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Wang M, Chen S, Zheng H, Li S, Chen L, Wang D. The responses of cadmium phytotoxicity in rice and the microbial community in contaminated paddy soils for the application of different long-term N fertilizers. CHEMOSPHERE 2020; 238:124700. [PMID: 31524602 DOI: 10.1016/j.chemosphere.2019.124700] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 08/25/2019] [Accepted: 08/27/2019] [Indexed: 06/10/2023]
Abstract
An eight-year field trial was conducted to investigate the effects of four different N fertilization treatments of urea (CO(NH2)2, the control), ammonium sulfate ((NH4)2SO4), ammonium chloride (NH4Cl), and ammonium hydrogen phosphate [(NH4)2HPO4]) on cadmium (Cd) phytotoxicity in rice and soil microbial communities in a Cd-contaminated paddy of southern China. The results demonstrate that the different N treatments exerted different effects: the application of (NH4)2HPO4 and (NH4)2SO4 significantly increased rice grain yield and decreased soil-extractable Cd content when compared with those of the control, while NH4Cl had a converse effect. Expression of genes related to Cd uptake (IRT and NRAPM genes) and transport (HMA genes) by roots may be responsible for Cd phytotoxicity in rice grown in the different N fertilization treatments. Our results further demonstrate that N fertilization had stronger effects on soil bacterial communities than fungal communities. The bacterial and fungal keystone species were identified by phylogenetic molecular ecological network (pMEN) analysis and mainly fell into the categories of Gammaproteobacteria, Acidobacteria and Actinobacteria for the bacterial species and Ascomycota for the fungal species; all of these keystone species were highly enriched in the (NH4)2HPO4 treatment. Soil pH and soil available-Cd content emerged as the major determinants of microbial network connectors. These results could provide effective fertilizing strategies for alleviating Cd phytotoxicity in rice and enhance the understanding of its underlying microbial mechanisms.
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Affiliation(s)
- Meng Wang
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs / Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Shibao Chen
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs / Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China.
| | - Han Zheng
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs / Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Shanshan Li
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs / Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Li Chen
- Institute of Plant Protection and Environmental Protection, Beijing Academy of Agriculture and Forestry Science, Beijing, 100097, PR China
| | - Duo Wang
- College of Energy, Xiamen University, Xiamen, Fujian, 361102, PR China
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52
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Wang S, Zhang B, Chen T, Li C, Fu X, Huang Q. Chemical Cross-Linking Controls in Vitro Fecal Fermentation Rate of High-Amylose Maize Starches and Regulates Gut Microbiota Composition. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:13728-13736. [PMID: 31617357 DOI: 10.1021/acs.jafc.9b04410] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A slow fermentation rate of dietary fiber could result in a steady metabolite production release and even distribution in the entire colon, increasing the likelihood of meeting the energy requirements of the distal colon. In the present study, we modulated the fermentation rate in an in vitro human fecal fermentation model by applying chemical cross-linking modification to a type 2 resistant starch [i.e., high-amylose maize starch (HAMS)]. Cross-linking modification decreased the gas production (an indicator of the fermentation rate) of HAMS throughout the whole fermentation progress. The butyrate production rate of cross-linked starches decreased gradually with the increase of the cross-linking degree. Certain beneficial gut microbiota such as genera of Blautia and Clostridiales members were remarkably promoted by starches with low and medium cross-linking degrees, whereas HAMS with a high cross-linking degree obviously promoted the abundance of Bacteroides uniformis and Ruminococcus bromii. This finding reveals that cross-linking modification effectively controls the fermentation rate and highlights the modulation metabolite profiles and gut microbiota composition through chemical modification.
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Affiliation(s)
- Shaokang Wang
- School of Food Science and Engineering, National Research Center for Tropical Health Food, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety , South China University of Technology , Guangzhou 510640 , China
| | - Bin Zhang
- School of Food Science and Engineering, National Research Center for Tropical Health Food, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety , South China University of Technology , Guangzhou 510640 , China
- Sino-Singapore International Research Institute , Guangzhou 510555 , China
- Overseas Expertise Introduction Center for Discipline Innovation of Food Nutrition and Human Health (111 Center) , Guangzhou 510640 , China
| | - Tingting Chen
- Department of Biochemistry and Microbiology , Rutgers University , New Brunswick , New Jersey 08901-8525 , United States
- School of Food Science and Technology , Nanchang University , Nanchang 330047 , China
| | - Chao Li
- School of Food Science and Engineering, National Research Center for Tropical Health Food, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety , South China University of Technology , Guangzhou 510640 , China
- Sino-Singapore International Research Institute , Guangzhou 510555 , China
- Overseas Expertise Introduction Center for Discipline Innovation of Food Nutrition and Human Health (111 Center) , Guangzhou 510640 , China
| | - Xiong Fu
- School of Food Science and Engineering, National Research Center for Tropical Health Food, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety , South China University of Technology , Guangzhou 510640 , China
- Overseas Expertise Introduction Center for Discipline Innovation of Food Nutrition and Human Health (111 Center) , Guangzhou 510640 , China
| | - Qiang Huang
- School of Food Science and Engineering, National Research Center for Tropical Health Food, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety , South China University of Technology , Guangzhou 510640 , China
- Sino-Singapore International Research Institute , Guangzhou 510555 , China
- Overseas Expertise Introduction Center for Discipline Innovation of Food Nutrition and Human Health (111 Center) , Guangzhou 510640 , China
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53
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Co-existence of Network Architectures Supporting the Human Gut Microbiome. iScience 2019; 22:380-391. [PMID: 31812808 PMCID: PMC6911941 DOI: 10.1016/j.isci.2019.11.032] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 09/27/2019] [Accepted: 11/15/2019] [Indexed: 01/29/2023] Open
Abstract
Microbial organisms of the human gut microbiome do not exist in isolation but form complex and diverse interactions to maintain health and reduce risk of disease development. The organization of the gut microbiome is assumed to be a singular assortative network, where interactions between operational taxonomic units (OTUs) can readily be clustered into segregated and distinct communities. Here, we leverage recent methodological advances in network modeling to assess whether communities in the human microbiome exhibit a single network structure or whether co-existing mesoscale network architectures are present. We found evidence for core-periphery structures in the microbiome, supported by strong, assortative community interactions. This complex architecture, coupled with previously reported functional roles of OTUs, provides a nuanced understanding of how the microbiome simultaneously promotes high microbial diversity and maintains functional redundancy.
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54
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Kauter A, Epping L, Semmler T, Antao EM, Kannapin D, Stoeckle SD, Gehlen H, Lübke-Becker A, Günther S, Wieler LH, Walther B. The gut microbiome of horses: current research on equine enteral microbiota and future perspectives. Anim Microbiome 2019; 1:14. [PMID: 33499951 PMCID: PMC7807895 DOI: 10.1186/s42523-019-0013-3] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 09/09/2019] [Indexed: 12/26/2022] Open
Abstract
Understanding the complex interactions of microbial communities including bacteria, archaea, parasites, viruses and fungi of the gastrointestinal tract (GIT) associated with states of either health or disease is still an expanding research field in both, human and veterinary medicine. GIT disorders and their consequences are among the most important diseases of domesticated Equidae, but current gaps of knowledge hinder adequate progress with respect to disease prevention and microbiome-based interventions. Current literature on enteral microbiomes mirrors a vast data and knowledge imbalance, with only few studies tackling archaea, viruses and eukaryotes compared with those addressing the bacterial components.Until recently, culture-dependent methods were used for the identification and description of compositional changes of enteral microorganisms, limiting the outcome to cultivatable bacteria only. Today, next generation sequencing technologies provide access to the entirety of genes (microbiome) associated with the microorganisms of the equine GIT including the mass of uncultured microbiota, or "microbial dark matter".This review illustrates methods commonly used for enteral microbiome analysis in horses and summarizes key findings reached for bacteria, viruses and fungi so far. Moreover, reasonable possibilities to combine different explorative techniques are described. As a future perspective, knowledge expansion concerning beneficial compositions of microorganisms within the equine GIT creates novel possibilities for early disorder diagnostics as well as innovative therapeutic approaches. In addition, analysis of shotgun metagenomic data enables tracking of certain microorganisms beyond species barriers: transmission events of bacteria including pathogens and opportunists harboring antibiotic resistance factors between different horses but also between humans and horses will reach new levels of depth concerning strain-level distinctions.
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Affiliation(s)
- Anne Kauter
- Advanced Light and Electron Microscopy (ZBS-4), Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Lennard Epping
- Microbial Genomics (NG1), Robert Koch Institute, Berlin, Germany
| | - Torsten Semmler
- Microbial Genomics (NG1), Robert Koch Institute, Berlin, Germany
| | | | - Dania Kannapin
- Equine Clinic, Surgery and Radiology, Freie Universität Berlin, Berlin, Germany
| | - Sabita D Stoeckle
- Equine Clinic, Surgery and Radiology, Freie Universität Berlin, Berlin, Germany
| | - Heidrun Gehlen
- Equine Clinic, Surgery and Radiology, Freie Universität Berlin, Berlin, Germany
| | - Antina Lübke-Becker
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Freie Universität Berlin, Berlin, Germany
| | - Sebastian Günther
- Pharmaceutical Biology Institute of Pharmacy, Universität Greifswald, Greifswald, Germany
| | | | - Birgit Walther
- Advanced Light and Electron Microscopy (ZBS-4), Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany.
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55
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Sanders ME, Merenstein DJ, Reid G, Gibson GR, Rastall RA. Probiotics and prebiotics in intestinal health and disease: from biology to the clinic. Nat Rev Gastroenterol Hepatol 2019; 16:605-616. [PMID: 31296969 DOI: 10.1038/s41575-019-0173-3] [Citation(s) in RCA: 864] [Impact Index Per Article: 172.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/14/2019] [Indexed: 12/14/2022]
Abstract
Probiotics and prebiotics are microbiota-management tools for improving host health. They target gastrointestinal effects via the gut, although direct application to other sites such as the oral cavity, vaginal tract and skin is being explored. Here, we describe gut-derived effects in humans. In the past decade, research on the gut microbiome has rapidly accumulated and has been accompanied by increased interest in probiotics and prebiotics as a means to modulate the gut microbiota. Given the importance of these approaches for public health, it is timely to reiterate factual and supporting information on their clinical application and use. In this Review, we discuss scientific evidence on probiotics and prebiotics, including mechanistic insights into health effects. Strains of Lactobacillus, Bifidobacterium and Saccharomyces have a long history of safe and effective use as probiotics, but Roseburia spp., Akkermansia spp., Propionibacterium spp. and Faecalibacterium spp. show promise for the future. For prebiotics, glucans and fructans are well proven, and evidence is building on the prebiotic effects of other substances (for example, oligomers of mannose, glucose, xylose, pectin, starches, human milk and polyphenols).
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Affiliation(s)
- Mary Ellen Sanders
- International Scientific Association for Probiotics and Prebiotics, Centennial, CO, USA
| | - Daniel J Merenstein
- Department of Family Medicine, Georgetown University Medical Center, Washington, DC, USA
| | - Gregor Reid
- Lawson Research Institute, and Western University, London, Ontario, Canada
| | - Glenn R Gibson
- Department of Food and Nutritional Sciences, University of Reading, Reading, UK.
| | - Robert A Rastall
- Department of Food and Nutritional Sciences, University of Reading, Reading, UK
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56
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Nourishing the gut microbiota: The potential of prebiotics in microbiota-gut-brain axis research. Behav Brain Sci 2019. [DOI: 10.1017/s0140525x18002856] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Abstract
Dietary fiber and prebiotics consistently modulate microbiota composition and function and hence may constitute a powerful tool in microbiota-gut-brain axis research. However, this is largely ignored in Hooks et al.’s analysis, which highlights the limitations of probiotics in establishing microbiome-mediated effects on neurobehavioral functioning and neglects discussing the potential of prebiotics in warranting the microbiota's role in such effects.
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57
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Youngblut ND, Reischer GH, Walters W, Schuster N, Walzer C, Stalder G, Ley RE, Farnleitner AH. Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades. Nat Commun 2019; 10:2200. [PMID: 31097702 PMCID: PMC6522487 DOI: 10.1038/s41467-019-10191-3] [Citation(s) in RCA: 247] [Impact Index Per Article: 49.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 04/25/2019] [Indexed: 02/06/2023] Open
Abstract
Multiple factors modulate microbial community assembly in the vertebrate gut, though studies disagree as to their relative contribution. One cause may be a reliance on captive animals, which can have very different gut microbiomes compared to their wild counterparts. To resolve this disagreement, we analyze a new, large, and highly diverse animal distal gut 16 S rRNA microbiome dataset, which comprises 80% wild animals and includes members of Mammalia, Aves, Reptilia, Amphibia, and Actinopterygii. We decouple the effects of host evolutionary history and diet on gut microbiome diversity and show that each factor modulates different aspects of diversity. Moreover, we resolve particular microbial taxa associated with host phylogeny or diet and show that Mammalia have a stronger signal of cophylogeny. Finally, we find that environmental filtering and microbe-microbe interactions differ among host clades. These findings provide a robust assessment of the processes driving microbial community assembly in the vertebrate intestine.
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Affiliation(s)
- Nicholas D Youngblut
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Max Planck Ring 5, 72076, Tübingen, Germany.
| | - Georg H Reischer
- TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, Research Group for Environmental Microbiology and Molecular Diagnostics 166/5/3, Gumpendorfer Straße 1a, 1060, Vienna, Austria
- ICC Interuniversity Cooperation Centre Water & Health, 1160, Vienna, Austria
| | - William Walters
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Max Planck Ring 5, 72076, Tübingen, Germany
| | - Nathalie Schuster
- TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, Research Group for Environmental Microbiology and Molecular Diagnostics 166/5/3, Gumpendorfer Straße 1a, 1060, Vienna, Austria
| | - Chris Walzer
- Research Institute of Wildlife Ecology, University of Veterinary Medicine, Vienna, 1160, Austria
| | - Gabrielle Stalder
- Research Institute of Wildlife Ecology, University of Veterinary Medicine, Vienna, 1160, Austria
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Max Planck Ring 5, 72076, Tübingen, Germany
| | - Andreas H Farnleitner
- TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, Research Group for Environmental Microbiology and Molecular Diagnostics 166/5/3, Gumpendorfer Straße 1a, 1060, Vienna, Austria
- ICC Interuniversity Cooperation Centre Water & Health, 1160, Vienna, Austria
- Research Division Water Quality and Health, Karl Landsteiner University for Health Sciences, 3500, Krems an der Donau, Austria
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58
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Smith NW, Shorten PR, Altermann E, Roy NC, McNabb WC. The Classification and Evolution of Bacterial Cross-Feeding. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00153] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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59
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Invited review: Application of meta-omics to understand the dynamic nature of the rumen microbiome and how it responds to diet in ruminants. Animal 2019; 13:1843-1854. [PMID: 31062682 DOI: 10.1017/s1751731119000752] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Ruminants are unique among livestock due to their ability to efficiently convert plant cell wall carbohydrates into meat and milk. This ability is a result of the evolution of an essential symbiotic association with a complex microbial community in the rumen that includes vast numbers of bacteria, methanogenic archaea, anaerobic fungi and protozoa. These microbes produce a diverse array of enzymes that convert ingested feedstuffs into volatile fatty acids and microbial protein which are used by the animal for growth. Recent advances in high-throughput sequencing and bioinformatic analyses have helped to reveal how the composition of the rumen microbiome varies significantly during the development of the ruminant host, and with changes in diet. These sequencing efforts are also beginning to explain how shifts in the microbiome affect feed efficiency. In this review, we provide an overview of how meta-omics technologies have been applied to understanding the rumen microbiome, and the impact that diet has on the rumen microbial community.
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60
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The Use of Defined Microbial Communities To Model Host-Microbe Interactions in the Human Gut. Microbiol Mol Biol Rev 2019; 83:83/2/e00054-18. [PMID: 30867232 DOI: 10.1128/mmbr.00054-18] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The human intestinal ecosystem is characterized by a complex interplay between different microorganisms and the host. The high variation within the human population further complicates the quest toward an adequate understanding of this complex system that is so relevant to human health and well-being. To study host-microbe interactions, defined synthetic bacterial communities have been introduced in gnotobiotic animals or in sophisticated in vitro cell models. This review reinforces that our limited understanding has often hampered the appropriate design of defined communities that represent the human gut microbiota. On top of this, some communities have been applied to in vivo models that differ appreciably from the human host. In this review, the advantages and disadvantages of using defined microbial communities are outlined, and suggestions for future improvement of host-microbe interaction models are provided. With respect to the host, technological advances, such as the development of a gut-on-a-chip system and intestinal organoids, may contribute to more-accurate in vitro models of the human host. With respect to the microbiota, due to the increasing availability of representative cultured isolates and their genomic sequences, our understanding and controllability of the human gut "core microbiota" are likely to increase. Taken together, these advancements could further unravel the molecular mechanisms underlying the human gut microbiota superorganism. Such a gain of insight would provide a solid basis for the improvement of pre-, pro-, and synbiotics as well as the development of new therapeutic microbes.
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61
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Gotoh A, Ojima MN, Katayama T. Minority species influences microbiota formation: the role of Bifidobacterium with extracellular glycosidases in bifidus flora formation in breastfed infant guts. Microb Biotechnol 2019; 12:259-264. [PMID: 30637938 PMCID: PMC6389856 DOI: 10.1111/1751-7915.13366] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 12/14/2018] [Indexed: 12/13/2022] Open
Abstract
The human body houses a variety of microbial ecosystems, such as the microbiotas on the skin, in the oral cavity and in the digestive tract. The gut microbiota is one such ecosystem that contains trillions of bacteria, and it is well established that it can significantly influence host health and diseases. With the advancement in bioinformatics tools, numerous comparative studies based on 16S ribosomal RNA (rRNA) gene sequences, metabolomics, pathological and epidemical analyses have revealed the correlative relationship between the abundance of certain taxa and disease states or amount of certain causative bioactive compounds. However, the 16S rRNA-based taxonomic analyses using next-generation sequencing (NGS) technology essentially detect only the majority species. Although the entire gut microbiome consists of 1013 microbial cells, NGS read counts are given in multiples of 106 , making it difficult to determine the diversity of the entire microbiota. Some recent studies have reported instances where certain minority species play a critical role in creating locally stable conditions for other species by stabilizing the fundamental microbiota, despite their low abundance. These minority species act as 'keystone species', which is a species whose effect on the community is disproportionately large compared to its relative abundance. One of the attributes of keystone species within the gut microbiota is its extensive enzymatic capacity for substrates that are rare or difficult to degrade for other species, such as dietary fibres or host-derived complex glycans, like human milk oligosaccharides (HMOs). In this paper, we propose that more emphasis should be placed on minority taxa and their possible role as keystone species in gut microbiota studies by referring to our recent studies on HMO-mediated microbiota formation in the infant gut.
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Affiliation(s)
- Aina Gotoh
- Graduate School of BiostudiesKyoto UniversitySakyo‐kuKyoto606‐8502Japan
| | | | - Takane Katayama
- Graduate School of BiostudiesKyoto UniversitySakyo‐kuKyoto606‐8502Japan
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62
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Snelson M, Kellow NJ, Coughlan MT. Modulation of the Gut Microbiota by Resistant Starch as a Treatment of Chronic Kidney Diseases: Evidence of Efficacy and Mechanistic Insights. Adv Nutr 2019; 10:303-320. [PMID: 30668615 PMCID: PMC6416045 DOI: 10.1093/advances/nmy068] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 07/17/2018] [Accepted: 08/12/2018] [Indexed: 12/14/2022] Open
Abstract
Chronic kidney disease (CKD) has been associated with changes in gut microbial ecology, or "dysbiosis," which may contribute to disease progression. Recent studies have focused on dietary approaches to favorably alter the composition of the gut microbial communities as a treatment method in CKD. Resistant starch (RS), a prebiotic that promotes proliferation of gut bacteria such as Bifidobacteria and Lactobacilli, increases the production of metabolites including short-chain fatty acids, which confer a number of health-promoting benefits. However, there is a lack of mechanistic insight into how these metabolites can positively influence renal health. Emerging evidence shows that microbiota-derived metabolites can regulate the incretin axis and mitigate inflammation via expansion of regulatory T cells. Studies from animal models and patients with CKD show that RS supplementation attenuates the concentrations of uremic retention solutes, including indoxyl sulfate and p-cresyl sulfate. Here, we present the current state of knowledge linking the microbiome to CKD, we explore the efficacy of RS in animal models of CKD and in humans with the condition, and we discuss how RS supplementation could be a promising dietary approach for slowing CKD progression.
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Affiliation(s)
- Matthew Snelson
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Nicole J Kellow
- Be Active Sleep & Eat (BASE) Facility, Department of Nutrition, Dietetics, and Food, Monash University, Notting Hill, Victoria, Australia
| | - Melinda T Coughlan
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Baker Heart Research Institute, Melbourne, Victoria, Australia
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63
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Fu X, Liu Z, Zhu C, Mou H, Kong Q. Nondigestible carbohydrates, butyrate, and butyrate-producing bacteria. Crit Rev Food Sci Nutr 2018; 59:S130-S152. [PMID: 30580556 DOI: 10.1080/10408398.2018.1542587] [Citation(s) in RCA: 265] [Impact Index Per Article: 44.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Nondigestible carbohydrates (NDCs) are fermentation substrates in the colon after escaping digestion in the upper gastrointestinal tract. Among NDCs, resistant starch is not hydrolyzed by pancreatic amylases but can be degraded by enzymes produced by large intestinal bacteria, including clostridia, bacteroides, and bifidobacteria. Nonstarch polysaccharides, such as pectin, guar gum, alginate, arabinoxylan, and inulin fructans, and nondigestible oligosaccharides and their derivatives, can also be fermented by beneficial bacteria in the large intestine. Butyrate is one of the most important metabolites produced through gastrointestinal microbial fermentation and functions as a major energy source for colonocytes by directly affecting the growth and differentiation of colonocytes. Moreover, butyrate has various physiological effects, including enhancement of intestinal barrier function and mucosal immunity. In this review, several representative NDCs are introduced, and their chemical components, structures, and physiological functions, including promotion of the proliferation of butyrate-producing bacteria and enhancement of butyrate production, are discussed. We also describe the strategies for achieving directional accumulation of colonic butyrate based on endogenous generation mechanisms.
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Affiliation(s)
- Xiaodan Fu
- a College of Food Science and Engineering , Ocean University of China , Qingdao , China
| | - Zhemin Liu
- a College of Food Science and Engineering , Ocean University of China , Qingdao , China
| | - Changliang Zhu
- a College of Food Science and Engineering , Ocean University of China , Qingdao , China
| | - Haijin Mou
- a College of Food Science and Engineering , Ocean University of China , Qingdao , China
| | - Qing Kong
- a College of Food Science and Engineering , Ocean University of China , Qingdao , China
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64
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Crost EH, Le Gall G, Laverde-Gomez JA, Mukhopadhya I, Flint HJ, Juge N. Mechanistic Insights Into the Cross-Feeding of Ruminococcus gnavus and Ruminococcus bromii on Host and Dietary Carbohydrates. Front Microbiol 2018; 9:2558. [PMID: 30455672 PMCID: PMC6231298 DOI: 10.3389/fmicb.2018.02558] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 10/08/2018] [Indexed: 12/13/2022] Open
Abstract
Dietary and host glycans shape the composition of the human gut microbiota with keystone carbohydrate-degrading species playing a critical role in maintaining the structure and function of gut microbial communities. Here, we focused on two major human gut symbionts, the mucin-degrader Ruminococcus gnavus ATCC 29149, and R. bromii L2-63, a keystone species for the degradation of resistant starch (RS) in human colon. Using anaerobic individual and co-cultures of R. bromii and R. gnavus grown on mucin or starch as sole carbon source, we showed that starch degradation by R. bromii supported the growth of R. gnavus whereas R. bromii did not benefit from mucin degradation by R. gnavus. Further we analyzed the growth (quantitative PCR), metabolite production (1H NMR analysis), and bacterial transcriptional response (RNA-Seq) of R. bromii cultured with RS or soluble starch (SS) in the presence or absence of R. gnavus. In co-culture fermentations on starch, 1H NMR analysis showed that R. gnavus benefits from transient glucose and malto-oligosaccharides released by R. bromii upon starch degradation, producing acetate, formate, and lactate as main fermentation end-products. Differential expression analysis (DESeq 2) on starch (SS and RS) showed that the presence of R. bromii induced changes in R. gnavus transcriptional response of genes encoding several maltose transporters and enzymes involved in its metabolism such as maltose phosphorylase, in line with the ability of R. gnavus to utilize R. bromii starch degradation products. In the RS co-culture, R. bromii showed a significant increase in the induction of tryptophan (Trp) biosynthesis genes and a decrease of vitamin B12 (VitB12)-dependent methionine biosynthesis as compared to the mono-culture, suggesting that Trp and VitB12 availability become limited in the presence of R. gnavus. Together this study showed a direct competition between R. bromii and R. gnavus on RS, suggesting that in vivo, the R. gnavus population inhabiting the mucus niche may be modulated by the supply of non-digestible carbohydrates reaching the colon such as RS.
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Affiliation(s)
- Emmanuelle H Crost
- Quadram Institute Bioscience, Gut Microbes and Health Institute Strategic Programme, Norwich Research Park, Norwich, United Kingdom
| | - Gwenaelle Le Gall
- Quadram Institute Bioscience, Gut Microbes and Health Institute Strategic Programme, Norwich Research Park, Norwich, United Kingdom
| | - Jenny A Laverde-Gomez
- Gut Health Group, The Rowett Institute, University of Aberdeen, Aberdeen, United Kingdom
| | - Indrani Mukhopadhya
- Gut Health Group, The Rowett Institute, University of Aberdeen, Aberdeen, United Kingdom
| | - Harry J Flint
- Gut Health Group, The Rowett Institute, University of Aberdeen, Aberdeen, United Kingdom
| | - Nathalie Juge
- Quadram Institute Bioscience, Gut Microbes and Health Institute Strategic Programme, Norwich Research Park, Norwich, United Kingdom
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65
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Cani PD, Jordan BF. Gut microbiota-mediated inflammation in obesity: a link with gastrointestinal cancer. Nat Rev Gastroenterol Hepatol 2018; 15:671-682. [PMID: 29844585 DOI: 10.1038/s41575-018-0025-6] [Citation(s) in RCA: 240] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Overweight and obesity are associated with increased risk of developing metabolic disorders such as diabetes and cardiovascular diseases. However, besides these metabolic diseases, excess body weight is also associated with different cancers, including gastrointestinal cancers, such as liver, pancreatic and colon cancers. Inflammation is a common feature of both obesity and cancer; however, the origin of this inflammation has been largely debated. Over the past decade, growing evidence has shown that the composition of the gut microbiota and its activity might be associated not only with the onset of inflammation but also with metabolic disorders and cancer. Here, we review the links between the gut microbiota, gut barrier function and the onset of low-grade inflammation in the development of gastrointestinal cancer. We also describe the mechanisms by which specific microorganism-associated molecular patterns crosstalk with the immune system and how the metabolic activity of bacteria induces specific signalling pathways beyond the gut that eventually trigger carcinogenesis.
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Affiliation(s)
- Patrice D Cani
- Université catholique de Louvain, Louvain Drug Research Institute, WELBIO (Walloon Excellence in Life sciences and BIOtechnology), Metabolism and Nutrition Research Group, Brussels, Belgium.
| | - Benedicte F Jordan
- Université catholique de Louvain, Louvain Drug Research Institute, Biomedical Magnetic Resonance Research Group, Brussels, Belgium
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66
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Cross-Feeding among Probiotic Bacterial Strains on Prebiotic Inulin Involves the Extracellular exo-Inulinase of Lactobacillus paracasei Strain W20. Appl Environ Microbiol 2018; 84:AEM.01539-18. [PMID: 30171006 DOI: 10.1128/aem.01539-18] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 08/23/2018] [Indexed: 11/20/2022] Open
Abstract
Probiotic gut bacteria employ specific metabolic pathways to degrade dietary carbohydrates beyond the capabilities of their human host. Here, we report how individual commercial probiotic strains degrade prebiotic (inulin type) fructans. First, a structural analysis of commercial fructose oligosaccharide-inulin samples was performed. These β-(2-1)-fructans differ in termination by either glucose (GF) or fructose (FF) residues, with a broad variation in the degrees of polymerization (DPs). The growth of individual probiotic bacteria on short-chain inulin (sc-inulin) (Frutafit CLR), a β-(2-1)-fructan (DP 2 to DP 40), was studied. Lactobacillus salivarius W57 and other bacteria grew relatively poorly on sc-inulin, with only fractions of DP 3 and DP 5 utilized, reflecting uptake via specific transport systems followed by intracellular metabolism. Lactobacillus paracasei subsp. paracasei W20 completely used all sc-inulin components, employing an extracellular exo-inulinase enzyme (glycoside hydrolase family GH32 [LpGH32], also found in other strains of this species); the purified enzyme converted high-DP compounds into fructose, sucrose, 1-kestose, and F2 (inulobiose). The cocultivation of L. salivarius W57 and L. paracasei W20 on sc-inulin resulted in cross-feeding of the former by the latter, supported by this extracellular exo-inulinase. The extent of cross-feeding depended on the type of fructan, i.e., the GF type (clearly stimulating) versus the FF type (relatively low stimulus), and on fructan chain length, since relatively low-DP β-(2-1)-fructans contain a relatively high content of GF-type molecules, thus resulting in higher concentrations of GF-type DP 2 to DP 3 degradation products. The results provide an example of how in vivo cross-feeding on prebiotic β-(2-1)-fructans may occur among probiotic lactobacilli.IMPORTANCE The human gut microbial community is associated strongly with host physiology and human diseases. This observation has prompted research on pre- and probiotics, two concepts enabling specific changes in the composition of the human gut microbiome that result in beneficial effects for the host. Here, we show how fructooligosaccharide-inulin prebiotics are fermented by commercial probiotic bacterial strains involving specific sets of enzymes and transporters. Cross-feeding strains such as Lactobacillus paracasei W20 may thus act as keystone strains in the degradation of prebiotic inulin in the human gut, and this strain-exo-inulinase combination may be used in commercial Lactobacillus-inulin synbiotics.
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Bifidobacterium pseudolongum in the Ceca of Rats Fed Hi-Maize Starch Has Characteristics of a Keystone Species in Bifidobacterial Blooms. Appl Environ Microbiol 2018; 84:AEM.00547-18. [PMID: 29802187 DOI: 10.1128/aem.00547-18] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 05/19/2018] [Indexed: 12/18/2022] Open
Abstract
Starches resistant to mammalian digestion are present in foods and pass to the large bowel, where they may be degraded and fermented by the microbiota. Increases in relative abundances of bifidobacteria (blooms) have been reported in rats whose diet was supplemented with Hi-Maize resistant starch. We determined that the bifidobacterial species present in the rat cecum under these circumstances mostly belonged to Bifidobacterium animalis However, cultures of B. animalis isolated from the rats failed to degrade Hi-Maize starch to any extent. In contrast, Bifidobacterium pseudolongum also detected in the rat microbiota had high starch-degrading ability. Transcriptional comparisons showed increased expression of a type 1 pullulanase, alpha-amylase, and glycogen debranching enzyme by B. pseudolongum when cultured in medium containing Hi-Maize starch. Maltose was released into the culture medium, and B. animalis cultures had shorter doubling times in maltose medium than did B. pseudolongum Thus, B. pseudolongum, which was present at a consistently low abundance in the microbiota, but which has extensive enzymatic capacity to degrade resistant starch, showed the attributes of a keystone species associated with the bifidobacterial bloom.IMPORTANCE This study addresses the microbiology and function of a natural ecosystem (the rat gut) using DNA-based observations and in vitro experimentation. The microbial community of the large bowel of animals, including humans, has been studied extensively through the use of high-throughput DNA sequencing methods and advanced bioinformatics analysis. These studies reveal the compositions and genetic capacities of microbiotas but not the intricacies of how microbial communities function. Our work, combining DNA sequence analysis and laboratory experiments with cultured strains of bacteria, revealed that the increased abundance of bifidobacteria in the rat gut, induced by feeding indigestible starch, involved a species that cannot itself degrade the starch (Bifidobacterium animalis) but cohabits with a species that can (Bifidobacterium pseudolongum). B. pseudolongum has the characteristics of a keystone species in the community because it had low abundance but high ability to perform a critical function, the hydrolysis of resistant starch.
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68
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So D, Whelan K, Rossi M, Morrison M, Holtmann G, Kelly JT, Shanahan ER, Staudacher HM, Campbell KL. Dietary fiber intervention on gut microbiota composition in healthy adults: a systematic review and meta-analysis. Am J Clin Nutr 2018; 107:965-983. [PMID: 29757343 DOI: 10.1093/ajcn/nqy041] [Citation(s) in RCA: 375] [Impact Index Per Article: 62.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 02/14/2018] [Indexed: 12/17/2022] Open
Abstract
Background Dysfunction of the gut microbiota is frequently reported as a manifestation of chronic diseases, and therefore presents as a modifiable risk factor in their development. Diet is a major regulator of the gut microbiota, and certain types of dietary fiber may modify bacterial numbers and metabolism, including short-chain fatty acid (SCFA) generation. Objective A systematic review and meta-analysis were undertaken to assess the effect of dietary fiber interventions on gut microbiota composition in healthy adults. Design A systematic search was conducted across MEDLINE, EMBASE, CENTRAL, and CINAHL for randomized controlled trials using culture and/or molecular microbiological techniques evaluating the effect of fiber intervention on gut microbiota composition in healthy adults. Meta-analyses via a random-effects model were performed on alpha diversity, prespecified bacterial abundances including Bifidobacterium and Lactobacillus spp., and fecal SCFA concentrations comparing dietary fiber interventions with placebo/low-fiber comparators. Results A total of 64 studies involving 2099 participants were included. Dietary fiber intervention resulted in higher abundance of Bifidobacterium spp. (standardized mean difference (SMD): 0.64; 95% CI: 0.42, 0.86; P < 0.00001) and Lactobacillus spp. (SMD: 0.22; 0.03, 0.41; P = 0.02) as well as fecal butyrate concentration (SMD: 0.24; 0.00, 0.47; P = 0.05) compared with placebo/low-fiber comparators. Subgroup analysis revealed that fructans and galacto-oligosaccharides led to significantly greater abundance of both Bifidobacterium spp. and Lactobacillus spp. compared with comparators (P < 0.00001 and P = 0.002, respectively). No differences in effect were found between fiber intervention and comparators for α-diversity, abundances of other prespecified bacteria, or other SCFA concentrations. Conclusions Dietary fiber intervention, particularly involving fructans and galacto-oligosaccharides, leads to higher fecal abundance of Bifidobacterium and Lactobacillus spp. but does not affect α-diversity. Further research is required to better understand the role of individual fiber types on the growth of microbes and the overall gut microbial community. This review was registered at PROSPERO as CRD42016053101.
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Affiliation(s)
- Daniel So
- Faculty of Health Sciences and Medicine, Bond University, Gold Coast, Australia
| | - Kevin Whelan
- Department of Nutritional Sciences, King's College, London, United Kingdom
| | - Megan Rossi
- Department of Nutritional Sciences, King's College, London, United Kingdom
| | - Mark Morrison
- The University of Queensland Diamantina Institute, Translational Research Institute.,Faculty of Medicine, University of Queensland, Brisbane, Australia
| | - Gerald Holtmann
- Faculty of Medicine, University of Queensland, Brisbane, Australia.,Department of Gastroenterology & Hepatology
| | - Jaimon T Kelly
- Faculty of Health Sciences and Medicine, Bond University, Gold Coast, Australia
| | - Erin R Shanahan
- The University of Queensland Diamantina Institute, Translational Research Institute.,Department of Gastroenterology & Hepatology
| | | | - Katrina L Campbell
- Faculty of Health Sciences and Medicine, Bond University, Gold Coast, Australia.,Department of Nutrition and Dietetics, Princess Alexandra Hospital, Brisbane, Australia
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69
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Feng G, Flanagan BM, Mikkelsen D, Williams BA, Yu W, Gilbert RG, Gidley MJ. Mechanisms of utilisation of arabinoxylans by a porcine faecal inoculum: competition and co-operation. Sci Rep 2018. [PMID: 29540852 PMCID: PMC5852058 DOI: 10.1038/s41598-018-22818-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Recent studies show that a single or small number of intestinal microbes can completely degrade complex carbohydrates. This suggests a drive towards competitive utilisation of dietary complex carbohydrates resulting in limited microbial diversity, at odds with the health benefits associated with a diverse microbiome. This study investigates the enzymatic metabolism of wheat and rye arabinoxylans (AX) using in vitro fermentation, with a porcine faecal inoculum. Through studying the activity of AX-degrading enzymes and the structural changes of residual AX during fermentation, we show that the AX-degrading enzymes are mainly cell-associated, which enables the microbes to utilise the AX competitively. However, potential for cross-feeding is also demonstrated to occur by two distinct mechanisms: (1) release of AX after partial degradation by cell-associated enzymes, and (2) release of enzymes during biomass turnover, indicative of co-operative AX degradation. This study provides a model for the combined competitive-co-operative utilisation of complex dietary carbohydrates by gut microorganisms.
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Affiliation(s)
- Guangli Feng
- ARC Centre of Excellence in Plant Cell Walls, Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Bernadine M Flanagan
- ARC Centre of Excellence in Plant Cell Walls, Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Deirdre Mikkelsen
- ARC Centre of Excellence in Plant Cell Walls, Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Barbara A Williams
- ARC Centre of Excellence in Plant Cell Walls, Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Wenwen Yu
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Robert G Gilbert
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, College of Agriculture, Yangzhou University, Yangzhou, Jiangsu Province, 225009, China
| | - Michael J Gidley
- ARC Centre of Excellence in Plant Cell Walls, Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia.
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70
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Abstract
In red algae, the most abundant principal cell wall polysaccharides are mixed galactan agars, of which agarose is a common component. While bioconversion of agarose is predominantly catalyzed by bacteria that live in the oceans, agarases have been discovered in microorganisms that inhabit diverse terrestrial ecosystems, including human intestines. Here we comprehensively define the structure-function relationship of the agarolytic pathway from the human intestinal bacterium Bacteroides uniformis (Bu) NP1. Using recombinant agarases from Bu NP1 to completely depolymerize agarose, we demonstrate that a non-agarolytic Bu strain can grow on GAL released from agarose. This relationship underscores that rare nutrient utilization by intestinal bacteria is facilitated by the acquisition of highly specific enzymes that unlock inaccessible carbohydrate resources contained within unusual polysaccharides. Intriguingly, the agarolytic pathway is differentially distributed throughout geographically distinct human microbiomes, reflecting a complex historical context for agarose consumption by human beings.
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71
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Mukhopadhya I, Moraïs S, Laverde‐Gomez J, Sheridan PO, Walker AW, Kelly W, Klieve AV, Ouwerkerk D, Duncan SH, Louis P, Koropatkin N, Cockburn D, Kibler R, Cooper PJ, Sandoval C, Crost E, Juge N, Bayer EA, Flint HJ. Sporulation capability and amylosome conservation among diverse human colonic and rumen isolates of the keystone starch-degrader Ruminococcus bromii. Environ Microbiol 2018; 20:324-336. [PMID: 29159997 PMCID: PMC5814915 DOI: 10.1111/1462-2920.14000] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 10/25/2017] [Accepted: 11/16/2017] [Indexed: 12/16/2022]
Abstract
Ruminococcus bromii is a dominant member of the human colonic microbiota that plays a 'keystone' role in degrading dietary resistant starch. Recent evidence from one strain has uncovered a unique cell surface 'amylosome' complex that organizes starch-degrading enzymes. New genome analysis presented here reveals further features of this complex and shows remarkable conservation of amylosome components between human colonic strains from three different continents and a R. bromii strain from the rumen of Australian cattle. These R. bromii strains encode a narrow spectrum of carbohydrate active enzymes (CAZymes) that reflect extreme specialization in starch utilization. Starch hydrolysis products are taken up mainly as oligosaccharides, with only one strain able to grow on glucose. The human strains, but not the rumen strain, also possess transporters that allow growth on galactose and fructose. R. bromii strains possess a full complement of sporulation and spore germination genes and we demonstrate the ability to form spores that survive exposure to air. Spore formation is likely to be a critical factor in the ecology of this nutritionally highly specialized bacterium, which was previously regarded as 'non-sporing', helping to explain its widespread occurrence in the gut microbiota through the ability to transmit between hosts.
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Affiliation(s)
| | - Sarah Moraïs
- Department of Biomolecular SciencesThe Weizmann Institute of ScienceRehovotIsrael
- Present address:
Faculty of Natural Sciences, Ben‐Gurion University of the NegevBeer‐Sheva 8499000Israel
| | | | - Paul O. Sheridan
- Microbiology GroupThe Rowett Institute, University of AberdeenAberdeenUK
| | - Alan W. Walker
- Microbiology GroupThe Rowett Institute, University of AberdeenAberdeenUK
| | - William Kelly
- AgResearch Limited, Grasslands Research Centre, Palmerston North 4442New Zealand
| | - Athol V. Klieve
- School of Agriculture and Food SciencesThe University of QueenslandQLDSt Lucia, Australia
- Queensland Alliance for Agriculture and Food InnovationThe University of QueenslandQLDSt Lucia, Australia
| | - Diane Ouwerkerk
- Queensland Alliance for Agriculture and Food InnovationThe University of QueenslandQLDSt Lucia, Australia
- Department of Agriculture and FisheriesAgri‐Science QueenslandBrisbaneQLDAustralia
| | - Sylvia H. Duncan
- Microbiology GroupThe Rowett Institute, University of AberdeenAberdeenUK
| | - Petra Louis
- Microbiology GroupThe Rowett Institute, University of AberdeenAberdeenUK
| | - Nicole Koropatkin
- Department of Microbiology and ImmunologyUniversity of Michigan Medical SchoolAnn ArborMIUSA
| | - Darrell Cockburn
- Department of Microbiology and ImmunologyUniversity of Michigan Medical SchoolAnn ArborMIUSA
| | - Ryan Kibler
- Department of Microbiology and ImmunologyUniversity of Michigan Medical SchoolAnn ArborMIUSA
| | - Philip J. Cooper
- Hospital Cantonal “Padre Alberto Buffoni”, Avenida 3 de Julio y Victor VillegasQuinindeEsmeraldas ProvinceEcuador
| | - Carlos Sandoval
- Hospital Cantonal “Padre Alberto Buffoni”, Avenida 3 de Julio y Victor VillegasQuinindeEsmeraldas ProvinceEcuador
| | - Emmanuelle Crost
- The Gut Health and Food Safety Institute Strategic Programme, Institute of Food ResearchNorwichUK
| | - Nathalie Juge
- The Gut Health and Food Safety Institute Strategic Programme, Institute of Food ResearchNorwichUK
| | - Edward A. Bayer
- Department of Biomolecular SciencesThe Weizmann Institute of ScienceRehovotIsrael
| | - Harry J. Flint
- Microbiology GroupThe Rowett Institute, University of AberdeenAberdeenUK
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72
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Reichardt N, Vollmer M, Holtrop G, Farquharson FM, Wefers D, Bunzel M, Duncan SH, Drew JE, Williams LM, Milligan G, Preston T, Morrison D, Flint HJ, Louis P. Specific substrate-driven changes in human faecal microbiota composition contrast with functional redundancy in short-chain fatty acid production. ISME JOURNAL 2017; 12:610-622. [PMID: 29192904 PMCID: PMC5776475 DOI: 10.1038/ismej.2017.196] [Citation(s) in RCA: 136] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 10/03/2017] [Accepted: 10/09/2017] [Indexed: 01/04/2023]
Abstract
The diet provides carbohydrates that are non-digestible in the upper gut and are major carbon and energy sources for the microbial community in the lower intestine, supporting a complex metabolic network. Fermentation produces the short-chain fatty acids (SCFAs) acetate, propionate and butyrate, which have health-promoting effects for the human host. Here we investigated microbial community changes and SCFA production during in vitro batch incubations of 15 different non-digestible carbohydrates, at two initial pH values with faecal microbiota from three different human donors. To investigate temporal stability and reproducibility, a further experiment was performed 1 year later with four of the carbohydrates. The lower pH (5.5) led to higher butyrate and the higher pH (6.5) to more propionate production. The strongest propionigenic effect was found with rhamnose, followed by galactomannans, whereas fructans and several α- and β-glucans led to higher butyrate production. 16S ribosomal RNA gene-based quantitative PCR analysis of 22 different microbial groups together with 454 sequencing revealed significant stimulation of specific bacteria in response to particular carbohydrates. Some changes were ascribed to metabolite cross-feeding, for example, utilisation by Eubacterium hallii of 1,2-propanediol produced from fermentation of rhamnose by Blautia spp. Despite marked inter-individual differences in microbiota composition, SCFA production was surprisingly reproducible for different carbohydrates, indicating a level of functional redundancy. Interestingly, butyrate formation was influenced not only by the overall % butyrate-producing bacteria in the community but also by the initial pH, consistent with a pH-dependent shift in the stoichiometry of butyrate production.
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Affiliation(s)
- Nicole Reichardt
- The Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen, UK.,Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Maren Vollmer
- The Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen, UK
| | - Grietje Holtrop
- Biomathematics and Statistics Scotland, Foresterhill, Aberdeen, UK
| | | | - Daniel Wefers
- Department of Food Chemistry and Phytochemistry, Karlsruhe Institute of Technology (KIT), Adenauerring 20A, Karlsruhe, Germany
| | - Mirko Bunzel
- Department of Food Chemistry and Phytochemistry, Karlsruhe Institute of Technology (KIT), Adenauerring 20A, Karlsruhe, Germany
| | - Sylvia H Duncan
- The Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen, UK
| | - Janice E Drew
- The Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen, UK
| | - Lynda M Williams
- The Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen, UK
| | - Graeme Milligan
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Thomas Preston
- Scottish Universities Environmental Research Centre, University of Glasgow, Rankine Avenue, East Kilbride, UK
| | - Douglas Morrison
- Scottish Universities Environmental Research Centre, University of Glasgow, Rankine Avenue, East Kilbride, UK
| | - Harry J Flint
- The Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen, UK
| | - Petra Louis
- The Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen, UK
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73
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Microbial Metabolic Networks at the Mucus Layer Lead to Diet-Independent Butyrate and Vitamin B 12 Production by Intestinal Symbionts. mBio 2017; 8:mBio.00770-17. [PMID: 28928206 PMCID: PMC5605934 DOI: 10.1128/mbio.00770-17] [Citation(s) in RCA: 235] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Akkermansia muciniphila has evolved to specialize in the degradation and utilization of host mucus, which it may use as the sole source of carbon and nitrogen. Mucus degradation and fermentation by A. muciniphila are known to result in the liberation of oligosaccharides and subsequent production of acetate, which becomes directly available to microorganisms in the vicinity of the intestinal mucosa. Coculturing experiments of A. muciniphila with non-mucus-degrading butyrate-producing bacteria Anaerostipes caccae, Eubacterium hallii, and Faecalibacterium prausnitzii resulted in syntrophic growth and production of butyrate. In addition, we demonstrate that the production of pseudovitamin B12 by E. hallii results in production of propionate by A. muciniphila, which suggests that this syntrophy is indeed bidirectional. These data are proof of concept for syntrophic and other symbiotic microbe-microbe interactions at the intestinal mucosal interface. The observed metabolic interactions between A. muciniphila and butyrogenic bacterial taxa support the existence of colonic vitamin and butyrate production pathways that are dependent on host glycan production and independent of dietary carbohydrates. We infer that the intestinal symbiont A. muciniphila can indirectly stimulate intestinal butyrate levels in the vicinity of the intestinal epithelial cells with potential health benefits to the host. The intestinal microbiota is said to be a stable ecosystem where many networks between microorganisms are formed. Here we present a proof of principle study of microbial interaction at the intestinal mucus layer. We show that indigestible oligosaccharide chains within mucus become available for a broad range of intestinal microbes after degradation and liberation of sugars by the species Akkermansia muciniphila. This leads to the microbial synthesis of vitamin B12, 1,2-propanediol, propionate, and butyrate, which are beneficial to the microbial ecosystem and host epithelial cells.
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74
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Flint HJ, Duncan SH, Louis P. The impact of nutrition on intestinal bacterial communities. Curr Opin Microbiol 2017; 38:59-65. [DOI: 10.1016/j.mib.2017.04.005] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 03/02/2017] [Accepted: 04/12/2017] [Indexed: 12/16/2022]
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75
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Selber-Hnatiw S, Rukundo B, Ahmadi M, Akoubi H, Al-Bizri H, Aliu AF, Ambeaghen TU, Avetisyan L, Bahar I, Baird A, Begum F, Ben Soussan H, Blondeau-Éthier V, Bordaries R, Bramwell H, Briggs A, Bui R, Carnevale M, Chancharoen M, Chevassus T, Choi JH, Coulombe K, Couvrette F, D'Abreau S, Davies M, Desbiens MP, Di Maulo T, Di Paolo SA, Do Ponte S, Dos Santos Ribeiro P, Dubuc-Kanary LA, Duncan PK, Dupuis F, El-Nounou S, Eyangos CN, Ferguson NK, Flores-Chinchilla NR, Fotakis T, Gado Oumarou H D M, Georgiev M, Ghiassy S, Glibetic N, Grégoire Bouchard J, Hassan T, Huseen I, Ibuna Quilatan MF, Iozzo T, Islam S, Jaunky DB, Jeyasegaram A, Johnston MA, Kahler MR, Kaler K, Kamani C, Karimian Rad H, Konidis E, Konieczny F, Kurianowicz S, Lamothe P, Legros K, Leroux S, Li J, Lozano Rodriguez ME, Luponio-Yoffe S, Maalouf Y, Mantha J, McCormick M, Mondragon P, Narayana T, Neretin E, Nguyen TTT, Niu I, Nkemazem RB, O'Donovan M, Oueis M, Paquette S, Patel N, Pecsi E, Peters J, Pettorelli A, Poirier C, Pompa VR, Rajen H, Ralph RO, Rosales-Vasquez J, Rubinshtein D, Sakr S, Sebai MS, Serravalle L, Sidibe F, Sinnathurai A, Soho D, Sundarakrishnan A, Svistkova V, Ugbeye TE, Vasconcelos MS, Vincelli M, Voitovich O, Vrabel P, Wang L, Wasfi M, Zha CY, Gamberi C. Human Gut Microbiota: Toward an Ecology of Disease. Front Microbiol 2017; 8:1265. [PMID: 28769880 PMCID: PMC5511848 DOI: 10.3389/fmicb.2017.01265] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 06/23/2017] [Indexed: 12/17/2022] Open
Abstract
Composed of trillions of individual microbes, the human gut microbiota has adapted to the uniquely diverse environments found in the human intestine. Quickly responding to the variances in the ingested food, the microbiota interacts with the host via reciprocal biochemical signaling to coordinate the exchange of nutrients and proper immune function. Host and microbiota function as a unit which guards its balance against invasion by potential pathogens and which undergoes natural selection. Disturbance of the microbiota composition, or dysbiosis, is often associated with human disease, indicating that, while there seems to be no unique optimal composition of the gut microbiota, a balanced community is crucial for human health. Emerging knowledge of the ecology of the microbiota-host synergy will have an impact on how we implement antibiotic treatment in therapeutics and prophylaxis and how we will consider alternative strategies of global remodeling of the microbiota such as fecal transplants. Here we examine the microbiota-human host relationship from the perspective of the microbial community dynamics.
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Affiliation(s)
| | - Belise Rukundo
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Masoumeh Ahmadi
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Hayfa Akoubi
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Hend Al-Bizri
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Adelekan F Aliu
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | - Lilit Avetisyan
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Irmak Bahar
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Alexandra Baird
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Fatema Begum
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | | | | | - Helene Bramwell
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Alicia Briggs
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Richard Bui
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | | | - Talia Chevassus
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Jin H Choi
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Karyne Coulombe
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | | | - Meghan Davies
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | - Tamara Di Maulo
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | | | | | | | - Paola K Duncan
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | - Sara El-Nounou
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | | | | | - Tanya Fotakis
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | - Metodi Georgiev
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | | | | | - Tazkia Hassan
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Iman Huseen
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | - Tania Iozzo
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Safina Islam
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Dilan B Jaunky
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | | | | | | | - Cedric Kamani
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | | | - Filip Konieczny
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | | | - Karina Legros
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | - Jun Li
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | | | - Yara Maalouf
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Jessica Mantha
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | | | | | | | - Thi T T Nguyen
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Ian Niu
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | | | - Matthew Oueis
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | - Nehal Patel
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Emily Pecsi
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Jackie Peters
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | | | | | | | | | | | | | - Surya Sakr
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | - Lisa Serravalle
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Fily Sidibe
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | - Dominique Soho
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | | | | | | | | | - Olga Voitovich
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Pamela Vrabel
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Lu Wang
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Maryse Wasfi
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Cong Y Zha
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Chiara Gamberi
- Department of Biology, Concordia UniversityMontréal, QC, Canada
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Duranti S, Ferrario C, van Sinderen D, Ventura M, Turroni F. Obesity and microbiota: an example of an intricate relationship. GENES AND NUTRITION 2017. [PMID: 28638490 PMCID: PMC5473000 DOI: 10.1186/s12263-017-0566-2] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
It is widely accepted that metabolic disorders, such as obesity, are closely linked to lifestyle and diet. Recently, the central role played by the intestinal microbiota in human metabolism and in progression of metabolic disorders has become evident. In this context, animal studies and human trials have demonstrated that alterations of the intestinal microbiota towards enhanced energy harvest is a characteristic of the obese phenotype. Many publications, involving both animal studies and clinical trials, have reported on the successful exploitation of probiotics and prebiotics to treat obesity. However, the molecular mechanisms underlying these observed anti-obesity effects of probiotics and prebiotic therapies are still obscure. The aim of this mini-review is to discuss the intricate relationship of various factors, including diet, gut microbiota, and host genetics, that are believed to impact on the development of obesity, and to understand how modulation of the gut microbiota with dietary intervention may alleviate obesity-associated symptoms.
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Affiliation(s)
- Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, 43124 Parma, Italy
| | - Chiara Ferrario
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, 43124 Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, 43124 Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, 43124 Parma, Italy
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Shetty SA, Hugenholtz F, Lahti L, Smidt H, de Vos WM. Intestinal microbiome landscaping: insight in community assemblage and implications for microbial modulation strategies. FEMS Microbiol Rev 2017; 41:182-199. [PMID: 28364729 PMCID: PMC5399919 DOI: 10.1093/femsre/fuw045] [Citation(s) in RCA: 130] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 12/03/2016] [Indexed: 02/07/2023] Open
Abstract
High individuality, large complexity and limited understanding of the mechanisms underlying human intestinal microbiome function remain the major challenges for designing beneficial modulation strategies. Exemplified by the analysis of intestinal bacteria in a thousand Western adults, we discuss key concepts of the human intestinal microbiome landscape, i.e. the compositional and functional 'core', the presence of community types and the existence of alternative stable states. Genomic investigation of core taxa revealed functional redundancy, which is expected to stabilize the ecosystem, as well as taxa with specialized functions that have the potential to shape the microbiome landscape. The contrast between Prevotella- and Bacteroides-dominated systems has been well described. However, less known is the effect of not so abundant bacteria, for example, Dialister spp. that have been proposed to exhibit distinct bistable dynamics. Studies employing time-series analysis have highlighted the dynamical variation in the microbiome landscape with and without the effect of defined perturbations, such as the use of antibiotics or dietary changes. We incorporate ecosystem-level observations of the human intestinal microbiota and its keystone species to suggest avenues for designing microbiome modulation strategies to improve host health.
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Affiliation(s)
- Sudarshan A. Shetty
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, Building 124, 6708 WE Wageningen, the Netherlands
| | - Floor Hugenholtz
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, Building 124, 6708 WE Wageningen, the Netherlands
| | - Leo Lahti
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, Building 124, 6708 WE Wageningen, the Netherlands
- VIB Lab for Bioinformatics and (Eco-)systems Biology, KU Leuven, Campus Gasthuisberg, 3000 Leuven, Belgium
- Department of Mathematics and Statistics, University of Turku, 20014 Turku, Finland
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, Building 124, 6708 WE Wageningen, the Netherlands
| | - Willem M. de Vos
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, Building 124, 6708 WE Wageningen, the Netherlands
- Research Programme Unit Immunobiology, Department of Bacteriology and Immunology, Helsinki University, P.O. Box 21, 00014 Helsinki, Finland
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78
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Hinsu AT, Parmar NR, Nathani NM, Pandit RJ, Patel AB, Patel AK, Joshi CG. Functional gene profiling through metaRNAseq approach reveals diet-dependent variation in rumen microbiota of buffalo (Bubalus bubalis). Anaerobe 2017; 44:106-116. [PMID: 28246035 DOI: 10.1016/j.anaerobe.2017.02.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 02/18/2017] [Accepted: 02/23/2017] [Indexed: 10/20/2022]
Abstract
Recent advances in next generation sequencing technology have enabled analysis of complex microbial community from genome to transcriptome level. In the present study, metatranscriptomic approach was applied to elucidate functionally active bacteria and their biological processes in rumen of buffalo (Bubalus bubalis) adapted to different dietary treatments. Buffaloes were adapted to a diet containing 50:50, 75:25 and 100:0 forage to concentrate ratio, each for 6 weeks, before ruminal content sample collection. Metatranscriptomes from rumen fiber adherent and fiber-free active bacteria were sequenced using Ion Torrent PGM platform followed by annotation using MG-RAST server and CAZYmes (Carbohydrate active enzymes) analysis toolkit. In all the samples Bacteroidetes was the most abundant phylum followed by Firmicutes. Functional analysis using KEGG Orthology database revealed Metabolism as the most abundant category at level 1 within which Carbohydrate metabolism was dominating. Diet treatments also exerted significant differences in proportion of enzymes involved in metabolic pathways for VFA production. Carbohydrate Active Enzyme(CAZy) analysis revealed the abundance of genes encoding glycoside hydrolases with the highest representation of GH13 CAZy family in all the samples. The findings provide an overview of the activities occurring in the rumen as well as active bacterial population and the changes occurring through different dietary treatments.
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Affiliation(s)
- Ankit T Hinsu
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University (AAU), Anand, Gujarat, India
| | - Nidhi R Parmar
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University (AAU), Anand, Gujarat, India
| | - Neelam M Nathani
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University (AAU), Anand, Gujarat, India
| | - Ramesh J Pandit
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University (AAU), Anand, Gujarat, India
| | - Anand B Patel
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University (AAU), Anand, Gujarat, India
| | - Amrutlal K Patel
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University (AAU), Anand, Gujarat, India
| | - Chaitanya G Joshi
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University (AAU), Anand, Gujarat, India.
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80
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Sheflin AM, Melby CL, Carbonero F, Weir TL. Linking dietary patterns with gut microbial composition and function. Gut Microbes 2016; 8:113-129. [PMID: 27960648 PMCID: PMC5390824 DOI: 10.1080/19490976.2016.1270809] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Emerging insights have implicated the gut microbiota as an important factor in the maintenance of human health. Although nutrition research has focused on how direct interactions between dietary components and host systems influence human health, it is becoming increasingly important to consider nutrient effects on the gut microbiome for a more complete picture. Understanding nutrient-host-microbiome interactions promises to reveal novel mechanisms of disease etiology and progression, offers new disease prevention strategies and therapeutic possibilities, and may mandate alternative criteria to evaluate the safety of food ingredients. Here we review the current literature on diet effects on the microbiome and the generation of microbial metabolites of dietary constituents that may influence human health. We conclude with a discussion of the relevance of these studies to nutrition and public health and summarize further research needs required to realize the potential of exploiting diet-microbiota interactions for improved health.
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Affiliation(s)
- Amy M. Sheflin
- Proteomics and Metabolomics Facility, Colorado State University, Fort Collins, CO, USA
| | - Christopher L. Melby
- Department of Food Science and Human Nutrition, Colorado State University, Fort Collins, CO, USA
| | - Franck Carbonero
- Department of Food Science, University of Arkansas, Fayetteville, AR, USA
| | - Tiffany L. Weir
- Department of Food Science and Human Nutrition, Colorado State University, Fort Collins, CO, USA,CONTACT Tiffany L. Weir 210 Gifford Building, 1571 Campus Delivery, Colorado State University, Fort Collins, CO 80521-1571, USA
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81
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Cockburn DW, Koropatkin NM. Polysaccharide Degradation by the Intestinal Microbiota and Its Influence on Human Health and Disease. J Mol Biol 2016; 428:3230-3252. [PMID: 27393306 DOI: 10.1016/j.jmb.2016.06.021] [Citation(s) in RCA: 330] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 06/29/2016] [Accepted: 06/30/2016] [Indexed: 02/06/2023]
Abstract
Carbohydrates comprise a large fraction of the typical diet, yet humans are only able to directly process some types of starch and simple sugars. The remainder transits the large intestine where it becomes food for the commensal bacterial community. This is an environment of not only intense competition but also impressive cooperation for available glycans, as these bacteria work to maximize their energy harvest from these carbohydrates during their limited transit time through the gut. The species within the gut microbiota use a variety of strategies to process and scavenge both dietary and host-produced glycans such as mucins. Some act as generalists that are able to degrade a wide range of polysaccharides, while others are specialists that are only able to target a few select glycans. All are members of a metabolic network where substantial cross-feeding takes place, as by-products of one organism serve as important resources for another. Much of this metabolic activity influences host physiology, as secondary metabolites and fermentation end products are absorbed either by the epithelial layer or by transit via the portal vein to the liver where they can have additional effects. These microbially derived compounds influence cell proliferation and apoptosis, modulate the immune response, and can alter host metabolism. This review summarizes the molecular underpinnings of these polysaccharide degradation processes, their impact on human health, and how we can manipulate them through the use of prebiotics.
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Affiliation(s)
- Darrell W Cockburn
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
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82
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Foley MH, Cockburn DW, Koropatkin NM. The Sus operon: a model system for starch uptake by the human gut Bacteroidetes. Cell Mol Life Sci 2016; 73:2603-17. [PMID: 27137179 PMCID: PMC4924478 DOI: 10.1007/s00018-016-2242-x] [Citation(s) in RCA: 157] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 04/22/2016] [Indexed: 12/16/2022]
Abstract
Resident bacteria in the densely populated human intestinal tract must efficiently compete for carbohydrate nutrition. The Bacteroidetes, a dominant bacterial phylum in the mammalian gut, encode a plethora of discrete polysaccharide utilization loci (PULs) that are selectively activated to facilitate glycan capture at the cell surface. The most well-studied PUL-encoded glycan-uptake system is the starch utilization system (Sus) of Bacteroides thetaiotaomicron. The Sus includes the requisite proteins for binding and degrading starch at the surface of the cell preceding oligosaccharide transport across the outer membrane for further depolymerization to glucose in the periplasm. All mammalian gut Bacteroidetes possess analogous Sus-like systems that target numerous diverse glycans. In this review, we discuss what is known about the eight Sus proteins of B. thetaiotaomicron that define the Sus-like paradigm of nutrient acquisition that is exclusive to the Gram-negative Bacteroidetes. We emphasize the well-characterized outer membrane proteins SusDEF and the α-amylase SusG, each of which have unique structural features that allow them to interact with starch on the cell surface. Despite the apparent redundancy in starch-binding sites among these proteins, each has a distinct role during starch catabolism. Additionally, we consider what is known about how these proteins dynamically interact and cooperate in the membrane and propose a model for the formation of the Sus outer membrane complex.
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Affiliation(s)
- Matthew H Foley
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Darrell W Cockburn
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
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83
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Duncan SH, Russell WR, Quartieri A, Rossi M, Parkhill J, Walker AW, Flint HJ. Wheat bran promotes enrichment within the human colonic microbiota of butyrate-producing bacteria that release ferulic acid. Environ Microbiol 2016; 18:2214-25. [PMID: 26636660 PMCID: PMC4949515 DOI: 10.1111/1462-2920.13158] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 11/09/2015] [Accepted: 11/27/2015] [Indexed: 01/02/2023]
Abstract
Cereal fibres such as wheat bran are considered to offer human health benefits via their impact on the intestinal microbiota. We show here by 16S rRNA gene-based community analysis that providing amylase-pretreated wheat bran as the sole added energy source to human intestinal microbial communities in anaerobic fermentors leads to the selective and progressive enrichment of a small number of bacterial species. In particular, OTUs corresponding to uncultured Lachnospiraceae (Firmicutes) related to Eubacterium xylanophilum and Butyrivibrio spp. were strongly enriched (by five to 160 fold) over 48 h in four independent experiments performed with different faecal inocula, while nine other Firmicutes OTUs showed > 5-fold enrichment in at least one experiment. Ferulic acid was released from the wheat bran during degradation but was rapidly converted to phenylpropionic acid derivatives via hydrogenation, demethylation and dehydroxylation to give metabolites that are detected in human faecal samples. Pure culture work using bacterial isolates related to the enriched OTUs, including several butyrate-producers, demonstrated that the strains caused substrate weight loss and released ferulic acid, but with limited further conversion. We conclude that breakdown of wheat bran involves specialist primary degraders while the conversion of released ferulic acid is likely to involve a multi-species pathway.
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Affiliation(s)
- Sylvia H Duncan
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK
| | - Wendy R Russell
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK
| | - Andrea Quartieri
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Maddalena Rossi
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Julian Parkhill
- Pathogen Genomics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Alan W Walker
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK
- Pathogen Genomics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Harry J Flint
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK
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84
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Julliand V, Grimm P. HORSE SPECIES SYMPOSIUM: The microbiome of the horse hindgut: History and current knowledge1. J Anim Sci 2016; 94:2262-74. [DOI: 10.2527/jas.2015-0198] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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85
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Munoz S, Guzman-Rodriguez M, Sun J, Zhang YG, Noordhof C, He SM, Allen-Vercoe E, Claud EC, Petrof EO. Rebooting the microbiome. Gut Microbes 2016; 7:353-363. [PMID: 27176179 PMCID: PMC4988458 DOI: 10.1080/19490976.2016.1188248] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Using a murine Salmonella model of colitis, we recently reported that mice receiving a community of defined gut microbiota (MET-1) lost less weight, had reduced systemic inflammation and splenic S. typhimurium infection, and decreased neutrophil infiltration in the cecum, compared to vehicle controls. In addition, animals receiving MET-1 exhibited preserved tight junction protein expression (Zonula occludens-1, claudin-1), suggesting important effects on barrier function. In this addendum, we describe additional in vitro experiments examining effects of MET-1, as well as in vivo experiments demonstrating that MET-1 is protective in a DSS model of colitis after administration of antibiotics. Placed in the context of our findings and those of others, we discuss differences in our findings between the Salmonella colitis and DSS colitis models, provide speculation as to which bacteria may be important in the protective effects of MET-1, and discuss potential implications for other GI diseases such as IBD.
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Affiliation(s)
- Sean Munoz
- Department of Medicine, Division of Infectious Diseases/GI Diseases Research Unit, Queen's University, Kingston, ON, Canada
| | - Mabel Guzman-Rodriguez
- Department of Medicine, Division of Infectious Diseases/GI Diseases Research Unit, Queen's University, Kingston, ON, Canada
| | - Jun Sun
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Illinois at Chicago, Chicago, IL, USA
| | - Yong-guo Zhang
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Illinois at Chicago, Chicago, IL, USA
| | - Curtis Noordhof
- Department of Medicine, Division of Infectious Diseases/GI Diseases Research Unit, Queen's University, Kingston, ON, Canada
| | - Shu-Mei He
- Department of Medicine, Division of Infectious Diseases/GI Diseases Research Unit, Queen's University, Kingston, ON, Canada
| | - Emma Allen-Vercoe
- Department of Molecular & Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Erika C. Claud
- Department of Pediatrics and Medicine, University of Chicago, Chicago, IL, USA
| | - Elaine O. Petrof
- Department of Medicine, Division of Infectious Diseases/GI Diseases Research Unit, Queen's University, Kingston, ON, Canada
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86
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Wetzels SU, Mann E, Metzler-Zebeli BU, Pourazad P, Qumar M, Klevenhusen F, Pinior B, Wagner M, Zebeli Q, Schmitz-Esser S. Epimural Indicator Phylotypes of Transiently-Induced Subacute Ruminal Acidosis in Dairy Cattle. Front Microbiol 2016; 7:274. [PMID: 26973642 PMCID: PMC4777738 DOI: 10.3389/fmicb.2016.00274] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 02/19/2016] [Indexed: 02/01/2023] Open
Abstract
The impact of a long-term subacute rumen acidosis (SARA) on the bovine epimural bacterial microbiome (BEBM) and its consequences for rumen health is poorly understood. This study aimed to investigate shifts in the BEBM during a long-term transient SARA model consisting of two concentrate-diet-induced SARA challenges separated by a 1-week challenge break. Eight cows were fed forage and varying concentrate amounts throughout the experiment. In total, 32 rumen papilla biopsies were taken for DNA isolation (4 sampling time points per cow: at the baseline before concentrate was fed, after the first SARA challenge, after the challenge break, and after the second SARA challenge). Ruminal pH was continuously monitored. The microbiome was determined using Illumina MiSeq sequencing of the 16S rRNA gene (V345 region). In total 1,215,618 sequences were obtained and clustered into 6833 operational taxonomic units (OTUs). Campylobacter and Kingella were the most abundant OTUs (16.5 and 7.1%). According to ruminal pH dynamics, the second challenge was more severe than the first challenge. Species diversity estimates and evenness increased during the challenge break compared to all other sampling time points (P < 0.05). During both SARA challenges, Kingella- and Azoarcus-OTUs decreased (0.5 and 0.4 fold-change) and a dominant Ruminobacter-OTU increased during the challenge break (18.9 fold-change; P < 0.05). qPCR confirmed SARA-related shifts. During the challenge break noticeably more OTUs increased compared to other sampling time points. Our results show that the BEBM re-establishes the baseline conditions slower after a SARA challenge than ruminal pH. Key phylotypes that were reduced during both challenges may help to establish a bacterial fingerprint to facilitate understanding effects of SARA conditions on the BEBM and their consequences for the ruminant host.
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Affiliation(s)
- Stefanie U Wetzels
- Department for Farm Animals and Veterinary Public Health, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine ViennaVienna, Austria; Department of Farm Animal and Public Health in Veterinary Medicine, Institute for Milk Hygiene, Milk Technology and Food Science, University of Veterinary Medicine ViennaVienna, Austria; Department for Farm Animals and Veterinary Public Health, Research Cluster Animal Gut Health, University of Veterinary Medicine ViennaVienna, Austria
| | - Evelyne Mann
- Department of Farm Animal and Public Health in Veterinary Medicine, Institute for Milk Hygiene, Milk Technology and Food Science, University of Veterinary Medicine ViennaVienna, Austria; Department for Farm Animals and Veterinary Public Health, Research Cluster Animal Gut Health, University of Veterinary Medicine ViennaVienna, Austria
| | - Barbara U Metzler-Zebeli
- Department for Farm Animals and Veterinary Public Health, Research Cluster Animal Gut Health, University of Veterinary Medicine ViennaVienna, Austria; Department for Farm Animals and Veterinary Public Health, University Clinic for Swine, University of Veterinary Medicine ViennaVienna, Austria
| | - Poulad Pourazad
- Department for Farm Animals and Veterinary Public Health, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna Vienna, Austria
| | - Muhammad Qumar
- Department for Farm Animals and Veterinary Public Health, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna Vienna, Austria
| | - Fenja Klevenhusen
- Department for Farm Animals and Veterinary Public Health, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine ViennaVienna, Austria; Department for Farm Animals and Veterinary Public Health, Research Cluster Animal Gut Health, University of Veterinary Medicine ViennaVienna, Austria
| | - Beate Pinior
- Department for Farm Animals and Veterinary Public Health, Institute for Veterinary Public Health, University of Veterinary Medicine Vienna Vienna, Austria
| | - Martin Wagner
- Department of Farm Animal and Public Health in Veterinary Medicine, Institute for Milk Hygiene, Milk Technology and Food Science, University of Veterinary Medicine ViennaVienna, Austria; Department for Farm Animals and Veterinary Public Health, Research Cluster Animal Gut Health, University of Veterinary Medicine ViennaVienna, Austria
| | - Qendrim Zebeli
- Department for Farm Animals and Veterinary Public Health, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine ViennaVienna, Austria; Department for Farm Animals and Veterinary Public Health, Research Cluster Animal Gut Health, University of Veterinary Medicine ViennaVienna, Austria
| | - Stephan Schmitz-Esser
- Department of Farm Animal and Public Health in Veterinary Medicine, Institute for Milk Hygiene, Milk Technology and Food Science, University of Veterinary Medicine ViennaVienna, Austria; Department for Farm Animals and Veterinary Public Health, Research Cluster Animal Gut Health, University of Veterinary Medicine ViennaVienna, Austria; Department of Animal Science, Iowa State UniversityAmes, IA, USA
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87
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Moraïs S, Ben David Y, Bensoussan L, Duncan SH, Koropatkin NM, Martens EC, Flint HJ, Bayer EA. Enzymatic profiling of cellulosomal enzymes from the human gut bacterium, Ruminococcus champanellensis, reveals a fine-tuned system for cohesin-dockerin recognition. Environ Microbiol 2016; 18:542-56. [PMID: 26347002 DOI: 10.1111/1462-2920.13047] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 09/02/2015] [Accepted: 09/02/2015] [Indexed: 12/16/2023]
Abstract
Ruminococcus champanellensis is considered a keystone species in the human gut that degrades microcrystalline cellulose efficiently and contains the genetic elements necessary for cellulosome production. The basic elements of its cellulosome architecture, mainly cohesin and dockerin modules from scaffoldins and enzyme-borne dockerins, have been characterized recently. In this study, we cloned, expressed and characterized all of the glycoside hydrolases that contain a dockerin module. Among the 25 enzymes, 10 cellulases, 4 xylanases, 3 mannanases, 2 xyloglucanases, 2 arabinofuranosidases, 2 arabinanases and one β-glucanase were assessed for their comparative enzymatic activity on their respective substrates. The dockerin specificities of the enzymes were examined by ELISA, and 80 positives out of 525 possible interactions were detected. Our analysis reveals a fine-tuned system for cohesin-dockerin specificity and the importance of diversity among the cohesin-dockerin sequences. Our results imply that cohesin-dockerin pairs are not necessarily assembled at random among the same specificity types, as generally believed for other cellulosome-producing bacteria, but reveal a more organized cellulosome architecture. Moreover, our results highlight the importance of the cellulosome paradigm for cellulose and hemicellulose degradation by R. champanellensis in the human gut.
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Affiliation(s)
- Sarah Moraïs
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
| | - Yonit Ben David
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
| | - Lizi Bensoussan
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
| | - Sylvia H Duncan
- Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Eric C Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Harry J Flint
- Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK
| | - Edward A Bayer
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
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88
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Marchesi JR, Adams DH, Fava F, Hermes GDA, Hirschfield GM, Hold G, Quraishi MN, Kinross J, Smidt H, Tuohy KM, Thomas LV, Zoetendal EG, Hart A. The gut microbiota and host health: a new clinical frontier. Gut 2016; 65:330-9. [PMID: 26338727 PMCID: PMC4752653 DOI: 10.1136/gutjnl-2015-309990] [Citation(s) in RCA: 1419] [Impact Index Per Article: 177.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 07/16/2015] [Indexed: 12/15/2022]
Abstract
Over the last 10-15 years, our understanding of the composition and functions of the human gut microbiota has increased exponentially. To a large extent, this has been due to new 'omic' technologies that have facilitated large-scale analysis of the genetic and metabolic profile of this microbial community, revealing it to be comparable in influence to a new organ in the body and offering the possibility of a new route for therapeutic intervention. Moreover, it might be more accurate to think of it like an immune system: a collection of cells that work in unison with the host and that can promote health but sometimes initiate disease. This review gives an update on the current knowledge in the area of gut disorders, in particular metabolic syndrome and obesity-related disease, liver disease, IBD and colorectal cancer. The potential of manipulating the gut microbiota in these disorders is assessed, with an examination of the latest and most relevant evidence relating to antibiotics, probiotics, prebiotics, polyphenols and faecal microbiota transplantation.
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Affiliation(s)
- Julian R Marchesi
- School of Biosciences, Museum Avenue, Cardiff University, Cardiff, UK,Centre for Digestive and Gut Health, Imperial College London, London, UK
| | - David H Adams
- NIHR Biomedical Research Unit, Centre for Liver Research, University of Birmingham, Birmingham, UK
| | - Francesca Fava
- Nutrition and Nutrigenomics Group, Department of Food Quality and Nutrition, Research and Innovation Centre, Trento, Italy
| | - Gerben D A Hermes
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands,Top Institute Food and Nutrition (TIFN), Wageningen, The Netherlands
| | - Gideon M Hirschfield
- NIHR Biomedical Research Unit, Centre for Liver Research, University of Birmingham, Birmingham, UK
| | - Georgina Hold
- Division of Applied Medicine, School of Medicine and Dentistry, University of Aberdeen, Institute of Medical Sciences, Aberdeen, UK
| | - Mohammed Nabil Quraishi
- NIHR Biomedical Research Unit, Centre for Liver Research, University of Birmingham, Birmingham, UK
| | - James Kinross
- Section of Computational and Systems Medicine, Faculty of Medicine, Imperial College London, London, UK
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Kieran M Tuohy
- Nutrition and Nutrigenomics Group, Department of Food Quality and Nutrition, Research and Innovation Centre, Trento, Italy
| | | | - Erwin G Zoetendal
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands,Top Institute Food and Nutrition (TIFN), Wageningen, The Netherlands
| | - Ailsa Hart
- IBD Unit, St Mark's Hospital and Imperial College London, London, UK
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89
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Abstract
Microbe communication with host mammalian cells and external factors such as diet influences this multifaceted ecosystem. A recent study shows that interactions between microbial genes and dietary elements are dynamic processes that may help to characterize an organism's niche and eventually its impact on the overall community and host metabolism.
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Affiliation(s)
- Patrice D Cani
- Université catholique de Louvain, Louvain Drug Research Institute, WELBIO (Walloon Excellence in Life Sciences and Biotechnology), Metabolism and Nutrition research group, Avenue E. Mounier, 73 Box B1.73.11, 1200 Brussels, Belgium.
| | - Amandine Everard
- Université catholique de Louvain, Louvain Drug Research Institute, WELBIO (Walloon Excellence in Life Sciences and Biotechnology), Metabolism and Nutrition research group, Avenue E. Mounier, 73 Box B1.73.11, 1200 Brussels, Belgium
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90
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Abbott DW, Martens EC, Gilbert HJ, Cuskin F, Lowe EC. Coevolution of yeast mannan digestion: Convergence of the civilized human diet, distal gut microbiome, and host immunity. Gut Microbes 2015; 6:334-9. [PMID: 26440374 PMCID: PMC4826095 DOI: 10.1080/19490976.2015.1091913] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The complex carbohydrates accessible to the distal gut microbiota (DGM) are key drivers in determining the structure of this ecosystem. Typically, plant cell wall polysaccharides and recalcitrant starch (i.e. dietary fiber), in addition to host glycans are considered the primary nutrients for the DGM; however, we recently demonstrated that α-mannans, highly branched polysaccharides that decorate the surface of yeast, are also nutrients for several members of Bacteroides spp. This relationship suggests that the advent of yeast in contemporary food technologies and the colonization of the intestine by endogenous fungi have roles in microbiome structure and function. Here we discuss the process of yeast mannan metabolism, and the intersection between various sources of intestinal fungi and their roles in recognition by the host innate immune system.
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Affiliation(s)
- D Wade Abbott
- Lethbridge Research Center; Agriculture and Agri-Food Canada; Lethbridge, Alberta, Canada,Correspondence to: D Wade Abbott; ; Eric C Martens; ; Harry J Gilbert;
| | - Eric C Martens
- Department of Microbiology and Immunology; University of Michigan Medical School; Ann Arbor, MI USA,Correspondence to: D Wade Abbott; ; Eric C Martens; ; Harry J Gilbert;
| | - Harry J Gilbert
- Institute for Cell and Molecular Biosciences; The Medical School; Newcastle University; Newcastle upon Tyne, UK,Correspondence to: D Wade Abbott; ; Eric C Martens; ; Harry J Gilbert;
| | - Fiona Cuskin
- Institute for Cell and Molecular Biosciences; The Medical School; Newcastle University; Newcastle upon Tyne, UK
| | - Elisabeth C Lowe
- Institute for Cell and Molecular Biosciences; The Medical School; Newcastle University; Newcastle upon Tyne, UK
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91
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Unique Organization of Extracellular Amylases into Amylosomes in the Resistant Starch-Utilizing Human Colonic Firmicutes Bacterium Ruminococcus bromii. mBio 2015; 6:e01058-15. [PMID: 26419877 PMCID: PMC4611034 DOI: 10.1128/mbio.01058-15] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
UNLABELLED Ruminococcus bromii is a dominant member of the human gut microbiota that plays a key role in releasing energy from dietary starches that escape digestion by host enzymes via its exceptional activity against particulate "resistant" starches. Genomic analysis of R. bromii shows that it is highly specialized, with 15 of its 21 glycoside hydrolases belonging to one family (GH13). We found that amylase activity in R. bromii is expressed constitutively, with the activity seen during growth with fructose as an energy source being similar to that seen with starch as an energy source. Six GH13 amylases that carry signal peptides were detected by proteomic analysis in R. bromii cultures. Four of these enzymes are among 26 R. bromii proteins predicted to carry dockerin modules, with one, Amy4, also carrying a cohesin module. Since cohesin-dockerin interactions are known to mediate the formation of protein complexes in cellulolytic ruminococci, the binding interactions of four cohesins and 11 dockerins from R. bromii were investigated after overexpressing them as recombinant fusion proteins. Dockerins possessed by the enzymes Amy4 and Amy9 are predicted to bind a cohesin present in protein scaffoldin 2 (Sca2), which resembles the ScaE cell wall-anchoring protein of a cellulolytic relative, R. flavefaciens. Further complexes are predicted between the dockerin-carrying amylases Amy4, Amy9, Amy10, and Amy12 and two other cohesin-carrying proteins, while Amy4 has the ability to autoaggregate, as its dockerin can recognize its own cohesin. This organization of starch-degrading enzymes is unprecedented and provides the first example of cohesin-dockerin interactions being involved in an amylolytic system, which we refer to as an "amylosome." IMPORTANCE Fermentation of dietary nondigestible carbohydrates by the human colonic microbiota supplies much of the energy that supports microbial growth in the intestine. This activity has important consequences for health via modulation of microbiota composition and the physiological and nutritional effects of microbial metabolites, including the supply of energy to the host from short-chain fatty acids. Recent evidence indicates that certain human colonic bacteria play keystone roles in degrading nondigestible substrates, with the dominant but little-studied species Ruminococcus bromii displaying an exceptional ability to degrade dietary resistant starches (i.e., dietary starches that escape digestion by host enzymes in the upper gastrointestinal tract because of protection provided by other polymers, particle structure, retrogradation, or chemical cross-linking). In this report, we reveal the unique organization of the amylolytic enzyme system of R. bromii that involves cohesin-dockerin interactions between component proteins. While dockerins and cohesins are fundamental to the organization of cellulosomal enzyme systems of cellulolytic ruminococci, their contribution to organization of amylases has not previously been recognized and may help to explain the starch-degrading abilities of R. bromii.
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92
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Ben David Y, Dassa B, Borovok I, Lamed R, Koropatkin NM, Martens EC, White BA, Bernalier-Donadille A, Duncan SH, Flint HJ, Bayer EA, Moraïs S. Ruminococcal cellulosome systems from rumen to human. Environ Microbiol 2015; 17:3407-26. [PMID: 25845888 DOI: 10.1111/1462-2920.12868] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 03/24/2015] [Accepted: 03/31/2015] [Indexed: 01/19/2023]
Abstract
A cellulolytic fiber-degrading bacterium, Ruminococcus champanellensis, was isolated from human faecal samples, and its genome was recently sequenced. Bioinformatic analysis of the R. champanellensis genome revealed numerous cohesin and dockerin modules, the basic elements of the cellulosome, and manual sequencing of partially sequenced genomic segments revealed two large tandem scaffoldin-coding genes that form part of a gene cluster. Representative R. champanellensis dockerins were tested against putative cohesins, and the results revealed three different cohesin-dockerin binding profiles which implied two major types of cellulosome architectures: (i) an intricate cell-bound system and (ii) a simplistic cell-free system composed of a single cohesin-containing scaffoldin. The cell-bound system can adopt various enzymatic architectures, ranging from a single enzyme to a large enzymatic complex comprising up to 11 enzymes. The variety of cellulosomal components together with adaptor proteins may infer a very tight regulation of its components. The cellulosome system of the human gut bacterium R. champanellensis closely resembles that of the bovine rumen bacterium Ruminococcus flavefaciens. The two species contain orthologous gene clusters comprising fundamental components of cellulosome architecture. Since R. champanellensis is the only human colonic bacterium known to degrade crystalline cellulose, it may thus represent a keystone species in the human gut.
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Affiliation(s)
- Yonit Ben David
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
| | - Bareket Dassa
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
| | - Ilya Borovok
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Raphael Lamed
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Eric C Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Bryan A White
- Department of Animal Sciences and Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
| | | | - Sylvia H Duncan
- Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK
| | - Harry J Flint
- Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK
| | - Edward A Bayer
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
| | - Sarah Moraïs
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
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93
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Glycan complexity dictates microbial resource allocation in the large intestine. Nat Commun 2015; 6:7481. [PMID: 26112186 PMCID: PMC4491172 DOI: 10.1038/ncomms8481] [Citation(s) in RCA: 289] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 05/13/2015] [Indexed: 12/20/2022] Open
Abstract
The structure of the human gut microbiota is controlled primarily through the degradation of complex dietary carbohydrates, but the extent to which carbohydrate breakdown products are shared between members of the microbiota is unclear. We show here, using xylan as a model, that sharing the breakdown products of complex carbohydrates by key members of the microbiota, such as Bacteroides ovatus, is dependent on the complexity of the target glycan. Characterization of the extensive xylan degrading apparatus expressed by B. ovatus reveals that the breakdown of the polysaccharide by the human gut microbiota is significantly more complex than previous models suggested, which were based on the deconstruction of xylans containing limited monosaccharide side chains. Our report presents a highly complex and dynamic xylan degrading apparatus that is fine-tuned to recognize the different forms of the polysaccharide presented to the human gut microbiota. The human gut microbiota helps us to degrade complex dietary carbohydrates such as xylan and, in turn, the carbohydrate breakdown products control the structure of the microbiota. Here the authors characterize the xylan-degrading apparatus of a key member of the gut microbiota, Bacteroides ovatus.
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94
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Hackmann TJ, Firkins JL. Maximizing efficiency of rumen microbial protein production. Front Microbiol 2015; 6:465. [PMID: 26029197 PMCID: PMC4432691 DOI: 10.3389/fmicb.2015.00465] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 04/28/2015] [Indexed: 11/13/2022] Open
Abstract
Rumen microbes produce cellular protein inefficiently partly because they do not direct all ATP toward growth. They direct some ATP toward maintenance functions, as long-recognized, but they also direct ATP toward reserve carbohydrate synthesis and energy spilling (futile cycles that dissipate heat). Rumen microbes expend ATP by vacillating between (1) accumulation of reserve carbohydrate after feeding (during carbohydrate excess) and (2) mobilization of that carbohydrate thereafter (during carbohydrate limitation). Protozoa account for most accumulation of reserve carbohydrate, and in competition experiments, protozoa accumulated nearly 35-fold more reserve carbohydrate than bacteria. Some pure cultures of bacteria spill energy, but only recently have mixed rumen communities been recognized as capable of the same. When these communities were dosed glucose in vitro, energy spilling could account for nearly 40% of heat production. We suspect that cycling of glycogen (a major reserve carbohydrate) is a major mechanism of spilling; such cycling has already been observed in single-species cultures of protozoa and bacteria. Interconversions of short-chain fatty acids (SCFA) may also expend ATP and depress efficiency of microbial protein production. These interconversions may involve extensive cycling of intermediates, such as cycling of acetate during butyrate production in certain butyrivibrios. We speculate this cycling may expend ATP directly or indirectly. By further quantifying the impact of reserve carbohydrate accumulation, energy spilling, and SCFA interconversions on growth efficiency, we can improve prediction of microbial protein production and guide efforts to improve efficiency of microbial protein production in the rumen.
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Affiliation(s)
| | - Jeffrey L. Firkins
- Department of Animal Sciences, The Ohio State UniversityColumbus, OH, USA
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95
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Heinken A, Thiele I. Systems biology of host-microbe metabolomics. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2015; 7:195-219. [PMID: 25929487 PMCID: PMC5029777 DOI: 10.1002/wsbm.1301] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 03/25/2015] [Accepted: 04/01/2015] [Indexed: 12/15/2022]
Abstract
The human gut microbiota performs essential functions for host and well‐being, but has also been linked to a variety of disease states, e.g., obesity and type 2 diabetes. The mammalian body fluid and tissue metabolomes are greatly influenced by the microbiota, with many health‐relevant metabolites being considered ‘mammalian–microbial co‐metabolites’. To systematically investigate this complex host–microbial co‐metabolism, a systems biology approach integrating high‐throughput data and computational network models is required. Here, we review established top‐down and bottom‐up systems biology approaches that have successfully elucidated relationships between gut microbiota‐derived metabolites and host health and disease. We focus particularly on the constraint‐based modeling and analysis approach, which enables the prediction of mechanisms behind metabolic host–microbe interactions on the molecular level. We illustrate that constraint‐based models are a useful tool for the contextualization of metabolomic measurements and can further our insight into host–microbe interactions, yielding, e.g., in potential novel drugs and biomarkers. WIREs Syst Biol Med 2015, 7:195–219. doi: 10.1002/wsbm.1301 For further resources related to this article, please visit the WIREs website. Conflict of interest: The authors have declared no conflicts of interest for this article.
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Affiliation(s)
- Almut Heinken
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belval, Luxembourg
| | - Ines Thiele
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belval, Luxembourg
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96
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Doré J, Blottière H. The influence of diet on the gut microbiota and its consequences for health. Curr Opin Biotechnol 2015; 32:195-199. [PMID: 25615931 DOI: 10.1016/j.copbio.2015.01.002] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 12/29/2014] [Accepted: 01/03/2015] [Indexed: 02/07/2023]
Abstract
Man is an intimate symbiosis between 10 trillion human cells and some 100 trillion bacteria, most of which inhabit the intestine where they constitute an extremely dense and diverse microbiota. This symbiotic balance that has to be established within each newborn is key to the maintenance of health and well being. Its development is markedly influenced by microbial exposure encountered very early in life. Mode of infant feeding, and the post-weaning transition to habitual diet will further shape the microbiota. Recent studies support the concept that diet should be viewed as a means to prevent potentially durable alterations of symbiosis observed in immune-mediated metabolic and inflammatory diseases. Non-digestible dietary fiber will play a major role in this context.
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Affiliation(s)
- Joël Doré
- INRA, Micalis & MetaGenoPolis, Jouy-en-Josas, France.
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97
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Microbiome changes in healthy volunteers treated with GSK1322322, a novel antibiotic targeting bacterial peptide deformylase. Antimicrob Agents Chemother 2014; 59:1182-92. [PMID: 25487798 DOI: 10.1128/aac.04506-14] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
GSK1322322 is a novel antibacterial agent under development, and it has known antibacterial activities against multidrug-resistant respiratory and skin pathogens through its inhibition of the bacterial peptide deformylase. Here, we used next-generation sequencing (NGS) of the bacterial 16S rRNA genes from stool samples collected from 61 healthy volunteers at the predosing and end-of-study time points to determine the effects of GSK1322322 on the gastrointestinal (GI) microbiota in a phase I, randomized, double-blind, and placebo-controlled study. GSK1322322 was administered either intravenously (i.v.) only or in an oral-i.v. combination in single- and repeat-dose-escalation infusions. Analysis of the 16S rRNA sequence data found no significant changes in the relative abundances of GI operational taxonomic units (OTUs) between the prestudy and end-of-study samples for either the placebo- or i.v.-only-treated subjects. However, oral-i.v. treatment resulted in significant decreases in some bacterial taxa, the Firmicutes and Bacteroidales, and increases in others, the Betaproteobacteria, Gammaproteobacteria, and Bifidobacteriaceae. Microbiome diversity plots clearly differentiated the end-of-study oral-i.v.-dosed samples from all others collected. The changes in genome function as inferred from species composition suggest an increase in bacterial transporter and xenobiotic metabolism pathways in these samples. A phylogenetic analysis of the peptide deformylase protein sequences collected from the published genomes of clinical isolates previously tested for GSK1322322 in vitro susceptibility and GI bacterial reference genomes suggests that antibiotic target homology is one of several factors that influences the response of GI microbiota to this antibiotic. Our study shows that dosing regimen and target class are important factors when considering the impact of antibiotic usage on GI microbiota. (This clinical trial was registered at the GlaxoSmithKline Clinical Study Register under study identifier PDF 113376.).
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98
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Peters JW, Schut GJ, Boyd ES, Mulder DW, Shepard EM, Broderick JB, King PW, Adams MWW. [FeFe]- and [NiFe]-hydrogenase diversity, mechanism, and maturation. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1853:1350-69. [PMID: 25461840 DOI: 10.1016/j.bbamcr.2014.11.021] [Citation(s) in RCA: 273] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 11/10/2014] [Accepted: 11/16/2014] [Indexed: 11/29/2022]
Abstract
The [FeFe]- and [NiFe]-hydrogenases catalyze the formal interconversion between hydrogen and protons and electrons, possess characteristic non-protein ligands at their catalytic sites and thus share common mechanistic features. Despite the similarities between these two types of hydrogenases, they clearly have distinct evolutionary origins and likely emerged from different selective pressures. [FeFe]-hydrogenases are widely distributed in fermentative anaerobic microorganisms and likely evolved under selective pressure to couple hydrogen production to the recycling of electron carriers that accumulate during anaerobic metabolism. In contrast, many [NiFe]-hydrogenases catalyze hydrogen oxidation as part of energy metabolism and were likely key enzymes in early life and arguably represent the predecessors of modern respiratory metabolism. Although the reversible combination of protons and electrons to generate hydrogen gas is the simplest of chemical reactions, the [FeFe]- and [NiFe]-hydrogenases have distinct mechanisms and differ in the fundamental chemistry associated with proton transfer and control of electron flow that also help to define catalytic bias. A unifying feature of these enzymes is that hydrogen activation itself has been restricted to one solution involving diatomic ligands (carbon monoxide and cyanide) bound to an Fe ion. On the other hand, and quite remarkably, the biosynthetic mechanisms to produce these ligands are exclusive to each type of enzyme. Furthermore, these mechanisms represent two independent solutions to the formation of complex bioinorganic active sites for catalyzing the simplest of chemical reactions, reversible hydrogen oxidation. As such, the [FeFe]- and [NiFe]-hydrogenases are arguably the most profound case of convergent evolution. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.
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Affiliation(s)
- John W Peters
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Gerrit J Schut
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Eric S Boyd
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - David W Mulder
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Eric M Shepard
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Joan B Broderick
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Paul W King
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
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99
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Exploring the influence of the gut microbiota and probiotics on health: a symposium report. Br J Nutr 2014; 112 Suppl 1:S1-18. [PMID: 24953670 PMCID: PMC4077244 DOI: 10.1017/s0007114514001275] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The present report describes the presentations delivered at the 7th International Yakult Symposium, ‘The Intestinal Microbiota and Probiotics: Exploiting Their Influence on Health’, in London on 22–23 April 2013. The following two themes associated with health risks were covered: (1) the impact of age and diet on the gut microbiota and (2) the gut microbiota's interaction with the host. The strong influence of the maternal gut microbiota on neonatal colonisation was reported, as well as rapid changes in the gut microbiome of older people who move from community living to residential care. The effects of dietary changes on gut metabolism were described and the potential influence of inter-individual microbiota differences was noted, in particular the presence/absence of keystone species involved in butyrate metabolism. Several speakers highlighted the association between certain metabolic disorders and imbalanced or less diverse microbiota. Data from metagenomic analyses and novel techniques (including an ex vivo human mucosa model) provided new insights into the microbiota's influence on coeliac, obesity-related and inflammatory diseases, as well as the potential of probiotics. Akkermansia muciniphila and Faecalibacterium prausnitzii were suggested as targets for intervention. Host–microbiota interactions were explored in the context of gut barrier function, pathogenic bacteria recognition, and the ability of the immune system to induce either tolerogenic or inflammatory responses. There was speculation that the gut microbiota should be considered a separate organ, and whether analysis of an individual's microbiota could be useful in identifying their disease risk and/or therapy; however, more research is needed into specific diseases, different population groups and microbial interventions including probiotics.
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100
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Functional metabolic map of Faecalibacterium prausnitzii, a beneficial human gut microbe. J Bacteriol 2014; 196:3289-302. [PMID: 25002542 DOI: 10.1128/jb.01780-14] [Citation(s) in RCA: 145] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The human gut microbiota plays a central role in human well-being and disease. In this study, we present an integrated, iterative approach of computational modeling, in vitro experiments, metabolomics, and genomic analysis to accelerate the identification of metabolic capabilities for poorly characterized (anaerobic) microorganisms. We demonstrate this approach for the beneficial human gut microbe Faecalibacterium prausnitzii strain A2-165. We generated an automated draft reconstruction, which we curated against the limited biochemical data. This reconstruction modeling was used to develop in silico and in vitro a chemically defined medium (CDM), which was validated experimentally. Subsequent metabolomic analysis of the spent medium for growth on CDM was performed. We refined our metabolic reconstruction according to in vitro observed metabolite consumption and secretion and propose improvements to the current genome annotation of F. prausnitzii A2-165. We then used the reconstruction to systematically characterize its metabolic properties. Novel carbon source utilization capabilities and inabilities were predicted based on metabolic modeling and validated experimentally. This study resulted in a functional metabolic map of F. prausnitzii, which is available for further applications. The presented workflow can be readily extended to other poorly characterized and uncharacterized organisms to yield novel biochemical insights about the target organism.
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