Paris Région, Paris, France (P.J.); Pharmabiotic Research Institute, Narbonne, France (C.D.); UMR 454 MEDIS, Université Clermont Auvergne, Clermont-Ferrand, France (S.B.D.); Global Bioinformatics, Evotec ID, Lyon, France (L.B.); Preclinical Sciences & Translational Safety, JNJ Innovative Medicine, Beerse, Belgium (S.K.); Biofortis, Saint-Herblain, France (F.L.V.); Translational Pharmacology Department, Oncodesign Services, Dijon, France (S.M.); Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France (S.R.); Center of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium (T.V.W.); TNO, Leiden, The Netherlands (F.S.); Lallemand Health Solutions, Blagnac, France (V.T.); Servier, Saclay, France (B.W.); and Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany (M.Z.)
| | - Stephanie Kourula
- Medicen Paris Région, Paris, France (P.J.); Pharmabiotic Research Institute, Narbonne, France (C.D.); UMR 454 MEDIS, Université Clermont Auvergne, Clermont-Ferrand, France (S.B.D.); Global Bioinformatics, Evotec ID, Lyon, France (L.B.); Preclinical Sciences & Translational Safety, JNJ Innovative Medicine, Beerse, Belgium (S.K.); Biofortis, Saint-Herblain, France (F.L.V.); Translational Pharmacology Department, Oncodesign Services, Dijon, France (S.M.); Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France (S.R.); Center of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium (T.V.W.); TNO, Leiden, The Netherlands (F.S.); Lallemand Health Solutions, Blagnac, France (V.T.); Servier, Saclay, France (B.W.); and Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany (M.Z.)
| | - Françoise Le Vacon
- Medicen Paris Région, Paris, France (P.J.); Pharmabiotic Research Institute, Narbonne, France (C.D.); UMR 454 MEDIS, Université Clermont Auvergne, Clermont-Ferrand, France (S.B.D.); Global Bioinformatics, Evotec ID, Lyon, France (L.B.); Preclinical Sciences & Translational Safety, JNJ Innovative Medicine, Beerse, Belgium (S.K.); Biofortis, Saint-Herblain, France (F.L.V.); Translational Pharmacology Department, Oncodesign Services, Dijon, France (S.M.); Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France (S.R.); Center of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium (T.V.W.); TNO, Leiden, The Netherlands (F.S.); Lallemand Health Solutions, Blagnac, France (V.T.); Servier, Saclay, France (B.W.); and Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany (M.Z.)
| | - Sylvie Maubant
- Medicen Paris Région, Paris, France (P.J.); Pharmabiotic Research Institute, Narbonne, France (C.D.); UMR 454 MEDIS, Université Clermont Auvergne, Clermont-Ferrand, France (S.B.D.); Global Bioinformatics, Evotec ID, Lyon, France (L.B.); Preclinical Sciences & Translational Safety, JNJ Innovative Medicine, Beerse, Belgium (S.K.); Biofortis, Saint-Herblain, France (F.L.V.); Translational Pharmacology Department, Oncodesign Services, Dijon, France (S.M.); Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France (S.R.); Center of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium (T.V.W.); TNO, Leiden, The Netherlands (F.S.); Lallemand Health Solutions, Blagnac, France (V.T.); Servier, Saclay, France (B.W.); and Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany (M.Z.)
| | - Sylvie Rabot
- Medicen Paris Région, Paris, France (P.J.); Pharmabiotic Research Institute, Narbonne, France (C.D.); UMR 454 MEDIS, Université Clermont Auvergne, Clermont-Ferrand, France (S.B.D.); Global Bioinformatics, Evotec ID, Lyon, France (L.B.); Preclinical Sciences & Translational Safety, JNJ Innovative Medicine, Beerse, Belgium (S.K.); Biofortis, Saint-Herblain, France (F.L.V.); Translational Pharmacology Department, Oncodesign Services, Dijon, France (S.M.); Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France (S.R.); Center of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium (T.V.W.); TNO, Leiden, The Netherlands (F.S.); Lallemand Health Solutions, Blagnac, France (V.T.); Servier, Saclay, France (B.W.); and Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany (M.Z.)
| | - Tom Van de Wiele
- Medicen Paris Région, Paris, France (P.J.); Pharmabiotic Research Institute, Narbonne, France (C.D.); UMR 454 MEDIS, Université Clermont Auvergne, Clermont-Ferrand, France (S.B.D.); Global Bioinformatics, Evotec ID, Lyon, France (L.B.); Preclinical Sciences & Translational Safety, JNJ Innovative Medicine, Beerse, Belgium (S.K.); Biofortis, Saint-Herblain, France (F.L.V.); Translational Pharmacology Department, Oncodesign Services, Dijon, France (S.M.); Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France (S.R.); Center of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium (T.V.W.); TNO, Leiden, The Netherlands (F.S.); Lallemand Health Solutions, Blagnac, France (V.T.); Servier, Saclay, France (B.W.); and Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany (M.Z.)
| | - Frank Schuren
- Medicen Paris Région, Paris, France (P.J.); Pharmabiotic Research Institute, Narbonne, France (C.D.); UMR 454 MEDIS, Université Clermont Auvergne, Clermont-Ferrand, France (S.B.D.); Global Bioinformatics, Evotec ID, Lyon, France (L.B.); Preclinical Sciences & Translational Safety, JNJ Innovative Medicine, Beerse, Belgium (S.K.); Biofortis, Saint-Herblain, France (F.L.V.); Translational Pharmacology Department, Oncodesign Services, Dijon, France (S.M.); Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France (S.R.); Center of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium (T.V.W.); TNO, Leiden, The Netherlands (F.S.); Lallemand Health Solutions, Blagnac, France (V.T.); Servier, Saclay, France (B.W.); and Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany (M.Z.)
| | - Vincent Thomas
- Medicen Paris Région, Paris, France (P.J.); Pharmabiotic Research Institute, Narbonne, France (C.D.); UMR 454 MEDIS, Université Clermont Auvergne, Clermont-Ferrand, France (S.B.D.); Global Bioinformatics, Evotec ID, Lyon, France (L.B.); Preclinical Sciences & Translational Safety, JNJ Innovative Medicine, Beerse, Belgium (S.K.); Biofortis, Saint-Herblain, France (F.L.V.); Translational Pharmacology Department, Oncodesign Services, Dijon, France (S.M.); Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France (S.R.); Center of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium (T.V.W.); TNO, Leiden, The Netherlands (F.S.); Lallemand Health Solutions, Blagnac, France (V.T.); Servier, Saclay, France (B.W.); and Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany (M.Z.)
| | - Bernard Walther
- Medicen Paris Région, Paris, France (P.J.); Pharmabiotic Research Institute, Narbonne, France (C.D.); UMR 454 MEDIS, Université Clermont Auvergne, Clermont-Ferrand, France (S.B.D.); Global Bioinformatics, Evotec ID, Lyon, France (L.B.); Preclinical Sciences & Translational Safety, JNJ Innovative Medicine, Beerse, Belgium (S.K.); Biofortis, Saint-Herblain, France (F.L.V.); Translational Pharmacology Department, Oncodesign Services, Dijon, France (S.M.); Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France (S.R.); Center of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium (T.V.W.); TNO, Leiden, The Netherlands (F.S.); Lallemand Health Solutions, Blagnac, France (V.T.); Servier, Saclay, France (B.W.); and Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany (M.Z.)
| | - Michael Zimmermann
- Medicen Paris Région, Paris, France (P.J.); Pharmabiotic Research Institute, Narbonne, France (C.D.); UMR 454 MEDIS, Université Clermont Auvergne, Clermont-Ferrand, France (S.B.D.); Global Bioinformatics, Evotec ID, Lyon, France (L.B.); Preclinical Sciences & Translational Safety, JNJ Innovative Medicine, Beerse, Belgium (S.K.); Biofortis, Saint-Herblain, France (F.L.V.); Translational Pharmacology Department, Oncodesign Services, Dijon, France (S.M.); Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France (S.R.); Center of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium (T.V.W.); TNO, Leiden, The Netherlands (F.S.); Lallemand Health Solutions, Blagnac, France (V.T.); Servier, Saclay, France (B.W.); and Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany (M.Z.)
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22
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Huang HJ, Zhang X, Sun XW, Chen B, Li XT, Zhou N, Abdugheni R, Cheng QY, Zhang TJ, Liu Y, Jiang Y, Deng Y, Liu SJ, Jiang CY. Xiashengella succiniciproducens gen. nov., sp. nov., a succinate-producing bacterium isolated from an anaerobic digestion tank in the family Marinilabiliaceae of the order Bacteroidales. Arch Microbiol 2024; 206:141. [PMID: 38441685 DOI: 10.1007/s00203-024-03909-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 01/26/2024] [Accepted: 02/24/2024] [Indexed: 03/07/2024]
Abstract
A strictly anaerobic, motile bacterium, designated as strain Ai-910T, was isolated from the sludge of an anaerobic digestion tank in China. Cells were Gram-stain-negative rods. Optimal growth was observed at 38 °C (growth range 25-42 °C), pH 8.5 (growth range 5.5-10.5), and under a NaCl concentration of 0.06% (w/v) (range 0-2.0%). Major cellular fatty acids were iso-C15 : 0 and anteiso-C15 : 0. The respiratory quinone was MK-7. Using xylose as the growth substrate, succinate was produced as the fermentation product. Phylogenetic analysis based on the 16 S rRNA gene sequences indicated that strain Ai-910T formed a distinct phylogenetic lineage that reflects a new genus in the family Marinilabiliaceae, sharing high similarities to Alkaliflexus imshenetskii Z-7010T (92.78%), Alkalitalea saponilacus SC/BZ-SP2T (92.51%), and Geofilum rubicundum JAM-BA0501T (92.36%). Genomic similarity (average nucleotide identity and digital DNA-DNA hybridization) values between strain Ai-910T and its phylogenetic neighbors were below 65.27 and 16.90%, respectively, indicating that strain Ai-910T represented a novel species. The average amino acid identity between strain Ai-910T and other related members of the family Marinilabiliaceae were below 69.41%, supporting that strain Ai-910T was a member of a new genus within the family Marinilabiliaceae. Phylogenetic, genomic, and phenotypic analysis revealed that strain Ai-910T was distinguished from other phylogenetic relatives within the family Marinilabiliaceae. The genome size was 3.10 Mbp, and the DNA G + C content of the isolate was 42.8 mol%. Collectively, differences of the phenotypic and phylogenetic features of strain Ai-910T from its close relatives suggest that strain Ai-910T represented a novel species in a new genus of the family Marinilabiliaceae, for which the name Xiashengella succiniciproducens gen. nov., sp. nov. was proposed. The type strain of Xiashengella succiniciproducens is Ai-910T (= CGMCC 1.17893T = KCTC 25,304T).
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Affiliation(s)
- Hao-Jie Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266000, China
| | - Xi Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xin-Wei Sun
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266000, China
| | - Biao Chen
- Xuzhou Medical University, Xuzhou, 221004, China
| | - Xiu-Tong Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Nan Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Rashidin Abdugheni
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiu-Yin Cheng
- Beijing Drainage Group Co., Ltd, Beijing, 100044, China
| | - Tie-Jun Zhang
- Beijing Drainage Group Co., Ltd, Beijing, 100044, China
| | - Yao Liu
- Beijing Drainage Group Co., Ltd, Beijing, 100044, China
| | - Yong Jiang
- Beijing Drainage Group Co., Ltd, Beijing, 100044, China
| | - Ye Deng
- IMCAS-RCEES Joint Lab at CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China.
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266000, China.
- IMCAS-RCEES Joint Lab at CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
| | - Cheng-Ying Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China.
- IMCAS-RCEES Joint Lab at CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
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23
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Xu C, Jiang H, Feng LJ, Jiang MZ, Wang YL, Liu SJ. Christensenella minuta interacts with multiple gut bacteria. Front Microbiol 2024; 15:1301073. [PMID: 38440147 PMCID: PMC10910051 DOI: 10.3389/fmicb.2024.1301073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 01/30/2024] [Indexed: 03/06/2024] Open
Abstract
Introduction Gut microbes form complex networks that significantly influence host health and disease treatment. Interventions with the probiotic bacteria on the gut microbiota have been demonstrated to improve host well-being. As a representative of next-generation probiotics, Christensenella minuta (C. minuta) plays a critical role in regulating energy balance and metabolic homeostasis in human bodies, showing potential in treating metabolic disorders and reducing inflammation. However, interactions of C. minuta with the members of the networked gut microbiota have rarely been explored. Methods In this study, we investigated the impact of C. minuta on fecal microbiota via metagenomic sequencing, focusing on retrieving bacterial strains and coculture assays of C. minuta with associated microbial partners. Results Our results showed that C. minuta intervention significantly reduced the diversity of fecal microorganisms, but specifically enhanced some groups of bacteria, such as Lactobacillaceae. C. minuta selectively enriched bacterial pathways that compensated for its metabolic defects on vitamin B1, B12, serine, and glutamate synthesis. Meanwhile, C. minuta cross-feeds Faecalibacterium prausnitzii and other bacteria via the production of arginine, branched-chain amino acids, fumaric acids and short-chain fatty acids (SCFAs), such as acetic. Both metagenomic data analysis and culture experiments revealed that C. minuta negatively correlated with Klebsiella pneumoniae and 14 other bacterial taxa, while positively correlated with F. prausnitzii. Our results advance our comprehension of C. minuta's in modulating the gut microbial network. Conclusions C. minuta disrupts the composition of the fecal microbiota. This disturbance is manifested through cross-feeding, nutritional competition, and supplementation of its own metabolic deficiencies, resulting in the specific enrichment or inhibition of the growth of certain bacteria. This study will shed light on the application of C. minuta as a probiotic for effective interventions on gut microbiomes and improvement of host health.
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Affiliation(s)
- Chang Xu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - He Jiang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Li-Juan Feng
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Min-Zhi Jiang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yu-Lin Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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24
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Liu C, Du MX, Xie LS, Wang WZ, Chen BS, Yun CY, Sun XW, Luo X, Jiang Y, Wang K, Jiang MZ, Qiao SS, Sun M, Cui BJ, Huang HJ, Qu SP, Li CK, Wu D, Wang LS, Jiang C, Liu HW, Liu SJ. Gut commensal Christensenella minuta modulates host metabolism via acylated secondary bile acids. Nat Microbiol 2024; 9:434-450. [PMID: 38233647 DOI: 10.1038/s41564-023-01570-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 11/29/2023] [Indexed: 01/19/2024]
Abstract
A strong correlation between gut microbes and host health has been observed in numerous gut metagenomic cohort studies. However, the underlying mechanisms governing host-microbe interactions in the gut remain largely unknown. Here we report that the gut commensal Christensenella minuta modulates host metabolism by generating a previously undescribed class of secondary bile acids with 3-O-acylation substitution that inhibit the intestinal farnesoid X receptor. Administration of C. minuta alleviated features of metabolic disease in high fat diet-induced obese mice associated with a significant increase in these acylated bile acids, which we refer to as 3-O-acyl-cholic acids. Specific knockout of intestinal farnesoid X receptor in mice counteracted the beneficial effects observed in their wild-type counterparts. Finally, we showed that 3-O-acyl-CAs were prevalent in healthy humans but significantly depleted in patients with type 2 diabetes. Our findings indicate a role for C. minuta and acylated bile acids in metabolic diseases.
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Affiliation(s)
- Chang Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
| | - Meng-Xuan Du
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China
| | - Li-Sheng Xie
- College of Life Science, Hebei University, Baoding, P. R. China
| | - Wen-Zhao Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
| | - Bao-Song Chen
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
| | - Chu-Yu Yun
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, P. R. China
| | - Xin-Wei Sun
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China
| | - Xi Luo
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, P. R. China
| | - Yu Jiang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China
| | - Kai Wang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, P. R. China
| | - Min-Zhi Jiang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China
| | - Shan-Shan Qiao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
| | - Min Sun
- The Second Hospital of Shandong University, Jinan, P. R. China
| | - Bao-Juan Cui
- The Second Hospital of Shandong University, Jinan, P. R. China
| | - Hao-Jie Huang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China
| | | | | | - Dalei Wu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China
| | - Lu-Shan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China
| | - Changtao Jiang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, P. R. China.
- Center of Basic Medical Research, Institute of Medical Innovation and Research, Third Hospital, Peking University, Beijing, P. R. China.
| | - Hong-Wei Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China.
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China.
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China.
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25
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Hu T, Chen J, Lin X, He W, Liang H, Wang M, Li W, Wu Z, Han M, Jin X, Kristiansen K, Xiao L, Zou Y. Comparison of the DNBSEQ platform and Illumina HiSeq 2000 for bacterial genome assembly. Sci Rep 2024; 14:1292. [PMID: 38221534 PMCID: PMC10788345 DOI: 10.1038/s41598-024-51725-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 01/09/2024] [Indexed: 01/16/2024] Open
Abstract
The Illumina HiSeq platform has been a commonly used option for bacterial genome sequencing. Now the BGI DNA nanoball (DNB) nanoarrays platform may provide an alternative platform for sequencing of bacterial genomes. To explore the impact of sequencing platforms on bacterial genome assembly, quality assessment, sequence alignment, functional annotation, mutation detection, and metagenome mapping, we compared genome assemblies based on sequencing of cultured bacterial species using the HiSeq 2000 and BGISEQ-500 platforms. In addition, simulated reads were used to evaluate the impact of insert size on genome assembly. Genome assemblies based on BGISEQ-500 sequencing exhibited higher completeness and fewer N bases in high GC genomes, whereas HiSeq 2000 assemblies exhibited higher N50. The majority of assembly assessment parameters, sequences of 16S rRNA genes and genomes, numbers of single nucleotide variants (SNV), and mapping to metagenome data did not differ significantly between platforms. More insertions were detected in HiSeq 2000 genome assemblies, whereas more deletions were detected in BGISEQ-500 genome assemblies. Insert size had no significant impact on genome assembly. Taken together, our results suggest that DNBSEQ platforms would be a valid substitute for HiSeq 2000 for bacterial genome sequencing.
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Affiliation(s)
- Tongyuan Hu
- BGI Research, Shenzhen, 518083, China
- BGI Research, Wuhan, 430074, China
| | | | - Xiaoqian Lin
- BGI Research, Shenzhen, 518083, China
- School of Bioscience and Biotechnology, South China University of Technology, Guangzhou, 510006, China
| | - Wenxin He
- BGI Research, Shenzhen, 518083, China
| | - Hewei Liang
- BGI Research, Shenzhen, 518083, China
- BGI Research, Wuhan, 430074, China
| | | | - Wenxi Li
- BGI Research, Shenzhen, 518083, China
- School of Bioscience and Biotechnology, South China University of Technology, Guangzhou, 510006, China
| | - Zhinan Wu
- BGI Research, Shenzhen, 518083, China
| | - Mo Han
- BGI Research, Shenzhen, 518083, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken 13, 2100, Copenhagen, Denmark
| | - Xin Jin
- BGI Research, Shenzhen, 518083, China
| | - Karsten Kristiansen
- BGI Research, Shenzhen, 518083, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken 13, 2100, Copenhagen, Denmark
| | - Liang Xiao
- BGI Research, Shenzhen, 518083, China
- Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI Research, Shenzhen, 518083, China
| | - Yuanqiang Zou
- BGI Research, Shenzhen, 518083, China.
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken 13, 2100, Copenhagen, Denmark.
- Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI Research, Shenzhen, 518083, China.
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26
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Zaplana T, Miele S, Tolonen AC. Lachnospiraceae are emerging industrial biocatalysts and biotherapeutics. Front Bioeng Biotechnol 2024; 11:1324396. [PMID: 38239921 PMCID: PMC10794557 DOI: 10.3389/fbioe.2023.1324396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 12/05/2023] [Indexed: 01/22/2024] Open
Abstract
The Lachnospiraceae is a family of anaerobic bacteria in the class Clostridia with potential to advance the bio-economy and intestinal therapeutics. Some species of Lachnospiraceae metabolize abundant, low-cost feedstocks such as lignocellulose and carbon dioxide into value-added chemicals. Others are among the dominant species of the human colon and animal rumen, where they ferment dietary fiber to promote healthy gut and immune function. Here, we summarize recent studies of the physiology, cultivation, and genetics of Lachnospiraceae, highlighting their wide substrate utilization and metabolic products with industrial applications. We examine studies of these bacteria as Live Biotherapeutic Products (LBPs), focusing on in vivo disease models and clinical studies using them to treat infection, inflammation, metabolic syndrome, and cancer. We discuss key research areas including elucidation of intra-specific diversity and genetic modification of candidate strains that will facilitate the exploitation of Lachnospiraceae in industry and medicine.
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Affiliation(s)
| | | | - Andrew C. Tolonen
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, University of Evry, Université Paris-Saclay, Evry, France
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27
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Sun XW, Huang HJ, Wang XM, Wei RQ, Niu HY, Chen HY, Luo M, Abdugheni R, Wang YL, Liu FL, Jiang H, Liu C, Liu SJ. Christensenella strain resources, genomic/metabolomic profiling, and association with host at species level. Gut Microbes 2024; 16:2347725. [PMID: 38722028 PMCID: PMC11085954 DOI: 10.1080/19490976.2024.2347725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 04/22/2024] [Indexed: 05/12/2024] Open
Abstract
The gut commensal bacteria Christensenellaceae species are negatively associated with many metabolic diseases, and have been seen as promising next-generation probiotics. However, the cultured Christensenellaceae strain resources were limited, and their beneficial mechanisms for improving metabolic diseases have yet to be explored. In this study, we developed a method that enabled the enrichment and cultivation of Christensenellaceae strains from fecal samples. Using this method, a collection of Christensenellaceae Gut Microbial Biobank (ChrisGMB) was established, composed of 87 strains and genomes that represent 14 species of 8 genera. Seven species were first described and the cultured Christensenellaceae resources have been significantly expanded at species and strain levels. Christensenella strains exerted different abilities in utilization of various complex polysaccharides and other carbon sources, exhibited host-adaptation capabilities such as acid tolerance and bile tolerance, produced a wide range of volatile probiotic metabolites and secondary bile acids. Cohort analyses demonstrated that Christensenellaceae and Christensenella were prevalent in various cohorts and the abundances were significantly reduced in T2D and OB cohorts. At species level, Christensenellaceae showed different changes among healthy and disease cohorts. C. faecalis, F. tenuis, L. tenuis, and Guo. tenuis significantly reduced in all the metabolic disease cohorts. The relative abundances of C. minuta, C. hongkongensis and C. massiliensis showed no significant change in NAFLD and ACVD. and C. tenuis and C. acetigenes showed no significant change in ACVD, and Q. tenuis and Geh. tenuis showed no significant change in NAFLD, when compared with the HC cohort. So far as we know, this is the largest collection of cultured resource and first exploration of Christensenellaceae prevalences and abundances at species level.
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Affiliation(s)
- Xin-Wei Sun
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China
| | - Hao-Jie Huang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China
| | - Xiao-Meng Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China
| | - Rui-Qi Wei
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China
| | - Han-Yu Niu
- College of Veterinary Medicine, Shanxi Agr icultural University, Taigu, China
| | - Hao-Yu Chen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China
| | - Man Luo
- College of Veterinary Medicine, Shanxi Agr icultural University, Taigu, China
| | - Rashidin Abdugheni
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürűmqi, P. R. China
| | - Yu-Lin Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China
| | - Feng-Lan Liu
- College of Life Sciences, Hebei University, Baoding, P. R. China
| | - He Jiang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China
| | - Chang Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
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28
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Yadav A, Ahlawat S, Sharma KK. Culturing the unculturables: strategies, challenges, and opportunities for gut microbiome study. J Appl Microbiol 2023; 134:lxad280. [PMID: 38006234 DOI: 10.1093/jambio/lxad280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 10/17/2023] [Accepted: 11/23/2023] [Indexed: 11/26/2023]
Abstract
Metagenome sequencing techniques revolutionized the field of gut microbiome study. However, it is equipped with experimental and computational biases, which affect the downstream analysis results. Also, live microbial strains are needed for a better understanding of host-microbial crosstalks and for designing next-generation treatment therapies based on probiotic strains and postbiotic molecules. Conventional culturing methodologies are insufficient to get the dark gut matter on the plate; therefore, there is an urgent need to propose novel culturing methods that can fill the limitations of metagenomics. The current work aims to provide a consolidated evaluation of the available methods for host-microbe interaction with an emphasis on in vitro culturing of gut microbes using organoids, gut on a chip, and gut bioreactor. Further, the knowledge of microbial crosstalk in the gut helps us to identify core microbiota, and key metabolites that will aid in designing culturing media and co-culturing systems for gut microbiome study. After the deeper mining of the current culturing methods, we recommend that 3D-printed intestinal cells in a multistage continuous flow reactor equipped with an extended organoid system might be a good practical choice for gut microbiota-based studies.
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Affiliation(s)
- Asha Yadav
- Laboratory of Enzymology and Gut Microbiology, Department of Microbiology, Maharshi Dayanand University, Rohtak 124001, Haryana, India
| | - Shruti Ahlawat
- Department of Microbiology, Faculty of Allied Health Sciences, SGT University, Gurugram 122505, Haryana, India
| | - Krishna K Sharma
- Laboratory of Enzymology and Gut Microbiology, Department of Microbiology, Maharshi Dayanand University, Rohtak 124001, Haryana, India
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Munson E, Carella A, Carroll KC. Valid and accepted novel bacterial taxa derived from human clinical specimens and taxonomic revisions published in 2022. J Clin Microbiol 2023; 61:e0083823. [PMID: 37889007 PMCID: PMC10662342 DOI: 10.1128/jcm.00838-23] [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] [Indexed: 10/28/2023] Open
Abstract
Although some nomenclature changes have caused consternation among clinical microbiologists, the discovery of novel taxa and improving classification of existing groups of organisms is exciting and adds to our understanding of microbial pathogenesis. In this mini-review, we present an in-depth summary of novel taxonomic designations and revisions to prokaryotic taxonomy that were published in 2022. Henceforth, these bacteriology taxonomic summaries will appear annually. Several of the novel Gram-positive organisms have been associated with disease, namely, the Corynebacterium kroppenstedtii-like organisms Corynebacterium parakroppenstedtii sp. nov. and Corynebacterium pseudokroppenstedtii sp. nov. A newly described Streptococcus species, Streptococcus toyakuensis sp. nov., is noteworthy for exhibiting multi-drug resistance. Among the novel Gram-negative pathogens, Vibrio paracholerae sp. nov. stands out as an organism associated with diarrhea and sepsis and has probably been co-circulating with pandemic Vibrio cholerae for decades. Many new anaerobic organisms have been described in this past year largely from genetic assessments of gastrointestinal microbiome collections. With respect to revised taxa, as discussed in previous reviews, the genus Bacillus continues to undergo further division into additional genera and reassignment of existing species into them. Reassignment of two subspecies of Fusobacterium nucleatum to species designations (Fusobacterium animalis sp. nov. and Fusobacterium vincentii sp. nov.) is also noteworthy. As was typical of previous reviews, literature updates for selected clinically relevant organisms discovered between 2017 and 2021 have been included.
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Affiliation(s)
- Erik Munson
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
| | - Arianna Carella
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
| | - Karen C. Carroll
- Division of Medical Microbiology, Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Byun JH, Cho HW, Lee H, Lee WK, Yong D. Parabacteroides leei sp. nov., isolated from human blood. Int J Syst Evol Microbiol 2023; 73. [PMID: 37999940 DOI: 10.1099/ijsem.0.006187] [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] [Indexed: 11/25/2023] Open
Abstract
An obligate anaerobic, Gram-negative, rod-shaped and non-spore-forming bacterium, designated as strain GYB001T, was isolated from the blood of a patient with a sigmoid colon perforation. Taxonomic characterization of the novel isolate was performed using a polyphasic approach. A phylogenetic analysis based on 16S rRNA gene and whole genome sequences revealed that GYB001T represented a member of the genus Parabacteroides, in the family Tannerellaceae. The closest species, based on 16S rRNA sequence, was Parabacteroides gordonii DSM 23371T with 97.4 % similarity. Average nucleotide identity and digital DNA-DNA hybridization values between strain GYB001T and P. gordonii DSM 23371T were 86.7 and 28.7% and between GYB001T and Parabacteroides faecis JCM 18682T were 86.6 and 27.7 %, respectively. The genome was 6.57 Mbp long with 43.3 mol% G+C content. Colonies on Brucella blood agar (BBA) were circular, convex, smooth, grey and small in size. Growth was observed on trypticase soy agar (TSA), TSA +5 % sheep blood and Euglena gracilis agar. Growth occurred at 18-42 °C on BBA in the presence of 0-3 % NaCl (w/v) and at pH 6.0-8.5. The major polar lipids were phosphatidylethanolamine and phospholipids. The major fatty acids in strain GYB001T were anteiso-C15 : 0 and iso-C17 : 0 3-OH, and the predominant respiratory quinones were menaquinone-10 (MK-10) and MK-9. The cell wall contained meso-diaminopimelic acid. Considering these phenotypic features and comparative genome analyses, we propose strain GYB001T as the type strain of Parabacteroides leei sp. nov. (=KCTC 25738T=KBN12P06525T=LMG 32797T).
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Affiliation(s)
- Jung-Hyun Byun
- Department of Laboratory Medicine, Gyeongsang National University College of Medicine, Gyeongsang National University Hospital, Jinju, Republic of Korea
| | - Hae Weon Cho
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department of Laboratory Medicine, Myongji Hospital, Goyang, Republic of Korea
| | - Hyukmin Lee
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Woo-Kon Lee
- Department of Microbiology, Gyeongsang National University College of Medicine, Jinju, Republic of Korea
| | - Dongeun Yong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Republic of Korea
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Li L, Yan S, Liu S, Wang P, Li W, Yi Y, Qin S. In-depth insight into correlations between gut microbiota and dietary fiber elucidates a dietary causal relationship with host health. Food Res Int 2023; 172:113133. [PMID: 37689844 DOI: 10.1016/j.foodres.2023.113133] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/09/2023] [Accepted: 06/10/2023] [Indexed: 09/11/2023]
Abstract
Dietary fiber exerts a wide range of biological benefits on host health, which not only provides a powerful source of nutrition for gut microbiota but also supplies key microbial metabolites that directly affect host health. This review mainly focuses on the decomposition and metabolism of dietary fiber and the essential genera Bacteroides and Bifidobacterium in dietary fiber fermentation. Dietary fiber plays an essential role in host health by impacting outcomes related to obesity, enteritis, immune health, cancer and neurodegenerative diseases. Additionally, the gut microbiota-independent pathway of dietary fiber affecting host health is also discussed. Personalized dietary fiber intake combined with microbiome, genetics, epigenetics, lifestyle and other factors has been highlighted for development in the future. A higher level of evidence is needed to demonstrate which microbial phenotype benefits from which kind of dietary fiber. In-depth insights into the correlation between gut microbiota and dietary fiber provide strong theoretical support for the precise application of dietary fiber, which elucidates a dietary causal relationship with host health.
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Affiliation(s)
- Lili Li
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China.
| | - Shuling Yan
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuangjiang Liu
- Shandong University, Qingdao 266237, China; Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Ping Wang
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China; Shandong University of Traditional Chinese Medicine, Jinan 250355, China.
| | - Wenjun Li
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China.
| | - Yuetao Yi
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China.
| | - Song Qin
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China.
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Magdy Wasfy R, Mbaye B, Borentain P, Tidjani Alou M, Murillo Ruiz ML, Caputo A, Andrieu C, Armstrong N, Million M, Gerolami R. Ethanol-Producing Enterocloster bolteae Is Enriched in Chronic Hepatitis B-Associated Gut Dysbiosis: A Case-Control Culturomics Study. Microorganisms 2023; 11:2437. [PMID: 37894093 PMCID: PMC10608849 DOI: 10.3390/microorganisms11102437] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 09/25/2023] [Accepted: 09/26/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND Hepatitis B virus (HBV) infection is a global health epidemic that causes fatal complications, leading to liver cirrhosis and hepatocellular carcinoma. The link between HBV-related dysbiosis and specific bacterial taxa is still under investigation. Enterocloster is emerging as a new genus (formerly Clostridium), including Enterocloster bolteae, a gut pathogen previously associated with dysbiosis and human diseases such as autism, multiple sclerosis, and inflammatory bowel diseases. Its role in liver diseases, especially HBV infection, is not reported. METHODS The fecal samples of eight patients with chronic HBV infection and ten healthy individuals were analyzed using the high-throughput culturomics approach and compared to 16S rRNA sequencing. Quantification of ethanol, known for its damaging effect on the liver, produced from bacterial strains enriched in chronic HBV was carried out by gas chromatography-mass spectrometry. RESULTS Using culturomics, 29,120 isolated colonies were analyzed by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry (MALDI-TOF); 340 species were identified (240 species in chronic HBV samples, 254 species in control samples) belonging to 169 genera and 6 phyla. In the chronic HBV group, 65 species were already known in the literature; 48 were associated with humans but had not been previously found in the gut, and 17 had never been associated with humans previously. Six species were newly isolated in our study. By comparing bacterial species frequency, three bacterial genera were serendipitously found with significantly enriched bacterial diversity in patients with chronic HBV: Enterocloster, Clostridium, and Streptococcus (p = 0.0016, p = 0.041, p = 0.053, respectively). However, metagenomics could not identify this enrichment, possibly concerning its insufficient taxonomical resolution (equivocal assignment of operational taxonomic units). At the species level, the significantly enriched species in the chronic HBV group almost all belonged to class Clostridia, such as Clostridium perfringens, Clostridium sporogenes, Enterocloster aldenensis, Enterocloster bolteae, Enterocloster clostridioformis, and Clostridium innocuum. Two E. bolteae strains, isolated from two patients with chronic HBV infection, showed high ethanol production (27 and 200 mM). CONCLUSIONS Culturomics allowed us to identify Enterocloster species, specifically, E. bolteae, enriched in the gut microbiota of patients with chronic HBV. These species had never been isolated in chronic HBV infection before. Moreover, ethanol production by E. bolteae strains isolated from the chronic HBV group could contribute to liver disease progression. Additionally, culturomics might be critical for better elucidating the relationship between dysbiosis and chronic HBV infection in the future.
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Affiliation(s)
- Reham Magdy Wasfy
- IHU Méditerranée Infection, 13005 Marseille, France (M.T.A.); (C.A.)
- MEPHI, IRD, Aix-Marseille Université, 13005 Marseille, France
| | - Babacar Mbaye
- IHU Méditerranée Infection, 13005 Marseille, France (M.T.A.); (C.A.)
- MEPHI, IRD, Aix-Marseille Université, 13005 Marseille, France
| | - Patrick Borentain
- Unité Hépatologie, Hôpital de la Timone, APHM, 13005 Marseille, France;
- Assistance Publique-Hôpitaux de Marseille (APHM), 13005 Marseille, France
| | - Maryam Tidjani Alou
- IHU Méditerranée Infection, 13005 Marseille, France (M.T.A.); (C.A.)
- MEPHI, IRD, Aix-Marseille Université, 13005 Marseille, France
| | - Maria Leticia Murillo Ruiz
- IHU Méditerranée Infection, 13005 Marseille, France (M.T.A.); (C.A.)
- MEPHI, IRD, Aix-Marseille Université, 13005 Marseille, France
| | - Aurelia Caputo
- IHU Méditerranée Infection, 13005 Marseille, France (M.T.A.); (C.A.)
- Assistance Publique-Hôpitaux de Marseille (APHM), 13005 Marseille, France
| | - Claudia Andrieu
- IHU Méditerranée Infection, 13005 Marseille, France (M.T.A.); (C.A.)
- Assistance Publique-Hôpitaux de Marseille (APHM), 13005 Marseille, France
| | - Nicholas Armstrong
- IHU Méditerranée Infection, 13005 Marseille, France (M.T.A.); (C.A.)
- Assistance Publique-Hôpitaux de Marseille (APHM), 13005 Marseille, France
| | - Matthieu Million
- IHU Méditerranée Infection, 13005 Marseille, France (M.T.A.); (C.A.)
- MEPHI, IRD, Aix-Marseille Université, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (APHM), 13005 Marseille, France
| | - Rene Gerolami
- IHU Méditerranée Infection, 13005 Marseille, France (M.T.A.); (C.A.)
- MEPHI, IRD, Aix-Marseille Université, 13005 Marseille, France
- Unité Hépatologie, Hôpital de la Timone, APHM, 13005 Marseille, France;
- Assistance Publique-Hôpitaux de Marseille (APHM), 13005 Marseille, France
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Huang Y, Abdugheni R, Ma J, Wang R, Gao L, Liu Y, Li W, Cai M, Li L. Halomonas flagellata sp. nov., a halophilic bacterium isolated from saline soil in Xinjiang. Arch Microbiol 2023; 205:340. [PMID: 37750964 DOI: 10.1007/s00203-023-03670-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 09/27/2023]
Abstract
A Gram-stain-negative, strictly aerobic, motile, slightly curved rod-shaped bacterium with multiple flagella, designated strain EGI 63088T, was isolated from a bulk soil of Kalidium foliatum, collected from Wujiaqu in Xinjiang Uighur Autonomous Region, PR China. The optimal growth temperature, salinity, and pH for strain EGI 63088T growth were 30 °C, 3% (w/v) NaCl and 8, respectively. Phylogenetic analysis using 16S rRNA gene sequences indicated that strain EGI 63088T showed the highest sequence similarities to Halomonas heilongjiangensis 9-2T (97.94%), H. lysinitropha 3(2)T (97.51%), and H. daqiaonensis CGMCC 1.9150T (97.08%). The average nucleotide identity and digital DNA-DNA hybridization values between the strain EGI 63088T and H. heilongjiangensis 9-2T were 89.03 and 41.10%, respectively. The DNA G + C content of the genome for strain EGI 63088T was 66.3 mol%. The most prevalent antibiotic resistance and virulence-related genes in Halomonas genomes were Streptomyces cinnamoneu EF-Tu mutant, pilT, and cheY, respectively. The predominant fatty acids of strain EGI 63088T were summed feature 8 (C18: 1 ω6c and/or C18: 1 ω7c), summed feature 3 (C16: 1 ω6c and/or C16: 1 ω7c), and C16: 0; its major respiratory quinone was ubiquinone-9 (Q-9), and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. According to the above results, strain EGI 63088T is considered a novel species of the genus Halomonas, for which the name Halomonas flagellata sp. nov. is proposed. The type strain is EGI 63088T (= KCTC 92047T = CGMCC 1.19133T).
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Affiliation(s)
- Yin Huang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Rashidin Abdugheni
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China
| | - Jinbiao Ma
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China
| | - Rui Wang
- School of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, People's Republic of China
| | - Lei Gao
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Yonghong Liu
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China
| | - Wenjun Li
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Man Cai
- China General Microbiological Culture Collection Center, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.
| | - Li Li
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China.
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Wang K, Zhang Z, Hang J, Liu J, Guo F, Ding Y, Li M, Nie Q, Lin J, Zhuo Y, Sun L, Luo X, Zhong Q, Ye C, Yun C, Zhang Y, Wang J, Bao R, Pang Y, Wang G, Gonzalez FJ, Lei X, Qiao J, Jiang C. Microbial-host-isozyme analyses reveal microbial DPP4 as a potential antidiabetic target. Science 2023; 381:eadd5787. [PMID: 37535747 DOI: 10.1126/science.add5787] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 06/14/2023] [Indexed: 08/05/2023]
Abstract
A mechanistic understanding of how microbial proteins affect the host could yield deeper insights into gut microbiota-host cross-talk. We developed an enzyme activity-screening platform to investigate how gut microbiota-derived enzymes might influence host physiology. We discovered that dipeptidyl peptidase 4 (DPP4) is expressed by specific bacterial taxa of the microbiota. Microbial DPP4 was able to decrease the active glucagon like peptide-1 (GLP-1) and disrupt glucose metabolism in mice with a leaky gut. Furthermore, the current drugs targeting human DPP4, including sitagliptin, had little effect on microbial DPP4. Using high-throughput screening, we identified daurisoline-d4 (Dau-d4) as a selective microbial DPP4 inhibitor that improves glucose tolerance in diabetic mice.
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Affiliation(s)
- Kai Wang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Peking University, Beijing, China
- Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
| | - Zhiwei Zhang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Peking University, Beijing, China
- Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
| | - Jing Hang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Peking University, Beijing, China
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, China
| | - Jia Liu
- Department of Endocrinology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Fusheng Guo
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Yong Ding
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Peking University, Beijing, China
- Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
| | - Meng Li
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Peking University, Beijing, China
- Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
| | - Qixing Nie
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Peking University, Beijing, China
- Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
| | - Jun Lin
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Peking University, Beijing, China
- Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
| | - Yingying Zhuo
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Peking University, Beijing, China
- Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
| | - Lulu Sun
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Xi Luo
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Peking University, Beijing, China
- Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
| | - Qihang Zhong
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Peking University, Beijing, China
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, China
| | - Chuan Ye
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Peking University, Beijing, China
- Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
| | - Chuyu Yun
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Peking University, Beijing, China
- Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
| | - Yi Zhang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Peking University, Beijing, China
- Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
| | - Jue Wang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Peking University, Beijing, China
| | - Rui Bao
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Yanli Pang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Peking University, Beijing, China
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, China
| | - Guang Wang
- Department of Endocrinology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Frank J Gonzalez
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Xiaoguang Lei
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Jie Qiao
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Peking University, Beijing, China
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, China
- Beijing Advanced Innovation Center for Genomics, Beijing, China
| | - Changtao Jiang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Peking University, Beijing, China
- Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
- Center of Basic Medical Research, Institute of Medical Innovation and Research, Third Hospital, Peking University, Beijing, China
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Sakamoto M, Sakurai N, Tanno H, Iino T, Ohkuma M, Endo A. Faecalibacterium hominis Liu et al. 2023 is a later heterotypic synonym of Faecalibacterium duncaniae Sakamoto et al. 2022. Int J Syst Evol Microbiol 2023; 73. [PMID: 37566461 DOI: 10.1099/ijsem.0.005995] [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] [Indexed: 08/12/2023] Open
Abstract
A strain of the recently validated species Faecalibacterium hominis shares 99.0 % 16S rRNA gene sequence similarity with the type strain of Faecalibacterium duncaniae. The aim of this study was to evaluate the taxonomic relationship between F. hominis and F. duncaniae. F. duncaniae JCM 31915T showed 73.0 % digital DNA-DNA hybridization (dDDH) value with F. hominis JCM 39347T. The average nucleotide identity (ANI) value between these two strains was 96.7 %. These results indicate that F. duncaniae JCM 31915T and F. hominis JCM 39347T represent members of the same species. Based on these data, we propose Faecalibacterium hominis as a later heterotypic synonym of Faecalibacterium duncaniae. An emended description is provided.
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Affiliation(s)
- Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Naomi Sakurai
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Hiroki Tanno
- Department of Food, Aroma and Cosmetic Chemistry, Faculty of Bioindustry, Tokyo University of Agriculture, Hokkaido 099-2493, Japan
| | - Takao Iino
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Akihito Endo
- Department of Food, Aroma and Cosmetic Chemistry, Faculty of Bioindustry, Tokyo University of Agriculture, Hokkaido 099-2493, Japan
- Department of Nutritional Science and Food Safety, Faculty of Applied Bioscience, Tokyo University of Agriculture, Tokyo 156-8502, Japan
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Abdugheni R, Liu C, Liu FL, Zhou N, Jiang CY, Liu Y, Li L, Li WJ, Liu SJ. Comparative genomics reveals extensive intra-species genetic divergence of the prevalent gut commensal Ruminococcus gnavus. Microb Genom 2023; 9:mgen001071. [PMID: 37486746 PMCID: PMC10438805 DOI: 10.1099/mgen.0.001071] [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: 04/05/2023] [Accepted: 06/23/2023] [Indexed: 07/25/2023] Open
Abstract
Ruminococcus gnavus is prevalent in the intestines of humans and animals, and ambiguities have been reported regarding its relations with the development of diseases and host well-being. We postulate the ambiguities of its function in different cases may be attributed to strain-level variability of genomic features of R. gnavus. We performed comparative genomic and pathogenicity prediction analysis on 152 filtered high-quality genomes, including 4 genomes of strains isolated from healthy adults in this study. The mean G+C content of genomes of R. gnavus was 42.73±0.33 mol%, and the mean genome size was 3.46±0.34 Mbp. Genome-wide evolutionary analysis revealed R. gnavus genomes were divided into three major phylogenetic clusters. Pan-core genome analysis revealed that there was a total of 28 072 predicted genes, and the core genes, soft-core genes, shell genes and cloud genes accounted for 3.74 % (1051/28 072), 1.75 % (491/28 072), 9.88 % (2774/28 072) and 84.63 % (23 756/28 072) of the total genes, respectively. The small proportion of core genes reflected the wide divergence among R. gnavus strains. We found certain coding sequences with determined health benefits (such as vitamin production and arsenic detoxification), whilst some had an implication of health adversity (such as sulfide dehydrogenase subunits). The functions of the majority of core genes were unknown. The most widespread genes functioning in antibiotic resistance and virulence are tetO (tetracycline-resistance gene, present in 75 strains) and cps4J (capsular polysaccharide biosynthesis protein Cps4J encoding gene, detected in 3 genomes), respectively. Our results revealed genomic divergence and the existence of certain safety-relevant factors of R. gnavus. This study provides new insights for understanding the genomic features and health relevance of R. gnavus, and raises concerns regarding predicted prevalent pathogenicity and antibiotic resistance among most of the strains.
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Affiliation(s)
- Rashidin Abdugheni
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China
| | - Chang Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266000, PR China
| | - Feng-Lan Liu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center (EMRC), Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
- College of Life Sciences, Hebei University, Baoding 071000, PR China
| | - Nan Zhou
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center (EMRC), Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Cheng-Ying Jiang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266000, PR China
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center (EMRC), Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
- University of the Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yonghong Liu
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China
| | - Li Li
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China
| | - Wen-Jun Li
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266000, PR China
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center (EMRC), Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
- University of the Chinese Academy of Sciences, Beijing 100049, PR China
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Jagare L, Rozenberga M, Silamikelis I, Ansone L, Elbere I, Briviba M, Megnis K, Konrade I, Birka I, Straume Z, Klovins J. Metatranscriptome analysis of blood in healthy individuals and irritable bowel syndrome patients. J Med Microbiol 2023; 72. [PMID: 37335601 DOI: 10.1099/jmm.0.001719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023] Open
Abstract
Introduction. Although the presence of micro-organisms in the blood of healthy humans is a relatively new concept, there is a growing amount of evidence that blood might have its own microbiome.Gap Statement. Previous research has targeted the taxonomic composition of the blood microbiome using DNA-based sequencing methods, while little information is known about the presence of microbial transcripts obtained from the blood and their relation to conditions connected with increased gut permeability.Aim. To detect potentially alive and active micro-organisms and investigate differences in taxonomic composition between healthy people and patients with irritable bowel syndrome (IBS), we used the metatranscriptomics approach.Methodology. We collected blood samples from 23 IBS patients and 26 volunteers from the general population, and performed RNAseq on the isolated RNA. Reads corresponding to microbial genomes were identified with Kraken 2's standard plus protozoa and fungi database, and re-estimated at genus level with Bracken 2.7. We looked for trends in the taxonomic composition, making a comparison between the IBS and control groups, accounting for other different factors.Results. The dominant genera in the blood microbiome were found to be Cutibacterium, Bradyrhizobium, Escherichia, Pseudomonas, Micrococcus, Delftia, Mediterraneibacter, Staphylococcus, Stutzerimonas and Ralstonia. Some of these are typical environmental bacteria and could partially represent contamination. However, analysis of sequences from the negative controls suggested that some genera which are characteristic of the gut microbiome (Mediterraneibacter, Blautia, Collinsella, Klebsiella, Coprococcus, Dysosmobacter, Anaerostipes, Faecalibacterium, Dorea, Simiaoa, Bifidobacterium, Alistipes, Prevotella, Ruminococcus) are less likely to be a result of contamination. Differential analysis of microbes between groups showed that some taxa associated with the gut microbiome (Blautia, Faecalibacterium, Dorea, Bifidobacterium, Clostridium, Christensenella) are more prevalent in IBS patients compared to the general population. No significant correlations with any other factors were identified.Conclusion. Our findings support the existence of the blood microbiome and suggest the gut and possibly the oral microbiome as its origin, while the skin microbiome is a possible but less certain source. The blood microbiome is likely influenced by states of increased gut permeability such as IBS.
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Affiliation(s)
- Lauma Jagare
- Latvian Biomedical Research and Study Centre, Human Genetics and Disease Mechanisms Group, Ratsupites iela 1, Riga, LV-1067, Latvia
| | - Maija Rozenberga
- Latvian Biomedical Research and Study Centre, Human Genetics and Disease Mechanisms Group, Ratsupites iela 1, Riga, LV-1067, Latvia
| | - Ivars Silamikelis
- Latvian Biomedical Research and Study Centre, Human Genetics and Disease Mechanisms Group, Ratsupites iela 1, Riga, LV-1067, Latvia
| | - Laura Ansone
- Latvian Biomedical Research and Study Centre, Human Genetics and Disease Mechanisms Group, Ratsupites iela 1, Riga, LV-1067, Latvia
| | - Ilze Elbere
- Latvian Biomedical Research and Study Centre, Human Genetics and Disease Mechanisms Group, Ratsupites iela 1, Riga, LV-1067, Latvia
| | - Monta Briviba
- Latvian Biomedical Research and Study Centre, Human Genetics and Disease Mechanisms Group, Ratsupites iela 1, Riga, LV-1067, Latvia
| | - Kaspars Megnis
- Latvian Biomedical Research and Study Centre, Human Genetics and Disease Mechanisms Group, Ratsupites iela 1, Riga, LV-1067, Latvia
| | - Ilze Konrade
- Riga Stradins University, Dzirciema iela 16, Riga, LV-1007, Latvia
| | - Ilze Birka
- Pauls Stradins Clinical University Hospital, Pilsonu iela 13, Riga, LV-1002, Latvia
| | - Zane Straume
- Ogre Regional Hospital, Slimnicas iela 2, Ogre, LV-5001, Latvia
| | - Janis Klovins
- Latvian Biomedical Research and Study Centre, Human Genetics and Disease Mechanisms Group, Ratsupites iela 1, Riga, LV-1067, Latvia
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Dahal RH, Kim S, Kim YK, Kim ES, Kim J. Insight into gut dysbiosis of patients with inflammatory bowel disease and ischemic colitis. Front Microbiol 2023; 14:1174832. [PMID: 37250025 PMCID: PMC10211348 DOI: 10.3389/fmicb.2023.1174832] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 04/17/2023] [Indexed: 05/31/2023] Open
Abstract
The collection of whole microbial communities (bacteria, archaea, fungi, and viruses) together constitutes the gut microbiome. Diet, age, stress, host genetics, and diseases cause increases or decreases in the relative abundance and diversity of bacterial species (dysbiosis). We aimed to investigate the gut microbial composition at different taxonomic levels of healthy controls (HCs) with active Crohn's disease (CD), ulcerative colitis (UC), and ischemic colitis (IC) using culture- and non-culture-based approaches and identify biomarkers to discriminate CD, UC, or IC. We determined the specific changes in the gut microbial profile using culture-independent (16S rRNA gene amplicon sequencing) as well as culture-based (culturomic) approaches. Biomarkers were validated using quantitative Real-Time PCR (qPCR). In both methods, bacterial diversity and species richness decreased in disease-associated conditions compared with that in HCs. Highly reduced abundance of Faecalibacterium prausnitzii and Prevotella sp. and an increased abundance of potentially pathogenic bacteria such as Enterococcus faecium, Enterococcus faecalis, and Escherichia coli in all CD, UC, or IC conditions were observed. We noted a high abundance of Latilactobacillus sakei in CD patients; Ligilactobacillus ruminis in UC patients; and Enterococcus faecium, Escherichia coli, and Enterococcus faecalis in IC patients. Highly reduced abundance of Faecalibacterium prausnitzii in all cases, and increased abundance of Latilactobacillus sakei and Enterococcus faecium in CD, Ligilactobacillus ruminis and Enterococcus faecium in UC, and Enterococcus faecium, Escherichia coli, and Enterococcus faecalis in IC could be biomarkers for CD, UC, and IC, respectively. These biomarkers may help in IBD (CD or UC) and IC diagnosis.
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Affiliation(s)
- Ram Hari Dahal
- Department of Microbiology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Shukho Kim
- Department of Microbiology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Yu Kyung Kim
- Department of Clinical Pathology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Eun Soo Kim
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Jungmin Kim
- Department of Microbiology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
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Zhu J, Dong G, Shih CJ, Wu YC, Lai SJ, You YT, Qiu W, Wu CH, Liao CH, Gong Y, Chen SC. Complete Genome Sequence of Tissierella sp. Strain Yu-01, Isolated from the Feces of the Black Soldier Fly. Microbiol Resour Announc 2023:e0027723. [PMID: 37154723 DOI: 10.1128/mra.00277-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023] Open
Abstract
We report the complete genome sequence of Tissierella sp. strain Yu-01 (=BCRC 81391), isolated from the feces of black soldier fly (Hermetia illucens) larvae. This fly has increasingly been gaining attention because of its usefulness for recycling organic waste. The genome of strain Yu-01 was selected for further species delineation.
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Affiliation(s)
- Junyu Zhu
- College of Environment and Safety Engineering, Fuzhou University, Fuzhou, Fujian, People's Republic of China
- School of Resources and Chemical Engineering, Sanming University, Sanming City, Fujian, People's Republic of China
| | - Guowen Dong
- College of Environment and Safety Engineering, Fuzhou University, Fuzhou, Fujian, People's Republic of China
- School of Resources and Chemical Engineering, Sanming University, Sanming City, Fujian, People's Republic of China
| | - Chao-Jen Shih
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan, Republic of China
| | - Yen-Chi Wu
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan, Republic of China
| | - Shu-Jung Lai
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung City, Taiwan, Republic of China
- Research Center for Cancer Biology, China Medical University, Taichung City, Taiwan, Republic of China
| | - Yi-Ting You
- Department of Life Sciences, National Chung Hsing University, Taichung City, Taiwan, Republic of China
| | - Wanling Qiu
- School of Resources and Chemical Engineering, Sanming University, Sanming City, Fujian, People's Republic of China
| | - Chih-Hung Wu
- College of Environment and Safety Engineering, Fuzhou University, Fuzhou, Fujian, People's Republic of China
- School of Resources and Chemical Engineering, Sanming University, Sanming City, Fujian, People's Republic of China
| | - Ching-Hua Liao
- School of Resources and Chemical Engineering, Sanming University, Sanming City, Fujian, People's Republic of China
| | - Yan Gong
- People's Government of Zhongcun Township, Sanyuan District, Sanming City, Fujian, People's Republic of China
| | - Sheng-Chung Chen
- College of Environment and Safety Engineering, Fuzhou University, Fuzhou, Fujian, People's Republic of China
- School of Resources and Chemical Engineering, Sanming University, Sanming City, Fujian, People's Republic of China
- Department of Life Sciences, National Chung Hsing University, Taichung City, Taiwan, Republic of China
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40
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Qu P, Rom O, Li K, Jia L, Gao X, Liu Z, Ding S, Zhao M, Wang H, Chen S, Xiong X, Zhao Y, Xue C, Zhao Y, Chu C, Wen B, Finney AC, Zheng Z, Cao W, Zhao J, Bai L, Zhao S, Sun D, Zeng R, Lin J, Liu W, Zheng L, Zhang J, Liu E, Chen YE. DT-109 ameliorates nonalcoholic steatohepatitis in nonhuman primates. Cell Metab 2023; 35:742-757.e10. [PMID: 37040763 DOI: 10.1016/j.cmet.2023.03.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 01/03/2023] [Accepted: 03/17/2023] [Indexed: 04/13/2023]
Abstract
Nonalcoholic steatohepatitis (NASH) prevalence is rising with no pharmacotherapy approved. A major hurdle in NASH drug development is the poor translatability of preclinical studies to safe/effective clinical outcomes, and recent failures highlight a need to identify new targetable pathways. Dysregulated glycine metabolism has emerged as a causative factor and therapeutic target in NASH. Here, we report that the tripeptide DT-109 (Gly-Gly-Leu) dose-dependently attenuates steatohepatitis and fibrosis in mice. To enhance the probability of successful translation, we developed a nonhuman primate model that histologically and transcriptionally mimics human NASH. Applying a multiomics approach combining transcriptomics, proteomics, metabolomics, and metagenomics, we found that DT-109 reverses hepatic steatosis and prevents fibrosis progression in nonhuman primates, not only by stimulating fatty acid degradation and glutathione formation, as found in mice, but also by modulating microbial bile acid metabolism. Our studies describe a highly translatable NASH model and highlight the need for clinical evaluation of DT-109.
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Affiliation(s)
- Pengxiang Qu
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Center, 76 Yanta West Road, Xi'an, Shaanxi 710061, China
| | - Oren Rom
- Department of Internal Medicine, Frankel Cardiovascular Center, University of Michigan, 2800 Plymouth Road, Ann Arbor, MI 48109, USA; Department of Pathology and Translational Pathobiology, Louisiana State University Health Sciences Center-Shreveport, Shreveport, LA 71103, USA; Department of Molecular and Cellular Physiology, Louisiana State University Health Sciences Center-Shreveport, Shreveport, LA 71103, USA; Center for Cardiovascular Diseases and Sciences, Louisiana State University Health Sciences Center-Shreveport, Shreveport, LA 71103, USA
| | - Ke Li
- Beijing Tiantan Hospital, China National Clinical Research Center for Neurological Diseases, Advanced Innovation Center for Human Brain Protection, Capital Medical University, 6 Tiantan Xili, Chongwen District, Beijing 100050, China
| | - Linying Jia
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Center, 76 Yanta West Road, Xi'an, Shaanxi 710061, China
| | - Xiaojing Gao
- Key Laboratory of Systems Health Science of Zhejiang Province, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China; CAS Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhipeng Liu
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
| | - Shusi Ding
- Beijing Tiantan Hospital, China National Clinical Research Center for Neurological Diseases, Advanced Innovation Center for Human Brain Protection, Capital Medical University, 6 Tiantan Xili, Chongwen District, Beijing 100050, China
| | - Mingming Zhao
- The Institute of Cardiovascular Sciences, School of Basic Medical Sciences, Key Laboratory of Molecular Cardiovascular Science of Ministry of Education, NHC Key Laboratory of Cardiovascular Molecular Biology and Regulatory Peptides, Beijing Key Laboratory of Cardiovascular Receptors Research, Health Science Center, Peking University, 38 Xue Yuan Road, Beijing 100191, China
| | - Huiqing Wang
- The Institute of Cardiovascular Sciences, School of Basic Medical Sciences, Key Laboratory of Molecular Cardiovascular Science of Ministry of Education, NHC Key Laboratory of Cardiovascular Molecular Biology and Regulatory Peptides, Beijing Key Laboratory of Cardiovascular Receptors Research, Health Science Center, Peking University, 38 Xue Yuan Road, Beijing 100191, China
| | - Shuangshuang Chen
- Department of Endocrinology and Metabolism, Fudan Institute of Metabolic Diseases, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Xuhui District, Shanghai 200031, China
| | - Xuelian Xiong
- Department of Endocrinology and Metabolism, Fudan Institute of Metabolic Diseases, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Xuhui District, Shanghai 200031, China
| | - Ying Zhao
- Department of Internal Medicine, Frankel Cardiovascular Center, University of Michigan, 2800 Plymouth Road, Ann Arbor, MI 48109, USA
| | - Chao Xue
- Department of Internal Medicine, Frankel Cardiovascular Center, University of Michigan, 2800 Plymouth Road, Ann Arbor, MI 48109, USA
| | - Yang Zhao
- Department of Internal Medicine, Frankel Cardiovascular Center, University of Michigan, 2800 Plymouth Road, Ann Arbor, MI 48109, USA
| | - Chengshuang Chu
- CAS Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Bo Wen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA
| | - Alexandra C Finney
- Department of Pathology and Translational Pathobiology, Louisiana State University Health Sciences Center-Shreveport, Shreveport, LA 71103, USA
| | - Zuowen Zheng
- Spring Biological Technology Development Co., Ltd, Fangchenggang, Guangxi 538000, China
| | - Wenbin Cao
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Center, 76 Yanta West Road, Xi'an, Shaanxi 710061, China
| | - Jinpeng Zhao
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Center, 76 Yanta West Road, Xi'an, Shaanxi 710061, China
| | - Liang Bai
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Center, 76 Yanta West Road, Xi'an, Shaanxi 710061, China
| | - Sihai Zhao
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Center, 76 Yanta West Road, Xi'an, Shaanxi 710061, China
| | - Duxin Sun
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rong Zeng
- Key Laboratory of Systems Health Science of Zhejiang Province, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China; CAS Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Jiandie Lin
- Life Sciences Institute and Department of Cell & Developmental Biology, University of Michigan Medical Center, Ann Arbor, MI 48109, USA
| | - Wanqing Liu
- Department of Pharmaceutical Sciences and Department of Pharmacology, Wayne State University, Detroit, MI 48201, USA
| | - Lemin Zheng
- Beijing Tiantan Hospital, China National Clinical Research Center for Neurological Diseases, Advanced Innovation Center for Human Brain Protection, Capital Medical University, 6 Tiantan Xili, Chongwen District, Beijing 100050, China; The Institute of Cardiovascular Sciences, School of Basic Medical Sciences, Key Laboratory of Molecular Cardiovascular Science of Ministry of Education, NHC Key Laboratory of Cardiovascular Molecular Biology and Regulatory Peptides, Beijing Key Laboratory of Cardiovascular Receptors Research, Health Science Center, Peking University, 38 Xue Yuan Road, Beijing 100191, China.
| | - Jifeng Zhang
- Department of Internal Medicine, Frankel Cardiovascular Center, University of Michigan, 2800 Plymouth Road, Ann Arbor, MI 48109, USA.
| | - Enqi Liu
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Center, 76 Yanta West Road, Xi'an, Shaanxi 710061, China.
| | - Y Eugene Chen
- Department of Internal Medicine, Frankel Cardiovascular Center, University of Michigan, 2800 Plymouth Road, Ann Arbor, MI 48109, USA.
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Lin X, Hu T, Chen J, Liang H, Zhou J, Wu Z, Ye C, Jin X, Xu X, Zhang W, Jing X, Yang T, Wang J, Yang H, Kristiansen K, Xiao L, Zou Y. The genomic landscape of reference genomes of cultivated human gut bacteria. Nat Commun 2023; 14:1663. [PMID: 36966151 PMCID: PMC10039858 DOI: 10.1038/s41467-023-37396-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 03/14/2023] [Indexed: 03/27/2023] Open
Abstract
Culture-independent metagenomic studies have revolutionized our understanding of the gut microbiota. However, the lack of full genomes from cultured species is still a limitation for in-depth studies of the gut microbiota. Here we present a substantially expanded version of our Cultivated Genome Reference (CGR), termed CGR2, providing 3324 high-quality draft genomes from isolates selected from a large-scale cultivation of bacterial isolates from fecal samples of healthy Chinese individuals. The CGR2 classifies 527 species (179 previously unidentified species) from 8 phyla, and uncovers a genomic and functional diversity of Collinsella aerofaciens. The CGR2 genomes match 126 metagenome-assembled genomes without cultured representatives in the Unified Human Gastrointestinal Genome (UHGG) collection and harbor 3767 unidentified secondary metabolite biosynthetic gene clusters, providing a source of natural compounds with pharmaceutical potentials. We uncover accurate phage-bacterium linkages providing information on the evolutionary characteristics of interaction between bacteriophages and bacteria at the strain level.
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Affiliation(s)
- Xiaoqian Lin
- BGI-Shenzhen, Shenzhen, 518083, China
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | | | - Jianwei Chen
- BGI-Shenzhen, Shenzhen, 518083, China
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, 266555, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken 13, 2100, Copenhagen, Denmark
| | | | - Jianwei Zhou
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, 266555, China
| | - Zhinan Wu
- BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chen Ye
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Xin Jin
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, 518083, China
| | | | - Xiaohuan Jing
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Tao Yang
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, 518083, China
- James D. Watson Institute of Genome Sciences, Hangzhou, 310058, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, 518083, China
- James D. Watson Institute of Genome Sciences, Hangzhou, 310058, China
| | - Karsten Kristiansen
- BGI-Shenzhen, Shenzhen, 518083, China.
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, 266555, China.
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken 13, 2100, Copenhagen, Denmark.
- PREDICT, Center for Molecular Prediction of Inflammatory Bowel Disease, Faculty of Medicine, Aalborg University, 2450, Copenhagen, Denmark.
| | - Liang Xiao
- BGI-Shenzhen, Shenzhen, 518083, China.
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, 266555, China.
- Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI-Shenzhen, Shenzhen, China.
| | - Yuanqiang Zou
- BGI-Shenzhen, Shenzhen, 518083, China.
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, 266555, China.
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken 13, 2100, Copenhagen, Denmark.
- Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI-Shenzhen, Shenzhen, China.
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Chen HH, Wang YX, Li DF, Liu C, Bi SY, Jiang CY, Liu SJ. Chemoreceptors from the commensal gut Roseburia rectibacter bind to mucin and trigger chemotaxis. Environ Microbiol 2023. [PMID: 36869629 DOI: 10.1111/1462-2920.16365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 03/02/2023] [Indexed: 03/05/2023]
Abstract
Chemotaxis is crucial for bacterial adherence and colonization of the host gastrointestinal tract. Previous studies have demonstrated that chemotaxis affects the virulence of causative pathogens and the infection in the host. However, the chemotactic abilities of non-pathogenic and commensal gut bacteria have rarely been explored. We observed that Roseburia rectibacter NSJ-69 exhibited flagella-dependent motility and chemotaxis to a variety of molecules, including mucin and propionate. A genome-wide analysis revealed that NSJ-69 has 28 putative chemoreceptors, 15 of which have periplasmic ligand-binding domains (LBDs). These LBD-coding genes were chemically synthesized and expressed heterologously in Escherichia coli. Intensive screening of ligands revealed four chemoreceptors bound to mucin and two bound to propionate. When expressed in Comamonas testosteroni or E. coli, these chemoreceptors elicited chemotaxis toward mucin and propionate. Hybrid chemoreceptors were constructed, and results showed that the chemotactic responses to mucin and propionate were dependent on the LBDs of R. rectibacter chemoreceptors. Our study identified and characterized R. rectibacter chemoreceptors. These results will facilitate further investigations on the involvement of microbial chemotaxis in host colonization.
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Affiliation(s)
- Hong-He Chen
- State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Yu-Xin Wang
- State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao, People's Republic of China
| | - De-Feng Li
- State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Chang Liu
- State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People's Republic of China.,State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao, People's Republic of China
| | - Shuang-Yu Bi
- State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao, People's Republic of China
| | - Cheng-Ying Jiang
- State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People's Republic of China.,State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao, People's Republic of China
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Abdugheni R, Li DH, Wang YJ, Du MX, Zhou N, Liu C, Liu SJ. Acidaminococcus homini s sp. nov., Amedibacillus hominis sp. nov., Lientehia hominis gen. nov. sp. nov., Merdimmobilis hominis gen. nov. sp. nov., and Paraeggerthella hominis sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2023; 73. [PMID: 36735588 DOI: 10.1099/ijsem.0.005648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The human gastrointestinal tract is inhabited by various microorganisms, including thousands of bacterial taxa that have yet to be cultured and characterized. In this report, we describe the isolation, cultivation, genotypic and phenotypic characterization and taxonomy of five novel anaerobic bacterial strains that were recovered during the massive cultivation and isolation of gut microbes from human faecal samples. On the basis of the polyphasic taxonomic results, we propose two novel genera and five novel species. They are Acidaminococcus hominis sp. nov. (type strain NSJ-142T=CGMCC 1.17903T=KCTC 25346T), Amedibacillus hominis sp. nov. (type strain NSJ-176T=CGMCC 1.17933T=KCTC 25355T), Lientehia hominis gen. nov. sp. nov. (type strain NSJ-141T=CGMCC 1.17902T=KCTC 25345T), Merdimmobilis hominis gen. nov. sp. nov. (type strain NSJ-153T=CGMCC 1.17915T=KCTC 25350T) and Paraeggerthella hominis sp. nov. (type strain NSJ-152T=CGMCC 1.17914T=KCTC 25349T).
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Affiliation(s)
- Rashidin Abdugheni
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China.,University of the Chinese Academy of Sciences, Beijing 100049, PR China.,State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, PR China
| | - Dan-Hua Li
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yu-Jing Wang
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China.,University of the Chinese Academy of Sciences, Beijing 100049, PR China
| | - Meng-Xuan Du
- State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao 266237, PR China
| | - Nan Zhou
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Chang Liu
- State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao 266237, PR China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China.,University of the Chinese Academy of Sciences, Beijing 100049, PR China.,State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao 266237, PR China
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44
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Gut microbiome studies in CKD: opportunities, pitfalls and therapeutic potential. Nat Rev Nephrol 2023; 19:87-101. [PMID: 36357577 DOI: 10.1038/s41581-022-00647-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/17/2022] [Indexed: 11/12/2022]
Abstract
Interest in gut microbiome dysbiosis and its potential association with the development and progression of chronic kidney disease (CKD) has increased substantially in the past 6 years. In parallel, the microbiome field has matured considerably as the importance of host-related and environmental factors is increasingly recognized. Past research output in the context of CKD insufficiently considered the myriad confounding factors that are characteristic of the disease. Gut microbiota-derived metabolites remain an interesting therapeutic target to decrease uraemic (cardio)toxicity. However, future studies on the effect of dietary and biotic interventions will require harmonization of relevant readouts to enable an in-depth understanding of the underlying beneficial mechanisms. High-quality standards throughout the entire microbiome analysis workflow are also of utmost importance to obtain reliable and reproducible results. Importantly, investigating the relative composition and abundance of gut bacteria, and their potential association with plasma uraemic toxins levels is not sufficient. As in other fields, the time has come to move towards in-depth quantitative and functional exploration of the patient's gut microbiome by relying on confounder-controlled quantitative microbial profiling, shotgun metagenomics and in vitro simulations of microorganism-microorganism and host-microorganism interactions. This step is crucial to enable the rational selection and monitoring of dietary and biotic intervention strategies that can be deployed as a personalized intervention in CKD.
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Bilal H, Xiao Y, Khan MN, Chen J, Wang Q, Zeng Y, Lin X. Stabilization of Acne Vulgaris-Associated Microbial Dysbiosis with 2% Supramolecular Salicylic Acid. Pharmaceuticals (Basel) 2023; 16:ph16010087. [PMID: 36678584 PMCID: PMC9864713 DOI: 10.3390/ph16010087] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/28/2022] [Accepted: 01/06/2023] [Indexed: 01/11/2023] Open
Abstract
Facial microbiota dysbiosis is an important factor in causing acne vulgaris. The present study aimed to analyze the effect of 2% Supramolecular Salicylic Acid (SSA) on acne-associated facial bacteria. In the current study, 30 acne vulgaris patients (treated with 2% SSA for eight weeks) and ten volunteers with no facial acne were selected. Samples from acne patients (before and after treatment) and volunteers (not treated) were analyzed via high throughput sequencing, Deblur algorithm, and R microbiome package. After treatment with 2% SSA, the total lesion count and global acne grading system (GAGS) score reduced significantly (p < 0.001). Metagenomic sequencing analysis revealed that the pre-treated acne group had low α and deviated β diversity compared to the control and post-treated acne groups. Due to the treatment with 2% SSA, α diversity index was increased and β diversity was stabilized significantly (p < 0.001). The relative abundance of bacterial genera in the pre-treated acne group was uneven and had a high proportion of Staphylococcus, Ralstonia, and Streptococcus. The proportion of these three genera was significantly decreased in the post-treated group, and overall bacteria genera distribution tends toward the healthy individual. It is concluded that 2% SSA normalizes the microbial communities associated with the skin.
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Affiliation(s)
- Hazrat Bilal
- Department of Dermatology, The Second Affiliated Hospital of Shantou University Medical College, Shantou 515041, China
| | - Yuanyuan Xiao
- Department of Dermatology, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, China
- Department of Dermatology, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
- Chinese Academy of Sciences, Sichuan Translational Medicine Research Hospital, Chengdu 610072, China
- Department of Dermatology, People’s Hospital of Deyang City, Deyang 618000, China
| | - Muhammad Nadeem Khan
- Faculty of Biological Sciences, Department of Microbiology, Quaid-I-Azam University, Islamabad 45320, Pakistan
| | - Jinyu Chen
- Department of Dermatology, Chengdu Second People’s Hospital, Chengdu 610017, China
| | - Qian Wang
- Department of Dermatology, The Second Affiliated Hospital of Shantou University Medical College, Shantou 515041, China
- Department of Medical, Surgical and Experimental Sciences, University of Sassari—Neurology Unit, Azienza Ospedaliera Universitaria (AOU), 07100 Sassari, Italy
| | - Yuebin Zeng
- Department of Dermatology, The Second Affiliated Hospital of Shantou University Medical College, Shantou 515041, China
- Correspondence: (Y.Z.); (X.L.)
| | - Xinyu Lin
- Department of Dermatology, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
- Chinese Academy of Sciences, Sichuan Translational Medicine Research Hospital, Chengdu 610072, China
- Correspondence: (Y.Z.); (X.L.)
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46
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Abdugheni R, Wang W, Wang Y, Du M, Liu F, Zhou N, Jiang C, Wang C, Wu L, Ma J, Liu C, Liu S. Metabolite profiling of human-originated Lachnospiraceae at the strain level. IMETA 2022; 1:e58. [PMID: 38867908 PMCID: PMC10989990 DOI: 10.1002/imt2.58] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/08/2022] [Accepted: 09/14/2022] [Indexed: 06/14/2024]
Abstract
The human gastrointestinal (GI) tract harbors diverse microbes, and the family Lachnospiraceae is one of the most abundant and widely occurring bacterial groups in the human GI tract. Beneficial and adverse effects of the Lachnospiraceae on host health were reported, but the diversities at species/strain levels as well as their metabolites of Lachnospiraceae have been, so far, not well documented. In the present study, we report on the collection of 77 human-originated Lachnospiraceae species (please refer hLchsp, https://hgmb.nmdc.cn/subject/lachnospiraceae) and the in vitro metabolite profiles of 110 Lachnospiraceae strains (https://hgmb.nmdc.cn/subject/lachnospiraceae/metabolites). The Lachnospiraceae strains in hLchsp produced 242 metabolites of 17 categories. The larger categories were alcohols (89), ketones (35), pyrazines (29), short (C2-C5), and long (C > 5) chain acids (31), phenols (14), aldehydes (14), and other 30 compounds. Among them, 22 metabolites were aromatic compounds. The well-known beneficial gut microbial metabolite, butyric acid, was generally produced by many Lachnospiraceae strains, and Agathobacter rectalis strain Lach-101 and Coprococcus comes strain NSJ-173 were the top 2 butyric acid producers, as 331.5 and 310.9 mg/L of butyric acids were produced in vitro, respectively. Further analysis of the publicly available cohort-based volatile-metabolomic data sets of human feces revealed that over 30% of the prevailing volatile metabolites were covered by Lachnospiraceae metabolites identified in this study. This study provides Lachnospiraceae strain resources together with their metabolic profiles for future studies on host-microbe interactions and developments of novel probiotics or biotherapies.
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Affiliation(s)
- Rashidin Abdugheni
- State Key Laboratory of Microbial Resources, Environmental Microbiology Research Center (EMRC)Institute of Microbiology, Chinese Academy of SciencesBeijingChina
- State Key Laboratory of Desert and Oasis EcologyXinjiang Institute of Ecology and Geography, Chinese Academy of SciencesUrumqiChina
| | - Wen‐Zhao Wang
- State Key Laboratory of MycologyInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
| | - Yu‐Jing Wang
- State Key Laboratory of Microbial Resources, Environmental Microbiology Research Center (EMRC)Institute of Microbiology, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Meng‐Xuan Du
- State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoChina
| | - Feng‐Lan Liu
- State Key Laboratory of Microbial Resources, Environmental Microbiology Research Center (EMRC)Institute of Microbiology, Chinese Academy of SciencesBeijingChina
- College of Life SciencesHebei UniversityBaodingChina
| | - Nan Zhou
- State Key Laboratory of Microbial Resources, Environmental Microbiology Research Center (EMRC)Institute of Microbiology, Chinese Academy of SciencesBeijingChina
| | - Cheng‐Ying Jiang
- State Key Laboratory of Microbial Resources, Environmental Microbiology Research Center (EMRC)Institute of Microbiology, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Chang‐Yu Wang
- Colleg of Life SciencesUniversity of Science and Technology of ChinaHefeiChina
| | - Linhuan Wu
- State Key Laboratory of Microbial Resources, Environmental Microbiology Research Center (EMRC)Institute of Microbiology, Chinese Academy of SciencesBeijingChina
| | - Juncai Ma
- State Key Laboratory of Microbial Resources, Environmental Microbiology Research Center (EMRC)Institute of Microbiology, Chinese Academy of SciencesBeijingChina
| | - Chang Liu
- State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoChina
| | - Shuang‐Jiang Liu
- State Key Laboratory of Microbial Resources, Environmental Microbiology Research Center (EMRC)Institute of Microbiology, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
- State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoChina
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47
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Chen CZ, Li P, Liu L, Li ZH. Exploring the interactions between the gut microbiome and the shifting surrounding aquatic environment in fisheries and aquaculture: A review. ENVIRONMENTAL RESEARCH 2022; 214:114202. [PMID: 36030922 DOI: 10.1016/j.envres.2022.114202] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 08/10/2022] [Accepted: 08/20/2022] [Indexed: 06/15/2023]
Abstract
The rise of "new" sequencing technologies and the development of sophisticated bioinformatics tools have dramatically increased the study of the aquaculture microbiome. Microbial communities exist in complex and dynamic communities that play a vital role in the stability of healthy ecosystems. The gut microbiome contributes to multiple aspects of the host's physiological health status, ranging from nutritional regulation to immune modulation. Although studies of the gut microbiome in aquaculture are growing rapidly, the interrelationships between the aquaculture microbiome and its aquatic environment have not been discussed and summarized. In particular, few reviews have focused on the potential mechanisms driving the alteration of the gut microbiome by surrounding aquatic environmental factors. Here, we review current knowledge on the host gut microbiome and its interrelationship with the microbiome of the surrounding environment, mainly including the main methods for characterizing the gut microbiome, the composition and function of microbial communities, the dynamics of microbial interactions, and the relationship between the gut microbiome and the surrounding water/sediment microbiome. Our review highlights two potential mechanisms for how surrounding aquatic environmental factors drive the gut microbiome. This may deepen the understanding of the interactions between the microbiome and environmental factors. Lastly, we also briefly describe the research gaps in current knowledge and prospects for the future orientation of research. This review provides a framework for studying the complex relationship between the host gut microbiome and environmental stresses to better facilitate the widespread application of microbiome technologies in fisheries and aquaculture.
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Affiliation(s)
- Cheng-Zhuang Chen
- Marine College, Shandong University, Weihai, Shandong, 264209, China
| | - Ping Li
- Marine College, Shandong University, Weihai, Shandong, 264209, China
| | - Ling Liu
- Marine College, Shandong University, Weihai, Shandong, 264209, China
| | - Zhi-Hua Li
- Marine College, Shandong University, Weihai, Shandong, 264209, China.
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48
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Jiang MZ, Zhu HZ, Zhou N, Liu C, Jiang CY, Wang Y, Liu SJ. Droplet microfluidics-based high-throughput bacterial cultivation for validation of taxon pairs in microbial co-occurrence networks. Sci Rep 2022; 12:18145. [PMID: 36307549 PMCID: PMC9616874 DOI: 10.1038/s41598-022-23000-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 10/21/2022] [Indexed: 12/31/2022] Open
Abstract
Co-occurrence networks inferred from the abundance data of microbial communities are widely applied to predict microbial interactions. However, the high workloads of bacterial isolation and the complexity of the networks themselves constrained experimental demonstrations of the predicted microbial associations and interactions. Here, we integrate droplet microfluidics and bar-coding logistics for high-throughput bacterial isolation and cultivation from environmental samples, and experimentally investigate the relationships between taxon pairs inferred from microbial co-occurrence networks. We collected Potamogeton perfoliatus plants (including roots) and associated sediments from Beijing Olympic Park wetland. Droplets of series diluted homogenates of wetland samples were inoculated into 126 96-well plates containing R2A and TSB media. After 10 days of cultivation, 65 plates with > 30% wells showed microbial growth were selected for the inference of microbial co-occurrence networks. We cultivated 129 bacterial isolates belonging to 15 species that could represent the zero-level OTUs (Zotus) in the inferred co-occurrence networks. The co-cultivations of bacterial isolates corresponding to the prevalent Zotus pairs in networks were performed on agar plates and in broth. Results suggested that positively associated Zotu pairs in the co-occurrence network implied complicated relations including neutralism, competition, and mutualism, depending on bacterial isolate combination and cultivation time.
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Affiliation(s)
- Min-Zhi Jiang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266000, People's Republic of China
| | - Hai-Zhen Zhu
- State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center (EMRC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Nan Zhou
- State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center (EMRC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Chang Liu
- State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center (EMRC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Cheng-Ying Jiang
- State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center (EMRC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Yulin Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266000, People's Republic of China.
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266000, People's Republic of China.
- State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center (EMRC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.
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49
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Kim CY, Ma J, Lee I. HiFi metagenomic sequencing enables assembly of accurate and complete genomes from human gut microbiota. Nat Commun 2022; 13:6367. [PMID: 36289209 PMCID: PMC9606305 DOI: 10.1038/s41467-022-34149-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 10/12/2022] [Indexed: 12/25/2022] Open
Abstract
Advances in metagenomic assembly have led to the discovery of genomes belonging to uncultured microorganisms. Metagenome-assembled genomes (MAGs) often suffer from fragmentation and chimerism. Recently, 20 complete MAGs (cMAGs) have been assembled from Oxford Nanopore long-read sequencing of 13 human fecal samples, but with low nucleotide accuracy. Here, we report 102 cMAGs obtained by Pacific Biosciences (PacBio) high-accuracy long-read (HiFi) metagenomic sequencing of five human fecal samples, whose initial circular contigs were selected for complete prokaryotic genomes using our bioinformatics workflow. Nucleotide accuracy of the final cMAGs was as high as that of Illumina sequencing. The cMAGs could exceed 6 Mbp and included complete genomes of diverse taxa, including entirely uncultured RF39 and TANB77 orders. Moreover, cMAGs revealed that regions hard to assemble by short-read sequencing comprised mostly genomic islands and rRNAs. HiFi metagenomic sequencing will facilitate cataloging accurate and complete genomes from complex microbial communities, including uncultured species.
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Affiliation(s)
- Chan Yeong Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Junyeong Ma
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Insuk Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea.
- POSTECH Biotech Center, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea.
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50
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Sanders JG, Yan W, Mjungu D, Lonsdorf EV, Hart JA, Sanz CM, Morgan DB, Peeters M, Hahn BH, Moeller AH. A low-cost genomics workflow enables isolate screening and strain-level analyses within microbiomes. Genome Biol 2022; 23:212. [PMID: 36224660 PMCID: PMC9558970 DOI: 10.1186/s13059-022-02777-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 09/30/2022] [Indexed: 11/10/2022] Open
Abstract
Earth's environments harbor complex consortia of microbes that affect processes ranging from host health to biogeochemical cycles. Understanding their evolution and function is limited by an inability to isolate genomes in a high-throughput manner. Here, we present a workflow for bacterial whole-genome sequencing using open-source labware and the OpenTrons robotics platform, reducing costs to approximately $10 per genome. We assess genomic diversity within 45 gut bacterial species from wild-living chimpanzees and bonobos. We quantify intraspecific genomic diversity and reveal divergence of homologous plasmids between hosts. This enables population genetic analyses of bacterial strains not currently possible with metagenomic data alone.
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Affiliation(s)
- Jon G Sanders
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA.
| | - Weiwei Yan
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Deus Mjungu
- Gombe Stream Research Center, Kigoma, Tanzania
| | - Elizabeth V Lonsdorf
- Department of Psychology and Biological Foundations of Behavior Program, Franklin and Marshall College, Lancaster, PA, USA
- Department of Anthropology, Emory University, Atlanta, GA, 30322, USA
| | - John A Hart
- Lukuru Wildlife Research Foundation, Tshuapa-Lomami-Lualaba Project, BP 2012, Kinshasa, Democratic Republic of the Congo
| | - Crickette M Sanz
- Department of Anthropology, Washington University in St. Louis, 1 Brookings Drive, Saint Louis, MO, USA
- Wildlife Conservation Society, Congo Program, Brazzaville, B.P. 14537, Republic of Congo
| | - David B Morgan
- Lester E. Fisher Center for the Study and Conservation of Apes, Lincoln Park Zoo, Chicago, IL, USA
| | - Martine Peeters
- Recherche Translationnelle Appliquée Au VIH Et Aux Maladies Infectieuses, Institut de Recherche Pour Le Développement, University of Montpellier, INSERM, 34090, Montpellier, France
| | - Beatrice H Hahn
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Andrew H Moeller
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA.
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