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Lee B, Lee SM, Song JW, Choi JW. Gut Microbiota Metabolite Messengers in Brain Function and Pathology at a View of Cell Type-Based Receptor and Enzyme Reaction. Biomol Ther (Seoul) 2024; 32:403-423. [PMID: 38898687 PMCID: PMC11214962 DOI: 10.4062/biomolther.2024.009] [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: 01/10/2024] [Revised: 05/02/2024] [Accepted: 05/25/2024] [Indexed: 06/21/2024] Open
Abstract
The human gastrointestinal (GI) tract houses a diverse microbial community, known as the gut microbiome comprising bacteria, viruses, fungi, and protozoa. The gut microbiome plays a crucial role in maintaining the body's equilibrium and has recently been discovered to influence the functioning of the central nervous system (CNS). The communication between the nervous system and the GI tract occurs through a two-way network called the gut-brain axis. The nervous system and the GI tract can modulate each other through activated neuronal cells, the immune system, and metabolites produced by the gut microbiome. Extensive research both in preclinical and clinical realms, has highlighted the complex relationship between the gut and diseases associated with the CNS, such as Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. This review aims to delineate receptor and target enzymes linked with gut microbiota metabolites and explore their specific roles within the brain, particularly their impact on CNS-related diseases.
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Affiliation(s)
- Bada Lee
- Department of Biomedicinal and Pharmaceutical Sciences, Graduate School, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Soo Min Lee
- Department of Biomedicinal and Pharmaceutical Sciences, Graduate School, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Jae Won Song
- Department of Regulatory Science, Graduate School, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Jin Woo Choi
- Department of Biomedicinal and Pharmaceutical Sciences, Graduate School, Kyung Hee University, Seoul 02447, Republic of Korea
- Department of Regulatory Science, Graduate School, Kyung Hee University, Seoul 02447, Republic of Korea
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Tyagi S, Katara P. A metagenome-wide association study of gut microbiome in patients with AMD, ASD, RA, T2D & VKH diseases. Comput Biol Chem 2024; 110:108076. [PMID: 38678728 DOI: 10.1016/j.compbiolchem.2024.108076] [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: 12/28/2023] [Revised: 03/18/2024] [Accepted: 04/16/2024] [Indexed: 05/01/2024]
Abstract
Clinical studies have already illustrated the associations between gut microbes and diseases, yet fundamental questions remain unclear that how we can universalize this knowledge. Considering the important role of human gut microbial composition in maintaining overall health, it is important to understand the microbial diversity and altered disease conditions of the human gut. Metagenomics provides a way to analyze and understand the microbes and their role in a community manner. It provides qualitative as well as quantitative measurements, in terms of relative abundance. Various studies are already going on to find out the association between microbes and diseases; still, the mined knowledge is limited. Considering the current scenario, using the targeted metagenomics approach, we analyzed the gut microbiome of 99 samples from healthy and diseased individuals. Our metagenomic analysis mainly targeted five diseased microbiomes (i.e., Age-related macular degeneration, Autism spectrum disorder, Rheumatoid arthritis, Type 2 diabetes and Vogt-Koyanagi harada), with compare to healthy microbiome, and reported disease-associated microbiome shift in different conditions.
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Affiliation(s)
- Shivani Tyagi
- Centre of Bioinformatics, IIDS, University of Allahabad, Prayagraj 211002, India
| | - Pramod Katara
- Centre of Bioinformatics, IIDS, University of Allahabad, Prayagraj 211002, India.
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Li W, Lin X, Liang H, Wu Z, Wang M, Sun J, Li X, He W, Gao X, Hu T, Xiao L, Zou Y. Genomic and functional diversity of the human-derived isolates of Faecalibacterium. Front Microbiol 2024; 15:1379500. [PMID: 38873165 PMCID: PMC11169845 DOI: 10.3389/fmicb.2024.1379500] [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: 01/31/2024] [Accepted: 05/06/2024] [Indexed: 06/15/2024] Open
Abstract
Introduction Faecalibacterium is one of the most abundant bacteria in the gut microbiota of healthy adults, highly regarded as a next-generation probiotic. However, the functions of Faecalibacterium genomes from cultured strains and the distribution of different species in populations may differ among different sources. Methods We here performed an extensive analysis of pan-genomes, functions, and safety evaluation of 136 Faecalibacterium genomes collected from 10 countries. Results The genomes are clustered into 11 clusters, with only five of them were characterized and validly nomenclated. Over 80% of the accessory genes and unique genes of Faecalibacterium are found with unknown function, which reflects the importance of expanding the collection of Faecalibacterium strains. All the genomes have the potential to produce acetic acid and butyric acid. Nine clusters of Faecalibacterium are found significantly enriched in the healthy individuals compared with patients with type II diabetes.. Discussion This study provides a comprehensive view of genomic characteristic and functions and of culturable Faecalibacterium bacterium from human gut, and enables clinical advances in the future.
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Affiliation(s)
- Wenxi Li
- BGI-Shenzhen, Shenzhen, China
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Xiaoqian Lin
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Hewei Liang
- BGI-Shenzhen, Shenzhen, China
- BGI Research, Wuhan, China
| | - Zhinan Wu
- BGI-Shenzhen, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Mengmeng Wang
- BGI-Shenzhen, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jingxi Sun
- BGI-Shenzhen, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaofang Li
- BGI-Shenzhen, Shenzhen, China
- BGI College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | | | | | - Tongyuan Hu
- BGI-Shenzhen, Shenzhen, China
- BGI Research, Wuhan, China
| | - Liang Xiao
- BGI-Shenzhen, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI-Shenzhen, Shenzhen, China
| | - Yuanqiang Zou
- BGI-Shenzhen, Shenzhen, China
- BGI College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
- Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI-Shenzhen, Shenzhen, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken, Copenhagen, Denmark
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Averina OV, Poluektova EU, Zorkina YA, Kovtun AS, Danilenko VN. Human Gut Microbiota for Diagnosis and Treatment of Depression. Int J Mol Sci 2024; 25:5782. [PMID: 38891970 PMCID: PMC11171505 DOI: 10.3390/ijms25115782] [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: 04/19/2024] [Revised: 05/21/2024] [Accepted: 05/23/2024] [Indexed: 06/21/2024] Open
Abstract
Nowadays, depressive disorder is spreading rapidly all over the world. Therefore, attention to the studies of the pathogenesis of the disease in order to find novel ways of early diagnosis and treatment is increasing among the scientific and medical communities. Special attention is drawn to a biomarker and therapeutic strategy through the microbiota-gut-brain axis. It is known that the symbiotic interactions between the gut microbes and the host can affect mental health. The review analyzes the mechanisms and ways of action of the gut microbiota on the pathophysiology of depression. The possibility of using knowledge about the taxonomic composition and metabolic profile of the microbiota of patients with depression to select gene compositions (metagenomic signature) as biomarkers of the disease is evaluated. The use of in silico technologies (machine learning) for the diagnosis of depression based on the biomarkers of the gut microbiota is given. Alternative approaches to the treatment of depression are being considered by balancing the microbial composition through dietary modifications and the use of additives, namely probiotics, postbiotics (including vesicles) and prebiotics as psychobiotics, and fecal transplantation. The bacterium Faecalibacterium prausnitzii is under consideration as a promising new-generation probiotic and auxiliary diagnostic biomarker of depression. The analysis conducted in this review may be useful for clinical practice and pharmacology.
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Affiliation(s)
- Olga V. Averina
- Vavilov Institute of General Genetics, Russian Academy of Sciences (RAS), 119333 Moscow, Russia; (E.U.P.); (Y.A.Z.); (A.S.K.); (V.N.D.)
| | - Elena U. Poluektova
- Vavilov Institute of General Genetics, Russian Academy of Sciences (RAS), 119333 Moscow, Russia; (E.U.P.); (Y.A.Z.); (A.S.K.); (V.N.D.)
| | - Yana A. Zorkina
- Vavilov Institute of General Genetics, Russian Academy of Sciences (RAS), 119333 Moscow, Russia; (E.U.P.); (Y.A.Z.); (A.S.K.); (V.N.D.)
- V. Serbsky National Medical Research Centre of Psychiatry and Narcology, Kropotkinsky per. 23, 119034 Moscow, Russia
- Mental-Health Clinic No. 1 Named after N.A. Alekseev, Zagorodnoe Highway 2, 115191 Moscow, Russia
| | - Alexey S. Kovtun
- Vavilov Institute of General Genetics, Russian Academy of Sciences (RAS), 119333 Moscow, Russia; (E.U.P.); (Y.A.Z.); (A.S.K.); (V.N.D.)
| | - Valery N. Danilenko
- Vavilov Institute of General Genetics, Russian Academy of Sciences (RAS), 119333 Moscow, Russia; (E.U.P.); (Y.A.Z.); (A.S.K.); (V.N.D.)
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Vilela FP, Felice AG, Seribelli AA, Rodrigues DP, Soares SC, Allard MW, Falcão JP. Comparative genomics reveals high genetic similarity among strains of Salmonella enterica serovar Infantis isolated from multiple sources in Brazil. PeerJ 2024; 12:e17306. [PMID: 38784399 PMCID: PMC11114117 DOI: 10.7717/peerj.17306] [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: 06/02/2023] [Accepted: 04/04/2024] [Indexed: 05/25/2024] Open
Abstract
Background Salmonella enterica serovar Infantis (Salmonella Infantis) is a zoonotic, ubiquitous and foodborne pathogen of worldwide distribution. Despite Brazil's relevance as a major meat exporter, few studies were conducted to characterize strains of this serovar by genomic analyses in this country. Therefore, this study aimed to assess the diversity of 80 Salmonella Infantis strains isolated from veterinary, food and human sources in Brazil between 2013 and 2018 by comparative genomic analyses. Additional genomes of non-Brazilian countries (n = 18) were included for comparison purposes in some analyses. Methods Analyses of whole-genome multi-locus sequence typing (wgMLST), using PGAdb-builder, and of fragmented genomes, using Gegenees, were conducted to compare the 80 Brazilian strains to the 18 non-Brazilian genomes. Pangenome analyses and calculations were performed for all Salmonella Infantis genomes analyzed. The presence of prophages was determined using PHASTER for the 80 Brazilian strains. The genome plasticity using BLAST Ring Image Generator (BRIG) and gene synteny using Mauve were evaluated for 20 selected Salmonella Infantis genomes from Brazil and ten from non-Brazilian countries. Unique orthologous protein clusters were searched in ten selected Salmonella Infantis genomes from Brazil and ten from non-Brazilian countries. Results wgMLST and Gegenees showed a high genomic similarity among some Brazilian Salmonella Infantis genomes, and also the correlation of some clusters with non-Brazilian genomes. Gegenees also showed an overall similarity >91% among all Salmonella Infantis genomes. Pangenome calculations revealed an open pangenome for all Salmonella Infantis subsets analyzed and a high gene content in the core genomes. Fifteen types of prophages were detected among 97.5% of the Brazilian strains. BRIG and Mauve demonstrated a high structural similarity among the Brazilian and non-Brazilian isolates. Unique orthologous protein clusters related to biological processes, molecular functions, and cellular components were detected among Brazilian and non-Brazilian genomes. Conclusion The results presented using different genomic approaches emphasized the significant genomic similarity among Brazilian Salmonella Infantis genomes analyzed, suggesting wide distribution of closely related genotypes among diverse sources in Brazil. The data generated contributed to novel information regarding the genomic diversity of Brazilian and non-Brazilian Salmonella Infantis in comparison. The different genetically related subtypes of Salmonella Infantis from Brazil can either occur exclusively within the country, or also in other countries, suggesting that some exportation of the Brazilian genotypes may have already occurred.
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Affiliation(s)
- Felipe P. Vilela
- School of Pharmaceutical Sciences of Ribeirão Preto, Department of Clinical Analyses, Toxicology and Food Science, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Andrei G. Felice
- Institute of Biological and Natural Sciences, Department of Microbiology, Immunology and Parasitology, Universidade Federal do Triângulo Mineiro, Uberaba, Minas Gerais, Brazil
| | - Amanda A. Seribelli
- Medical School of Ribeirão Preto, Department of Cellular and Molecular Biology, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Dália P. Rodrigues
- Oswaldo Cruz Institute, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Siomar C. Soares
- Institute of Biological and Natural Sciences, Department of Microbiology, Immunology and Parasitology, Universidade Federal do Triângulo Mineiro, Uberaba, Minas Gerais, Brazil
| | - Marc W. Allard
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, United States of America
| | - Juliana P. Falcão
- School of Pharmaceutical Sciences of Ribeirão Preto, Department of Clinical Analyses, Toxicology and Food Science, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
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Sun X, Chen S, Zhao S, Wang J, Cheng H. Causal relationship of genetically predicted gut microbiota with thyroid cancer: a bidirectional two-sample mendelian randomization study. Front Endocrinol (Lausanne) 2024; 15:1284472. [PMID: 38495789 PMCID: PMC10940398 DOI: 10.3389/fendo.2024.1284472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 01/08/2024] [Indexed: 03/19/2024] Open
Abstract
Background Previous investigations have demonstrated a correlation between the composition of gut microbiota and the development of thyroid cancer (TC). Nonetheless, there was no consensus on the causal effect of gut microbiota composition on TC risk. Therefore, the present study aimed to perform a bidirectional two-sample Mendelian randomization (MR) analysis to explore potential causal associations between gut microbiota and TC risk. Methods Utilizing data from the MiBioGen consortium's genome-wide association studies (GWAS) meta-analysis involving a sample size of 18,340, we identified instrumental variables for 211 gut microbiota taxa. The summary statistics for TC was from relevant large-scale GWAS conducted by the FinnGen consortium. In the first stage, the Inverse-variance weighted (IVW) method was used as the primary estimate method, and the stability of estimations was tested by a battery of sensitivity analyses. In the second stage, a reverse MR analysis was applied to determine whether reverse causality existed. Results According to the IVW method, we identified 9 genetically predicted gut microbiota that were causally correlated with TC risk. Among them, we observed a positive causal effect of Family Christensenellaceae (OR = 1.664, 95% CI: 1.103-2.511, P = 0.015), Family Victivallaceae (OR = 1.268, 95% CI: 1.009-1.594, P = 0.042), Genus Methanobrevibacter (OR = 1.505, 95% CI: 1.049-2.159, P = 0.027), Genus Ruminococcus2 (OR = 1.846, 95% CI: 1.261-2.704, P = 0.002), Genus Subdoligranulum (OR = 1.907, 95% CI: 1.165-3.121, P = 0.010), Phylum Verrucomicrobia (OR = 1.309, 95% CI: 1.027-1.668, P = 0.029) on TC risk, while Class Betaproteobacteria (OR = 0.522, 95% CI: 0.310-0.879, P = 0.015), Family Family XI (OR = 0.753, 95% CI: 0.577-0.983, P = 0.037), Genus Sutterella (OR = 0.596, 95% CI: 0.381-0.933, P = 0.024) might be correlated with a decreased risk of TC. Subsequently, various sensitivity analyses indicated no heterogeneity, directional pleiotropy or outliers. In addition, reverse analysis demonstrated a negative causal effect of TC risk on the abundance of the gut microbiota (Genus Ruminococcus2, OR = 0.947, 95% CI: 0.907-0.989, P = 0.014). Conclusion Genetic evidence suggested that bidirectional causal associations of specific bacteria taxa and the risk of TC, highlighting the association of the "gut-thyroid" axis. Further exploration of the potential microbiota-related mechanisms might have profound implications for public health in terms of the early prevention and treatment of TC.
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Affiliation(s)
- Xiaohe Sun
- Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
- Jiangsu Collaborative Innovation Center of TCM Prevention and Treatment of Tumor, The First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Shuai Chen
- The Second Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Shuoqi Zhao
- Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
- Jiangsu Collaborative Innovation Center of TCM Prevention and Treatment of Tumor, The First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Jingwen Wang
- Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
- Jiangsu Collaborative Innovation Center of TCM Prevention and Treatment of Tumor, The First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Haibo Cheng
- Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
- Jiangsu Collaborative Innovation Center of TCM Prevention and Treatment of Tumor, The First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
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Wang M, Zheng H, Wang S, Luo H, Li Z, Song X, Xu H, Li P, Sun S, Wang Y, Yuan Z. Comparative analysis of changes in diarrhea and gut microbiota in Beigang pigs. Microb Pathog 2023; 185:106441. [PMID: 37944676 DOI: 10.1016/j.micpath.2023.106441] [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: 09/21/2023] [Revised: 10/30/2023] [Accepted: 11/03/2023] [Indexed: 11/12/2023]
Abstract
Increasing evidence indicated that the gut microbiota is a large and complex organic combination, which is closely related to the host health. Diarrhea is a disease with devastating effects on livestock that has been demonstrated to be associated with gut microbiota. Currently, studies on gut microbiota and diarrhea have involved multiple species, but changes in gut microbiota of Beigang pigs during diarrhea have not been characterized. Here, we described gut microbial changes of Beigang pigs during diarrhea. Results indicated that a total of 4423 OTUs were recognized in diarrheic and healthy Beigang pigs, and Firmicutes and Bacteroidota were the most dominant phyla regardless of health status. However, the major components of the gut microbiota changed between diarrheic and healthy Beigang pigs. Bacterial taxonomic analysis revealed that the relative abundances of 3 phyla (Synergistota, Actinobacteriota and Spirochaetota) and 30 genera increased significantly during diarrhea, whereas the relative abundances of 3 phyla (Patescibacteria, Bacteroidota and Fibrobacterota) and 41 genera decreased significantly. In conclusion, this study found significant changes in the gut microbiota of Beigang pigs during diarrhea. Meanwhile, this also lays the foundation for the prevention and treatment of diarrhea in Beigang pigs and the further discovery of more anti-diarrhea probiotics.
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Affiliation(s)
- Meng Wang
- College of Animal Science, Wenzhou Vocational College of Science and Technology, Wenzhou, 325006, China; College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Hao Zheng
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Shuaiwei Wang
- College of Animal Science, Wenzhou Vocational College of Science and Technology, Wenzhou, 325006, China
| | - Houqiang Luo
- College of Animal Science, Wenzhou Vocational College of Science and Technology, Wenzhou, 325006, China
| | - Ziwei Li
- College of Animal Science, Wenzhou Vocational College of Science and Technology, Wenzhou, 325006, China
| | - Xianzhang Song
- College of Animal Science, Wenzhou Vocational College of Science and Technology, Wenzhou, 325006, China
| | - Hongxi Xu
- College of Animal Science, Wenzhou Vocational College of Science and Technology, Wenzhou, 325006, China
| | - Peide Li
- College of Animal Science, Wenzhou Vocational College of Science and Technology, Wenzhou, 325006, China
| | - Siyu Sun
- College of Animal Science, Wenzhou Vocational College of Science and Technology, Wenzhou, 325006, China
| | - Yan Wang
- Tibet Livestock Research Institute, Tibet Academy of Agriculture and Animal Science, Lhasa, 850009, China.
| | - Zhenjie Yuan
- Tibet Livestock Research Institute, Tibet Academy of Agriculture and Animal Science, Lhasa, 850009, China.
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Ding XJ, Li HY, Wang H, Zhang XH, Song M, Jiang XH, Zhang X, Yue YX, Li XH. Altered gut microbiota and metabolites in untreated myasthenia gravis patients. Front Neurol 2023; 14:1248336. [PMID: 37789892 PMCID: PMC10542407 DOI: 10.3389/fneur.2023.1248336] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 08/31/2023] [Indexed: 10/05/2023] Open
Abstract
Objective The homeostasis of the immune system is influenced by the gut microbiota. Previous studies have reported dysbiosis in the gut microbiota of myasthenia gravis (MG) patients. To investigate potential alterations in gut microbiota and metabolites in newly diagnosed and untreated MG patients, we conducted a case-control study. Methods Fecal samples were collected from 11 newly diagnosed and untreated MG patients as well as 11 age-and sex-matched healthy controls. These samples underwent analysis for gut microbiota using 16S ribosomal RNA (rRNA) gene sequencing, while fecal metabolome was analyzed using liquid chromatography-electrospray tandem mass spectrometry system (LC-ESI-MS/MS). Results The microbial community richness (observed species) and diversity (Shannon and Simpson indices) were significantly lower in the MG group compared to the control group. Microbiota composition analysis revealed significant differences between the MG and control groups at phylum, family, and genus levels. Linear discriminant analysis effect size (LEfSe) analysis showed a substantial decrease in abundance of the genus Faecalibacterium within the MG group. Fecal metabolome analysis identified three up-regulated metabolites involved in amino acid metabolism (taurine, creatinine, L-carnitine), one up-regulated metabolite involved in lipid metabolism (oleic acid), with correlation analysis indicating a positive association between Faecalibacterium abundance and creatinine levels. Conclusion Our findings suggest that dysbiosis already exists in newly diagnosed and untreated MG patients, implying that dysbiosis within the gut microbiota may be an initiating factor contributing to MG pathogenesis. Furthermore, F. prausnitzii may hold promise as a probiotic for treating MG.
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Affiliation(s)
- Xiao-Jun Ding
- Department of Neurology, Qilu Hospital (Qingdao) of Shandong University, Qingdao, China
| | - Hong-Yan Li
- Department of Neurology, Qilu Hospital (Qingdao) of Shandong University, Qingdao, China
| | - Huaiping Wang
- Department of Geriatric Medicine, Qingdao Fuwai Cardiovascular Hospital, Qingdao, China
| | - Xue-Hua Zhang
- Department of Neurology, Qilu Hospital (Qingdao) of Shandong University, Qingdao, China
| | - Min Song
- Department of Neurology, Qilu Hospital (Qingdao) of Shandong University, Qingdao, China
| | - Xiao-Han Jiang
- Department of Neurology, Qilu Hospital (Qingdao) of Shandong University, Qingdao, China
| | - Xu Zhang
- Department of Clinical Psychology, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yao-Xian Yue
- Department of Neurology, Qilu Hospital (Qingdao) of Shandong University, Qingdao, China
| | - Xiao-Hong Li
- Department of Neurology, Jinan Central Hospital, Shandong University, Jinan, China
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Botin T, Ramirez-Chamorro L, Vidic J, Langella P, Martin-Verstraete I, Chatel JM, Auger S. The Tolerance of Gut Commensal Faecalibacterium to Oxidative Stress Is Strain Dependent and Relies on Detoxifying Enzymes. Appl Environ Microbiol 2023; 89:e0060623. [PMID: 37382539 PMCID: PMC10370306 DOI: 10.1128/aem.00606-23] [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] [Received: 04/12/2023] [Accepted: 06/12/2023] [Indexed: 06/30/2023] Open
Abstract
Obligate anaerobic bacteria in genus Faecalibacterium are among the most dominant taxa in the colon of healthy individuals and contribute to intestinal homeostasis. A decline in the abundance of this genus is associated with the occurrence of various gastrointestinal disorders, including inflammatory bowel diseases. In the colon, these diseases are accompanied by an imbalance between the generation and elimination of reactive oxygen species (ROS), and oxidative stress is closely linked to disruptions in anaerobiosis. In this work, we explored the impact of oxidative stress on several strains of faecalibacteria. An in silico analysis of complete genomes of faecalibacteria revealed the presence of genes encoding O2- and/or ROS-detoxifying enzymes, including flavodiiron proteins, rubrerythrins, reverse rubrerythrins, superoxide reductases, and alkyl peroxidase. However, the presence and the number of these detoxification systems varied greatly among faecalibacteria. These results were confirmed by O2 stress survival tests, in which we found that strains differed widely in their sensitivity. We showed the protective role of cysteine, which limited the production of extracellular O2•- and improved the survival of Faecalibacterium longum L2-6 under high O2 tension. In the strain F. longum L2-6, we observed that the expression of genes encoding detoxifying enzymes was upregulated in the response to O2 or H2O2 stress but with different patterns of regulation. Based on these results, we propose a first model of the gene regulatory network involved in the response to oxidative stress in F. longum L2-6. IMPORTANCE Commensal bacteria in the genus Faecalibacterium have been proposed for use as next-generation probiotics, but efforts to cultivate and exploit the potential of these strains have been limited by their sensitivity to O2. More broadly, little is known about how commensal and health-associated bacterial species in the human microbiome respond to the oxidative stress that occurs as a result of inflammation in the colon. In this work, we provide insights regarding the genes that encode potential mechanisms of protection against O2 or ROS stress in faecalibacteria, which may facilitate future advances in work with these important bacteria.
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Affiliation(s)
- Tatiana Botin
- Université Paris Saclay, INRAE, AgroParisTech, UMR1319, MICALIS, Jouy-en-Josas, France
| | - Luis Ramirez-Chamorro
- Université Paris Saclay, INRAE, AgroParisTech, UMR1319, MICALIS, Jouy-en-Josas, France
| | - Jasmina Vidic
- Université Paris Saclay, INRAE, AgroParisTech, UMR1319, MICALIS, Jouy-en-Josas, France
| | - Philippe Langella
- Université Paris Saclay, INRAE, AgroParisTech, UMR1319, MICALIS, Jouy-en-Josas, France
| | - Isabelle Martin-Verstraete
- Institut Pasteur, Université Paris Cité, UMR CNRS 6047, Laboratoire Pathogénèse des Bactéries Anaérobies, Paris, France
- Institut Universitaire de France, Paris, France
| | - Jean-Marc Chatel
- Université Paris Saclay, INRAE, AgroParisTech, UMR1319, MICALIS, Jouy-en-Josas, France
| | - Sandrine Auger
- Université Paris Saclay, INRAE, AgroParisTech, UMR1319, MICALIS, Jouy-en-Josas, France
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Martín R, Rios-Covian D, Huillet E, Auger S, Khazaal S, Bermúdez-Humarán LG, Sokol H, Chatel JM, Langella P. Faecalibacterium: a bacterial genus with promising human health applications. FEMS Microbiol Rev 2023; 47:fuad039. [PMID: 37451743 PMCID: PMC10410495 DOI: 10.1093/femsre/fuad039] [Citation(s) in RCA: 42] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 06/08/2023] [Accepted: 07/12/2023] [Indexed: 07/18/2023] Open
Abstract
In humans, many diseases are associated with alterations in gut microbiota, namely increases or decreases in the abundance of specific bacterial groups. One example is the genus Faecalibacterium. Numerous studies have underscored that low levels of Faecalibacterium are correlated with inflammatory conditions, with inflammatory bowel disease (IBD) in the forefront. Its representation is also diminished in the case of several diseases, including colorectal cancer (CRC), dermatitis, and depression. Additionally, the relative presence of this genus is considered to reflect, at least in part, intestinal health status because Faecalibacterium is frequently present at reduced levels in individuals with gastrointestinal diseases or disorders. In this review, we first thoroughly describe updates to the taxonomy of Faecalibacterium, which has transformed a single-species taxon to a multispecies taxon over the last decade. We then explore the links discovered between Faecalibacterium abundance and various diseases since the first IBD-focused studies were published. Next, we examine current available strategies for modulating Faecalibacterium levels in the gut. Finally, we summarize the mechanisms underlying the beneficial effects that have been attributed to this genus. Together, epidemiological and experimental data strongly support the use of Faecalibacterium as a next-generation probiotic (NGP) or live biotherapeutic product (LBP).
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Affiliation(s)
- Rebeca Martín
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - David Rios-Covian
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Eugénie Huillet
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Sandrine Auger
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Sarah Khazaal
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Luis G Bermúdez-Humarán
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Harry Sokol
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
- Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, Gastroenterology Department, F-75012 Paris, France
- Paris Centre for Microbiome Medicine (PaCeMM) FHU, F-75012, Paris, France
| | - Jean-Marc Chatel
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Philippe Langella
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
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11
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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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12
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Souza CMM, Bastos TS, Kaelle GCB, Bortolo M, de Oliveira SG, Félix AP. Fine cassava fibre utilization as a dietary fibre source for dogs: Effects on kibble characteristics, diet digestibility and palatability, faecal metabolites and microbiota. J Anim Physiol Anim Nutr (Berl) 2023. [PMID: 36807651 DOI: 10.1111/jpn.13812] [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: 04/20/2022] [Revised: 12/18/2022] [Accepted: 02/08/2023] [Indexed: 02/21/2023]
Abstract
The objective was to evaluate through three experiments the effects of a fine cassava fibre (CA: 106 µm) on kibble characteristics, coefficients of total tract apparent digestibility (CTTAD) of macronutrients, diet palatability and faecal metabolites and microbiota of dogs. Dietary treatments consisted of a control diet (CO), without an added fibre source and with 4.3% total dietary fibre (TDF), and a diet with 9.6% CA (106 µm), with 8.4% TDF. Experiment I evaluated the physical characteristics of the kibbles. The palatability test was evaluated in experiment II, which compared the diets CO versus CA. In experiment III, 12 adult dogs were randomly assigned to one of the two dietary treatments for 15 days, totalling six replicates/treatment, to assess the CTTAD of macronutrients; faecal characteristics, faecal metabolites and microbiota. The expansion index, kibble size and friability of diets with CA were higher than the CO (p < 0.05). Additionally, the CA diet presented higher palatability than the CO (p < 0.05) but did not affect CTTAD except for those of fibre (p > 0.05). Moreover, a greater faecal concentration of acetate, butyrate and total short-chain fatty acids (SCFA) and a lower faecal concentration of phenol, indole and isobutyrate were observed in dogs fed the CA diet (p < 0.05). Dogs fed with the CA diet presented a greater bacterial diversity and richness and a greater abundance of genera considered to be beneficial for gut health, such as Blautia, Faecalibacterium and Fusobacterium when compared to the CO group (p < 0.05). The inclusion of 9.6% of a fine CA improves the expansion of kibbles and diet palatability without affecting most of the CTTAD of nutrients. Besides, it improves the production of some SCFA and modulates the faecal microbiota of dogs.
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Affiliation(s)
- Camilla M M Souza
- Department of Animal Science, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Taís S Bastos
- Department of Animal Science, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Gislaine C B Kaelle
- Department of Animal Science, Federal University of Paraná, Curitiba, Paraná, Brazil
| | | | - Simone G de Oliveira
- Department of Animal Science, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Ananda P Félix
- Department of Animal Science, Federal University of Paraná, Curitiba, Paraná, Brazil
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13
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Bai Z, Zhang N, Jin Y, Chen L, Mao Y, Sun L, Fang F, Liu Y, Han M, Li G. Comprehensive analysis of 84 Faecalibacterium prausnitzii strains uncovers their genetic diversity, functional characteristics, and potential risks. Front Cell Infect Microbiol 2023; 12:919701. [PMID: 36683686 PMCID: PMC9846645 DOI: 10.3389/fcimb.2022.919701] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 12/09/2022] [Indexed: 01/06/2023] Open
Abstract
Faecalibacterium prausnitzii is a beneficial human gut microbe and a candidate for next-generation probiotics. With probiotics now being used in clinical treatments, concerns about their safety and side effects need to be considered. Therefore, it is essential to obtain a comprehensive understanding of the genetic diversity, functional characteristics, and potential risks of different F. prausnitzii strains. In this study, we collected the genetic information of 84 F . prausnitzii strains to conduct a pan-genome analysis with multiple perspectives. Based on single-copy genes and the sequences of 16S rRNA and the compositions of the pan-genome, different phylogenetic analyses of F. prausnitzii strains were performed, which showed the genetic diversity among them. Among the proteins of the pan-genome, we found that the accessory clusters made a greater contribution to the primary genetic functions of F. prausnitzii strains than the core and specific clusters. The functional annotations of F. prausnitzii showed that only a very small number of proteins were related to human diseases and there were no secondary metabolic gene clusters encoding harmful products. At the same time, complete fatty acid metabolism was detected in F. prausnitzii. In addition, we detected harmful elements, including antibiotic resistance genes, virulence factors, and pathogenic genes, and proposed the probiotic potential risk index (PPRI) and probiotic potential risk score (PPRS) to classify these 84 strains into low-, medium-, and high-risk groups. Finally, 15 strains were identified as low-risk strains and prioritized for clinical application. Undoubtedly, our results provide a comprehensive understanding and insight into F. prausnitzii, and PPRI and PPRS can be applied to evaluate the potential risks of probiotics in general and to guide the application of probiotics in clinical application.
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Affiliation(s)
- Zipeng Bai
- School of Life Sciences, Anhui Medical University, Hefei, Anhui, China
| | - Na Zhang
- School of Life Sciences, Anhui Medical University, Hefei, Anhui, China
| | - Yu Jin
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Long Chen
- School of Life Sciences, Anhui Medical University, Hefei, Anhui, China
| | - Yujie Mao
- School of Life Sciences, Anhui Medical University, Hefei, Anhui, China
| | - Lingna Sun
- School of Life Sciences, Anhui Medical University, Hefei, Anhui, China
| | - Feifei Fang
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ying Liu
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Maozhen Han
- School of Life Sciences, Anhui Medical University, Hefei, Anhui, China
| | - Gangping Li
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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14
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Loayza JJ, Kang S, Schooth L, Teh JJ, de Klerk A, Noon EK, Zhang J, Hu J, Hamilton AL, Wilson-O’Brien A, Trakman GL, Lin W, Ching J, Or L, Sung J, Yu J, Ng S, Kamm M, Morrison M. Effect of food additives on key bacterial taxa and the mucosa-associated microbiota in Crohn's disease. The ENIGMA study. Gut Microbes 2023; 15:2172670. [PMID: 36852457 PMCID: PMC9980662 DOI: 10.1080/19490976.2023.2172670] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
Food additives have been linked to the pro-inflammatory microbial dysbiosis associated with Crohn's disease (CD) but the underlying ecological dynamics are unknown. Here, we examine how selection of food additives affects the growth of multiple strains of a key beneficial bacterium (Faecalibacterium prausnitzii), axenic clinical isolates of proinflammatory bacteria from CD patients (Proteus, Morganella, and Klebsiella spp.), and the consortia of mucosa-associated microbiota recovered from multiple Crohn's disease patients. Bacterial growth of the axenic isolates was evaluated using a habitat-simulating medium supplemented with either sodium sulfite, aluminum silicate, carrageenan, carboxymethylcellulose, polysorbate 80, saccharin, sucralose, or aspartame, intended to approximate concentrations found in food. The microbial consortia recovered from post-operative CD patient mucosal biopsy samples were challenged with either carboxymethylcellulose and/or polysorbate 80, and the bacterial communities compared to unchallenged consortia by 16S rRNA gene amplicon profiling. Growth of all F. prausnitzii strains was arrested when either sodium sulfite or polysorbate 80 was added to cultures at baseline or mid-exponential phase of growth, and the inhibitory effects on the Gram-negative bacteria by sodium sulfite were conditional on oxygen availability. The effects from polysorbate 80, saccharin, carrageenan, and/or carboxymethylcellulose on these bacteria were strain-specific. In addition to their direct effects on bacterial growth, polysorbate 80 and/or carboxymethylcellulose can drive profound changes in the CD mucosa-associated microbiota via niche expansion of Proteus and/or Veillonellaceae - both implicated in early Crohn's disease recurrence. These studies on the interaction of food additives with the enteric microbiota provide a basis for dietary management in Crohn's disease.
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Affiliation(s)
- J.J. Jimenez Loayza
- Frazer Institute, Faculty of Medicine, University of Queensland, Brisbane, Australia
| | - S. Kang
- Frazer Institute, Faculty of Medicine, University of Queensland, Brisbane, Australia
| | - L. Schooth
- Frazer Institute, Faculty of Medicine, University of Queensland, Brisbane, Australia
| | - J. J. Teh
- Frazer Institute, Faculty of Medicine, University of Queensland, Brisbane, Australia
| | - A. de Klerk
- Frazer Institute, Faculty of Medicine, University of Queensland, Brisbane, Australia
| | - E. K. Noon
- Frazer Institute, Faculty of Medicine, University of Queensland, Brisbane, Australia
| | - J. Zhang
- Department of Medicine and Therapeutics, the Chinese University of Hong Kong, Hong Kong, China,State Key Laboratory of Digestive Diseases, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Hong Kong, China,Microbiota I-Center (Magic), Hong Kong, China
| | - J. Hu
- Department of Medicine and Therapeutics, the Chinese University of Hong Kong, Hong Kong, China,State Key Laboratory of Digestive Diseases, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Hong Kong, China,Microbiota I-Center (Magic), Hong Kong, China
| | - A. L. Hamilton
- Department of Gastroenterology, St Vincent’s Hospital, Melbourne, Australia,Department of Medicine, the University of Melbourne, Melbourne, Australia
| | - A. Wilson-O’Brien
- Department of Gastroenterology, St Vincent’s Hospital, Melbourne, Australia,Department of Medicine, the University of Melbourne, Melbourne, Australia
| | - G. L. Trakman
- Department of Gastroenterology, St Vincent’s Hospital, Melbourne, Australia,Department of Medicine, the University of Melbourne, Melbourne, Australia
| | - W. Lin
- Microbiota I-Center (Magic), Hong Kong, China
| | - J. Ching
- Department of Medicine and Therapeutics, the Chinese University of Hong Kong, Hong Kong, China,State Key Laboratory of Digestive Diseases, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Hong Kong, China,Microbiota I-Center (Magic), Hong Kong, China
| | - L. Or
- Department of Medicine and Therapeutics, the Chinese University of Hong Kong, Hong Kong, China,State Key Laboratory of Digestive Diseases, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Hong Kong, China
| | - J.J.Y. Sung
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - J. Yu
- Department of Medicine and Therapeutics, the Chinese University of Hong Kong, Hong Kong, China,State Key Laboratory of Digestive Diseases, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Hong Kong, China
| | - S.C. Ng
- Department of Medicine and Therapeutics, the Chinese University of Hong Kong, Hong Kong, China,State Key Laboratory of Digestive Diseases, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Hong Kong, China,Microbiota I-Center (Magic), Hong Kong, China,Centre for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - M.A. Kamm
- Department of Gastroenterology, St Vincent’s Hospital, Melbourne, Australia,Department of Medicine, the University of Melbourne, Melbourne, Australia
| | - M. Morrison
- Frazer Institute, Faculty of Medicine, University of Queensland, Brisbane, Australia,CONTACT M. Morrison Mark Morrison Frazer Institute, Faculty of Medicine, University of Queensland Woolloongabba, Australia
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15
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Functional Fermented Milk with Fruit Pulp Modulates the In Vitro Intestinal Microbiota. Foods 2022; 11:foods11244113. [PMID: 36553855 PMCID: PMC9778618 DOI: 10.3390/foods11244113] [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: 11/13/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
The effect of putative probiotic fermented milk (FM) with buriti pulp (FMB) or passion fruit pulp (FMPF) or without fruit pulp (FMC) on the microbiota of healthy humans was evaluated. FM formulations were administered into a simulator of the human intestinal microbial ecosystem (SHIME®) to evaluate the viability of lactic acid bacteria (LAB), microbiota composition, presence of short-chain fatty acids (SCFA), and ammonium ions. The probiotic LAB viability in FM was affected by the addition of the fruit pulp. Phocaeicola was dominant in the FMPF and FMB samples; Bifidobacterium was related to FM formulations, while Alistipes was associated with FMPF and FMB, and Lactobacillus and Lacticaseibacillus were predominant in FMC. Trabulsiella was the central element in the FMC, while Mediterraneibacter was the central one in the FMPF and FMB networks. The FM formulations increased the acetic acid, and a remarkably high amount of propionic and butyric acids were detected in the FMB treatment. All FM formulations decreased the ammonium ions compared to the control; FMPF samples stood out for having lower amounts of ammonia. The probiotic FM with fruit pulp boosted the beneficial effects on the intestinal microbiota of healthy humans in addition to increasing SCFA in SHIME® and decreasing ammonium ions, which could be related to the presence of bioactive compounds.
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16
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Morales C, Rojas G, Rebolledo C, Rojas-Herrera M, Arias-Carrasco R, Cuadros-Orellana S, Maracaja-Coutinho V, Saavedra K, Leal P, Lanas F, Salazar LA, Saavedra N. Characterization of microbial communities from gut microbiota of hypercholesterolemic and control subjects. Front Cell Infect Microbiol 2022; 12:943609. [PMID: 36523636 PMCID: PMC9745040 DOI: 10.3389/fcimb.2022.943609] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 10/31/2022] [Indexed: 11/30/2022] Open
Abstract
Introduction In recent years, several studies have evidenced the importance of the microbiome to host physiology as metabolism regulator, along with its potential role in triggering various diseases. In this study, we analyzed the gut microbiota in hypercholesterolemic (cases) and normocholesterolemic (controls) individuals to identify characteristic microbial signature for each condition. Methods Stool samples were obtained from 57 adult volunteers (27 hypercholesterolemic and 30 controls). The taxonomic profiling of microbial communities was performed using high-throughput sequencing of 16S rRNA V3-V4 amplicons, followed by data analysis using Quantitative Insights Into Microbial Ecology 2 (QIIME2) and linear discriminant analysis (LDA) effect size (LEfSe). Results Significant differences were observed in weight, height, body mass index (BMI) and serum levels of triglycerides, total cholesterol and low-density lipoprotein cholesterol (LDL-C) between the groups (p<0.05). LEfSe showed differentially abundant prokaryotic taxa (α=0.05, LDA score > 2.0) in the group of hypercholesterolemic individuals (Methanosphaera, Rothia, Chromatiales, Clostridiales, Bacillaceae and Coriobacteriaceae) and controls (Faecalibacterium, Victivallis and Selenomonas) at various taxonomic levels. In addition, through the application of Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2 (PICRUSt2), the predominance of pathways related to biosynthesis in hypercholesterolemic patients was established, compared to controls in which degradation pathways were predominant. Finally, in the analysis of co-occurrence networks, it was possible to identify associations between the microorganisms present in both studied groups. Conclusion Our results point out to unique microbial signatures, which likely play a role on the cholesterol metabolism in the studied population.
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Affiliation(s)
- Cristian Morales
- Centro de Biología Molecular y Farmacogenética, Núcleo Científico-Tecnológico en Biorecursos BIOREN, Universidad de La Frontera, Temuco, Chile,Tecnología Médica, Facultad de Salud, Universidad Santo Tomás, Temuco, Chile
| | - Gabriel Rojas
- Centro de Biología Molecular y Farmacogenética, Núcleo Científico-Tecnológico en Biorecursos BIOREN, Universidad de La Frontera, Temuco, Chile
| | - Camilo Rebolledo
- Centro de Biología Molecular y Farmacogenética, Núcleo Científico-Tecnológico en Biorecursos BIOREN, Universidad de La Frontera, Temuco, Chile
| | - Marcelo Rojas-Herrera
- Centro de Genética y Genómica, Facultad de Medicina, Universidad del Desarrollo, Santiago, Chile,Subdepartamento de Genética Molecular, Instituto de Salud Pública de Chile, Santiago, Chile
| | - Raúl Arias-Carrasco
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación, Universidad Tecnológica Metropolitana, Santiago, Chile
| | - Sara Cuadros-Orellana
- Centro de Biotecnología de los Recursos Naturales, Facultad de Ciencias Agrarias y Forestales, Universidad Católica del Maule, Talca, Chile
| | - Vinicius Maracaja-Coutinho
- Advanced Center for Chronic Diseases - ACCDiS, Facultad de Química y Ciencias Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Kathleen Saavedra
- Centro de Biología Molecular y Farmacogenética, Núcleo Científico-Tecnológico en Biorecursos BIOREN, Universidad de La Frontera, Temuco, Chile
| | - Pamela Leal
- Departamento de Ciencias Agronómicas y Recursos Naturales, Facultad de Ciencias Agropecuarias y Medioambiente, Temuco, Chile
| | - Fernando Lanas
- Departamento de Medicina Interna, Facultad de Medicina, Universidad de La Frontera, Temuco, Chile
| | - Luis A. Salazar
- Centro de Biología Molecular y Farmacogenética, Núcleo Científico-Tecnológico en Biorecursos BIOREN, Universidad de La Frontera, Temuco, Chile
| | - Nicolás Saavedra
- Centro de Biología Molecular y Farmacogenética, Núcleo Científico-Tecnológico en Biorecursos BIOREN, Universidad de La Frontera, Temuco, Chile,*Correspondence: Nicolás Saavedra,
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17
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Shang P, Dong S, Han Y, Bo S, Ye Y, Duan M, Chamba Y. Environmental exposure to swine farms reshapes human gut microbiota. CHEMOSPHERE 2022; 307:135558. [PMID: 35780983 DOI: 10.1016/j.chemosphere.2022.135558] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/21/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
The gut microbiota can change to varying degrees because of changes in the environment. In the present study, we performed microbial amplicon sequencing on the feces of people who had long-term exposure to swine farms (F) and that of people living in normal environments (S) to investigate the impact of the environment on the human gut microbiota. A total of 1,283,503 high-quality ordered sequences were obtained, which provided different levels of microbial classification and statistics. We found that different environments did not alter the richness and diversity of the microbial communities in participants, but caused significant changes in the proportion of some bacteria. The main bacterial phyla found in group F participants were Firmicutes (69.44-89.03%), Actinobacteria (1.7-18.95%), and Bacteroidetes (1.17-22.35%); those found in group S participants were Firmicutes (49.93-95.04%), Bacteroidetes (0.62-39.59%), and Proteobacteria (0.98-11.95%). Additionally, because of changes in phylum proportions, the Bugbase phenotypic classification predicted an increase in the proportion of Gram-positive bacteria in group F and an increase in the proportion of Gram-negative bacteria in group S. In conclusion, our findings suggest that human exposure to swine farms can reshape the gut microbiota, resulting in changes in the microbial abundances. This change can potentially reduce the odds of developing bowel disease and contribute to the prevention of intestinal diseases, providing a theoretical basis for improving human health.
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Affiliation(s)
- Peng Shang
- College of Animal Science, Tibet Agriculture and Animal Husbandry University, Linzhi, Tibet, People's Republic of China; The Provincial and Ministerial Co-founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, People's Republic of China
| | - Shixiong Dong
- College of Animal Science, Tibet Agriculture and Animal Husbandry University, Linzhi, Tibet, People's Republic of China; The Provincial and Ministerial Co-founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, People's Republic of China
| | - Yuqing Han
- College of Animal Science, Tibet Agriculture and Animal Husbandry University, Linzhi, Tibet, People's Republic of China; The Provincial and Ministerial Co-founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, People's Republic of China
| | - Suxue Bo
- College of Animal Science, Tibet Agriculture and Animal Husbandry University, Linzhi, Tibet, People's Republic of China; The Provincial and Ministerial Co-founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, People's Republic of China
| | - Yourong Ye
- College of Animal Science, Tibet Agriculture and Animal Husbandry University, Linzhi, Tibet, People's Republic of China; The Provincial and Ministerial Co-founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, People's Republic of China
| | - Mengqi Duan
- College of Animal Science, Tibet Agriculture and Animal Husbandry University, Linzhi, Tibet, People's Republic of China; The Provincial and Ministerial Co-founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, People's Republic of China
| | - Yangzom Chamba
- College of Animal Science, Tibet Agriculture and Animal Husbandry University, Linzhi, Tibet, People's Republic of China; The Provincial and Ministerial Co-founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, People's Republic of China.
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18
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Reconfiguration of Gut Microbiota and Reprogramming of Liver Metabolism with Phycobiliproteins Bioactive Peptides to Rehabilitate Obese Rats. Nutrients 2022; 14:nu14173635. [PMID: 36079890 PMCID: PMC9460120 DOI: 10.3390/nu14173635] [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: 07/21/2022] [Revised: 08/10/2022] [Accepted: 08/31/2022] [Indexed: 11/23/2022] Open
Abstract
Phycobiliproteins (derived from Arthrospira platensis) bioactive peptide extracts (PPE) possess multiple pharmacological effects in the mitigation of human metabolic disorders. The role of PPE in the treatment of diet-induced obesity and the understanding of the underlying mechanism between the gut microbiome and metabolic blood circulation for obese patients remains poorly understood. In this study, we showed that PPE attenuated obesity by reducing body weight, and ameliorated glucose and lipid indexes in serum. In particular, PPE is postulated to mitigate liver steatosis and insulin resistance. On the other hand, dietary treatment with PPE was found to “reconfigure” the gut microbiota in the way that the abundances were elevated for Akkermansia_muciniphila, beneficial Lactobacillus and Romboutsia, SCFA-producing species Faecalibacterium prausnitzii, Lachnospiraceae_bacterium, Clostridiales_bacterium, probiotics Clostridium sp., Enterococcus faecium, and Lactobacillus_johnsonii, while the abundance of Firmicutes was reduced and that of Bacteroidetes was increased to reverse the imbalance of Firmicutes/Bacteroidetes ratio. Finally, the metabolomics of circulating serum using UHPLC-MS/MS illustrated that PPE supplementation indeed promoted lipid metabolism in obese rats. As summary, it was seen that PPE reprogrammed the cell metabolism to prevent the aggravation of obesity. Our findings strongly support that PPE can be regarded as a potential therapeutic dietary supplement for obesity.
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19
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Hankel J, Chuppava B, Wilke V, Hartung CB, Muthukumarasamy U, Strowig T, Bach Knudsen KE, Kamphues J, Visscher C. High Dietary Intake of Rye Affects Porcine Gut Microbiota in a Salmonella Typhimurium Infection Study. PLANTS 2022; 11:plants11172232. [PMID: 36079614 PMCID: PMC9460007 DOI: 10.3390/plants11172232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 08/25/2022] [Accepted: 08/25/2022] [Indexed: 11/16/2022]
Abstract
Bacterial fermentation of undigested carbohydrates in the hindgut has considerable potential for the stimulation or inhibition of the growth of distinct bacteria within microbiota. The aim of the present study was to evaluate whether high levels of rye affect porcine gut microbiota composition with subsequent effects on the load of Salmonella Typhimurium, an intestinal pathogen with zoonotic relevance. Therefore, forty-two 25-day-old piglets were allocated to two groups and fed a diet containing either 69% wheat or 69% rye for 35 days. One week after introducing the two different diets, the piglets were experimentally infected with Salmonella Typhimurium. The microbiota composition of cecal and fecal samples of the piglets were evaluated 28 days after infection. In the cecum, promoted growth of Bifidobacterium, several lactic acid bacteria and Faecalibacterium prausnitzii were seen in pigs fed the diet containing 69% rye. Bacterial species belonging to the genera Bifidobacterium and Catenisphaera were associated with differing bacterial counts of Salmonella Typhimurium detected in the cecal contents of all piglets in both feeding groups via cultural cultivation. The high intake of rye instead of wheat seems to promote the growth of beneficial intestinal bacteria accompanied by impaired growth conditions for the foodborne pathogen Salmonella Typhimurium.
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Affiliation(s)
- Julia Hankel
- Institute for Animal Nutrition, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany
- Correspondence:
| | - Bussarakam Chuppava
- Institute for Animal Nutrition, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany
| | - Volker Wilke
- Institute for Animal Nutrition, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany
| | - Clara Berenike Hartung
- Institute for Animal Nutrition, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany
| | - Uthayakumar Muthukumarasamy
- Helmholtz Center for Infection Research, 38124 Braunschweig, Germany
- Hannover Medical School, 30625 Hannover, Germany
| | - Till Strowig
- Helmholtz Center for Infection Research, 38124 Braunschweig, Germany
- Hannover Medical School, 30625 Hannover, Germany
| | | | - Josef Kamphues
- Institute for Animal Nutrition, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany
| | - Christian Visscher
- Institute for Animal Nutrition, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany
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20
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Genome-based, phenotypic and chemotaxonomic classification of Faecalibacterium strains: proposal of three novel species Faecalibacterium duncaniae sp. nov., Faecalibacterium hattorii sp. nov. and Faecalibacterium gallinarum sp. nov. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005379] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Faecalibacterium prausnitzii
is one of the most important butyrate-producing bacteria in the human gut. Previous studies have suggested the presence of several phylogenetic groups, with differences at the species level, in the species, and a taxonomic re-evaluation is thus essential for further understanding of ecology of the important human symbiont. Here we examine the phenotypic, physiological, chemotaxonomic and phylogenomic characteristics of six
F. prausnitzii
strains (BCRC 81047T=ATCC 27768T, A2-165T=JCM 31915T, APC918/95b=JCM 39207, APC942/30−2=JCM 39208, APC924/119=JCM 39209 and APC922/41−1T=JCM 39210T) deposited in public culture collections with two reference strains of
Faecalibacterium butyricigenerans
JCM 39212T and
Faecalibacterium longum
JCM 39211T.
Faecalibacterium
sp. JCM 17207T isolated from caecum of broiler chicken was also included. Three strains of
F. prausnitzii
(BCRC 81047T, JCM 39207 and JCM 39209) shared more than 96.6 % average nucleotide identity (ANI) and 69.6 % digital DNA–DNA hybridization (dDDH) values, indicating that the three strains are members of the same species. On the other hand, the remaining three strains of
F. prausnitzii
(JCM 31915T, JCM 39208 and JCM 39210T) were clearly separated from the above three strains based on the ANI and dDDH values. Rather, JCM 39208 showed ANI and dDDH values over the cut-off values of species discrimination (>70 % dDDH and >95–96 % ANI) with
F. longum
JCM 39211T, whereas JCM 31915T, JCM 39210T and JCM 17207T did not share dDDH and ANI values over the currently accepted cut-off values with any of the tested strains, including among them. Furthermore, the cellular fatty acid patterns of these strains were slightly different from other
F. prausnitzii
strains. Based on the collected data,
F. prausnitzii
JCM 31915T,
F. prausnitzii
JCM 39210T and
Faecalibacterium
sp. JCM 17207T represent three novel species of the genus
Faecalibacterium
, for which the names Faecalibacterium duncaniae sp. nov. (type strain JCM 31915T=DSM 17677T=A2-165T), Faecalibacterium hattorii sp. nov. (type strain JCM 39210T=DSM 107841T=APC922/41-1T) and Faecalibacterium gallinarum sp. nov. (type strain JCM 17207T=DSM 23680T=ic1379T) are proposed.
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21
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Bellais S, Nehlich M, Ania M, Duquenoy A, Mazier W, van den Engh G, Baijer J, Treichel NS, Clavel T, Belotserkovsky I, Thomas V. Species-targeted sorting and cultivation of commensal bacteria from the gut microbiome using flow cytometry under anaerobic conditions. MICROBIOME 2022; 10:24. [PMID: 35115054 PMCID: PMC8812257 DOI: 10.1186/s40168-021-01206-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 12/04/2021] [Indexed: 05/20/2023]
Abstract
BACKGROUND There is a growing interest in using gut commensal bacteria as "next generation" probiotics. However, this approach is still hampered by the fact that there are few or no strains available for specific species that are difficult to cultivate. Our objective was to adapt flow cytometry and cell sorting to be able to detect, separate, isolate, and cultivate new strains of commensal species from fecal material. We focused on the extremely oxygen sensitive (EOS) species Faecalibacterium prausnitzii and the under-represented, health-associated keystone species Christensenella minuta as proof-of-concept. RESULTS A BD Influx® cell sorter was equipped with a glovebox that covered the sorting area. This box was flushed with nitrogen to deplete oxygen in the enclosure. Anaerobic conditions were maintained during the whole process, resulting in only minor viability loss during sorting and culture of unstained F. prausnitzii strains ATCC 27766, ATCC 27768, and DSM 17677. We then generated polyclonal antibodies against target species by immunizing rabbits with heat-inactivated bacteria. Two polyclonal antibodies were directed against F. prausnitzii type strains that belong to different phylogroups, whereas one was directed against C. minuta strain DSM 22607. The specificity of the antibodies was demonstrated by sorting and sequencing the stained bacterial fractions from fecal material. In addition, staining solutions including LIVE/DEAD™ BacLight™ Bacterial Viability staining and polyclonal antibodies did not severely impact bacterial viability while allowing discrimination between groups of strains. Finally, we combined these staining strategies as well as additional criteria based on bacterial shape for C. minuta and were able to detect, isolate, and cultivate new F. prausnitzii and C. minuta strains from healthy volunteer's fecal samples. CONCLUSIONS Targeted cell-sorting under anaerobic conditions is a promising tool for the study of fecal microbiota. It gives the opportunity to quickly analyze microbial populations, and can be used to sort EOS and/or under-represented strains of interest using specific antibodies, thus opening new avenues for culture experiments. Video abstract.
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Affiliation(s)
| | | | - Maryne Ania
- BIOASTER, 28 rue du Docteur Roux, 75015, Paris, France
| | | | | | | | - Jan Baijer
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Département de la Recherche Fondamentale, Institut de Biologie François Jacob, Institut de Radiobiologie Cellulaire et Moléculaire, Fontenay-aux-Roses, France
| | - Nicole Simone Treichel
- Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital of RWTH, Aachen, Germany
| | - Thomas Clavel
- Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital of RWTH, Aachen, Germany
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22
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Derosa L, Routy B, Thomas AM, Iebba V, Zalcman G, Friard S, Mazieres J, Audigier-Valette C, Moro-Sibilot D, Goldwasser F, Silva CAC, Terrisse S, Bonvalet M, Scherpereel A, Pegliasco H, Richard C, Ghiringhelli F, Elkrief A, Desilets A, Blanc-Durand F, Cumbo F, Blanco A, Boidot R, Chevrier S, Daillère R, Kroemer G, Alla L, Pons N, Le Chatelier E, Galleron N, Roume H, Dubuisson A, Bouchard N, Messaoudene M, Drubay D, Deutsch E, Barlesi F, Planchard D, Segata N, Martinez S, Zitvogel L, Soria JC, Besse B. Intestinal Akkermansia muciniphila predicts clinical response to PD-1 blockade in patients with advanced non-small-cell lung cancer. Nat Med 2022; 28:315-324. [PMID: 35115705 DOI: 10.1038/s41591-021-01655-5] [Citation(s) in RCA: 228] [Impact Index Per Article: 114.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 12/06/2021] [Indexed: 12/13/2022]
Abstract
Aside from PD-L1 expression, biomarkers of response to immune checkpoint inhibitors (ICIs) in non-small-cell lung cancer (NSCLC) are needed. In a previous retrospective analysis, we documented that fecal Akkermansia muciniphila (Akk) was associated with clinical benefit of ICI in patients with NSCLC or kidney cancer. In the current study, we performed shotgun-metagenomics-based microbiome profiling in a large cohort of patients with advanced NSCLC (n = 338) treated with first- or second-line ICIs to prospectively validate the predictive value of fecal Akk. Baseline stool Akk was associated with increased objective response rates and overall survival in multivariate analyses, independent of PD-L1 expression, antibiotics, and performance status. Intestinal Akk was accompanied by a richer commensalism, including Eubacterium hallii and Bifidobacterium adolescentis, and a more inflamed tumor microenvironment in a subset of patients. However, antibiotic use (20% of cases) coincided with a relative dominance of Akk above 4.8% accompanied with the genus Clostridium, both associated with resistance to ICI. Our study shows significant differences in relative abundance of Akk that may represent potential biomarkers to refine patient stratification in future studies.
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Affiliation(s)
- Lisa Derosa
- Gustave Roussy Cancer Campus, Villejuif, France.,Cancer Medicine Department, Gustave Roussy, Villejuif, France.,Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée, Ligue Nationale contre le Cancer, Villejuif, France.,Université Paris-Saclay, Ile-de-France, France
| | - Bertrand Routy
- Department of Medicine, Centre Hospitalier de l'Université de Montréal (CHUM), Hematology-Oncology Division, Montréal, Quebec, Canada.,Centre de Recherche du CHUM (CRCHUM), Montréal, Quebec, Canada
| | - Andrew Maltez Thomas
- Department CIBIO, University of Trento, Trento, Italy.,European Institute of Oncology (IEO) IRCCS, Milan, Italy
| | - Valerio Iebba
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
| | - Gerard Zalcman
- Thoracic Oncology Department-CIC1425/CLIP2 Paris-Nord, Hospital Bichat-Claude Bernard, AP-HP, Université Paris-Diderot, Paris, France
| | - Sylvie Friard
- Pneumology Department, Foch Hospital, Suresnes, France
| | - Julien Mazieres
- Department of Pneumology, Toulouse University Hospital, Toulouse, France
| | | | - Denis Moro-Sibilot
- Department of Thoracic Oncology, Centre Hospitalier Universitaire, Grenoble, France
| | - François Goldwasser
- UPR 4466, Paris Descartes University, Sorbonne Paris Cité, Paris, France.,Department of Medical Oncology, Cochin Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France.,Immunomodulatory Therapies Multidisciplinary Study Group (CERTIM), Paris, France
| | - Carolina Alves Costa Silva
- Gustave Roussy Cancer Campus, Villejuif, France.,Cancer Medicine Department, Gustave Roussy, Villejuif, France
| | | | | | - Arnaud Scherpereel
- Department of Pulmonary and Thoracic Oncology, University of Lille, University Hospital (CHU), Lille, France
| | | | - Corentin Richard
- Department of Medicine, Centre Hospitalier de l'Université de Montréal (CHUM), Hematology-Oncology Division, Montréal, Quebec, Canada.,Centre de Recherche du CHUM (CRCHUM), Montréal, Quebec, Canada
| | - François Ghiringhelli
- Cancer Biology Transfer Platform, Centre Georges-François Leclerc, Dijon, France.,Centre de Recherche INSERM LNC-UMR1231, Dijon, France.,Department of Medical Oncology, Centre Georges-François Leclerc, Dijon, France
| | - Arielle Elkrief
- Department of Medicine, Centre Hospitalier de l'Université de Montréal (CHUM), Hematology-Oncology Division, Montréal, Quebec, Canada.,Centre de Recherche du CHUM (CRCHUM), Montréal, Quebec, Canada
| | - Antoine Desilets
- Department of Medicine, Centre Hospitalier de l'Université de Montréal (CHUM), Hematology-Oncology Division, Montréal, Quebec, Canada.,Centre de Recherche du CHUM (CRCHUM), Montréal, Quebec, Canada
| | | | - Fabio Cumbo
- Department CIBIO, University of Trento, Trento, Italy
| | - Aitor Blanco
- Department CIBIO, University of Trento, Trento, Italy
| | - Romain Boidot
- Unit of Molecular Biology, Department of Biology and Pathology of Tumors, Georges-François Leclerc Cancer Center, UNICANCER, Dijon, France
| | - Sandy Chevrier
- Unit of Molecular Biology, Department of Biology and Pathology of Tumors, Georges-François Leclerc Cancer Center, UNICANCER, Dijon, France
| | | | - Guido Kroemer
- Gustave Roussy Cancer Campus, Villejuif, France.,UPR 4466, Paris Descartes University, Sorbonne Paris Cité, Paris, France.,Centre de Recherche des Cordeliers, INSERM U1138, Equipe labellisée-Ligue contre le cancer, Université de Paris, Institut Universitaire de France, Paris, France.,Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France.,Pôle de Biologie, Hôpital Européen Georges Pompidou, AP-HP, Paris, France
| | - Laurie Alla
- Université Paris-Saclay, INRAE, MGP, Jouy en Josas, France
| | - Nicolas Pons
- Université Paris-Saclay, INRAE, MGP, Jouy en Josas, France
| | | | | | - Hugo Roume
- Université Paris-Saclay, INRAE, MGP, Jouy en Josas, France
| | | | - Nicole Bouchard
- Centre Hospitalier de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Meriem Messaoudene
- Department of Medicine, Centre Hospitalier de l'Université de Montréal (CHUM), Hematology-Oncology Division, Montréal, Quebec, Canada.,Centre de Recherche du CHUM (CRCHUM), Montréal, Quebec, Canada
| | | | - Eric Deutsch
- Gustave Roussy Cancer Campus, Villejuif, France.,Université Paris-Saclay, Ile-de-France, France.,Department of Radiation Oncology, Gustave Roussy, Villejuif, France.,INSERM U1030, Radiothérapie Moléculaire et Innovation Thérapeutique, Villejuif, France
| | - Fabrice Barlesi
- Gustave Roussy Cancer Campus, Villejuif, France.,Cancer Medicine Department, Gustave Roussy, Villejuif, France
| | - David Planchard
- Gustave Roussy Cancer Campus, Villejuif, France.,Cancer Medicine Department, Gustave Roussy, Villejuif, France
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy.,European Institute of Oncology (IEO) IRCCS, Milan, Italy
| | - Stéphanie Martinez
- Service des Maladies Respiratoires, Centre Hospitalier d'Aix-en-Provence, Aix-en-Provence, France
| | - Laurence Zitvogel
- Gustave Roussy Cancer Campus, Villejuif, France. .,Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée, Ligue Nationale contre le Cancer, Villejuif, France. .,Université Paris-Saclay, Ile-de-France, France. .,Center of Clinical Investigations in Biotherapies of Cancer (BIOTHERIS) 1428, Villejuif, France.
| | | | - Benjamin Besse
- Gustave Roussy Cancer Campus, Villejuif, France.,Cancer Medicine Department, Gustave Roussy, Villejuif, France.,Université Paris-Saclay, Ile-de-France, France
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23
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Genomic Features and Pervasive Negative Selection in Rhodanobacter Strains Isolated from Nitrate and Heavy Metal Contaminated Aquifer. Microbiol Spectr 2022; 10:e0259121. [PMID: 35107332 PMCID: PMC8809349 DOI: 10.1128/spectrum.02591-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Rhodanobacter species dominate in the Oak Ridge Reservation (ORR) subsurface environments contaminated with acids, nitrate, metal radionuclides, and other heavy metals. To uncover the genomic features underlying adaptations to these mixed-waste environments and to guide genetic tool development, we sequenced the whole genomes of eight Rhodanobacter strains isolated from the ORR site. The genome sizes ranged from 3.9 to 4.2 Mb harboring 3,695 to 4,035 protein-coding genes and GC contents approximately 67%. Seven strains were classified as R. denitrificans and one strain, FW510-R12, as R. thiooxydans based on full length 16S rRNA sequences. According to gene annotation, the top two Cluster of Orthologous Groups (COGs) with high pan-genome expansion rates (Pan/Core gene ratio) were “replication, recombination and repair” and “defense mechanisms.” The denitrifying genes had high DNA homologies except the predicted protein structure variances in NosZ. In contrast, heavy metal resistance genes were diverse with between 7 to 34% of them were located in genomic islands, and these results suggested origins from horizontal gene transfer. Analysis of the methylation patterns in four strains revealed the unique 5mC methylation motifs. Most orthologs (78%) had ratios of nonsynonymous to synonymous substitutions (dN/dS) less than one when compared to the type strain 2APBS1, suggesting the prevalence of negative selection. Overall, the results provide evidence for the important roles of horizontal gene transfer and negative selection in genomic adaptation at the contaminated field site. The complex restriction-modification system genes and the unique methylation motifs in Rhodanobacter strains suggest the potential recalcitrance to genetic manipulation. IMPORTANCE Despite the dominance of Rhodanobacter species in the subsurface of the contaminated Oak Ridge Reservation (ORR) site, very little is known about the mechanisms underlying their adaptions to the various stressors present at ORR. Recently, multiple Rhodanobacter strains have been isolated from the ORR groundwater samples from several wells with varying geochemical properties. Using Illumina, PacBio, and Oxford Nanopore sequencing platforms, we obtained the whole genome sequences of eight Rhodanobacter strains. Comparison of the whole genomes demonstrated the genetic diversity, and analysis of the long nanopore reads revealed the heterogeneity of methylation patterns in strains isolated from the same well. Although all strains contained a complete set of denitrifying genes, the predicted tertiary structures of NosZ differed. The sequence comparison results demonstrate the important roles of horizontal gene transfer and negative selection in adaptation. In addition, these strains may be recalcitrant to genetic manipulation due to the complex restriction-modification systems and methylations.
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24
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Intraspecific Diversity of Microbial Anti-Inflammatory Molecule (MAM) from Faecalibacterium prausnitzii. Int J Mol Sci 2022; 23:ijms23031705. [PMID: 35163630 PMCID: PMC8836110 DOI: 10.3390/ijms23031705] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 01/24/2022] [Accepted: 01/27/2022] [Indexed: 11/17/2022] Open
Abstract
The commensal bacterium Faecalibacterium prausnitzii has unique anti-inflammatory properties, at least some of which have been attributed to its production of MAM, the Microbial Anti-inflammatory Molecule. Previous phylogenetic studies of F. prausnitzii strains have revealed the existence of various phylogroups. In this work, we address the question of whether MAMs from different phylogroups display distinct anti-inflammatory properties. We first performed wide-scale identification, classification, and phylogenetic analysis of MAM-like proteins encoded in different genomes of F. prausnitzii. When combined with a gene context analysis, this approach distinguished at least 10 distinct clusters of MAMs, providing evidence for functional diversity within this protein. We then selected 11 MAMs from various clusters and evaluated their anti-inflammatory capacities in vitro. A wide range of anti-inflammatory activity was detected. MAM from the M21/2 strain had the highest inhibitory effect (96% inhibition), while MAM from reference strain A2-165 demonstrated only 56% inhibition, and MAM from strain CNCM4541 was almost inactive. These results were confirmed in vivo in murine models of acute and chronic colitis. This study provides insights into the family of MAM proteins and generates clues regarding the choice of F. prausnitzii strains as probiotics for use in targeting chronic inflammatory diseases.
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25
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Hu W, Gao W, Liu Z, Fang Z, Zhao J, Zhang H, Lu W, Chen W. Biodiversity and Physiological Characteristics of Novel Faecalibacterium prausnitzii Strains Isolated from Human Feces. Microorganisms 2022; 10:microorganisms10020297. [PMID: 35208752 PMCID: PMC8876097 DOI: 10.3390/microorganisms10020297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 01/15/2022] [Accepted: 01/16/2022] [Indexed: 01/27/2023] Open
Abstract
Faecalibacterium prausnitzii is prevalent in the human gut and is a potential candidate for next-generation probiotics (NGPs) or biotherapeutics. However, the biodiversity and physiological characteristics of Faecalibacterium prausnitzii remain unclear. This study isolated 26 novel F. prausnitzii strains from human feces using a combination of negative screening and prime-specific PCR amplification (NSPA). Based on a 16S rRNA gene analysis, F. prausnitzii strains can be classified into two main phylogroups (phylogroups I and II), which were further clustered into five subgroups (I-A, II-B, II-C, II-D, and II-E). The ultrastructure, colony morphology, growth performance, and short-chain fatty acids (SCFAs)-producing ability were found to be variable among these F. prausnitzii isolates. The optimal pH for the isolates growth ranged between 6.0 and 7.0, while most isolates were inhibited by 0.1% of bile salts. Antimicrobial resistance profiles showed that all F. prausnitzii isolates were susceptible to vancomycin, whereas >80% were kanamycin and gentamicin resistant. Additionally, all strains can utilize maltose, cellulose, and fructose but not xylose, sorbose, and 2′-FL. Overall, our work provides new insights into the biodiversity and physiological characteristics of F. prausnitzii, as well as the choices of strains suitable for NGPs.
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Affiliation(s)
- Wenbing Hu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (W.H.); (W.G.); (Z.L.); (Z.F.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Wenyu Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (W.H.); (W.G.); (Z.L.); (Z.F.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Zongmin Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (W.H.); (W.G.); (Z.L.); (Z.F.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Zhifeng Fang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (W.H.); (W.G.); (Z.L.); (Z.F.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (W.H.); (W.G.); (Z.L.); (Z.F.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (W.H.); (W.G.); (Z.L.); (Z.F.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
- (Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou 225004, China
- Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi 214122, China
| | - Wenwei Lu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (W.H.); (W.G.); (Z.L.); (Z.F.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
- Correspondence: ; Tel./Fax: +86-510-85197302
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (W.H.); (W.G.); (Z.L.); (Z.F.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
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Yu X, Jiang W, Kosik RO, Song Y, Luo Q, Qiao T, Tong J, Liu S, Deng C, Qin S, Lv Z, Li D. Gut microbiota changes and its potential relations with thyroid carcinoma. J Adv Res 2022; 35:61-70. [PMID: 35003794 PMCID: PMC8721249 DOI: 10.1016/j.jare.2021.04.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 03/28/2021] [Accepted: 04/02/2021] [Indexed: 02/07/2023] Open
Abstract
Thyroid cancer patients have reduced richness and diversity of gut microbiota. A predictive model of 10 genera could distinguish thyroid cancer patients from healthy controls. The loss of the short-chain fatty acid-producing bacteria may promote thyroid carcinoma. The functional changes that occur in thyroid cancer patients affect the processing of genetic information. A four-genus microbial signature may be able to distinguish thyroid carcinoma patients with metastatic lymphadenopathy from those without metastatic lymphadenopathy.
Introduction Emerging evidence suggests that the essence of life is the ecological balance of the neural, endocrine, metabolic, microbial, and immune systems. Gut microbiota have been implicated as an important factor affecting thyroid homeostasis. Objectives This study aims to explore the relationship between gut microbiota and the development of thyroid carcinoma. Methods Stool samples were collected from 90 thyroid carcinoma patients (TCs) and 90 healthy controls (HCs). Microbiota were analyzed using 16S ribosomal RNA gene sequencing. A cross-sectional study of an exploratory cohort of 60 TCs and 60 HCs was conducted. The gut microbiota signature of TCs was established by LEfSe, stepwise logistic regression, lasso regression, and random forest model analysis. An independent cohort of 30 TCs and 30 HCs was used to validate the findings. Functional prediction was achieved using Tax4Fun and PICRUSt2. TC patients were subsequently divided into subgroups to analyze the relationship between microbiota and metastatic lymphadenopathy. Results In the exploratory cohorts, TCs had reduced richness and diversity of gut microbiota compared to HCs. No significant difference was found between TCs and HCs on the phylum level, though 70% of TCs had increased levels of Proteobacteria-types based on dominant microbiota typing. A prediction model of 10 genera generated with LEfSe analysis and lasso regression distinguished TCs from HCs with areas under the curves of 0.809 and 0.746 in the exploration and validation cohorts respectively. Functional prediction suggested that the microbial changes observed in TCs resulted in a decline in aminoacyl-tRNA biosynthesis, homologous recombination, mismatch repair, DNA replication, and nucleotide excision repair. A four-genus microbial signature was able to distinguish TC patients with metastatic lymphadenopathy from those without metastatic lymphadenopathy. Conclusion Our study shows that thyroid carcinoma patients demonstrate significant changes in gut microbiota, which will help delineate the relationship between gut microbiota and TC pathogenesis.
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Affiliation(s)
- Xiaqing Yu
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Wen Jiang
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Russell Oliver Kosik
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yingchun Song
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Qiong Luo
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Tingting Qiao
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Junyu Tong
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Simin Liu
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Chengwen Deng
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Shanshan Qin
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Zhongwei Lv
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China.,Clinical Nuclear Medicine Center, Tongji University School of Medicine, Shanghai, China.,Imaging Clinical Medical Center, Tongji University School of Medicine, Shanghai, China
| | - Dan Li
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China.,Clinical Nuclear Medicine Center, Tongji University School of Medicine, Shanghai, China
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Lawrence D, Campbell DE, Schriefer LA, Rodgers R, Walker FC, Turkin M, Droit L, Parkes M, Handley SA, Baldridge MT. Single-cell genomics for resolution of conserved bacterial genes and mobile genetic elements of the human intestinal microbiota using flow cytometry. Gut Microbes 2022; 14:2029673. [PMID: 35130125 PMCID: PMC8824198 DOI: 10.1080/19490976.2022.2029673] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 12/03/2021] [Accepted: 01/07/2022] [Indexed: 02/04/2023] Open
Abstract
As our understanding of the importance of the human microbiota in health and disease grows, so does our need to carefully resolve and delineate its genomic content. 16S rRNA gene-based analyses yield important insights into taxonomic composition, and metagenomics-based approaches reveal the functional potential of microbial communities. However, these methods generally fail to directly link genetic features, including bacterial genes and mobile genetic elements, to each other and to their source bacterial genomes. Further, they are inadequate to capture the microdiversity present within a genus, species, or strain of bacteria within these complex communities. Here, we present a method utilizing fluorescence-activated cell sorting for isolation of single bacterial cells, amplifying their genomes, screening them by 16S rRNA gene analysis, and selecting cells for genomic sequencing. We apply this method to both a cultured laboratory strain of Escherichia coli and human stool samples. Our analyses reveal the capacity of this method to provide nearly complete coverage of bacterial genomes when applied to isolates and partial genomes of bacterial species recovered from complex communities. Additionally, this method permits exploration and comparison of conserved and variable genomic features between individual cells. We generate assemblies of novel genomes within the Ruminococcaceae family and the Holdemanella genus by combining several 16S rRNA gene-matched single cells, and report novel prophages and conjugative transposons for both Bifidobacterium and Ruminococcaceae. Thus, we demonstrate an approach for flow cytometric separation and sequencing of single bacterial cells from the human microbiota, which yields a variety of critical insights into both the functional potential of individual microbes and the variation among those microbes. This method definitively links a variety of conserved and mobile genomic features, and can be extended to further resolve diverse elements present in the human microbiota.
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Affiliation(s)
- Dylan Lawrence
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Danielle E. Campbell
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Lawrence A. Schriefer
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Rachel Rodgers
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Forrest C. Walker
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Marissa Turkin
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Lindsay Droit
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Miles Parkes
- Division of Gastroenterology Addenbrooke’s Hospital and Department of Medicine, University of Cambridge, Cambridge, UK
| | - Scott A. Handley
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Megan T. Baldridge
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
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OUP accepted manuscript. FEMS Microbiol Ecol 2022; 98:6516937. [DOI: 10.1093/femsec/fiac004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 12/26/2021] [Accepted: 01/24/2022] [Indexed: 11/13/2022] Open
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Zhu LB, Zhang YC, Huang HH, Lin J. Prospects for clinical applications of butyrate-producing bacteria. World J Clin Pediatr 2021; 10:84-92. [PMID: 34616650 PMCID: PMC8465514 DOI: 10.5409/wjcp.v10.i5.84] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/23/2021] [Accepted: 08/24/2021] [Indexed: 02/06/2023] Open
Abstract
As the major source of energy for colonic mucosal cells and as an important regulator of gene expression, inflammation, differentiation, and apoptosis in host cells, microbiota-derived butyrate can enhance the intestinal mucosal immune barrier, modulate systemic immune response, and prevent infections. Maintaining a certain level of butyrate production in the gut can help balance intestinal microbiota, regulate host immune response, and promote the development and maintenance of the intestinal mucosal barrier. Butyrate-producing bacteria act as probiotics and play important roles in a variety of normal biological functions. Bacteriotherapeutic supplementation by using fecal microbiota transplantation to restore butyrate-producing commensal bacteria in the gut has been very successful in the treatment of recurrent and refractory Clostridium difficile (C. difficile) infection or C. difficile-negative nosocomial diarrhea. Administration of probiotics that include butyrate-producing bacteria may have a role in the treatment of inflammatory bowel diseases and in the prevention of necrotizing enterocolitis and late-onset sepsis in premature infants. Furthermore, modulating gut microbiota with dietary approaches may improve intestinal dysbiosis commonly seen in patients with obesity-associated metabolic disorders. Supplementation with a butyrate-producing bacterial stain might be used to increase energy expenditure, improve insulin sensitivity, and to help control obesity and metabolic syndrome.
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Affiliation(s)
- Li-Bin Zhu
- Department of Pediatric Surgery, The Second Affiliated Hospital & Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou 325027, Zhejiang Province, China
| | - Yu-Chen Zhang
- Department of Pediatric Surgery, The Second School of Clinical Medicine, Wenzhou Medical University, Wenzhou 325027, Zhejiang Province, China
| | - Han-Hui Huang
- Department of Pediatric Surgery, The Second School of Clinical Medicine, Wenzhou Medical University, Wenzhou 325027, Zhejiang Province, China
| | - Jing Lin
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
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Chen Y, Liu P, Liu R, Hu S, He Z, Dong G, Feng C, An S, Ying X. Comprehensive Strain-Level Analysis of the Gut Microbe Faecalibacterium prausnitzii in Patients with Liver Cirrhosis. mSystems 2021; 6:e0077521. [PMID: 34342541 PMCID: PMC8407477 DOI: 10.1128/msystems.00775-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 07/09/2021] [Indexed: 01/11/2023] Open
Abstract
Liver cirrhosis (LC) has been associated with gut microbes. However, the strain diversity of species and its association with LC have received little attention. Here, we constructed a computational framework to study the strain heterogeneity in the gut microbiome of patients with LC. Only Faecalibacterium prausnitzii shows different single-nucleotide polymorphism (SNP) patterns between the LC and healthy control (HC) groups. Strain diversity analysis discovered that although most F. prausnitzii genomes are more deficient in the LC group than in the HC group at the strain level, a subgroup of 19 F. prausnitzii strains showed no sensitivity to LC, which is inconsistent with the species-level result. The functional differences between this subgroup and other strains may involve short-chain fatty acid production and chlorine-related pathways. These findings demonstrate functional differences among F. prausnitzii subgroups, which extend current knowledge about strain heterogeneity and relationships between F. prausnitzii and LC at the strain level. IMPORTANCE Most metagenomic studies focus on microbes at the species level, thus ignoring the different effects of different strains of the same species on the host. In this study, we explored the different microbes at the strain level in the intestines of patients with liver cirrhosis and of healthy people. Previous studies have shown that the species Faecalibacterium prausnitzii has a lower abundance in patients with liver cirrhosis than in healthy people. However, our results found multiple F. prausnitzii strains that do not decrease in abundance in patients with liver cirrhosis. It is more sensitive to select the appropriate strains as indicators to distinguish between the disease and the control samples than to use the entire species as an indicator. We clustered multiple F. prausnitzii strains and discuss the functional differences of different clusters. Our findings suggest that more attention should be paid to metagenomic studies at the strain level.
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Affiliation(s)
- Yaowen Chen
- Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Pu Liu
- Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Runyan Liu
- Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Shuofeng Hu
- Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Zhen He
- Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Guohua Dong
- Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Chao Feng
- Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Sijing An
- Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Xiaomin Ying
- Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, China
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Brereton N, Pitre F, Gonzalez E. Reanalysis of the Mars500 experiment reveals common gut microbiome alterations in astronauts induced by long-duration confinement. Comput Struct Biotechnol J 2021; 19:2223-2235. [PMID: 33995915 PMCID: PMC8099722 DOI: 10.1016/j.csbj.2021.03.040] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 12/16/2022] Open
Abstract
Maintaining astronaut health throughout long-duration spaceflight is essential to the feasibility of a manned mission to Mars. The ground-based Mars500 experiment investigated long-duration health by isolating six astronauts for 520 days, the longest controlled human confinement study conducted to date. After 520 days, astronauts had uniform strength and lean body mass losses, and increased fasting plasma glucose, calprotectin, and neutrophil levels characteristic of intestinal inflammation but previous analyses revealed no common significant changes in gut microbiota. This study reanalysed data from early (days 7–45) and late (days 420–520) faecal samples and identified 408 exact sequence variants (ESVs), including 213 shared by all astronauts. Thirty-two ESVs were significantly differentially abundant over time, including depletion of keystone resistant starch degrading, anti-inflammatory and insulin sensitivity-associated species, such as Faecalibacterium prausnitzii, Ruminococcus bromii, Blautia luti, Anaerostipes hadrus, Roseburia faecis, and Lactobacillus rogosae, and enrichment of yet-to-be-cultured bacteria. Additionally, the extraordinary experimental confinement allowed observation of microbiota potentially shared between astronauts and their habitat. Forty-nine species were shared, representing 49% and 12% of the human and environmental microbiome diversity, respectively. These findings reveal the microbiota which significantly altered in relative abundance throughout confinement, including species known to influence inflammation and host glucose homeostasis consistent with astronaut symptoms. Identification of microbiome alterations after 520 days of isolation represents a missing piece connecting Mars500 astronaut physiological studies. Knowledge of the impact of long-term confinement upon the human microbiome helps to improve our understanding of how humans interact with their habitats and is a valuable step forward towards enabling long-duration spaceflight.
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Affiliation(s)
- N.J.B. Brereton
- Institut de Recherche en Biologie Végétale, University of Montreal, Montreal, QC H1X 2B2, Canada
- Corresponding author.
| | - F.E. Pitre
- Institut de Recherche en Biologie Végétale, University of Montreal, Montreal, QC H1X 2B2, Canada
| | - E. Gonzalez
- Canadian Centre for Computational Genomics (C3G), Department of Human Genetics, McGill University, 740 Dr. Penfield Avenue, Montréal, QC H3A 0G1, Canada
- Microbiome Research Platform, McGill Interdisciplinary Initiative in Infection and Immunity (MI4), Genome Centre, McGill University, Montréal, QC, Canada
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De Filippis F, Pasolli E, Ercolini D. Newly Explored Faecalibacterium Diversity Is Connected to Age, Lifestyle, Geography, and Disease. Curr Biol 2020; 30:4932-4943.e4. [PMID: 33065016 DOI: 10.1016/j.cub.2020.09.063] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/02/2020] [Accepted: 09/18/2020] [Indexed: 12/16/2022]
Abstract
Faecalibacterium is prevalent in the human gut and a promising microbe for the development of next-generation probiotics (NGPs) or biotherapeutics. Analyzing reference Faecalibacterium genomes and almost 3,000 Faecalibacterium-like metagenome-assembled genomes (MAGs) reconstructed from 7,907 human and 203 non-human primate gut metagenomes, we identified the presence of 22 different Faecalibacterium-like species-level genome bins (SGBs), some further divided in different strains according to the subject geographical origin. Twelve SGBs are globally spread in the human gut and show different genomic potential in the utilization of complex polysaccharides, suggesting that higher SGB diversity may be related with increased utilization of plant-based foods. Moreover, up to 11 different species may co-occur in the same subject, with lower diversity in Western populations, as well as intestinal inflammatory states and obesity. The newly explored Faecalibacterium diversity will be able to support the choice of strains suitable as NGPs, guided by the consideration of the differences existing in their functional potential.
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Affiliation(s)
- Francesca De Filippis
- Department of Agricultural Sciences, University of Naples Federico II, Portici 80055, Italy; Task Force on Microbiome Studies, University of Naples Federico II, Naples 80100, Italy
| | - Edoardo Pasolli
- Department of Agricultural Sciences, University of Naples Federico II, Portici 80055, Italy; Task Force on Microbiome Studies, University of Naples Federico II, Naples 80100, Italy
| | - Danilo Ercolini
- Department of Agricultural Sciences, University of Naples Federico II, Portici 80055, Italy; Task Force on Microbiome Studies, University of Naples Federico II, Naples 80100, Italy.
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Seribelli AA, Cruz MF, Vilela FP, Frazão MR, Paziani MH, Almeida F, Medeiros MIC, Rodrigues DDP, Kress MRVZ, Allard MW, Falcão JP. Phenotypic and genotypic characterization of Salmonella Typhimurium isolates from humans and foods in Brazil. PLoS One 2020; 15:e0237886. [PMID: 32810191 PMCID: PMC7437471 DOI: 10.1371/journal.pone.0237886] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 08/04/2020] [Indexed: 01/25/2023] Open
Abstract
Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) causes gastroenteritis in many countries. However, in Brazil there are few studies that have conducted a virulence characterization of this serovar. The aim of this study was to evaluate the virulence potential of S. Typhimurium strains isolated in Brazil. Forty S. Typhimurium strains isolated from humans (n = 20) and food (n = 20) from Brazil were studied regarding their invasion and survival in human epithelial cells (Caco-2) and macrophages (U937). Their virulence potential was determined using the Galleria mellonella larvae model combined with the analysis of virulence genes by whole genome sequencing (WGS). A total of 67.5% of the S. Typhimurium studied (32.5% isolated from humans and 35% isolated from food) invaded Caco-2 epithelial cells at levels similar to or greater than the S. Typhimurium SL1344 prototype strain. In addition, 37.5% of the studied strains (25% isolated from humans and 12.5% isolated from food) survived in U937 human macrophages at levels similar to or greater than SL1344. S. Typhimurium strains isolated from humans (40%) and food (25%) showed high or intermediate virulence in G. mellonella larvae after seven days exposure. Approximately, 153 virulence genes of chromosomal and plasmidial origin were detected in the strains studied. In conclusion, the ability of the S. Typhimurium to invade Caco-2 epithelial cells was strain dependent and was not related to the source or the year of isolation. However, S. Typhimurium strains isolated from humans showed greater survival rates in U937 human macrophages, and presented higher proportion of isolates with a virulent profile in G. mellonella in comparison to strains isolated from food suggesting that this difference may be related to the higher frequency of human isolates which contained plasmid genes, such as spvABCDR operon, pefABCD operon, rck and mig-5.
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Affiliation(s)
- Amanda Aparecida Seribelli
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto–Universidade de São Paulo—USP, Brazil
| | - Marcelo Ferreira Cruz
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto–Universidade de São Paulo—USP, Brazil
| | - Felipe Pinheiro Vilela
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto–Universidade de São Paulo—USP, Brazil
| | - Miliane Rodrigues Frazão
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto–Universidade de São Paulo—USP, Brazil
| | - Mario H. Paziani
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto–Universidade de São Paulo—USP, Brazil
| | - Fernanda Almeida
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto–Universidade de São Paulo—USP, Brazil
| | | | | | - Marcia R. von Zeska Kress
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto–Universidade de São Paulo—USP, Brazil
| | - Marc W. Allard
- Food and Drug Administration—FDA, College Park, Maryland, United States of America
- * E-mail: (JPF); (MWA)
| | - Juliana Pfrimer Falcão
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto–Universidade de São Paulo—USP, Brazil
- * E-mail: (JPF); (MWA)
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Guo M, Li M, Zhang C, Zhang X, Wu Y. Dietary Administration of the Bacillus subtilis Enhances Immune Responses and Disease Resistance in Chickens. Front Microbiol 2020; 11:1768. [PMID: 32849392 PMCID: PMC7396511 DOI: 10.3389/fmicb.2020.01768] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 07/06/2020] [Indexed: 12/25/2022] Open
Abstract
Bacillus subtilis (B. subtilis) has a variety of proposed beneficial effects for chickens, including growth promotion and disease prevention. In this study, chickens were fed a diet containing B. subtilis for 21 days and growth performance, intestinal morphology, intestinal microbiota, immune responses, and disease resistance were investigated. After 21 days of feeding, chickens fed a diet containing B. subtilis had higher body weights. The concentrations of serum immunoglobulins IgA and IgM were significantly increased by B. subtilis in the diet. Moreover, chickens fed with B. subtilis had greater villus height (VH), shallower crypt depth (CD), and a higher VH/CD ratio in the jejunum than chickens fed a standard control diet. Diet with B. subtilis can balance intestinal microbiota, facilitate an increase in beneficial bacteria, and inhibit the pathogenic bacteria after 21 days of feeding. After an Escherichia coli (E. coli) challenge, the survival rate of chickens fed with B. subtilis was 66.67%, which was significantly higher than the controls. The E. coli contents in spleens and lungs from chickens fed a diet with B. subtilis were lower than those in controls. In addition, B. subtilis can trigger the toll-like receptor 4 and cause induction of proinflammatory cytokine (Il1β, Il6, and Il8) production to develop innate immune responses in chickens. In conclusion, diets containing B. subtilis can improve growth performance, serum immunoglobulin levels, the intestinal villus-crypt system, intestinal homeostasis, immune responses, and disease resistance against E. coli in chickens.
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Affiliation(s)
- Mengjiao Guo
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Mingtao Li
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Chengcheng Zhang
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Xiaorong Zhang
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Yantao Wu
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture & Agri-Product Safety (JIRLAAPS), Yangzhou University, Yangzhou, China
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Andrade JC, Almeida D, Domingos M, Seabra CL, Machado D, Freitas AC, Gomes AM. Commensal Obligate Anaerobic Bacteria and Health: Production, Storage, and Delivery Strategies. Front Bioeng Biotechnol 2020; 8:550. [PMID: 32582673 PMCID: PMC7291883 DOI: 10.3389/fbioe.2020.00550] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 05/07/2020] [Indexed: 12/12/2022] Open
Abstract
In the last years several human commensals have emerged from the gut microbiota studies as potential probiotics or therapeutic agents. Strains of human gut inhabitants such as Akkermansia, Bacteroides, or Faecalibacterium have shown several interesting bioactivities and are thus currently being considered as food supplements or as live biotherapeutics, as is already the case with other human commensals such as bifidobacteria. The large-scale use of these bacteria will pose many challenges and drawbacks mainly because they are quite sensitive to oxygen and/or very difficult to cultivate. This review highlights the properties of some of the most promising human commensals bacteria and summarizes the most up-to-date knowledge on their potential health effects. A comprehensive outlook on the potential strategies currently employed and/or available to produce, stabilize, and deliver these microorganisms is also presented.
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Affiliation(s)
- José Carlos Andrade
- CESPU, Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde, Gandra, Portugal
| | - Diana Almeida
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Porto, Portugal
| | - Melany Domingos
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Porto, Portugal
| | - Catarina Leal Seabra
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Porto, Portugal
| | - Daniela Machado
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Porto, Portugal
| | - Ana Cristina Freitas
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Porto, Portugal
| | - Ana Maria Gomes
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Porto, Portugal
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Stefia LV, Lee J, Patel J, de Sousa SR, Legrand J, Rodero M, Burman S, Linedale R, Morrison M, Khosrotehrani K. Secretome Components from Faecalibacterium prausnitzii Strains A2-165 and AHMP21 Modulate Cutaneous Wound Inflammation. J Invest Dermatol 2020; 140:2312-2315.e6. [PMID: 32247858 DOI: 10.1016/j.jid.2020.02.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 02/12/2020] [Accepted: 02/17/2020] [Indexed: 01/07/2023]
Affiliation(s)
- Laurancia Vina Stefia
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - James Lee
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Jatin Patel
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Silmara Rodrigues de Sousa
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Julien Legrand
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Mathieu Rodero
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Sriti Burman
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Richard Linedale
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Mark Morrison
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Kiarash Khosrotehrani
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Queensland, Australia.
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Seribelli AA, Gonzales JC, de Almeida F, Benevides L, Cazentini Medeiros MI, Dos Prazeres Rodrigues D, de C Soares S, Allard MW, Falcão JP. Phylogenetic analysis revealed that Salmonella Typhimurium ST313 isolated from humans and food in Brazil presented a high genomic similarity. Braz J Microbiol 2020; 51:53-64. [PMID: 31728978 PMCID: PMC7058764 DOI: 10.1007/s42770-019-00155-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 09/07/2019] [Indexed: 12/16/2022] Open
Abstract
Salmonella Typhimurium sequence type 313 (S. Typhimurium ST313) has caused invasive disease mainly in sub-Saharan Africa. In Brazil, ST313 strains have been recently described, and there is a lack of studies that assessed by whole genome sequencing (WGS)-the relationship of these strains. The aims of this work were to study the phylogenetic relationship of 70 S. Typhimurium genomes comparing strains of ST313 (n = 9) isolated from humans and food in Brazil among themselves, with other STs isolated in this country (n = 31) and in other parts of the globe (n = 30) by 16S rRNA sequences, the Gegenees software, whole genome multilocus sequence typing (wgMLST), and average nucleotide identity (ANI) for the genomes of ST313. Additionally, pangenome analysis was performed to verify the heterogeneity of these genomes. The phylogenetic analyses showed that the ST313 genomes were very similar among themselves. However, the ST313 genomes were usually clustered more distantly to other STs of strains isolated in Brazil and in other parts of the world. By pangenome calculation, the core genome was 2,880 CDSs and 4,171 CDSs singletons for all the 70 S. Typhimurium genomes studied. Considering the 10 ST313 genomes analyzed the core genome was 4,112 CDSs and 76 CDSs singletons. In conclusion, the ST313 genomes from Brazil showed a high similarity among them which information might eventually help in the development of vaccines and antibiotics. The pangenome analysis showed that the S. Typhimurium genomes studied presented an open pangenome, but specifically tending to become close for the ST313 strains.
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Affiliation(s)
- Amanda Ap Seribelli
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo - USP, Av. do Café, s/n°-Campus Universitário USP, Ribeirão Preto, SP, 14040-903, Brazil.
| | - Júlia C Gonzales
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo - USP, Av. do Café, s/n°-Campus Universitário USP, Ribeirão Preto, SP, 14040-903, Brazil
| | - Fernanda de Almeida
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo - USP, Av. do Café, s/n°-Campus Universitário USP, Ribeirão Preto, SP, 14040-903, Brazil
| | - Leandro Benevides
- National Laboratory of Scientific Computation - LNCC, Petrópolis, Brazil
| | | | | | | | - Marc W Allard
- Food and Drug Administration - FDA, College Park, MA, USA
| | - Juliana P Falcão
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo - USP, Av. do Café, s/n°-Campus Universitário USP, Ribeirão Preto, SP, 14040-903, Brazil
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Xu J, Liang R, Zhang W, Tian K, Li J, Chen X, Yu T, Chen Q. Faecalibacterium prausnitzii-derived microbial anti-inflammatory molecule regulates intestinal integrity in diabetes mellitus mice via modulating tight junction protein expression. J Diabetes 2020; 12:224-236. [PMID: 31503404 PMCID: PMC7064962 DOI: 10.1111/1753-0407.12986] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 08/28/2019] [Accepted: 09/06/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Impaired intestinal barrier structure and function have been validated as an important pathogenic process in type 2 diabetes mellitus (T2DM). Gut dysbiosis is thought to be the critical factor in diabetic intestinal pathogenesis. As the most abundant commensal bacteria, Faecalibacterium prausnitzii (F. prausnitzii) play important roles in gut homeostasis. The microbial anti-inflammatory molecule (MAM), an F. prausnitzii metabolite, has anti-inflammatory potential in inflammatory bowel disease (IBD). Thus, we aimed to explore the function and mechanism of MAM on the diabetic intestinal epithelium. METHODS 16S high-throughput sequencing was used to analyze the gut microbiota of db/db mice (T2DM mouse model). We transfected a FLAG-tagged MAM plasmid into human colonic cells to explore the protein-protein interactions and observe cell monolayer permeability. For in vivo experiments, db/db mice were supplemented with recombinant His-tagged MAM protein from E. coli BL21 (DE3). RESULTS The abundance of F. prausnitzii was downregulated in the gut microbiota of db/db mice. Immunoprecipitation (IP) and mass spectroscopy (MS) analyses revealed that MAM potentially interacts with proteins in the tight junction pathway, including zona occludens 1 (ZO-1). FLAG-tagged MAM plasmid transfection stabilized the cell permeability and increased ZO-1 expression in NCM460, Caco2, and HT-29 cells. The db/db mice supplemented with recombinant His-tagged MAM protein showed restored intestinal barrier function and elevated ZO-1 expression. CONCLUSIONS Our study shows that MAM from F. prausnitzii can restore the intestinal barrier structure and function in DM conditions via the regulation of the tight junction pathway and ZO-1 expression.
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Affiliation(s)
- Jihao Xu
- Department of GastroenterologySun Yat‐Sen Memorial Hospital, Sun Yat‐Sen UniversityGuangzhouGuangdongPeople's Republic of China
| | - Rongrong Liang
- Department of PediatricsSun Yat‐Sen Memorial Hospital, Sun Yat‐Sen UniversityGuangzhouGuangdongPeople's Republic of China
| | - Wang Zhang
- Department of GastroenterologySun Yat‐Sen Memorial Hospital, Sun Yat‐Sen UniversityGuangzhouGuangdongPeople's Republic of China
- Department of GastroenterologyGuangdong Provincial Hospital of Chinese Medicine (2nd Clinical Hospital of Guangzhou University of Chinese Medicine), Guangzhou University of Chinese MedicineGuangzhouGuangdongPeople's Republic of China
| | - Kuangyi Tian
- Department of GastroenterologySun Yat‐Sen Memorial Hospital, Sun Yat‐Sen UniversityGuangzhouGuangdongPeople's Republic of China
| | - Jieyao Li
- Department of GastroenterologySun Yat‐Sen Memorial Hospital, Sun Yat‐Sen UniversityGuangzhouGuangdongPeople's Republic of China
| | - Xianming Chen
- Department of Medical Microbiology and ImmunologyCreighton University School of MedicineOmahaNebraska
| | - Tao Yu
- Department of GastroenterologySun Yat‐Sen Memorial Hospital, Sun Yat‐Sen UniversityGuangzhouGuangdongPeople's Republic of China
| | - Qikui Chen
- Department of GastroenterologySun Yat‐Sen Memorial Hospital, Sun Yat‐Sen UniversityGuangzhouGuangdongPeople's Republic of China
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Deng X, Tian H, Yang R, Han Y, Wei K, Zheng C, Liu Z, Chen T. Oral Probiotics Alleviate Intestinal Dysbacteriosis for People Receiving Bowel Preparation. Front Med (Lausanne) 2020; 7:73. [PMID: 32181256 PMCID: PMC7059130 DOI: 10.3389/fmed.2020.00073] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 02/19/2020] [Indexed: 12/13/2022] Open
Abstract
Background: Bowel preparation is necessary for successful colonoscopy, while it can seriously affect intestinal microbial composition and damage the intestinal mucosal barriers in humans. Methods: To figure out whether probiotics can sustain intestinal homeostasis and guard people's health, the probiotic drug of Bifidobacterium Tetragenous viable Bacteria Tablets (P group, n = 16) or placebo (C group, n = 16) was used for volunteers receiving bowel preparation, and high-throughput sequencing method was applied to monitor their intestinal microbial changes. Results: The present results suggested that bowel preparation obviously reduced the intestinal microbial diversity, while taking probiotics significantly restored it to normal level. In addition, probiotics sharply reduced the abundance of pathogenic Proteobacteria, and obviously lowered the ratio of Firmicutes/Bacteroidetes compared with control group at phylum level (P < 0.05). And probiotics markedly decreased the abundance of pathogenic Acinetobacter and Streptococcus, while greatly enriched the relative abundance of beneficial bacteria Bacteroides, Roseburia, Faecalibacterium, and Parabacteroides at genus level (P < 0.05). Conclusion: Probiotic drugs, e.g., Bifidobacterium Tetragenous viable Bacteria Tablets, can be used to restore intestinal dysbacteriosis caused by bowel preparation, and reduce side effects during colonoscopy.
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Affiliation(s)
- Xiaorong Deng
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Huakai Tian
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Rong Yang
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yiwen Han
- National Engineering Research Center for Bioengineering Drugs and the Technologies, Institute of Translational Medicine, Nanchang University, Nanchang, China
| | - Kehong Wei
- National Engineering Research Center for Bioengineering Drugs and the Technologies, Institute of Translational Medicine, Nanchang University, Nanchang, China
| | - Cihua Zheng
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zhaoxia Liu
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Tingtao Chen
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China.,National Engineering Research Center for Bioengineering Drugs and the Technologies, Institute of Translational Medicine, Nanchang University, Nanchang, China
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40
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Kumar H, Park W, Lim D, Srikanth K, Kim JM, Jia XZ, Han JL, Hanotte O, Park JE, Oyola SO. Whole metagenome sequencing of cecum microbiomes in Ethiopian indigenous chickens from two different altitudes reveals antibiotic resistance genes. Genomics 2019; 112:1988-1999. [PMID: 31759120 DOI: 10.1016/j.ygeno.2019.11.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 10/11/2019] [Accepted: 11/18/2019] [Indexed: 12/24/2022]
Abstract
We analyzed the whole genomes of cecum microbiomes of Ethiopian indigenous chickens from two distinct geographical zones: Afar (AF) district (Dulecha, 730 m above sea level) and Amhara (AM) district (Menz Gera Midir, 3300 m). Through metagenomic analysis we found that microbial populations were mainly dominated by Bacteroidetes and Firmicutes. We identified 2210 common genes in the two groups. LEfSe showed that the distribution of Coprobacter, Geobacter, Cronobacter, Alloprevotella, and Dysgonomonas were more abundant in AF than AM. Analyses using KEGG, eggNOG, and CAZy databases indicated that the pathways of metabolism, genetic information processing, environmental information processing, and cellular process were significantly enriched. Functional abundance was found to be associated with the nutrient absorption and microbial localization of indigenous chickens. We also investigated antibiotic resistant genes and found antibiotics like LSM, cephalosporin, and tetracycline were significantly more abundant in AF than AM.
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Affiliation(s)
- Himansu Kumar
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Republic of Korea
| | - Woncheoul Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Republic of Korea
| | - Dajeong Lim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Republic of Korea
| | - Krishnamoorthy Srikanth
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Republic of Korea
| | - Jun-Mo Kim
- Department of Animal Science and Technology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Xin-Zheng Jia
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, PR China; International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, PR China; International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Olivier Hanotte
- International Livestock Research Institute (ILRI), Nairobi, Kenya; Faculty of Medicine & Health Sciences, University of Nottingham, UK; International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| | - Jong-Eun Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Republic of Korea.
| | - Samuel O Oyola
- International Livestock Research Institute (ILRI), Nairobi, Kenya.
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Dietary intake influences gut microbiota development of healthy Australian children from the age of one to two years. Sci Rep 2019; 9:12476. [PMID: 31462648 PMCID: PMC6713781 DOI: 10.1038/s41598-019-48658-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 08/08/2019] [Indexed: 02/07/2023] Open
Abstract
Early life nutrition is a vital determinant of an individual’s life-long health and also directly influences the ecological and functional development of the gut microbiota. However, there are limited longitudinal studies examining the effect of diet on the gut microbiota development in early childhood. Here, up to seven stool samples were collected from each of 48 healthy children during their second year of life, and microbiota dynamics were assessed using 16S rRNA gene amplicon sequencing. Children’s dietary information was also collected during the same period using a validated food frequency questionnaire designed for this age group, over five time points. We observed significant changes in gut microbiota community, concordant with changes in the children’s dietary pattern over the 12-month period. In particular, we found differential effects on specific Firmicutes-affiliated lineages in response to frequent intake of either processed or unprocessed foods. Additionally, the consumption of fortified milk supplemented with a Bifidobacterium probiotic and prebiotics (synbiotics) further increased the presence of Bifidobacterium spp., highlighting the potential use of synbiotics to prolong and sustain changes in these lineages and shaping the gut microbiota community in young children.
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42
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Savin KW, Zawadzki J, Auldist MJ, Wang J, Ram D, Rochfort S, Cocks BG. Faecalibacterium diversity in dairy cow milk. PLoS One 2019; 14:e0221055. [PMID: 31419254 PMCID: PMC6697359 DOI: 10.1371/journal.pone.0221055] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 07/29/2019] [Indexed: 12/30/2022] Open
Abstract
The bacterial species, Faecalibacterium prausnitzii, beneficial to humans and animals and found in mammalian and avian gut, is also occasionally found in dairy cow milk. It is one of the butyrate-producing bacteria of the colon, has anti-inflammatory properties and its abundance in the gut is negatively correlated with obesity in humans. Several strains differing in their functional capability, have been identified. It is important therefore, milk being a potential source of F. prausnitzii as a novel probiotic, to investigate the diversity of this species in bovine milk. Using 16s rRNA gene amplicons we find 292 different dereplicated Faecalibacterium-related amplicons in a herd of 21 dairy cows. The distribution of the 20 most abundant amplicons with >97% identity to a Greengenes OTU varies from cow to cow. Clustering of the 292 pooled sequences from all cows at 99.6% identity finds 4 likely Faecalibacterium phylotypes with >98.5% identity to an F. prausnitzii reference sequence. Sequence alignment and phylogenetic analysis shows these phylotypes are distinct from 34 other species from the Ruminococcaceae family and displaying the sequence clusters as a network illustrates how each cluster is composed of sequences from multiple cows. We conclude there are several phylotypes of Faecalibacterium prausnitzii (the only species so far defined for the genus) in this dairy herd with cows being inoculated with a mixture of several strains from a common source. We conclude that not only can Faecalibacterium be detected in dairy cow milk (as noted by others) but that there exist multiple different strains in the milk of a dairy herd. Therefore milk, as an alternative to faeces, offers the opportunity of discovering new strains with potential probiotic application.
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Affiliation(s)
- Keith W. Savin
- AgriBio Centre, Agriculture Victoria Research, Bundoora, Victoria, Australia
- * E-mail:
| | - Jody Zawadzki
- AgriBio Centre, Agriculture Victoria Research, Bundoora, Victoria, Australia
| | | | - Jianghui Wang
- AgriBio Centre, Agriculture Victoria Research, Bundoora, Victoria, Australia
| | - Doris Ram
- AgriBio Centre, Agriculture Victoria Research, Bundoora, Victoria, Australia
| | - Simone Rochfort
- AgriBio Centre, Agriculture Victoria Research, Bundoora, Victoria, Australia
| | - Benjamin G. Cocks
- AgriBio Centre, Agriculture Victoria Research, Bundoora, Victoria, Australia
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Blanco G, Sánchez B, Fdez-Riverola F, Margolles A, Lourenço A. In silico Approach for Unveiling the Glycoside Hydrolase Activities in Faecalibacterium prausnitzii Through a Systematic and Integrative Large-Scale Analysis. Front Microbiol 2019; 10:517. [PMID: 31024464 PMCID: PMC6460054 DOI: 10.3389/fmicb.2019.00517] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 02/28/2019] [Indexed: 01/14/2023] Open
Abstract
This work presents a novel in silico approach to the prediction and characterization of the glycolytic capacities of the beneficial intestinal bacterium Faecalibacterium prausnitzii. Available F. prausnitzii genomes were explored taking the glycolytic capacities of F. prausnitzii SL3/3 and F. prausnitzii L2-6 as reference. The comparison of the generated glycolytic profiles offered insights into the particular capabilities of F. prausnitzii SL3/3 and F. prausnitzii L2-6 as well as the potential of the rest of strains. Glycoside hydrolases were mostly detected in the pathways responsible for the starch and sucrose metabolism and the biosynthesis of secondary metabolites, but this analysis also identified some other potentially interesting, but still uncharacterized activities, such as several hexosyltransferases and some hydrolases. Gene neighborhood maps offered additional understanding of the genes coding for relevant glycoside hydrolases. Although information about the carbohydrate preferences of F. prausnitzii is scarce, the in silico metabolic predictions were consistent with previous knowledge about the impact of fermentable sugars on the growth promotion and metabolism of F. prausnitzii. So, while the predictions still need to be validated using culturing methods, the approach holds the potential to be reproduced and scaled to accommodate the analysis of other strains (or even families and genus) as well as other metabolic activities. This will allow the exploration of novel methodologies to design or obtain targeted probiotics for F. prausnitzii and other strains of interest.
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Affiliation(s)
- Guillermo Blanco
- ESEI - Department of Computer Science, University of Vigo, Ourense, Spain.,Department of Microbiology and Biochemistry of Dairy Products, Superior Council of Scientific Investigations, Institute of Dairy Products of Asturias, Villaviciosa, Spain.,SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Borja Sánchez
- Department of Microbiology and Biochemistry of Dairy Products, Superior Council of Scientific Investigations, Institute of Dairy Products of Asturias, Villaviciosa, Spain
| | - Florentino Fdez-Riverola
- ESEI - Department of Computer Science, University of Vigo, Ourense, Spain.,SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain.,Centre for Biomedical Research, University of Vigo, Vigo, Spain
| | - Abelardo Margolles
- Department of Microbiology and Biochemistry of Dairy Products, Superior Council of Scientific Investigations, Institute of Dairy Products of Asturias, Villaviciosa, Spain
| | - Anália Lourenço
- ESEI - Department of Computer Science, University of Vigo, Ourense, Spain.,SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain.,Centre for Biomedical Research, University of Vigo, Vigo, Spain.,Centre of Biological Engineering, University of Minho, Braga, Portugal
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Douillard FP, de Vos WM. Biotechnology of health-promoting bacteria. Biotechnol Adv 2019; 37:107369. [PMID: 30876799 DOI: 10.1016/j.biotechadv.2019.03.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 02/15/2019] [Accepted: 03/11/2019] [Indexed: 12/20/2022]
Abstract
Over the last decade, there has been an increasing scientific and public interest in bacteria that may positively contribute to human gut health and well-being. This interest is reflected by the ever-increasing number of developed functional food products containing health-promoting bacteria and reaching the market place as well as by the growing revenue and profits of notably bacterial supplements worldwide. Traditionally, the origin of probiotic-marketed bacteria was limited to a rather small number of bacterial species that mostly belong to lactic acid bacteria and bifidobacteria. Intensifying research efforts on the human gut microbiome offered novel insights into the role of human gut microbiota in health and disease, while also providing a deep and increasingly comprehensive understanding of the bacterial communities present in this complex ecosystem and their interactions with the gut-liver-brain axis. This resulted in rational and systematic approaches to select novel health-promoting bacteria or to engineer existing bacteria with enhanced probiotic properties. In parallel, the field of gut microbiomics developed into a fertile framework for the identification, isolation and characterization of a phylogenetically diverse array of health-promoting bacterial species, also called next-generation therapeutic bacteria. The present review will address these developments with specific attention for the selection and improvement of a selected number of health-promoting bacterial species and strains that are extensively studied or hold promise for future food or pharma product development.
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Affiliation(s)
- François P Douillard
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Willem M de Vos
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands.
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45
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Livingstone PG, Morphew RM, Whitworth DE. Genome Sequencing and Pan-Genome Analysis of 23 Corallococcus spp. Strains Reveal Unexpected Diversity, With Particular Plasticity of Predatory Gene Sets. Front Microbiol 2018; 9:3187. [PMID: 30619233 PMCID: PMC6306037 DOI: 10.3389/fmicb.2018.03187] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 12/10/2018] [Indexed: 11/13/2022] Open
Abstract
Corallococcus is an abundant genus of predatory soil myxobacteria, containing two species, C. coralloides (for which a genome sequence is available) and C. exiguus. To investigate the genomic basis of predation, we genome-sequenced 23 Corallococcus strains. Genomic similarity metrics grouped the sequenced strains into at least nine distinct genomospecies, divided between two major sub-divisions of the genus, encompassing previously described diversity. The Corallococcus pan-genome was found to be open, with strains exhibiting highly individual gene sets. On average, only 30.5% of each strain's gene set belonged to the core pan-genome, while more than 75% of the accessory pan-genome genes were present in less than four of the 24 genomes. The Corallococcus accessory pan-proteome was enriched for the COG functional category "Secondary metabolism," with each genome containing on average 55 biosynthetic gene clusters (BGCs), of which only 20 belonged to the core pan-genome. Predatory activity was assayed against ten prey microbes and found to be mostly incongruent with phylogeny or BGC complement. Thus, predation seems multifactorial, depending partially on BGC complement, but also on the accessory pan-genome - genes most likely acquired horizontally. These observations encourage further exploration of Corallococcus as a source for novel bioactive secondary metabolites and predatory proteins.
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Affiliation(s)
- Paul G Livingstone
- Institute of Biological Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - Russell M Morphew
- Institute of Biological Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - David E Whitworth
- Institute of Biological Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
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46
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Fitzgerald CB, Shkoporov AN, Sutton TDS, Chaplin AV, Velayudhan V, Ross RP, Hill C. Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa. BMC Genomics 2018; 19:931. [PMID: 30547746 PMCID: PMC6295017 DOI: 10.1186/s12864-018-5313-6] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 11/27/2018] [Indexed: 02/08/2023] Open
Abstract
Background Faecalibacterium prausnitzii is a ubiquitous member of the human gut microbiome, constituting up to 15% of the total bacteria in the human gut. Substantial evidence connects decreased levels of F. prausnitzii with the onset and progression of certain forms of inflammatory bowel disease, which has been attributed to its anti-inflammatory potential. Two phylogroups of F. prausnitzii have been identified, with a decrease in phylogroup I being a more sensitive marker of intestinal inflammation. Much of the genomic and physiological data available to date was collected using phylogroup II strains. Little analysis of F. prausnitzii genomes has been performed so far and genetic differences between phylogroups I and II are poorly understood. Results In this study we sequenced 11 additional F. prausnitzii genomes and performed comparative genomics to investigate intraspecies diversity, functional gene complement and the mobilome of 31 high-quality draft and complete genomes. We reveal a very low level of average nucleotide identity among F. prausnitzii genomes and a high level of genome plasticity. Two genomogroups can be separated based on differences in functional gene complement, albeit that this division does not fully agree with separation based on conserved gene phylogeny, highlighting the importance of horizontal gene transfer in shaping F. prausnitzii genomes. The difference between the two genomogroups is mainly in the complement of genes associated with catabolism of carbohydrates (such as a predicted sialidase gene in genomogroup I) and amino acids, as well as defense mechanisms. Conclusions Based on the combination of ANI of genomic sequences, phylogenetic analysis of core proteomes and functional differences we propose to separate the species F. prausnitzii into two new species level taxa: F. prausnitzii sensu stricto (neotype strain A2–165T = DSM 17677T = JCM 31915T) and F. moorei sp. nov. (type strain ATCC 27768T = NCIMB 13872T). Electronic supplementary material The online version of this article (10.1186/s12864-018-5313-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Cormac Brian Fitzgerald
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | | | | | - Andrei V Chaplin
- Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Moscow, Russia
| | | | - R Paul Ross
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,Department of Food Biosciences, Teagasc Food Research Centre, Moorepark, Fermoy, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, Cork, Ireland. .,Department of Food Biosciences, Teagasc Food Research Centre, Moorepark, Fermoy, Ireland. .,School of Microbiology, University College Cork, Cork, Ireland.
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47
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Lopez-Siles M, Enrich-Capó N, Aldeguer X, Sabat-Mir M, Duncan SH, Garcia-Gil LJ, Martinez-Medina M. Alterations in the Abundance and Co-occurrence of Akkermansia muciniphila and Faecalibacterium prausnitzii in the Colonic Mucosa of Inflammatory Bowel Disease Subjects. Front Cell Infect Microbiol 2018; 8:281. [PMID: 30245977 PMCID: PMC6137959 DOI: 10.3389/fcimb.2018.00281] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 07/25/2018] [Indexed: 12/21/2022] Open
Abstract
Akkermansia muciniphila and Faecalibacterium prausnitzii, cohabitants in the intestinal mucosa, are considered members of a healthy microbiota and reduction of both species occurs in several intestinal disorders, including inflammatory bowel disease. Little is known however about a possible link between the reduction in quantity of these species, and in which circumstances this may occur. This study aims to determine the abundances and co-occurrence of the two species in order to elucidate conditions that may compromise their presence in the gut. Loads of A. muciniphila, total F. prausnitzii and its two phylogroup (16S rRNA gene copies) were determined by quantitative polymerase chain reaction in colonic biopsies from 17 healthy controls (H), 23 patients with ulcerative colitis (UC), 31 patients with Crohn's disease (CD), 3 with irritable bowel syndrome (IBS) and 3 with colorectal cancer (CRC). Data were normalized to total bacterial 16S rRNA gene copies in the same sample. Prevalence, relative abundances and correlation analyses were performed according to type of disease and considering relevant clinical characteristics of patients such as IBD location, age of disease onset, CD behavior, current medication and activity status. Co-occurrence of both species was found in 29% of H, 65% of UC and 29% of CD. Lower levels of total F. prausnitzii and phylogroups were found in subjects with CD, compared with H subjects (P ≤ 0.044). In contrast, no differences were found with the regard to A. muciniphila abundance across different disease states, but CD patients with disease onset below 16 years of age featured a marked depletion of this species. In CD patients, correlation between A. muciniphila and total F. prausnitzii (ρ = 0.362, P = 0.045) was observed, and particularly in those with non-stricturing, non-penetrating disease behavior and under moderate immunosuppressants therapy. Altogether, this study revealed that co-occurrence of both species differs between disease status. In addition, IBD patients featured a reduction of F. prausnitzii but similar loads of A. muciniphila when compared to H subjects, with the exception of those with early onset CD. Depletion of A. muciniphila in this subgroup of subjects suggests that it could be a potential biomarker to assist in pediatric CD diagnosis.
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Affiliation(s)
- Mireia Lopez-Siles
- Laboratory of Molecular Microbiology, Biology Department, Universitat de Girona, Girona, Spain
| | - Núria Enrich-Capó
- Laboratory of Molecular Microbiology, Biology Department, Universitat de Girona, Girona, Spain
| | - Xavier Aldeguer
- Department of Gastroenterology, Hospital Dr. Josep Trueta, Girona, Spain
| | - Miriam Sabat-Mir
- Department of Gastroenterology, Hospital Santa Caterina, Girona, Spain
| | - Sylvia H Duncan
- Microbiology Group, Rowett Institute of Nutrition and Health, Aberdeen, United Kingdom
| | - L Jesús Garcia-Gil
- Laboratory of Molecular Microbiology, Biology Department, Universitat de Girona, Girona, Spain
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48
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Gerhardt S, Mohajeri MH. Changes of Colonic Bacterial Composition in Parkinson's Disease and Other Neurodegenerative Diseases. Nutrients 2018; 10:E708. [PMID: 29857583 PMCID: PMC6024871 DOI: 10.3390/nu10060708] [Citation(s) in RCA: 171] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 05/28/2018] [Accepted: 05/30/2018] [Indexed: 12/12/2022] Open
Abstract
In recent years evidence has emerged that neurodegenerative diseases (NDs) are strongly associated with the microbiome composition in the gut. Parkinson's disease (PD) is the most intensively studied neurodegenerative disease in this context. In this review, we performed a systematic evaluation of the published literature comparing changes in colonic microbiome in PD to the ones observed in other NDs including Alzheimer's disease (AD), multiple system atrophy (MSA), multiple sclerosis (MS), neuromyelitis optica (NMO) and amyotrophic lateral sclerosis (ALS). To enhance the comparability of different studies, only human case-control studies were included. Several studies showed an increase of Lactobacillus, Bifidobacterium, Verrucomicrobiaceae and Akkermansia in PD. A decrease of Faecalibacterium spp., Coprococcus spp., Blautia spp., Prevotella spp. and Prevotellaceae was observed in PD. On a low taxonomic resolution, like the phylum level, the changes are not disease-specific and are inconsistent. However, on a higher taxonomic resolution like genus or species level, a minor overlap was observed between PD and MSA, both alpha synucleinopathies. We show that standardization of sample collection and analysis is necessary for ensuring the reproducibility and comparability of data. We also provide evidence that assessing the microbiota composition at high taxonomic resolution reveals changes in relative abundance that may be specific to or characteristic of one disease or disease group, and might evolve discriminative power. The interactions between bacterial species and strains and the co-abundances must be investigated before assumptions about the effects of specific bacteria on the host can be made with certainty.
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Affiliation(s)
- Sara Gerhardt
- Departement of human medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.
| | - M Hasan Mohajeri
- Departement of human medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.
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49
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Cornuault JK, Petit MA, Mariadassou M, Benevides L, Moncaut E, Langella P, Sokol H, De Paepe M. Phages infecting Faecalibacterium prausnitzii belong to novel viral genera that help to decipher intestinal viromes. MICROBIOME 2018; 6:65. [PMID: 29615108 PMCID: PMC5883640 DOI: 10.1186/s40168-018-0452-1] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 03/21/2018] [Indexed: 05/11/2023]
Abstract
BACKGROUND Viral metagenomic studies have suggested a role for bacteriophages in intestinal dysbiosis associated with several human diseases. However, interpretation of viral metagenomic studies is limited by the lack of knowledge of phages infecting major human gut commensal bacteria, such as Faecalibacterium prausnitzii, a bacterial symbiont repeatedly found depleted in inflammatory bowel disease (IBD) patients. In particular, no complete genomes of phages infecting F. prausnitzii are present in viral databases. METHODS We identified 18 prophages in 15 genomes of F. prausnitzii, used comparative genomics to define eight phage clades, and annotated the genome of the type phage of each clade. For two of the phages, we studied prophage induction in vitro and in vivo in mice. Finally, we aligned reads from already published viral metagenomic data onto the newly identified phages. RESULTS We show that each phage clade represents a novel viral genus and that a surprisingly large fraction of them (10 of the 18 phages) codes for a diversity-generating retroelement, which could contribute to their adaptation to the digestive tract environment. We obtained either experimental or in silico evidence of activity for at least one member of each genus. In addition, four of these phages are either significantly more prevalent or more abundant in stools of IBD patients than in those of healthy controls. CONCLUSION Since IBD patients generally have less F. prausnitzii in their microbiota than healthy controls, the higher prevalence or abundance of some of its phages may indicate that they are activated during disease. This in turn suggests that phages could trigger or aggravate F. prausnitzii depletion in patients. Our results show that prophage detection in sequenced strains of the microbiota can usefully complement viral metagenomic studies.
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Affiliation(s)
- Jeffrey K Cornuault
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Marie-Agnès Petit
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | | | - Leandro Benevides
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Elisabeth Moncaut
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Philippe Langella
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Harry Sokol
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
- Sorbonne Universités, UPMC Univ. Paris 06, École normale supérieure, CNRS, INSERM, APHP Laboratoire des Biomolécules (LBM), 27 rue de Chaligny, 75012, Paris, France
- Department of Gastroenterology, Saint Antoine Hospital, Assistance Publique - Hopitaux de Paris, UPMC, Paris, France
| | - Marianne De Paepe
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.
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50
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Martín R, Bermúdez-Humarán LG, Langella P. Searching for the Bacterial Effector: The Example of the Multi-Skilled Commensal Bacterium Faecalibacterium prausnitzii. Front Microbiol 2018; 9:346. [PMID: 29559959 PMCID: PMC5845625 DOI: 10.3389/fmicb.2018.00346] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 02/13/2018] [Indexed: 01/02/2023] Open
Abstract
Faecalibacterium prausnitzii represents approximately 5% of the total fecal microbiota in healthy adults being one of the most abundant bacterium in the human intestinal microbiota of healthy adults. Furthermore, this bacterium has been proposed to be a sensor and a major actor of the human intestinal health because of its importance in the gut ecosystem. In this context, F. prausnitzii population levels have been found to be reduced in patients suffering from several syndromes and diseases such as inflammatory bowel diseases. These diseases are characterized by a breakage of the intestinal homeostasis called dysbiosis and the use of F. prausnitzii as a next generation probiotic (also called live biotherapeutics) has been proposed as a natural tool to restore such dysbiosis within the gut. Nevertheless, despite the potential importance of this bacterium in human health, little is known about its main effectors underlying its beneficial effects. In this perspective note, we aim to present the actual state in the research about F. prausnitzii effectors and the future milestones in this field.
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Affiliation(s)
- Rebeca Martín
- National Institute of Agricultural Research, Commensals and Probiotics-Host Interactions Laboratory, Micalis Institute, AgroParisTech, Paris-Sud University, Jouy-en-Josas, France
| | - Luis G Bermúdez-Humarán
- National Institute of Agricultural Research, Commensals and Probiotics-Host Interactions Laboratory, Micalis Institute, AgroParisTech, Paris-Sud University, Jouy-en-Josas, France
| | - Philippe Langella
- National Institute of Agricultural Research, Commensals and Probiotics-Host Interactions Laboratory, Micalis Institute, AgroParisTech, Paris-Sud University, Jouy-en-Josas, France
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