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Wu L, Wang XW, Tao Z, Wang T, Zuo W, Zeng Y, Liu YY, Dai L. Data-driven prediction of colonization outcomes for complex microbial communities. Nat Commun 2024; 15:2406. [PMID: 38493186 PMCID: PMC10944475 DOI: 10.1038/s41467-024-46766-y] [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: 07/07/2023] [Accepted: 03/08/2024] [Indexed: 03/18/2024] Open
Abstract
Microbial interactions can lead to different colonization outcomes of exogenous species, be they pathogenic or beneficial in nature. Predicting the colonization of exogenous species in complex communities remains a fundamental challenge in microbial ecology, mainly due to our limited knowledge of the diverse mechanisms governing microbial dynamics. Here, we propose a data-driven approach independent of any dynamics model to predict colonization outcomes of exogenous species from the baseline compositions of microbial communities. We systematically validate this approach using synthetic data, finding that machine learning models can predict not only the binary colonization outcome but also the post-invasion steady-state abundance of the invading species. Then we conduct colonization experiments for commensal gut bacteria species Enterococcus faecium and Akkermansia muciniphila in hundreds of human stool-derived in vitro microbial communities, confirming that the data-driven approaches can predict the colonization outcomes in experiments. Furthermore, we find that while most resident species are predicted to have a weak negative impact on the colonization of exogenous species, strongly interacting species could significantly alter the colonization outcomes, e.g., Enterococcus faecalis inhibits the invasion of E. faecium invasion. The presented results suggest that the data-driven approaches are powerful tools to inform the ecology and management of microbial communities.
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Affiliation(s)
- Lu Wu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Xu-Wen Wang
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Zining Tao
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Shandong Agricultural University, Tai'an, China
| | - Tong Wang
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Wenlong Zuo
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yu Zeng
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yang-Yu Liu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Center for Artificial Intelligence and Modeling, The Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, USA.
| | - Lei Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
- University of Chinese Academy of Sciences, Beijing, China.
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2
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Yang P, Yang J, Long H, Huang K, Ji L, Lin H, Jiang X, Wang AK, Tian G, Ning K. MicroEXPERT: Microbiome profiling platform with cross-study metagenome-wide association analysis functionality. IMETA 2023; 2:e131. [PMID: 38868224 PMCID: PMC10989818 DOI: 10.1002/imt2.131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/06/2023] [Accepted: 07/10/2023] [Indexed: 06/14/2024]
Abstract
The framework of the MicroEXPERT platform. Our Platform was composed of five modules. Data management module: Users upload raw data and metadata to the system using a guided workflow. Data processing module: Uploaded data is processed to generate taxonomical distribution and functional composition results. Metagenome-wide association studies module (MWAS): Various methods, including biomarker analysis, PCA, co-occurrence networks, and sample classification, are employed using metadata. Data search module: Users can query nucleotide sequences to retrieve information in the MicroEXPERT database. Data visualization module: Visualization tools are used to illustrate the metagenome analysis results.
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Affiliation(s)
- Pengshuo Yang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular‐imaging, Center of AI Biology, Department of Bioinformatics and Systems BiologyCollege of Life Science and Technology, Huazhong University of Science and TechnologyWuhanHubeiChina
- Institute of Medical GenomicsBiomedical Sciences College, Shandong First Medical UniversityJinanShandongChina
| | - Jialiang Yang
- Department of SciencesGeneis Beijing Co., Ltd.BeijingChina
- Department of SciencesQingdao Geneis Institute of Big Data Mining and Precision MedicineQingdaoChina
- Department of SciencesAcademician Workstation, Changsha Medical UniversityChangshaChina
| | - Haixia Long
- Department of Information Science TechnologyHainan Normal UniversityHaikouChina
| | - Kaimei Huang
- Department of MathematicsZhejiang Normal UniversityJinhuaChina
| | - Lei Ji
- Department of SciencesGeneis Beijing Co., Ltd.BeijingChina
- Department of SciencesQingdao Geneis Institute of Big Data Mining and Precision MedicineQingdaoChina
| | - Hanyang Lin
- Department of SciencesSequenxe Biological Technology Co., Ltd.XiamenChina
| | - Xiuli Jiang
- Department of SciencesSequenxe Biological Technology Co., Ltd.XiamenChina
| | | | - Geng Tian
- Department of SciencesGeneis Beijing Co., Ltd.BeijingChina
- Department of SciencesQingdao Geneis Institute of Big Data Mining and Precision MedicineQingdaoChina
| | - Kang Ning
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular‐imaging, Center of AI Biology, Department of Bioinformatics and Systems BiologyCollege of Life Science and Technology, Huazhong University of Science and TechnologyWuhanHubeiChina
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3
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Qi F, Fan S, Fang C, Ge L, Lyu J, Huang Z, Zhao S, Zou Y, Huang L, Liu X, Liang Y, Zhang Y, Zhong Y, Zhang H, Xiao L, Zhang X. Orally administrated Lactobacillus gasseri TM13 and Lactobacillus crispatus LG55 can restore the vaginal health of patients recovering from bacterial vaginosis. Front Immunol 2023; 14:1125239. [PMID: 37575226 PMCID: PMC10415204 DOI: 10.3389/fimmu.2023.1125239] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 06/19/2023] [Indexed: 08/15/2023] Open
Abstract
Bacterial vaginosis (BV) is a common infection of the lower genital tract with a vaginal microbiome dysbiosis caused by decreasing of lactobacilli. Previous studies suggested that supplementation with live Lactobacillus may benefit the recovery of BV, however, the outcomes vary in people from different regions. Herein, we aim to evaluate the effectiveness of oral Chinese-origin Lactobacillus with adjuvant metronidazole (MET) on treating Chinese BV patients. In total, 67 Chinese women with BV were enrolled in this parallel controlled trial and randomly assigned to two study groups: a control group treated with MET vaginal suppositories for 7 days and a probiotic group treated with oral Lactobacillus gasseri TM13 and Lactobacillus crispatus LG55 as an adjuvant to MET for 30 days. By comparing the participants with Nugent Scores ≥ 7 and < 7 on days 14, 30, and 90, we found that oral administration of probiotics did not improve BV cure rates (72.73% and 84.00% at day 14, 57.14% and 60.00% at day 30, 32.14% and 48.39% at day 90 for probiotic and control group respectively). However, the probiotics were effective in restoring vaginal health after cure by showing higher proportion of participants with Nugent Scores < 4 in the probiotic group compared to the control group (87.50% and 71.43% on day 14, 93.75% and 88.89% on day 30, and 77.78% and 66.67% on day 90). The relative abundance of the probiotic strains was significantly increased in the intestinal microbiome of the probiotic group compared to the control group at day 14, but no significance was detected after 30 and 90 days. Also, the probiotics were not detected in vaginal microbiome, suggesting that L. gasseri TM13 and L. crispatus LG55 mainly acted through the intestine. A higher abundance of Prevotella timonensis at baseline was significantly associated with long-term cure failure of BV and greatly contributed to the enrichment of the lipid IVA synthesis pathway, which could aggravate inflammation response. To sum up, L. gasseri TM13 and L. crispatus LG55 can restore the vaginal health of patients recovering from BV, and individualized intervention mode should be developed to restore the vaginal health of patients recovering from BV. Clinical trial registration https://classic.clinicaltrials.gov/ct2/show/, identifier NCT04771728.
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Affiliation(s)
- Fengyuan Qi
- Department of Obstetrics and Gynecology, Peking University Shenzhen Hospital, Shenzhen, China
- BGI-Shenzhen, Shenzhen, China
- ShenZhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Shangrong Fan
- Department of Obstetrics and Gynecology, Peking University Shenzhen Hospital, Shenzhen, China
- Institute of Obstetrics and Gynecology, Shenzhen Peking University Hong Kong University of Science and Technology Medical Center, Shenzhen, China
- Shenzhen Key Laboratory on Technology for Early Diagnosis of Major Gynecological Diseases, Peking University Shenzhen Hospital, Shenzhen, China
| | - Chao Fang
- BGI-Shenzhen, Shenzhen, China
- ShenZhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, Shenzhen, China
| | - Lan Ge
- BGI Precision Nutrition (Shenzhen) Technology Co., Ltd, Shenzhen, China
| | - Jinli Lyu
- Department of Obstetrics and Gynecology, Peking University Shenzhen Hospital, Shenzhen, China
- Institute of Obstetrics and Gynecology, Shenzhen Peking University Hong Kong University of Science and Technology Medical Center, Shenzhen, China
- Shenzhen Key Laboratory on Technology for Early Diagnosis of Major Gynecological Diseases, Peking University Shenzhen Hospital, Shenzhen, China
| | - Zhuoqi Huang
- BGI-Shenzhen, Shenzhen, China
- ShenZhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, Shenzhen, China
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Shaowei Zhao
- BGI-Shenzhen, Shenzhen, China
- ShenZhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, Shenzhen, China
| | - Yuanqiang Zou
- BGI-Shenzhen, Shenzhen, China
- ShenZhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, Shenzhen, China
| | - Liting Huang
- Department of Obstetrics and Gynecology, Peking University Shenzhen Hospital, Shenzhen, China
- Institute of Obstetrics and Gynecology, Shenzhen Peking University Hong Kong University of Science and Technology Medical Center, Shenzhen, China
- Shenzhen Key Laboratory on Technology for Early Diagnosis of Major Gynecological Diseases, Peking University Shenzhen Hospital, Shenzhen, China
| | - Xinyang Liu
- Department of Obstetrics and Gynecology, Peking University Shenzhen Hospital, Shenzhen, China
- Institute of Obstetrics and Gynecology, Shenzhen Peking University Hong Kong University of Science and Technology Medical Center, Shenzhen, China
- Shenzhen Key Laboratory on Technology for Early Diagnosis of Major Gynecological Diseases, Peking University Shenzhen Hospital, Shenzhen, China
| | - Yiheng Liang
- Department of Obstetrics and Gynecology, Peking University Shenzhen Hospital, Shenzhen, China
- Institute of Obstetrics and Gynecology, Shenzhen Peking University Hong Kong University of Science and Technology Medical Center, Shenzhen, China
- Shenzhen Key Laboratory on Technology for Early Diagnosis of Major Gynecological Diseases, Peking University Shenzhen Hospital, Shenzhen, China
| | - Yongke Zhang
- Department of Obstetrics and Gynecology, Peking University Shenzhen Hospital, Shenzhen, China
- Institute of Obstetrics and Gynecology, Shenzhen Peking University Hong Kong University of Science and Technology Medical Center, Shenzhen, China
- Shenzhen Key Laboratory on Technology for Early Diagnosis of Major Gynecological Diseases, Peking University Shenzhen Hospital, Shenzhen, China
| | - Yiyi Zhong
- BGI Precision Nutrition (Shenzhen) Technology Co., Ltd, Shenzhen, China
| | - Haifeng Zhang
- BGI Precision Nutrition (Shenzhen) Technology Co., Ltd, Shenzhen, China
| | - Liang Xiao
- BGI-Shenzhen, Shenzhen, China
- ShenZhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, Shenzhen, China
| | - Xiaowei Zhang
- Department of Obstetrics and Gynecology, Peking University Shenzhen Hospital, Shenzhen, China
- Institute of Obstetrics and Gynecology, Shenzhen Peking University Hong Kong University of Science and Technology Medical Center, Shenzhen, China
- Shenzhen Key Laboratory on Technology for Early Diagnosis of Major Gynecological Diseases, Peking University Shenzhen Hospital, Shenzhen, China
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Li L, Wang T, Ning Z, Zhang X, Butcher J, Serrana JM, Simopoulos CMA, Mayne J, Stintzi A, Mack DR, Liu YY, Figeys D. Revealing proteome-level functional redundancy in the human gut microbiome using ultra-deep metaproteomics. Nat Commun 2023; 14:3428. [PMID: 37301875 PMCID: PMC10257714 DOI: 10.1038/s41467-023-39149-2] [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: 11/05/2022] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
Functional redundancy is a key ecosystem property representing the fact that different taxa contribute to an ecosystem in similar ways through the expression of redundant functions. The redundancy of potential functions (or genome-level functional redundancy [Formula: see text]) of human microbiomes has been recently quantified using metagenomics data. Yet, the redundancy of expressed functions in the human microbiome has never been quantitatively explored. Here, we present an approach to quantify the proteome-level functional redundancy [Formula: see text] in the human gut microbiome using metaproteomics. Ultra-deep metaproteomics reveals high proteome-level functional redundancy and high nestedness in the human gut proteomic content networks (i.e., the bipartite graphs connecting taxa to functions). We find that the nested topology of proteomic content networks and relatively small functional distances between proteomes of certain pairs of taxa together contribute to high [Formula: see text] in the human gut microbiome. As a metric comprehensively incorporating the factors of presence/absence of each function, protein abundances of each function and biomass of each taxon, [Formula: see text] outcompetes diversity indices in detecting significant microbiome responses to environmental factors, including individuality, biogeography, xenobiotics, and disease. We show that gut inflammation and exposure to specific xenobiotics can significantly diminish the [Formula: see text] with no significant change in taxonomic diversity.
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Affiliation(s)
- Leyuan Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, 102206, Beijing, China
- School of Pharmaceutical Sciences and Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Tong Wang
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Zhibin Ning
- School of Pharmaceutical Sciences and Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Xu Zhang
- School of Pharmaceutical Sciences and Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - James Butcher
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Joeselle M Serrana
- School of Pharmaceutical Sciences and Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Caitlin M A Simopoulos
- School of Pharmaceutical Sciences and Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Janice Mayne
- School of Pharmaceutical Sciences and Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Alain Stintzi
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - David R Mack
- Department of Paediatrics, Faculty of Medicine, University of Ottawa and Children's Hospital of Eastern Ontario Inflammatory Bowel Disease Centre and Research Institute, Ottawa, ON, K1H 8L1, Canada
| | - Yang-Yu Liu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
- Center for Artificial Intelligence and Modeling, The Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Daniel Figeys
- School of Pharmaceutical Sciences and Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada.
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Wu L, Wang XW, Tao Z, Wang T, Zuo W, Zeng Y, Liu YY, Dai L. Data-driven prediction of colonization outcomes for complex microbial communities. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.19.537502. [PMID: 37131715 PMCID: PMC10153232 DOI: 10.1101/2023.04.19.537502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Complex microbial interactions can lead to different colonization outcomes of exogenous species, be they pathogenic or beneficial in nature. Predicting the colonization of exogenous species in complex communities remains a fundamental challenge in microbial ecology, mainly due to our limited knowledge of the diverse physical, biochemical, and ecological processes governing microbial dynamics. Here, we proposed a data-driven approach independent of any dynamics model to predict colonization outcomes of exogenous species from the baseline compositions of microbial communities. We systematically validated this approach using synthetic data, finding that machine learning models (including Random Forest and neural ODE) can predict not only the binary colonization outcome but also the post-invasion steady-state abundance of the invading species. Then we conducted colonization experiments for two commensal gut bacteria species Enterococcus faecium and Akkermansia muciniphila in hundreds of human stool-derived in vitro microbial communities, confirming that the data-driven approach can successfully predict the colonization outcomes. Furthermore, we found that while most resident species were predicted to have a weak negative impact on the colonization of exogenous species, strongly interacting species could significantly alter the colonization outcomes, e.g., the presence of Enterococcus faecalis inhibits the invasion of E. faecium . The presented results suggest that the data-driven approach is a powerful tool to inform the ecology and management of complex microbial communities.
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