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Tanca A, Abbondio M, Palomba A, Fraumene C, Marongiu F, Serra M, Pagnozzi D, Laconi E, Uzzau S. Caloric restriction promotes functional changes involving short-chain fatty acid biosynthesis in the rat gut microbiota. Sci Rep 2018; 8:14778. [PMID: 30283130 PMCID: PMC6170429 DOI: 10.1038/s41598-018-33100-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 08/22/2018] [Indexed: 12/22/2022] Open
Abstract
Caloric restriction (CR) is known to promote health and longevity, likely via modification of the gut microbiota (GM). However, functional and metabolic changes induced in the GM during CR are still unidentified. Here, we investigated the short- and long-term effects of CR on the rat GM using a metaproteogenomic approach. We show that a switch from ad libitum (AL) low fat diet to CR in young rats is able to induce rapid and deep changes in their GM metaproteomic profile, related to a reduction of the Firmicutes/Bacteroidetes ratio and an expansion of lactobacilli. Specifically, we observed a significant change in the expression of the microbial enzymes responsible for short-chain fatty acid biosynthesis, with CR boosting propionogenesis and limiting butyrogenesis and acetogenesis. Furthermore, these CR-induced effects were maintained up to adulthood and started to be reversed after a short-term diet change. We also found that CR alters the abundance of an array of host proteins released in stool, mainly related to epithelial barrier integrity and inflammation. Hence, our results provide thorough information about CR-induced modifications to GM and host functional activity, and might constitute the basis for novel GM-based approaches aimed at monitoring the effectiveness of dietary interventions.
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Affiliation(s)
- Alessandro Tanca
- Porto Conte Ricerche, Science and Technology Park of Sardinia, Tramariglio, Alghero, Italy
| | - Marcello Abbondio
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Antonio Palomba
- Porto Conte Ricerche, Science and Technology Park of Sardinia, Tramariglio, Alghero, Italy
| | - Cristina Fraumene
- Porto Conte Ricerche, Science and Technology Park of Sardinia, Tramariglio, Alghero, Italy
| | - Fabio Marongiu
- Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Monica Serra
- Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Daniela Pagnozzi
- Porto Conte Ricerche, Science and Technology Park of Sardinia, Tramariglio, Alghero, Italy
| | - Ezio Laconi
- Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Sergio Uzzau
- Porto Conte Ricerche, Science and Technology Park of Sardinia, Tramariglio, Alghero, Italy.
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy.
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52
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Chhabra P, Spano AJ, Bowers D, Ren T, Moore DJ, Timko MP, Wu M, Brayman KL. Evidence for the Role of the Cecal Microbiome in Maintenance of Immune Regulation and Homeostasis. Ann Surg 2018; 268:541-549. [PMID: 29994931 DOI: 10.1097/sla.0000000000002930] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
OBJECTIVE (S) Our objective was to investigate alterations in the cecal microbial composition during the development of type 1 diabetes (T1D) with or without IgM therapy, and correlate these alterations with the corresponding immune profile. METHODS (1) Female nonobese diabetic (NOD) mice treated with IgM or saline (n = 20/group) were divided into 5-week-old nondiabetic; 9 to 12-week-old prehyperglycemic stage-1; ≥13-week-old prehyperglycemic stage-2; and diabetic groups. 16S rRNA libraries were prepared from bacterial DNA and deep-sequenced. (2) New-onset diabetic mice were treated with IgM (200 μg on Days 1, 3, and 5) and their blood glucose monitored for 2 months. RESULTS Significant dysbiosis was observed in the cecal microbiome with the progression of T1D development. The alteration in microbiome composition was characterized by an increase in the bacteroidetes:firmicutes ratio. In contrast, IgM conserved normal bacteroidetes:firmicutes ratio and this effect was long-lasting. Furthermore, oral gavage using cecal content from IgM-treated mice significantly diminished the incidence of diabetes compared with controls, indicating that IgM specifically affected mucosa-associated microbes, and that the affect was causal and not an epiphenomenon. Also, regulatory immune cell populations (myeloid-derived suppressor cells and regulatory T cells) were expanded and insulin autoantibody production diminished in the IgM-treated mice. In addition, IgM therapy reversed hyperglycemia in 70% of new-onset diabetic mice (n = 10) and the mice remained normoglycemic for the entire post-treatment observation period. CONCLUSIONS The cecal microbiome appears to be important in maintaining immune homeostasis and normal immune responses.
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Affiliation(s)
- Preeti Chhabra
- Department of Surgery, University of Virginia, Charlottesville, VA
| | - Anthony J Spano
- Department of Biology, University of Virginia, Charlottesville, VA
| | - Daniel Bowers
- Department of Surgery, University of Virginia, Charlottesville, VA
| | - Tiantian Ren
- Department of Biology, University of Virginia, Charlottesville, VA
| | - Daniel J Moore
- Department of Pediatrics, Vanderbilt University, Nashville, TN
| | - Michael P Timko
- Department of Biology, University of Virginia, Charlottesville, VA
| | - Martin Wu
- Department of Biology, University of Virginia, Charlottesville, VA
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53
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Wu H, Xing Y, Sun H, Mao X. Gut microbial diversity in two insectivorous bats: Insights into the effect of different sampling sources. Microbiologyopen 2018; 8:e00670. [PMID: 29971963 PMCID: PMC6530527 DOI: 10.1002/mbo3.670] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 04/03/2018] [Accepted: 05/17/2018] [Indexed: 11/30/2022] Open
Abstract
The gut microbiota is now known as a key factor in mammalian physiology and health. Our understanding of the gut microbial communities and their effects on ecology and evolution of their hosts is extremely limited in bats which represent the second largest mammalian order. In the current study, gut microbiota of three sampling sources (small intestine, large intestine, and feces) were characterized in two sympatric and insectivorous bats (Rhinolophus sinicus and Myotis altarium) by high‐throughput sequencing of the V3‐V4 region of the 16S rRNA gene. Combining with published studies, this work reveals that Gammaproteobacteria may be a dominant class in the whole Chiroptera and Fusobacteria is less observed in bats although it has been proven to be dominant in other mammals. Our results reveal that the sampling source influences alpha diversity of the microbial community in both studied species although no significant variations of beta diversity were observed, which support that fecal samples cannot be used as a proxy of the microbiota in other gut regions in wild animals.
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Affiliation(s)
- Haonan Wu
- Institute of Estuarine and Coastal Research, East China Normal University, Shanghai, China
| | - Yutong Xing
- Institute of Estuarine and Coastal Research, East China Normal University, Shanghai, China
| | - Haijian Sun
- Institute of Estuarine and Coastal Research, East China Normal University, Shanghai, China
| | - Xiuguang Mao
- Institute of Estuarine and Coastal Research, East China Normal University, Shanghai, China
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54
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Fraumene C, Manghina V, Cadoni E, Marongiu F, Abbondio M, Serra M, Palomba A, Tanca A, Laconi E, Uzzau S. Caloric restriction promotes rapid expansion and long-lasting increase of Lactobacillus in the rat fecal microbiota. Gut Microbes 2018; 9:104-114. [PMID: 28891744 PMCID: PMC5989789 DOI: 10.1080/19490976.2017.1371894] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 07/06/2017] [Accepted: 08/22/2017] [Indexed: 02/07/2023] Open
Abstract
Previous studies indicated that caloric restricted diet enables to lower significantly the risk of cardiovascular and metabolic diseases. In experimental animal models, life-long lasting caloric restriction (CR) was demonstrated to induce changes of the intestinal microbiota composition, regardless of fat content and/or exercise. To explore the potential impact of short and long-term CR treatment on the gut microbiota, we conducted an analysis of fecal microbiota composition in young and adult Fisher 344 rats treated with a low fat feed under ad libitum (AL) or CR conditions (70%). We report here significant changes of the rat fecal microbiota that arise rapidly in young growing animals after short-term administration of a CR diet. In particular, Lactobacillus increased significantly after 8 weeks of CR treatment and its relative abundance was significantly higher in CR vs AL fed animals after 36 weeks of dietary intervention. Taken together, our data suggest that Lactobacillus intestinal colonization is hampered in AL fed young rats compared to CR fed ones, while health-promoting CR diet intervention enables the expansion of this genus rapidly and persistently up to adulthood.
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Affiliation(s)
- Cristina Fraumene
- Porto Conte Ricerche, Science and Technology Park of Sardinia, Tramariglio, Alghero, Italy
| | - Valeria Manghina
- Porto Conte Ricerche, Science and Technology Park of Sardinia, Tramariglio, Alghero, Italy
| | - Erika Cadoni
- Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Fabio Marongiu
- Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Marcello Abbondio
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Monica Serra
- Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Antonio Palomba
- Porto Conte Ricerche, Science and Technology Park of Sardinia, Tramariglio, Alghero, Italy
| | - Alessandro Tanca
- Porto Conte Ricerche, Science and Technology Park of Sardinia, Tramariglio, Alghero, Italy
| | - Ezio Laconi
- Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Sergio Uzzau
- Porto Conte Ricerche, Science and Technology Park of Sardinia, Tramariglio, Alghero, Italy
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
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55
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Shi Y, Zhao X, Zhao J, Zhang H, Zhai Q, Narbad A, Chen W. A mixture of Lactobacillus species isolated from traditional fermented foods promote recovery from antibiotic-induced intestinal disruption in mice. J Appl Microbiol 2018; 124:842-854. [PMID: 29314490 DOI: 10.1111/jam.13687] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 11/30/2017] [Accepted: 12/12/2017] [Indexed: 12/18/2022]
Abstract
AIMS This study evaluated the antibiotic-induced changes in microbial ecology, intestinal dysbiosis and low-grade inflammation; and the combined effect of four different Lactobacillus species on recovery of microbiota composition and improvement of gut barrier function in mice. METHODS AND RESULTS Administration of the antibiotic ampicillin for 2 weeks decreased microbial community diversity, induced caecum tumefaction and increased gut permeability in mice. Application of a probiotic cocktail of four Lactobacillus species (JUP-Y4) modulated the microbiota community structure and promoted the abundance of potentially beneficial bacteria such as Akkermansia. Ampicillin administration led to a decline in Bacteroidetes from 46·6 ± 3·91% to 0·264 ± 0·0362%; the addition of JUP-Y4 restored this to 41·4 ± 2·87%. This probiotic supplementation was more effective than natural restoration, where the levels of Bacteroidetes were only restored to 29·3 ± 2·07%. Interestingly, JUP-Y4 treatment was more effective in the restoration of microbiota in faecal samples than in caecal samples. JUP-Y4 also significantly reduced the levels of d-lactate and endotoxin (lipopolysaccharide, LPS) in the serum of mice, and increased the expression of tight-junction proteins while reducing the production of inflammatory cytokines (TNF-α, IL-6, MCP-1, IFN-γ and IL-1β) in the ileum and the colon of antibiotic-treated mice. CONCLUSIONS JUP-Y4 not only promoted recovery from antibiotic-induced gut dysbiosis, but also enhanced the function of the gut barrier, reduced inflammation and lowered levels of circulating endotoxin in mice. SIGNIFICANCE AND IMPACT OF THE STUDY Consumption of a mixture of Lactobacillus species may encourage faster recovery from antibiotic-induced gut dysbiosis and gut microbiota-related immune disturbance.
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Affiliation(s)
- Y Shi
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi, Jiangsu, China
| | - X Zhao
- School of Life Science and Technology, Shanghai Tech University, Shanghai, China
| | - J Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - H Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,National Engineering Research Centre for Functional Food, Wuxi, Jiangsu, China
| | - Q Zhai
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi, Jiangsu, China.,National Engineering Research Centre for Functional Food, Wuxi, Jiangsu, China
| | - A Narbad
- UK-China Joint Centre on Probiotic Bacteria, Norwich, UK.,Gut Health and Food Safety Programme, Quadram Institute Bioscience, Norwich, UK
| | - W Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,National Engineering Research Centre for Functional Food, Wuxi, Jiangsu, China.,Beijing Innovation Centre of Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing, China
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56
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Li L, Zhang X, Ning Z, Mayne J, Moore JI, Butcher J, Chiang CK, Mack D, Stintzi A, Figeys D. Evaluating in Vitro Culture Medium of Gut Microbiome with Orthogonal Experimental Design and a Metaproteomics Approach. J Proteome Res 2017; 17:154-163. [PMID: 29130306 DOI: 10.1021/acs.jproteome.7b00461] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In vitro culture based approaches are time- and cost-effective solutions for rapidly evaluating the effects of drugs or natural compounds against microbiomes. The nutritional composition of the culture medium is an important determinant for effectively maintaining the gut microbiome in vitro. This study combines orthogonal experimental design and a metaproteomics approach to obtaining functional insights into the effects of different medium components on the microbiome. Our results show that the metaproteomic profile respond differently to medium components, including inorganic salts, bile salts, mucin, and short-chain fatty acids. Multifactor analysis of variance further revealed significant main and interaction effects of inorganic salts, bile salts, and mucin on the different functional groups of gut microbial proteins. While a broad regulating effect was observed on basic metabolic pathways, different medium components also showed significant modulations on cell wall, membrane, and envelope biogenesis and cell motility related functions. In particular, flagellar assembly related proteins were significantly responsive to the presence of mucin. This study provides information on the functional influences of medium components on the in vitro growth of microbiome communities and gives insight on the key components that must be considered when selecting and optimizing media for culturing ex vivo microbiotas.
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Affiliation(s)
- Leyuan Li
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa , Ottawa, Ontario K1H 8M5, Canada
| | - Xu Zhang
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa , Ottawa, Ontario K1H 8M5, Canada
| | - Zhibin Ning
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa , Ottawa, Ontario K1H 8M5, Canada
| | - Janice Mayne
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa , Ottawa, Ontario K1H 8M5, Canada
| | - Jasmine I Moore
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa , Ottawa, Ontario K1H 8M5, Canada
| | - James Butcher
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa , Ottawa, Ontario K1H 8M5, Canada
| | - Cheng-Kang Chiang
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa , Ottawa, Ontario K1H 8M5, Canada
| | - David Mack
- Department of Paediatrics, CHEO Inflammatory Bowel Disease Centre and Research Institute, University of Ottawa , Ottawa, Ontario K1H 8L1, Canada
| | - Alain Stintzi
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa , Ottawa, Ontario K1H 8M5, Canada
| | - Daniel Figeys
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa , Ottawa, Ontario K1H 8M5, Canada.,Canadian Institute for Advanced Research , Toronto, Ontario M5G 1Z8, Canada
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57
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Starr AE, Deeke SA, Li L, Zhang X, Daoud R, Ryan J, Ning Z, Cheng K, Nguyen LVH, Abou-Samra E, Lavallée-Adam M, Figeys D. Proteomic and Metaproteomic Approaches to Understand Host–Microbe Interactions. Anal Chem 2017; 90:86-109. [DOI: 10.1021/acs.analchem.7b04340] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Amanda E. Starr
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Shelley A. Deeke
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Leyuan Li
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Xu Zhang
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Rachid Daoud
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - James Ryan
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Zhibin Ning
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Kai Cheng
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Linh V. H. Nguyen
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Elias Abou-Samra
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Mathieu Lavallée-Adam
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Daniel Figeys
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
- Molecular Architecture of Life Program, Canadian Institute for Advanced Research, Toronto, Ontario, M5G 1M1, Canada
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58
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Metagenome Analysis: a Powerful Tool for Enzyme Bioprospecting. Appl Biochem Biotechnol 2017; 183:636-651. [PMID: 28815469 DOI: 10.1007/s12010-017-2568-3] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 07/24/2017] [Indexed: 01/05/2023]
Abstract
Microorganisms are found throughout every corner of nature, and vast number of microorganisms is difficult to cultivate by classical microbiological techniques. The advent of metagenomics has revolutionized the field of microbial biotechnology. Metagenomics allow the recovery of genetic material directly from environmental niches without any cultivation techniques. Currently, metagenomic tools are widely employed as powerful tools to isolate and identify enzymes with novel biocatalytic activities from the uncultivable component of microbial communities. The employment of next-generation sequencing techniques for metagenomics resulted in the generation of large sequence data sets derived from various environments, such as soil, the human body and ocean water. This review article describes the state-of-the-art techniques and tools in metagenomics and discusses the potential of metagenomic approaches for the bioprospecting of industrial enzymes from various environmental samples. We also describe the unusual novel enzymes discovered via metagenomic approaches and discuss the future prospects for metagenome technologies.
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59
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Tanca A, Abbondio M, Palomba A, Fraumene C, Manghina V, Cucca F, Fiorillo E, Uzzau S. Potential and active functions in the gut microbiota of a healthy human cohort. MICROBIOME 2017; 5:79. [PMID: 28709472 PMCID: PMC5513205 DOI: 10.1186/s40168-017-0293-3] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 06/28/2017] [Indexed: 05/20/2023]
Abstract
BACKGROUND The study of the gut microbiota (GM) is rapidly moving towards its functional characterization by means of shotgun meta-omics. In this context, there is still no consensus on which microbial functions are consistently and constitutively expressed in the human gut in physiological conditions. Here, we selected a cohort of 15 healthy subjects from a native and highly monitored Sardinian population and analyzed their GMs using shotgun metaproteomics, with the aim of investigating GM functions actually expressed in a healthy human population. In addition, shotgun metagenomics was employed to reveal GM functional potential and to compare metagenome and metaproteome profiles in a combined taxonomic and functional fashion. RESULTS Metagenomic and metaproteomic data concerning the taxonomic structure of the GM under study were globally comparable. On the contrary, a considerable divergence between genetic potential and functional activity of the human healthy GM was observed, with the metaproteome displaying a higher plasticity, compared to the lower inter-individual variability of metagenome profiles. The taxon-specific contribution to functional activities and metabolic tasks was also examined, giving insights into the peculiar role of several GM members in carbohydrate metabolism (including polysaccharide degradation, glycan transport, glycolysis, and short-chain fatty acid production). Noteworthy, Firmicutes-driven butyrogenesis (mainly due to Faecalibacterium spp.) was shown to be the metabolic activity with the highest expression rate and the lowest inter-individual variability in the study cohort, in line with the previously reported importance of the biosynthesis of this microbial product for the gut homeostasis. CONCLUSIONS Our results provide detailed and taxon-specific information regarding functions and pathways actively working in a healthy GM. The reported discrepancy between expressed functions and functional potential suggests that caution should be used before drawing functional conclusions from metagenomic data, further supporting metaproteomics as a fundamental approach to characterize the human GM metabolic functions and activities.
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Affiliation(s)
- Alessandro Tanca
- Porto Conte Ricerche, Science and Technology Park of Sardinia, S.P. 55 Porto Conte - Capo Caccia km 8,400, Località Tramariglio, 07041, Alghero, SS, Italy
| | - Marcello Abbondio
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Antonio Palomba
- Porto Conte Ricerche, Science and Technology Park of Sardinia, S.P. 55 Porto Conte - Capo Caccia km 8,400, Località Tramariglio, 07041, Alghero, SS, Italy
| | - Cristina Fraumene
- Porto Conte Ricerche, Science and Technology Park of Sardinia, S.P. 55 Porto Conte - Capo Caccia km 8,400, Località Tramariglio, 07041, Alghero, SS, Italy
| | - Valeria Manghina
- Porto Conte Ricerche, Science and Technology Park of Sardinia, S.P. 55 Porto Conte - Capo Caccia km 8,400, Località Tramariglio, 07041, Alghero, SS, Italy
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Francesco Cucca
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - Edoardo Fiorillo
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - Sergio Uzzau
- Porto Conte Ricerche, Science and Technology Park of Sardinia, S.P. 55 Porto Conte - Capo Caccia km 8,400, Località Tramariglio, 07041, Alghero, SS, Italy.
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy.
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