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Shi C, Liang Z, Li T, Hao Q, Xiang H, Xie Q. Metabolome and microbiome analyses of the anti-fatigue mechanism of Acanthopanax senticosus leaves. Food Funct 2024; 15:3791-3809. [PMID: 38511300 DOI: 10.1039/d3fo05311c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Acanthopanax senticosus leaves, widely used as a vegetable and tea, are reported to be beneficial in treating neurological disorders. At present, their anti-fatigue effect remains to be established. In this study, we analyzed the composition of the extracts from A. senticosus leaves and confirmed their antioxidant and anti-inflammatory properties at the cellular level. In mice subjected to exhaustive running on a treadmill, supplementation with A. senticosus leaf extracts enhanced exercise performance and alleviated fatigue via the reversal of exercise-induced 5-HT elevation, metabolic waste accumulation, organ damage, and glucose metabolism-related gene expression. The collective findings from microbiome and metabolomic analyses indicate that A. senticosus leaf extracts increase α-diversity, regulate microbial composition, and reverse exercise-mediated disruption of carbohydrate, creatine, amino acid, and trimethylamine metabolism. This study provides preliminary evidence for the utility of A. senticosus leaves as a promising anti-fatigue food and offers insights into the underlying mechanism.
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Affiliation(s)
- Chao Shi
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, P.R. China.
- School of Life Sciences, Jilin University, Changchun 130012, P.R. China
| | - Zehua Liang
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, P.R. China.
- School of Life Sciences, Jilin University, Changchun 130012, P.R. China
| | - Ting Li
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, P.R. China.
- School of Life Sciences, Jilin University, Changchun 130012, P.R. China
| | - Qi Hao
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, P.R. China.
- School of Life Sciences, Jilin University, Changchun 130012, P.R. China
| | - Hongyu Xiang
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, P.R. China.
- School of Life Sciences, Jilin University, Changchun 130012, P.R. China
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, P.R. China
- Institute of Changbai Mountain Resource and Health, Jilin University, Fusong 134504, P.R. China
| | - Qiuhong Xie
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, P.R. China.
- School of Life Sciences, Jilin University, Changchun 130012, P.R. China
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, P.R. China
- Institute of Changbai Mountain Resource and Health, Jilin University, Fusong 134504, P.R. China
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Molano LAG, Vega-Abellaneda S, Manichanh C. GSR-DB: a manually curated and optimized taxonomical database for 16S rRNA amplicon analysis. mSystems 2024; 9:e0095023. [PMID: 38189256 PMCID: PMC10946287 DOI: 10.1128/msystems.00950-23] [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: 09/08/2023] [Accepted: 11/27/2023] [Indexed: 01/09/2024] Open
Abstract
Amplicon-based 16S ribosomal RNA sequencing remains a widely used method to profile microbial communities, especially in low biomass samples, due to its cost-effectiveness and low-complexity approach. Reference databases are a mainstay for taxonomic assignments, which typically rely on popular databases such as SILVA, Greengenes, Genome Taxonomy Database (GTDB), or Ribosomal Database Project (RDP). However, the inconsistency of the nomenclature across databases and the presence of shortcomings in the annotation of these databases are limiting the resolution of the analysis. To overcome these limitations, we created the GSR database (Greengenes, SILVA, and RDP database), an integrated and manually curated database for bacterial and archaeal 16S amplicon taxonomy analysis. Unlike previous integration approaches, this database creation pipeline includes a taxonomy unification step to ensure consistency in taxonomical annotations. The database was validated with three mock communities, two real data sets, and a 10-fold cross-validation method and compared with existing 16S databases such as Greengenes, Greengenes 2, GTDB, ITGDB, SILVA, RDP, and MetaSquare. Results showed that the GSR database enhances taxonomical annotations of 16S sequences, outperforming current 16S databases at the species level, based on the evaluation of the mock communities. This was confirmed by the 10-fold cross-validation, except for Greengenes 2. The GSR database is available for full-length 16S sequences and the most commonly used hypervariable regions: V4, V1-V3, V3-V4, and V3-V5.IMPORTANCETaxonomic assignments of microorganisms have long been hindered by inconsistent nomenclature and annotation issues in existing databases like SILVA, Greengenes, Greengenes2, Genome Taxonomy Database, or Ribosomal Database Project. To overcome these issues, we created Greengenes-SILVA-RDP database (GSR-DB), accurate and comprehensive taxonomic annotations of 16S amplicon data. Unlike previous approaches, our innovative pipeline includes a unique taxonomy unification step, ensuring consistent and reliable annotations. Our evaluation analyses showed that GSR-DB outperforms existing databases in providing species-level resolution, especially based on mock-community analysis, making it a game-changer for microbiome studies. Moreover, GSR-DB is designed to be accessible to researchers with limited computational resources, making it a powerful tool for scientists across the board. Available for full-length 16S sequences and commonly used hypervariable regions, including V4, V1-V3, V3-V4, and V3-V5, GSR-DB is a go-to database for robust and accurate microbial taxonomy analysis.
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Affiliation(s)
- Leidy-Alejandra G. Molano
- Microbiome Lab, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron, Barcelona, Spain
| | - Sara Vega-Abellaneda
- Microbiome Lab, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron, Barcelona, Spain
| | - Chaysavanh Manichanh
- Microbiome Lab, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron, Barcelona, Spain
- Medicine Department, Universitat Autònoma de Barcelona, Barcelona, Spain
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Xie Z, Canalda-Baltrons A, d'Enfert C, Manichanh C. Shotgun metagenomics reveals interkingdom association between intestinal bacteria and fungi involving competition for nutrients. MICROBIOME 2023; 11:275. [PMID: 38098063 PMCID: PMC10720197 DOI: 10.1186/s40168-023-01693-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 10/08/2023] [Indexed: 12/18/2023]
Abstract
BACKGROUND The accuracy of internal-transcribed-spacer (ITS) and shotgun metagenomics has not been robustly evaluated, and the effect of diet on the composition and function of the bacterial and fungal gut microbiome in a longitudinal setting has been poorly investigated. Here we compared two approaches to study the fungal community (ITS and shotgun metagenomics), proposed an enrichment protocol to perform a reliable mycobiome analysis using a comprehensive in-house fungal database, and correlated dietary data with both bacterial and fungal communities. RESULTS We found that shotgun DNA sequencing after a new enrichment protocol combined with the most comprehensive and novel fungal databases provided a cost-effective approach to perform gut mycobiome profiling at the species level and to integrate bacterial and fungal community analyses in fecal samples. The mycobiome was significantly more variable than the bacterial community at the compositional and functional levels. Notably, we showed that microbial diversity, composition, and functions were associated with habitual diet composition instead of driven by global dietary changes. Our study indicates a potential competitive inter-kingdom interaction between bacteria and fungi for food foraging. CONCLUSION Together, our present work proposes an efficient workflow to study the human gut microbiome integrating robustly fungal, bacterial, and dietary data. These findings will further advance our knowledge of the interaction between gut bacteria and fungi and pave the way for future investigations in human mycobiome. Video Abstract.
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Affiliation(s)
- Zixuan Xie
- Microbiome Lab, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
- Departament de Medicina, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Aleix Canalda-Baltrons
- Microbiome Lab, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Christophe d'Enfert
- Institut Pasteur, Université Paris Cité, INRAE USC2019, Unité Biologie et Pathogénicité Fongiques, Paris, France
| | - Chaysavanh Manichanh
- Microbiome Lab, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain.
- Departament de Medicina, Universitat Autònoma de Barcelona, Barcelona, Spain.
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Cuenca S, Soler Z, Serrano-Gómez G, Xie Z, Barquinero J, Roca J, Sirvent JM, Manichanh C. Dysbiosis: An Indicator of COVID-19 Severity in Critically Ill Patients. Int J Mol Sci 2022; 23:ijms232415808. [PMID: 36555453 PMCID: PMC9779860 DOI: 10.3390/ijms232415808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 11/29/2022] [Accepted: 12/10/2022] [Indexed: 12/15/2022] Open
Abstract
Here, we examined the dynamics of the gut and respiratory microbiomes in severe COVID-19 patients in need of mechanical ventilation in the intensive care unit (ICU). We recruited 85 critically ill patients (53 with COVID-19 and 32 without COVID-19) and 17 healthy controls (HCs) and monitored them for up to 4 weeks. We analyzed the bacterial and fungal taxonomic profiles and loads of 232 gut and respiratory samples and we measured the blood levels of Interleukin 6, IgG, and IgM in COVID-19 patients. Upon ICU admission, the bacterial composition and load in the gut and respiratory samples were altered in critically ill patients compared with HCs. During their ICU stay, the patients experienced increased bacterial and fungal loads, drastic decreased bacterial richness, and progressive changes in bacterial and fungal taxonomic profiles. In the gut samples, six bacterial taxa could discriminate ICU-COV(+) from ICU-COV(-) cases upon ICU admission and the bacterial taxa were associated according to age, PaO2/FiO2, and CRP levels. In the respiratory samples of the ICU-COV(+) patients, bacterial signatures including Pseudomonas and Streptococcus were found to be correlated with the length of ICU stay. Our findings demonstrated that the gut and respiratory microbiome dysbiosis and bacterial signatures associated with critical illness emerged as biomarkers of COVID-19 severity and could be a potential predictor of ICU length of stay. We propose using a high-throughput sequencing approach as an alternative to traditional isolation techniques to monitor ICU patient infection.
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Affiliation(s)
- Silvia Cuenca
- Intensive Care Department (ICU), University Hospital of Girona Dr. Josep Trueta, Avda. França s/n, 17007 Girona, Spain
- Medicine Department, Autonomous University of Barcelona (UAB), 08193 Cerdanyola del Vallès, Spain
| | - Zaida Soler
- Medicine Department, Autonomous University of Barcelona (UAB), 08193 Cerdanyola del Vallès, Spain
- Gut Microbiome Group, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
| | - Gerard Serrano-Gómez
- Medicine Department, Autonomous University of Barcelona (UAB), 08193 Cerdanyola del Vallès, Spain
| | - Zixuan Xie
- Medicine Department, Autonomous University of Barcelona (UAB), 08193 Cerdanyola del Vallès, Spain
- Gut Microbiome Group, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
| | - Jordi Barquinero
- Gene and Cell Therapy, VHIR, Vall d’Hebron Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
| | - Joaquim Roca
- Molecular Biology Institute of Barcelona (IBMB), Spanish National Research Council (CSIC), 08028 Barcelona, Spain
| | - Jose-Maria Sirvent
- Intensive Care Department (ICU), University Hospital of Girona Dr. Josep Trueta, Avda. França s/n, 17007 Girona, Spain
- Institute of Biomedical Research of Girona Dr. Josep Trueta (IDIBGI), 17190 Salt, Spain
| | - Chaysavanh Manichanh
- Medicine Department, Autonomous University of Barcelona (UAB), 08193 Cerdanyola del Vallès, Spain
- Gut Microbiome Group, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
- Correspondence: ; Tel.:+34-934894036
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Oyarzun I, Le Nevé B, Yañez F, Xie Z, Pichaud M, Serrano-Gómez G, Roca J, Veiga P, Azpiroz F, Tap J, Manichanh C. Human gut metatranscriptome changes induced by a fermented milk product are associated with improved tolerance to a flatulogenic diet. Comput Struct Biotechnol J 2022; 20:1632-1641. [PMID: 35465165 PMCID: PMC9014321 DOI: 10.1016/j.csbj.2022.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 04/02/2022] [Accepted: 04/02/2022] [Indexed: 11/29/2022] Open
Abstract
Healthy plant-based diets rich in fermentable residues may induce gas-related symptoms, possibly mediated by the gut microbiota. We previously showed that consumption of a fermented milk product (FMP) containing Bifidobacterium animalis subsp. lactis CNCM I-2494 and lactic acid bacteria improved gastrointestinal (GI) comfort in response to a flatulogenic dietary challenge in healthy individuals. To study the effects of the FMP on gut microbiota activity from those participants, we conducted a metatranscriptomic analysis of fecal samples (n = 262), which were collected during the ingestion of a habitual diet and two series of a 3-day high-residue challenge diet, before and following 28-days of FMP consumption. Most of the FMP species were detected or found enriched upon consumption of the product. FMP mitigated the effect of a flatulogenic diet on gas-related symptoms in several ways. First, FMP consumption was associated with the depletion of gas-producing bacteria and increased hydrogen to methane conversion. It also led to the upregulation of activities such as replication and downregulation of functions related to motility and chemotaxis. Furthermore, upon FMP intake, metabolic activities such as carbohydrate metabolism, attributed to B. animalis and S. thermophilus, were enriched; these activities were coincidentally found to be negatively associated with several GI symptoms. Finally, a more connected microbial ecosystem or mutualistic relationship among microbes was found in responders to the FMP intervention. Taken together, these findings suggest that consumption of the FMP improved the tolerance of a flatulogenic diet through active interactions with the resident gut microbiota.
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Affiliation(s)
- Iñigo Oyarzun
- Microbiome Lab, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | | | - Francisca Yañez
- Microbiome Lab, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | - Zixuan Xie
- Microbiome Lab, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | | | | | - Joaquim Roca
- Molecular Biology Institute of Barcelona (IBMB), Spanish National Research Council (CSIC), Barcelona, Spain
| | | | - Fernando Azpiroz
- Microbiome Lab, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
| | - Julien Tap
- Danone Nutricia Research, Palaiseau, France
| | - Chaysavanh Manichanh
- Microbiome Lab, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
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