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Fernandez-Julia P, Commane DM, van Sinderen D, Munoz-Munoz J. Cross-feeding interactions between human gut commensals belonging to the Bacteroides and Bifidobacterium genera when grown on dietary glycans. MICROBIOME RESEARCH REPORTS 2022; 1:12. [PMID: 38045648 PMCID: PMC10688802 DOI: 10.20517/mrr.2021.05] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/20/2022] [Accepted: 02/25/2022] [Indexed: 12/05/2023]
Abstract
Elements of the human gut microbiota metabolise many host- and diet-derived, non-digestible carbohydrates (NDCs). Intestinal fermentation of NDCs salvages energy and resources for the host and generates beneficial metabolites, such as short chain fatty acids, which contribute to host health. The development of functional NDCs that support the growth and/or metabolic activity of specific beneficial gut bacteria, is desirable, but dependent on an in-depth understanding of the pathways of carbohydrate fermentation. The purpose of this review is to provide an appraisal of what is known about the roles of, and interactions between, Bacteroides and Bifidobacterium as key members involved in NDC utilisation. Bacteroides is considered an important primary degrader of complex NDCs, thereby generating oligosaccharides, which in turn can be fermented by secondary degraders. In this review, we will therefore focus on Bacteroides as an NDC-degrading specialist and Bifidobacterium as an important and purported probiotic representative of secondary degraders. We will describe cross-feeding interactions between members of these two genera. We note that there are limited studies exploring the interactions between Bacteroides and Bifidobacterium, specifically concerning β-glucan and arabinoxylan metabolism. This review therefore summarises the roles of these organisms in the breakdown of dietary fibre and the molecular mechanisms and interactions involved. Finally, it also highlights the need for further research into the phenomenon of cross-feeding between these organisms for an improved understanding of these cross-feeding mechanisms to guide the rational development of prebiotics to support host health or to prevent or combat disease associated with microbial dysbiosis.
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Affiliation(s)
- Pedro Fernandez-Julia
- Microbial Enzymology Group, Department of Applied Sciences, Ellison Building A, University of Northumbria, Newcastle Upon Tyne NE1 8ST, UK
| | - Daniel M. Commane
- Microbial Enzymology Group, Department of Applied Sciences, Ellison Building A, University of Northumbria, Newcastle Upon Tyne NE1 8ST, UK
| | - Douwe van Sinderen
- APC Microbiome Ireland and School of Microbiology, University College Cork, Western Road, Cork T12 YT20, Ireland
| | - Jose Munoz-Munoz
- Microbial Enzymology Group, Department of Applied Sciences, Ellison Building A, University of Northumbria, Newcastle Upon Tyne NE1 8ST, UK
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52
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Bacillus velezensis stimulates resident rhizosphere Pseudomonas stutzeri for plant health through metabolic interactions. THE ISME JOURNAL 2022; 16:774-787. [PMID: 34593997 PMCID: PMC8483172 DOI: 10.1038/s41396-021-01125-3] [Citation(s) in RCA: 121] [Impact Index Per Article: 60.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 09/16/2021] [Accepted: 09/20/2021] [Indexed: 02/08/2023]
Abstract
Trophic interactions play a central role in driving microbial community assembly and function. In gut or soil ecosystems, successful inoculants are always facilitated by efficient colonization; however, the metabolite exchanges between inoculants and resident bacteria are rarely studied, particularly in the rhizosphere. Here, we used bioinformatic, genetic, transcriptomic, and metabonomic analyses to uncover syntrophic cooperation between inoculant (Bacillus velezensis SQR9) and plant-beneficial indigenous Pseudomonas stutzeri in the cucumber rhizosphere. We found that the synergistic interaction of these two species is highly environmental dependent, the emergence of syntrophic cooperation was only evident in a static nutrient-rich niche, such as pellicle biofilm in addition to the rhizosphere. Our results identified branched-chain amino acids (BCAAs) biosynthesis pathways are involved in syntrophic cooperation. Genome-scale metabolic modeling and metabolic profiling also demonstrated metabolic facilitation among the bacterial strains. In addition, biofilm matrix components from Bacillus were essential for the interaction. Importantly, the two-species consortium promoted plant growth and helped plants alleviate salt stress. In summary, we propose a mechanism in which synergic interactions between a biocontrol bacterium and a partner species promote plant health.
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53
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Liang Y, Ma A, Zhuang G. Construction of Environmental Synthetic Microbial Consortia: Based on Engineering and Ecological Principles. Front Microbiol 2022; 13:829717. [PMID: 35283862 PMCID: PMC8905317 DOI: 10.3389/fmicb.2022.829717] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 01/31/2022] [Indexed: 01/30/2023] Open
Abstract
In synthetic biology, engineering principles are applied to system design. The development of synthetic microbial consortia represents the intersection of synthetic biology and microbiology. Synthetic community systems are constructed by co-cultivating two or more microorganisms under certain environmental conditions, with broad applications in many fields including ecological restoration and ecological theory. Synthetic microbial consortia tend to have high biological processing efficiencies, because the division of labor reduces the metabolic burden of individual members. In this review, we focus on the environmental applications of synthetic microbial consortia. Although there are many strategies for the construction of synthetic microbial consortia, we mainly introduce the most widely used construction principles based on cross-feeding. Additionally, we propose methods for constructing synthetic microbial consortia based on traits and spatial structure from the perspective of ecology to provide a basis for future work.
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Affiliation(s)
- Yu Liang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resource and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Anzhou Ma
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resource and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Guoqiang Zhuang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resource and Environment, University of Chinese Academy of Sciences, Beijing, China
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54
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Ellis JL, Karl JP, Oliverio AM, Fu X, Soares JW, Wolfe BE, Hernandez CJ, Mason JB, Booth SL. Dietary vitamin K is remodeled by gut microbiota and influences community composition. Gut Microbes 2022; 13:1-16. [PMID: 33651646 PMCID: PMC7928036 DOI: 10.1080/19490976.2021.1887721] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Vitamins have well-established roles in bacterial metabolism. Menaquinones (MKn, n = prenyl units in sidechain) are bacterially produced forms of vitamin K produced by the gut microbiota and consumed in the diet. Little is known about the influence of dietary vitamin K quinones on gut microbial composition and MKn production. Here, male and female C57BL6 mice were fed a vitamin K deficient diet or vitamin K sufficient diets containing phylloquinone (PK, plant-based vitamin K form), MK4, and/or MK9. DNA was extracted from cecal contents and 16S sequencing conducted to assess microbial composition. Cecal microbial community composition was significantly different in vitamin K deficient female mice compared to females on vitamin K sufficient diets (all p < .007). Parallel trends were seen in male mice, but were not statistically significant (all p > .05 but <0.1). Next, stable isotope-labeled vitamin K quinones were supplemented to male and female C57BL6 mice (2H7PK, 13C11MK4, 2H7MK7, 2H7MK9) and to an in vitro fermentation model inoculated with human stool (2H7PK, 2H7MK4, 2H7MK9, or vitamin K precursor 2H8-menadione). Vitamin K quinones in feces and culture aliquots were measured using LC-MS. In vivo, supplemented vitamin K quinones were remodeled to other MKn (2H7- or 13C6-labeled MK4, MK10, MK11, and MK12), but in vitro only the precursor 2H8-menadione was remodeled to 2H7MK4, 2H7MK9, 2H7MK10, and 2H7MK11. These results suggest that dietary vitamin K deficiency alters the gut microbial community composition. Further studies are needed to determine if menadione generated by host metabolism may serve as an intermediate in dietary vitamin K remodeling in vivo.
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Affiliation(s)
- Jessie L. Ellis
- Jean Mayer USDA Human Nutrition Research Center on Aging, Tufts University, Boston, MA, USA,The Friedman School of Nutrition Science & Policy, Tufts University, Boston, MA, USA
| | - J. Philip Karl
- Military Nutrition Division, US Army Research Institute of Environmental Medicine, Natick, MA, USA
| | - Angela M. Oliverio
- Department of Ecology and Evolutionary Biology, University of Colorado-Boulder, Boulder, CO, USA
| | - Xueyan Fu
- Jean Mayer USDA Human Nutrition Research Center on Aging, Tufts University, Boston, MA, USA
| | - Jason W. Soares
- Soldier Effectiveness Directorate, US Army Combat Capabilities Developmental Command Soldier Center, Natick, MA, USA
| | | | - Christopher J. Hernandez
- Schools of Mechanical and Aerospace Engineering & Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Joel B. Mason
- Jean Mayer USDA Human Nutrition Research Center on Aging, Tufts University, Boston, MA, USA,The Friedman School of Nutrition Science & Policy, Tufts University, Boston, MA, USA
| | - Sarah L. Booth
- Jean Mayer USDA Human Nutrition Research Center on Aging, Tufts University, Boston, MA, USA,CONTACT Sarah L. Booth 711 Washington Street, Boston, MA 02111, USA
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55
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Mataigne V, Vannier N, Vandenkoornhuyse P, Hacquard S. Microbial Systems Ecology to Understand Cross-Feeding in Microbiomes. Front Microbiol 2021; 12:780469. [PMID: 34987488 PMCID: PMC8721230 DOI: 10.3389/fmicb.2021.780469] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 11/25/2021] [Indexed: 12/26/2022] Open
Abstract
Understanding how microorganism-microorganism interactions shape microbial assemblages is a key to deciphering the evolution of dependencies and co-existence in complex microbiomes. Metabolic dependencies in cross-feeding exist in microbial communities and can at least partially determine microbial community composition. To parry the complexity and experimental limitations caused by the large number of possible interactions, new concepts from systems biology aim to decipher how the components of a system interact with each other. The idea that cross-feeding does impact microbiome assemblages has developed both theoretically and empirically, following a systems biology framework applied to microbial communities, formalized as microbial systems ecology (MSE) and relying on integrated-omics data. This framework merges cellular and community scales and offers new avenues to untangle microbial coexistence primarily by metabolic modeling, one of the main approaches used for mechanistic studies. In this mini-review, we first give a concise explanation of microbial cross-feeding. We then discuss how MSE can enable progress in microbial research. Finally, we provide an overview of a MSE framework mostly based on genome-scale metabolic-network reconstruction that combines top-down and bottom-up approaches to assess the molecular mechanisms of deterministic processes of microbial community assembly that is particularly suitable for use in synthetic biology and microbiome engineering.
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Affiliation(s)
- Victor Mataigne
- Université de Rennes 1, CNRS, UMR6553 ECOBIO, Rennes, France
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Nathan Vannier
- Université de Rennes 1, CNRS, UMR6553 ECOBIO, Rennes, France
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56
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Díaz-Pascual F, Lempp M, Nosho K, Jeckel H, Jo JK, Neuhaus K, Hartmann R, Jelli E, Hansen MF, Price-Whelan A, Dietrich LEP, Link H, Drescher K. Spatial alanine metabolism determines local growth dynamics of Escherichia coli colonies. eLife 2021; 10:e70794. [PMID: 34751128 PMCID: PMC8579308 DOI: 10.7554/elife.70794] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 10/18/2021] [Indexed: 12/17/2022] Open
Abstract
Bacteria commonly live in spatially structured biofilm assemblages, which are encased by an extracellular matrix. Metabolic activity of the cells inside biofilms causes gradients in local environmental conditions, which leads to the emergence of physiologically differentiated subpopulations. Information about the properties and spatial arrangement of such metabolic subpopulations, as well as their interaction strength and interaction length scales are lacking, even for model systems like Escherichia coli colony biofilms grown on agar-solidified media. Here, we use an unbiased approach, based on temporal and spatial transcriptome and metabolome data acquired during E. coli colony biofilm growth, to study the spatial organization of metabolism. We discovered that alanine displays a unique pattern among amino acids and that alanine metabolism is spatially and temporally heterogeneous. At the anoxic base of the colony, where carbon and nitrogen sources are abundant, cells secrete alanine via the transporter AlaE. In contrast, cells utilize alanine as a carbon and nitrogen source in the oxic nutrient-deprived region at the colony mid-height, via the enzymes DadA and DadX. This spatially structured alanine cross-feeding influences cellular viability and growth in the cross-feeding-dependent region, which shapes the overall colony morphology. More generally, our results on this precisely controllable biofilm model system demonstrate a remarkable spatiotemporal complexity of metabolism in biofilms. A better characterization of the spatiotemporal metabolic heterogeneities and dependencies is essential for understanding the physiology, architecture, and function of biofilms.
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Affiliation(s)
| | - Martin Lempp
- Max Planck Institute for Terrestrial
MicrobiologyMarburgGermany
| | - Kazuki Nosho
- Max Planck Institute for Terrestrial
MicrobiologyMarburgGermany
| | - Hannah Jeckel
- Max Planck Institute for Terrestrial
MicrobiologyMarburgGermany
- Department of Physics,
Philipps-Universität MarburgMarburgGermany
- Biozentrum, University of
BaselBaselSwitzerland
| | - Jeanyoung K Jo
- Department of Biological Sciences,
Columbia UniversityNew YorkUnited
States
| | - Konstantin Neuhaus
- Max Planck Institute for Terrestrial
MicrobiologyMarburgGermany
- Department of Physics,
Philipps-Universität MarburgMarburgGermany
- Biozentrum, University of
BaselBaselSwitzerland
| | - Raimo Hartmann
- Max Planck Institute for Terrestrial
MicrobiologyMarburgGermany
| | - Eric Jelli
- Max Planck Institute for Terrestrial
MicrobiologyMarburgGermany
- Department of Physics,
Philipps-Universität MarburgMarburgGermany
| | | | - Alexa Price-Whelan
- Department of Biological Sciences,
Columbia UniversityNew YorkUnited
States
| | - Lars EP Dietrich
- Department of Biological Sciences,
Columbia UniversityNew YorkUnited
States
| | - Hannes Link
- Max Planck Institute for Terrestrial
MicrobiologyMarburgGermany
- Interfaculty Institute for Microbiology
and Infection Medicine, Eberhard Karls Universität
TübingenTübingenGermany
| | - Knut Drescher
- Max Planck Institute for Terrestrial
MicrobiologyMarburgGermany
- Department of Physics,
Philipps-Universität MarburgMarburgGermany
- Biozentrum, University of
BaselBaselSwitzerland
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57
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Berkhout MD, Plugge CM, Belzer C. How microbial glycosyl hydrolase activity in the gut mucosa initiates microbial cross-feeding. Glycobiology 2021; 32:182-200. [PMID: 34939101 PMCID: PMC8966484 DOI: 10.1093/glycob/cwab105] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/30/2021] [Accepted: 10/06/2021] [Indexed: 11/12/2022] Open
Abstract
The intestinal epithelium is protected from direct contact with gut microbes by a mucus layer. This mucus layer consists of secreted mucin glycoproteins. The outer mucus layer in the large intestine forms a niche that attracts specific gut microbiota members of which several gut commensals can degrade mucin. Mucin glycan degradation is a complex process that requires a broad range of glycan degrading enzymes, as mucin glycans are intricate and diverse molecules. Consequently, it is hypothesised that microbial mucin breakdown requires concerted action of various enzymes in a network of multiple resident microbes at the gut mucosa. This review investigates the evolutionary relationships of microbial CAZymes that are potentially involved in mucin glycan degradation and focuses on the role that microbial enzymes play in the degradation of gut mucin glycans in microbial cross-feeding and syntrophic interactions.
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Affiliation(s)
- Maryse D Berkhout
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708WE Wageningen, The Netherlands
| | - Caroline M Plugge
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708WE Wageningen, The Netherlands
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708WE Wageningen, The Netherlands
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58
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Feller FM, Eilebrecht S, Nedielkov R, Yücel O, Alvincz J, Salinas G, Ludwig KC, Möller H, Philipp B. Investigations on the Degradation of the Bile Salt Cholate via the 9,10- Seco-Pathway Reveals the Formation of a Novel Recalcitrant Steroid Compound by a Side Reaction in Sphingobium sp. Strain Chol11. Microorganisms 2021; 9:microorganisms9102146. [PMID: 34683472 PMCID: PMC8540908 DOI: 10.3390/microorganisms9102146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/07/2021] [Accepted: 10/11/2021] [Indexed: 01/30/2023] Open
Abstract
Bile salts such as cholate are steroid compounds from the digestive tracts of vertebrates, which enter the environment upon excretion, e.g., in manure. Environmental bacteria degrade bile salts aerobically via two pathway variants involving intermediates with Δ1,4- or Δ4,6-3-keto-structures of the steroid skeleton. Recent studies indicated that degradation of bile salts via Δ4,6-3-keto intermediates in Sphingobium sp. strain Chol11 proceeds via 9,10-seco cleavage of the steroid skeleton. For further elucidation, the presumptive product of this cleavage, 3,12β-dihydroxy-9,10-seco-androsta-1,3,5(10),6-tetraene-9,17-dione (DHSATD), was provided to strain Chol11 in a co-culture approach with Pseudomonas stutzeri Chol1 and as purified substrate. Strain Chol11 converted DHSATD to the so far unknown compound 4-methyl-3-deoxy-1,9,12-trihydroxyestra-1,3,5(10)7-tetraene-6,17-dione (MDTETD), presumably in a side reaction involving an unusual ring closure. MDTETD was neither degraded by strains Chol1 and Chol11 nor in enrichment cultures. Functional transcriptome profiling of zebrafish embryos after exposure to MDTETD identified a significant overrepresentation of genes linked to hormone responses. In both pathway variants, steroid degradation intermediates transiently accumulate in supernatants of laboratory cultures. Soil slurry experiments indicated that bacteria using both pathway variants were active and also released their respective intermediates into the environment. This instance could enable the formation of recalcitrant steroid metabolites by interspecies cross-feeding in agricultural soils.
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Affiliation(s)
- Franziska Maria Feller
- Institute for Molecular Microbiology and Biotechnology, University of Münster, Corrensstr. 3, 48149 Münster, Germany; (F.M.F.); (O.Y.); (K.C.L.)
| | - Sebastian Eilebrecht
- Fraunhofer Attract Eco’n’OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Auf dem Aberg 1, 57392 Schmallenberg, Germany; (S.E.); (J.A.)
| | - Ruslan Nedielkov
- Institute for Chemistry, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476 Potsdam, Germany; (R.N.); (H.M.)
| | - Onur Yücel
- Institute for Molecular Microbiology and Biotechnology, University of Münster, Corrensstr. 3, 48149 Münster, Germany; (F.M.F.); (O.Y.); (K.C.L.)
| | - Julia Alvincz
- Fraunhofer Attract Eco’n’OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Auf dem Aberg 1, 57392 Schmallenberg, Germany; (S.E.); (J.A.)
| | - Gabriela Salinas
- NGS-Services for Integrative Genomics, Institute for Human Genetics, University of Göttingen, 37077 Göttingen, Germany;
| | - Kevin Christopher Ludwig
- Institute for Molecular Microbiology and Biotechnology, University of Münster, Corrensstr. 3, 48149 Münster, Germany; (F.M.F.); (O.Y.); (K.C.L.)
| | - Heiko Möller
- Institute for Chemistry, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476 Potsdam, Germany; (R.N.); (H.M.)
| | - Bodo Philipp
- Institute for Molecular Microbiology and Biotechnology, University of Münster, Corrensstr. 3, 48149 Münster, Germany; (F.M.F.); (O.Y.); (K.C.L.)
- Department for Environmental Microbiology, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Auf dem Aberg 1, 57392 Schmallenberg, Germany
- Correspondence: ; Tel.: +49-251-8339827; Fax: +49-251-8338388
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59
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Méndez-Salazar EO, Martínez-Nava GA. Uric acid extrarenal excretion: the gut microbiome as an evident yet understated factor in gout development. Rheumatol Int 2021; 42:403-412. [PMID: 34586473 DOI: 10.1007/s00296-021-05007-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/19/2021] [Indexed: 12/19/2022]
Abstract
Humans do not produce uricase, an enzyme responsible for degrading uric acid. However, some bacteria residing in the gut can degrade one-third of the dietary and endogenous uric acid generated daily. New insights based on metagenomic and metabolomic approaches provide a new interest in exploring the involvement of gut microbiota in gout. Nevertheless, the exact mechanisms underlying this association are complex and have not been widely discussed. In this study, we aimed to review the evidence that suggests uric acid extrarenal excretion and gut microbiome are potential risk factors for developing gout. A literature search was performed in PubMed, Web of Science, and Google Scholar using several keywords, including "gut microbiome AND gout". A remarkable intestinal dysbiosis and shifts in abundance of certain bacterial taxa in gout patients have been consistently reported among different studies. Under this condition, bacteria might have developed adaptive mechanisms for de novo biosynthesis and salvage of purines, and thus, a concomitant alteration in uric acid metabolism. Moreover, gut microbiota can produce substrates that might cross the portal vein so the liver can generate de novo purinogenic amino acids, as well as uric acid. Therefore, the extrarenal excretion of uric acid needs to be considered as a factor in gout development. Nevertheless, further studies are needed to fully understand the role of gut microbiome in uric acid production and its extrarenal excretion, and to point out possible bacteria or bacterial enzymes that could be used as probiotic coadjutant treatment in gout patients.
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Affiliation(s)
| | - Gabriela Angélica Martínez-Nava
- Laboratorio de Líquido Sinovial, Instituto Nacional de Rehabilitación "Luis Guillermo Ibarra Ibarra", Calzada México-Xochimilco 289, Arenal de Guadalupe, 14389, Mexico City, Mexico.
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60
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Cell Growth Model with Stochastic Gene Expression Helps Understand the Growth Advantage of Metabolic Exchange and Auxotrophy. mSystems 2021; 6:e0044821. [PMID: 34342540 PMCID: PMC8407474 DOI: 10.1128/msystems.00448-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
During cooperative growth, microbes often experience higher fitness by sharing resources via metabolite exchange. How competitive species evolve to cooperate is, however, not known. Moreover, existing models (based on optimization of steady-state resources or fluxes) are often unable to explain the growth advantage for the cooperating species, even for simple reciprocally cross-feeding auxotrophic pairs. We present here an abstract model of cell growth that considers the stochastic burst-like gene expression of biosynthetic pathways of limiting biomass precursor metabolites and directly connect the amount of metabolite produced to cell growth and division, using a "metabolic sizer/adder" rule. Our model recapitulates Monod's law and yields the experimentally observed right-skewed long-tailed distribution of cell doubling times. The model further predicts the growth effect of secretion and uptake of metabolites by linking it to changes in the internal metabolite levels. The model also explains why auxotrophs may grow faster when supplied with the metabolite they cannot produce and why two reciprocally cross-feeding auxotrophs can grow faster than prototrophs. Overall, our framework allows us to predict the growth effect of metabolic interactions in independent microbes and microbial communities, setting up the stage to study the evolution of these interactions. IMPORTANCE Cooperative behaviors are highly prevalent in the wild, but their evolution is not understood. Metabolic flux models can demonstrate the viability of metabolic exchange as cooperative interactions, but steady-state growth models cannot explain why cooperators grow faster. We present a stochastic model that connects growth to the cell's internal metabolite levels and quantifies the growth effect of metabolite exchange and auxotrophy. We show that a reduction in gene expression noise can explain why cells that import metabolites or become auxotrophs can grow faster and why reciprocal cross-feeding of metabolites between complementary auxotrophs allows them to grow faster. Furthermore, our framework can simulate the growth of interacting cells, which will enable us to understand the possible trajectories of the evolution of cooperation in silico.
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61
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Jimenez P, Scheuring I. Density-dependent private benefit leads to bacterial mutualism. Evolution 2021; 75:1619-1635. [PMID: 33954986 DOI: 10.1111/evo.14241] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 03/25/2021] [Indexed: 01/26/2023]
Abstract
Microorganisms produce and secrete materials that are beneficial for themselves and their neighbors. We modeled the situation when cells can produce different costly secretions which increase the carrying capacity of the population. Strains that lose the function of producing one or more secretions avoid the cost of production and can exhaust the producers. However, secreting substances provides a private benefit for the producers in a density-dependent way. We developed a model to examine the outcome of the selection among different types of producer strains from the nonproducer strain to the partial producers, to the full producer strain. We were interested in circumstances under which selection maintains partners that produce complementary secreted materials thus forming an interdependent mutualistic interaction. We show that interdependent mutualism is selected under a broad range of conditions if private benefit decreases with density. Selection frequently causes the coexistence of more and less generalist cooperative strains, thus cooperation and exploitation co-occur. Interdependent mutualism is evolved under more specific circumstances if private benefit increases with density and these general observations are valid in a well-mixed and a structured deme model. We show that the applied population structure allows the invasion of rare cooperators and supports cooperation in general.
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Affiliation(s)
- Paul Jimenez
- Department of Plant Systematics, Ecology and Theoretical Biology, Eötvös Loránd University, Pázmány P. sétány 1/c, Budapest, 1117, Hungary
| | - István Scheuring
- MTA-ELTE Theoretical Biology and Evolutionary Ecology Research Group, Eotvos University, Budapest, 1117, Hungary.,Centre for Ecological Research, Institute of Evolution, Konkoly-Thege Miklós út 29-33, Budapest, 1121, Hungary
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62
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Wei N, Russell AL, Jarrett AR, Ashman TL. Pollinators mediate floral microbial diversity and microbial network under agrochemical disturbance. Mol Ecol 2021; 30:2235-2247. [PMID: 33738885 DOI: 10.1111/mec.15890] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 03/07/2021] [Accepted: 03/10/2021] [Indexed: 12/14/2022]
Abstract
How pollinators mediate microbiome assembly in the anthosphere is a major unresolved question of theoretical and applied importance in the face of anthropogenic disturbance. We addressed this question by linking visitation of diverse pollinator functional groups (bees, wasps, flies, butterflies, beetles, true bugs and other taxa) to the key properties of the floral microbiome (microbial α- and β-diversity and microbial network) under agrochemical disturbance, using a field experiment of bactericide and fungicide treatments on cultivated strawberries that differ in flower abundance. Structural equation modelling was used to link agrochemical disturbance and flower abundance to pollinator visitation to floral microbiome properties. Our results revealed that (i) pollinator visitation influenced the α- and β-diversity and network centrality of the floral microbiome, with different pollinator functional groups affecting different microbiome properties; (ii) flower abundance influenced the floral microbiome both directly by governing the source pool of microbes and indirectly by enhancing pollinator visitation; and (iii) agrochemical disturbance affected the floral microbiome primarily directly by fungicide, and less so indirectly via pollinator visitation. These findings improve the mechanistic understanding of floral microbiome assembly, and may be generalizable to many other plants that are visited by diverse insect pollinators in natural and managed ecosystems.
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Affiliation(s)
- Na Wei
- The Holden Arboretum, Kirtland, Ohio, USA.,Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Avery L Russell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Biology, Missouri State University, Springfield, Missouri, USA
| | - Abigail R Jarrett
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Tia-Lynn Ashman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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van Bel N, van der Wielen P, Wullings B, van Rijn J, van der Mark E, Ketelaars H, Hijnen W. Aeromonas species from non-chlorinated distribution systems and their competitive planktonic growth in drinking water. Appl Environ Microbiol 2021; 87:AEM.02867-20. [PMID: 33310721 PMCID: PMC8090877 DOI: 10.1128/aem.02867-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 11/25/2020] [Indexed: 11/20/2022] Open
Abstract
Aeromonas is included in the Dutch Drinking Water Decree as an indicator for elevated microbial regrowth in non-chlorinated drinking water distribution systems (DWDS). The temporal and spatial diversity of Aeromonas species in ten DWDS and their planktonic growth characteristics for different carbon sources was investigated. Genotyping of the gyrB gene of isolates showed a non-systematic temporal and spatial variable prevalence of seven different Aeromonas species in these DWDS and no correlation with AOC-P17/NOX and Aeromonas concentrations. Pure cultures of these seven species showed a high affinity to low concentrations (μg/L) of individual amino acids and fatty acids, compounds associated with biomass. Growth occurred at 0.5 μg-C/L of an amino acid mixture. Growth of a mixed community of A. rivuli, A. salmonicida, A. sobria and A. veronii in drinking water occurred in pasteurized samples, however, no growth and decay occurred in competition with the autochthonous bacteria (non-pasteurized samples). This community also failed to grow in non-pasteurized distribution samples from a location with clear increase in planktonic Aeromonas concentrations in the transported drinking water. For competitive planktonic growth of Aeromonas an amino acid concentration of ≥5 μg-C/L is required. AOC-P17/NOX concentrations showed that such concentrations are not expected in Dutch drinking water. Therefore, we suspect that competitive planktonic growth is not the major cause of the observed non-compliance with the Aeromonas standard in non-chlorinated DWSD.Importance The occurrence of the bacterial genus Aeromonas in non-chlorinated drinking water in the Netherlands is regarded as an indication for elevated microbial regrowth in the distribution system. Identification of the prevalent species in ten distribution systems by genotyping yielded seven different species, with A. rivuli, A. veronii and A. sobria as the most dominant ones. Planktonic growth experiments of pure cultures confirmed former published affinity of Aeromonas for certain biomass compounds (amino and fatty acids). In competition with the autochthonous microflora, however, planktonic growth was not observed, only after addition of a threshold amino acid concentration of 5 μg-C/L. Based on our results and further observations we deduced that planktonic growth of Aeromonas in the DWDS is not very likely. Benthic growth in loose deposits and planktonic release is a more plausible explanation for the observed planktonic increase of Aeromonas.
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Affiliation(s)
- Nikki van Bel
- KWR Water Research Institute, Nieuwegein, the Netherlands
| | - Paul van der Wielen
- KWR Water Research Institute, Nieuwegein, the Netherlands
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | - Bart Wullings
- KWR Water Research Institute, Nieuwegein, the Netherlands
| | | | | | | | - Wim Hijnen
- KWR Water Research Institute, Nieuwegein, the Netherlands
- Evides Water Company, Rotterdam, the Netherlands
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64
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Shanahan ER, McMaster JJ, Staudacher HM. Conducting research on diet-microbiome interactions: A review of current challenges, essential methodological principles, and recommendations for best practice in study design. J Hum Nutr Diet 2021; 34:631-644. [PMID: 33639033 DOI: 10.1111/jhn.12868] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 01/07/2021] [Accepted: 01/19/2021] [Indexed: 12/21/2022]
Abstract
Diet is one of the strongest modulators of the gut microbiome. However, the complexity of the interactions between diet and the microbial community emphasises the need for a robust study design and continued methodological development. This review aims to summarise considerations for conducting high-quality diet-microbiome research, outline key challenges unique to the field, and provide advice for addressing these in a practical manner useful to dietitians, microbiologists, gastroenterologists and other diet-microbiome researchers. Searches of databases and references from relevant articles were conducted using the primary search terms 'diet', 'diet intervention', 'dietary analysis', 'microbiome' and 'microbiota', alone or in combination. Publications were considered relevant if they addressed methods for diet and/or microbiome research, or were a human study relevant to diet-microbiome interactions. Best-practice design in diet-microbiome research requires appropriate consideration of the study population and careful choice of trial design and data collection methodology. Ongoing challenges include the collection of dietary data that accurately reflects intake at a timescale relevant to microbial community structure and metabolism, measurement of nutrients in foods pertinent to microbes, improving ability to measure and understand microbial metabolic and functional properties, adequately powering studies, and the considered analysis of multivariate compositional datasets. Collaboration across the disciplines of nutrition science and microbiology is crucial for high-quality diet-microbiome research. Improvements in our understanding of the interaction between nutrient intake and microbial metabolism, as well as continued methodological innovation, will facilitate development of effective evidence-based personalised dietary treatments.
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Affiliation(s)
- Erin R Shanahan
- School of Life and Environmental Sciences, Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | | | - Heidi M Staudacher
- IMPACT (The Institute for Mental and Physical Health and Clinical Translation) Food & Mood Centre, Deakin University, Geelong, VIC, Australia
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Fritts RK, McCully AL, McKinlay JB. Extracellular Metabolism Sets the Table for Microbial Cross-Feeding. Microbiol Mol Biol Rev 2021; 85:e00135-20. [PMID: 33441489 PMCID: PMC7849352 DOI: 10.1128/mmbr.00135-20] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The transfer of nutrients between cells, or cross-feeding, is a ubiquitous feature of microbial communities with emergent properties that influence our health and orchestrate global biogeochemical cycles. Cross-feeding inevitably involves the externalization of molecules. Some of these molecules directly serve as cross-fed nutrients, while others can facilitate cross-feeding. Altogether, externalized molecules that promote cross-feeding are diverse in structure, ranging from small molecules to macromolecules. The functions of these molecules are equally diverse, encompassing waste products, enzymes, toxins, signaling molecules, biofilm components, and nutrients of high value to most microbes, including the producer cell. As diverse as the externalized and transferred molecules are the cross-feeding relationships that can be derived from them. Many cross-feeding relationships can be summarized as cooperative but are also subject to exploitation. Even those relationships that appear to be cooperative exhibit some level of competition between partners. In this review, we summarize the major types of actively secreted, passively excreted, and directly transferred molecules that either form the basis of cross-feeding relationships or facilitate them. Drawing on examples from both natural and synthetic communities, we explore how the interplay between microbial physiology, environmental parameters, and the diverse functional attributes of extracellular molecules can influence cross-feeding dynamics. Though microbial cross-feeding interactions represent a burgeoning field of interest, we may have only begun to scratch the surface.
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Affiliation(s)
- Ryan K Fritts
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | | | - James B McKinlay
- Department of Biology, Indiana University, Bloomington, Indiana, USA
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66
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Yang F, Tomberlin JK, Jordan HR. Starvation Alters Gut Microbiome in Black Soldier Fly (Diptera: Stratiomyidae) Larvae. Front Microbiol 2021; 12:601253. [PMID: 33664713 PMCID: PMC7921171 DOI: 10.3389/fmicb.2021.601253] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 01/18/2021] [Indexed: 12/18/2022] Open
Abstract
Unlike for vertebrates, the impact of starvation on the gut microbiome of invertebrates is poorly studied. Deciphering shifts in metabolically active associated bacterial communities in vertebrates has led to determining the role of the associated microbiome in the sensation of hunger and discoveries of associated regulatory mechanisms. From an invertebrate perspective, such as the black soldier fly, such information could lead to enhanced processes for optimized biomass production and waste conversion. Bacteria associated with food substrates of black soldier fly are known to impact corresponding larval life-history traits (e.g., larval development); however, whether black soldier fly larval host state (i.e., starved) impacts the gut microbiome is not known. In this study, we measured microbial community structural and functional shifts due to black soldier fly larvae starvation. Data generated demonstrate such a physiological state (i.e., starvation) does in fact impact both aspects of the microbiome. At the phylum level, community diversity decreased significantly during black soldier fly larval starvation (p = 0.0025). Genus level DESeq2 analysis identified five genera with significantly different relative abundance (q < 0.05) across the 24 and 48 H post initiation of starvation: Actinomyces, Microbacterium, Enterococcus, Sphingobacterium, and Leucobacter. Finally, we inferred potential gene function and significantly predicted functional KEGG Orthology (KO) abundance. We demonstrated the metabolically active microbial community structure and function could be influenced by host-feeding status. Such perturbations, even when short in duration (e.g., 24 H) could stunt larval growth and waste conversion due to lacking a full complement of bacteria and associated functions.
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Affiliation(s)
- Fengchun Yang
- Department of Entomology, Texas A&M University, College Station, TX, United States
| | - Jeffery K Tomberlin
- Department of Entomology, Texas A&M University, College Station, TX, United States
| | - Heather R Jordan
- Department of Biological Sciences, Mississippi State University, Starkville, MS, United States
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67
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Raimundo I, Silva R, Meunier L, Valente SM, Lago-Lestón A, Keller-Costa T, Costa R. Functional metagenomics reveals differential chitin degradation and utilization features across free-living and host-associated marine microbiomes. MICROBIOME 2021; 9:43. [PMID: 33583433 PMCID: PMC7883442 DOI: 10.1186/s40168-020-00970-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 10/18/2020] [Indexed: 06/01/2023]
Abstract
BACKGROUND Chitin ranks as the most abundant polysaccharide in the oceans yet knowledge of shifts in structure and diversity of chitin-degrading communities across marine niches is scarce. Here, we integrate cultivation-dependent and -independent approaches to shed light on the chitin processing potential within the microbiomes of marine sponges, octocorals, sediments, and seawater. RESULTS We found that cultivatable host-associated bacteria in the genera Aquimarina, Enterovibrio, Microbulbifer, Pseudoalteromonas, Shewanella, and Vibrio were able to degrade colloidal chitin in vitro. Congruent with enzymatic activity bioassays, genome-wide inspection of cultivated symbionts revealed that Vibrio and Aquimarina species, particularly, possess several endo- and exo-chitinase-encoding genes underlying their ability to cleave the large chitin polymer into oligomers and dimers. Conversely, Alphaproteobacteria species were found to specialize in the utilization of the chitin monomer N-acetylglucosamine more often. Phylogenetic assessments uncovered a high degree of within-genome diversification of multiple, full-length endo-chitinase genes for Aquimarina and Vibrio strains, suggestive of a versatile chitin catabolism aptitude. We then analyzed the abundance distributions of chitin metabolism-related genes across 30 Illumina-sequenced microbial metagenomes and found that the endosymbiotic consortium of Spongia officinalis is enriched in polysaccharide deacetylases, suggesting the ability of the marine sponge microbiome to convert chitin into its deacetylated-and biotechnologically versatile-form chitosan. Instead, the abundance of endo-chitinase and chitin-binding protein-encoding genes in healthy octocorals leveled up with those from the surrounding environment but was found to be depleted in necrotic octocoral tissue. Using cultivation-independent, taxonomic assignments of endo-chitinase encoding genes, we unveiled previously unsuspected richness and divergent structures of chitinolytic communities across host-associated and free-living biotopes, revealing putative roles for uncultivated Gammaproteobacteria and Chloroflexi symbionts in chitin processing within sessile marine invertebrates. CONCLUSIONS Our findings suggest that differential chitin degradation pathways, utilization, and turnover dictate the processing of chitin across marine micro-niches and support the hypothesis that inter-species cross-feeding could facilitate the co-existence of chitin utilizers within marine invertebrate microbiomes. We further identified chitin metabolism functions which may serve as indicators of microbiome integrity/dysbiosis in corals and reveal putative novel chitinolytic enzymes in the genus Aquimarina that may find applications in the blue biotechnology sector. Video abstract.
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Affiliation(s)
- I. Raimundo
- Instituto de Bioengenharia e Biociências, Instituto Superior Técnico (IST), Universidade de Lisboa, Av. Rovisco Pais 1, Torre Sul, Piso 11, 11.6.11b, 1049-001 Lisbon, Portugal
| | - R. Silva
- Instituto de Bioengenharia e Biociências, Instituto Superior Técnico (IST), Universidade de Lisboa, Av. Rovisco Pais 1, Torre Sul, Piso 11, 11.6.11b, 1049-001 Lisbon, Portugal
| | - L. Meunier
- Instituto de Bioengenharia e Biociências, Instituto Superior Técnico (IST), Universidade de Lisboa, Av. Rovisco Pais 1, Torre Sul, Piso 11, 11.6.11b, 1049-001 Lisbon, Portugal
- Laboratory of Aquatic Systems Ecology, Université Libre de Bruxelles, Brussels, Belgium
| | - S. M. Valente
- Instituto de Bioengenharia e Biociências, Instituto Superior Técnico (IST), Universidade de Lisboa, Av. Rovisco Pais 1, Torre Sul, Piso 11, 11.6.11b, 1049-001 Lisbon, Portugal
| | - A. Lago-Lestón
- Department of Medical Innovation, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), 22860 Ensenada, Mexico
| | - T. Keller-Costa
- Instituto de Bioengenharia e Biociências, Instituto Superior Técnico (IST), Universidade de Lisboa, Av. Rovisco Pais 1, Torre Sul, Piso 11, 11.6.11b, 1049-001 Lisbon, Portugal
| | - R. Costa
- Instituto de Bioengenharia e Biociências, Instituto Superior Técnico (IST), Universidade de Lisboa, Av. Rovisco Pais 1, Torre Sul, Piso 11, 11.6.11b, 1049-001 Lisbon, Portugal
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, 8005-139 Faro, Portugal
- Department of Energy, Joint Genome Institute, Berkeley, CA 94720 USA
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
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68
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Associations between the Gut Microbiota, Immune Reconstitution, and Outcomes of Allogeneic Hematopoietic Stem Cell Transplantation. ACTA ACUST UNITED AC 2021; 3. [PMID: 33552594 PMCID: PMC7864222 DOI: 10.20900/immunometab20210004] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Immune reconstitution following allogeneic hematopoietic stem cell transplantation (allo-HSCT) sets the stage for the goal of a successful transplant—the prevention of disease relapse without graft versus host disease (GVHD) and opportunistic infection. In both epidemiologic studies and in controlled animal studies, it is known that the gut microbiome (GM) can profoundly influence normal innate and adaptive immune development and can be altered by microbial transfer and antibiotics. Following allo-HSCT the GM has been shown to influence clinical outcomes but published associations between the GM and immune reconstitution post-allo-HSCT are lacking. In this viewpoint we propose that the extensive knowledge garnered from studying normal immune development can serve as a framework for studying immune development post-allo-HSCT. We summarize existing studies addressing the effect of the GM on immune ontogeny and draw associations with immune reconstitution and the GM post-allo-HSCT.
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69
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Aylward FO. The coevolutionary history of the microbial planet. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:12-14. [PMID: 32939975 DOI: 10.1111/1758-2229.12888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 09/15/2020] [Indexed: 06/11/2023]
Affiliation(s)
- Frank O Aylward
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
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70
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71
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Tourigny DS. Cooperative metabolic resource allocation in spatially-structured systems. J Math Biol 2021; 82:5. [PMID: 33479850 DOI: 10.1007/s00285-021-01558-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 06/30/2020] [Accepted: 10/27/2020] [Indexed: 10/22/2022]
Abstract
Natural selection has shaped the evolution of cells and multi-cellular organisms such that social cooperation can often be preferred over an individualistic approach to metabolic regulation. This paper extends a framework for dynamic metabolic resource allocation based on the maximum entropy principle to spatiotemporal models of metabolism with cooperation. Much like the maximum entropy principle encapsulates 'bet-hedging' behaviour displayed by organisms dealing with future uncertainty in a fluctuating environment, its cooperative extension describes how individuals adapt their metabolic resource allocation strategy to further accommodate limited knowledge about the welfare of others within a community. The resulting theory explains why local regulation of metabolic cross-feeding can fulfil a community-wide metabolic objective if individuals take into consideration an ensemble measure of total population performance as the only form of global information. The latter is likely supplied by quorum sensing in microbial systems or signalling molecules such as hormones in multi-cellular eukaryotic organisms.
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Affiliation(s)
- David S Tourigny
- Columbia University Irving Medical Center, 630 West 168th Street, New York, NY, 10032, USA.
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72
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Lee JS, Wang RX, Alexeev EE, Colgan SP. Intestinal Inflammation as a Dysbiosis of Energy Procurement: New Insights into an Old Topic. Gut Microbes 2021; 13:1-20. [PMID: 33583319 PMCID: PMC7889129 DOI: 10.1080/19490976.2021.1880241] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 01/04/2021] [Accepted: 01/11/2021] [Indexed: 02/07/2023] Open
Abstract
Inflammatory bowel disease (IBD) coincides with profound shifts in microbiota and host metabolic energy supply and demand. The gastrointestinal epithelium is anatomically positioned to provide a selective barrier between the anaerobic luminal microbiota and host lamina propria, with the microbiota and epithelium participating in an intricate energy exchange necessary for homeostasis. Maintenance and restoration of the barrier requires high energy flux and places significant demands on available substrates to generate ATP. It is recently appreciated that components of the microbiota contribute significantly to a multitude of biochemical pathways within and outside of the mucosa. Decades-old studies have appreciated that byproducts of the microbiota provide essential sources of energy to the intestinal epithelium, especially the colon. More recent work has unveiled the existence of numerous microbial-derived metabolites that support energy procurement within the mucosa. It is now appreciated that disease-associated shifts in the microbiota, termed dysbiosis, places significant demands on energy acquisition within the mucosa. Here, we review the topic of host- and microbial-derived components that influence tissue energetics in health and during disease.
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Affiliation(s)
- J. Scott Lee
- Department of Medicine and the Mucosal Inflammation Program, University of Colorado School of Medicine, Aurora, United States
| | - Ruth X. Wang
- Department of Medicine and the Mucosal Inflammation Program, University of Colorado School of Medicine, Aurora, United States
| | - Erica E. Alexeev
- Department of Medicine and the Mucosal Inflammation Program, University of Colorado School of Medicine, Aurora, United States
- Department of Gastroenterology, Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, United States
| | - Sean P. Colgan
- Department of Medicine and the Mucosal Inflammation Program, University of Colorado School of Medicine, Aurora, United States
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Arora K, Green M, Prakash S. The Microbiome and Alzheimer's Disease: Potential and Limitations of Prebiotic, Synbiotic, and Probiotic Formulations. Front Bioeng Biotechnol 2020; 8:537847. [PMID: 33384986 PMCID: PMC7771210 DOI: 10.3389/fbioe.2020.537847] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 11/17/2020] [Indexed: 12/20/2022] Open
Abstract
The Microbiome has generated significant attention for its impacts not only on gastrointestinal health, but also on signaling pathways of the enteric and central nervous system via the microbiome gut-brain axis. In light of this, microbiome modulation may be an effective therapeutic strategy for treating or mitigating many somatic and neural pathologies, including neurodegenerative disorders. Alzheimer's disease (AD) is a chronic neurodegenerative disease that interferes with cerebral function by progressively impairing memory, thinking and learning through the continuous depletion of neurons. Although its etiopathogenesis remains uncertain, recent literature endorses the hypothesis that probiotic, prebiotic and synbiotic supplementation alters AD-like symptoms and improves many of its associated disease biomarkers. Alternatively, a dysfunctional microbiota impairs the gut epithelial barrier by inducing chronic gastric inflammation, culminating in neuroinflammation and accelerating AD progression. The findings in this review suggest that probiotics, prebiotics or synbiotics have potential as novel biological prophylactics in treatment of AD, due to their anti-inflammatory and antioxidant properties, their ability to improve cognition and metabolic activity, as well as their capacity of producing essential metabolites for gut and brain barrier permeability.
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Affiliation(s)
- Karan Arora
- Biomedical Technology and Cell Therapy Research Laboratory, Department of Biomedical Engineering, Faculty of Medicine, McGill University, Montreal, QC, Canada
- Department of Bioengineering, Faculty of Engineering, McGill University, Montreal, QC, Canada
- Biena Inc., Saint-Hyacinthe, QC, Canada
| | - Miranda Green
- Biomedical Technology and Cell Therapy Research Laboratory, Department of Biomedical Engineering, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Satya Prakash
- Biomedical Technology and Cell Therapy Research Laboratory, Department of Biomedical Engineering, Faculty of Medicine, McGill University, Montreal, QC, Canada
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Figueiredo ART, Kümmerli R. Microbial Mutualism: Will You Still Need Me, Will You Still Feed Me? Curr Biol 2020; 30:R1041-R1043. [PMID: 32961158 DOI: 10.1016/j.cub.2020.07.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
How might costly cooperation evolve from scratch? A new study using cross-feeding in a bacterial system suggests that spatial proximity between partners and reciprocal fitness feedbacks between them are essential drivers of stable cooperative partnerships.
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Affiliation(s)
- Alexandre R T Figueiredo
- Department of Quantitative Biomedicine, University of Zurich, 8057 Zurich, Switzerland; Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zurich, Switzerland; University Research Priority Program on Evolution in Action, University of Zurich, 8008 Zurich, Switzerland
| | - Rolf Kümmerli
- Department of Quantitative Biomedicine, University of Zurich, 8057 Zurich, Switzerland; University Research Priority Program on Evolution in Action, University of Zurich, 8008 Zurich, Switzerland.
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Zachar I, Boza G. Endosymbiosis before eukaryotes: mitochondrial establishment in protoeukaryotes. Cell Mol Life Sci 2020; 77:3503-3523. [PMID: 32008087 PMCID: PMC7452879 DOI: 10.1007/s00018-020-03462-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 12/25/2019] [Accepted: 01/14/2020] [Indexed: 02/07/2023]
Abstract
Endosymbiosis and organellogenesis are virtually unknown among prokaryotes. The single presumed example is the endosymbiogenetic origin of mitochondria, which is hidden behind the event horizon of the last eukaryotic common ancestor. While eukaryotes are monophyletic, it is unlikely that during billions of years, there were no other prokaryote-prokaryote endosymbioses as symbiosis is extremely common among prokaryotes, e.g., in biofilms. Therefore, it is even more precarious to draw conclusions about potentially existing (or once existing) prokaryotic endosymbioses based on a single example. It is yet unknown if the bacterial endosymbiont was captured by a prokaryote or by a (proto-)eukaryote, and if the process of internalization was parasitic infection, slow engulfment, or phagocytosis. In this review, we accordingly explore multiple mechanisms and processes that could drive the evolution of unicellular microbial symbioses with a special attention to prokaryote-prokaryote interactions and to the mitochondrion, possibly the single prokaryotic endosymbiosis that turned out to be a major evolutionary transition. We investigate the ecology and evolutionary stability of inter-species microbial interactions based on dependence, physical proximity, cost-benefit budget, and the types of benefits, investments, and controls. We identify challenges that had to be conquered for the mitochondrial host to establish a stable eukaryotic lineage. Any assumption about the initial interaction of the mitochondrial ancestor and its contemporary host based solely on their modern relationship is rather perilous. As a result, we warn against assuming an initial mutually beneficial interaction based on modern mitochondria-host cooperation. This assumption is twice fallacious: (i) endosymbioses are known to evolve from exploitative interactions and (ii) cooperativity does not necessarily lead to stable mutualism. We point out that the lack of evidence so far on the evolution of endosymbiosis from mutual syntrophy supports the idea that mitochondria emerged from an exploitative (parasitic or phagotrophic) interaction rather than from syntrophy.
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Affiliation(s)
- István Zachar
- Evolutionary Systems Research Group, Institute of Evolution, Centre for Ecological Research, Klebelsberg Kunó str. 3., Tihany, 8237, Hungary.
- MTA-ELTE Theoretical Biology and Evolutionary Ecology Research Group, Department of Plant Taxonomy and Ecology, Eötvös Loránd University, Pázmány Péter sétány 1/c, Budapest, 1117, Hungary.
- Center for the Conceptual Foundations of Science, Parmenides Foundation, Kirchplatz 1, 82049, Munich, Germany.
| | - Gergely Boza
- Evolutionary Systems Research Group, Institute of Evolution, Centre for Ecological Research, Klebelsberg Kunó str. 3., Tihany, 8237, Hungary
- Evolution and Ecology Program, International Institute for Applied Systems Analysis (IIASA), Schlossplatz 1, 2361, Laxenburg, Austria
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Phenotypic Parallelism during Experimental Adaptation of a Free-Living Bacterium to the Zebrafish Gut. mBio 2020; 11:mBio.01519-20. [PMID: 32817106 PMCID: PMC7439477 DOI: 10.1128/mbio.01519-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Although animals encounter many bacterial species throughout their lives, only a subset colonize vertebrate digestive tracts, and these bacteria can profoundly influence the health and development of their animal hosts. We used experimental evolution to study a free-living bacterium as it adapts to a novel vertebrate host by serially passaging replicate populations of Shewanella oneidensis through the intestines of larval zebrafish (Danio rerio). Our results demonstrate that adaptation to the zebrafish gut is complex, with multiple evolutionary pathways capable of improving colonization, but that motility plays an important role during the onset of host association. Although animals encounter a plethora of bacterial species throughout their lives, only a subset colonize vertebrate digestive tracts, and these bacteria can profoundly influence the health and development of their animal hosts. However, our understanding of how bacteria initiate symbioses with animal hosts remains underexplored, and this process is central to the assembly and function of gut bacterial communities. Therefore, we used experimental evolution to study a free-living bacterium as it adapts to a novel vertebrate host by serially passaging replicate populations of Shewanella oneidensis through the intestines of larval zebrafish (Danio rerio). After approximately 200 bacterial generations, isolates from evolved populations improved their ability to colonize larval zebrafish during competition against their unpassaged ancestor. Genome sequencing revealed unique sets of mutations in the two evolved isolates exhibiting the highest mean competitive fitness. One isolate exhibited increased swimming motility and decreased biofilm formation compared to the ancestor, and we identified a missense mutation in the mannose-sensitive hemagglutinin pilus operon that is sufficient to increase fitness and reproduce these phenotypes. The second isolate exhibited enhanced swimming motility but unchanged biofilm formation, and here the genetic basis for adaptation is less clear. These parallel enhancements in motility and fitness resemble the behavior of a closely related Shewanella strain previously isolated from larval zebrafish and suggest phenotypic convergence with this isolate. Our results demonstrate that adaptation to the zebrafish gut is complex, with multiple evolutionary pathways capable of improving colonization, but that motility plays an important role during the onset of host association.
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Gubelit YI, Grossart HP. New Methods, New Concepts: What Can Be Applied to Freshwater Periphyton? Front Microbiol 2020; 11:1275. [PMID: 32670226 PMCID: PMC7328189 DOI: 10.3389/fmicb.2020.01275] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 05/19/2020] [Indexed: 12/24/2022] Open
Abstract
Microbial interactions play an essential role in aquatic ecosystems and are of the great interest for both marine and freshwater ecologists. Recent development of new technologies and methods allowed to reveal many functional mechanisms and create new concepts. Yet, many fundamental aspects of microbial interactions have been almost exclusively studied for marine pelagic and benthic ecosystems. These studies resulted in a formulation of the Black Queen Hypothesis, a development of the phycosphere concept for pelagic communities, and a realization of microbial communication as a key mechanism for microbial interactions. In freshwater ecosystems, especially for periphyton communities, studies focus mainly on physiology, biodiversity, biological indication, and assessment, but the many aspects of microbial interactions are neglected to a large extent. Since periphyton plays a great role for aquatic nutrient cycling, provides the basis for water purification, and can be regarded as a hotspot of microbial biodiversity, we highlight that more in-depth studies on microbial interactions in periphyton are needed to improve our understanding on functioning of freshwater ecosystems. In this paper we first present an overview on recent concepts (e.g., the "Black Queen Hypothesis") derived from state-of-the-art OMICS methods including metagenomics, metatranscriptomics, and metabolomics. We then point to the avenues how these methods can be applied for future studies on biodiversity and the ecological role of freshwater periphyton, a yet largely neglected component of many freshwater ecosystems.
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Affiliation(s)
- Yulia I. Gubelit
- Laboratory of Freshwater Hydrobiology, Zoological Institute, Russian Academy of Science, Saint Petersburg, Russia
| | - Hans-Peter Grossart
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Department of Experimental Limnology, Leibniz-Institute for Freshwater Ecology and Inland Fisheries, Stechlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
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78
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Pacheco AR, Segrè D. A multidimensional perspective on microbial interactions. FEMS Microbiol Lett 2020; 366:5513995. [PMID: 31187139 PMCID: PMC6610204 DOI: 10.1093/femsle/fnz125] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 06/10/2019] [Indexed: 12/16/2022] Open
Abstract
Beyond being simply positive or negative, beneficial or inhibitory, microbial interactions can involve a diverse set of mechanisms, dependencies and dynamical properties. These more nuanced features have been described in great detail for some specific types of interactions, (e.g. pairwise metabolic cross-feeding, quorum sensing or antibiotic killing), often with the use of quantitative measurements and insight derived from modeling. With a growing understanding of the composition and dynamics of complex microbial communities for human health and other applications, we face the challenge of integrating information about these different interactions into comprehensive quantitative frameworks. Here, we review the literature on a wide set of microbial interactions, and explore the potential value of a formal categorization based on multidimensional vectors of attributes. We propose that such an encoding can facilitate systematic, direct comparisons of interaction mechanisms and dependencies, and we discuss the relevance of an atlas of interactions for future modeling and rational design efforts.
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Affiliation(s)
- Alan R Pacheco
- Graduate Program in Bioinformatics and Biological Design Center, Boston University, 24 Cummington Mall, Boston, MA, 02215, USA
| | - Daniel Segrè
- Graduate Program in Bioinformatics and Biological Design Center, Boston University, 24 Cummington Mall, Boston, MA, 02215, USA.,Department of Biomedical Engineering, Department of Biology and Department of Physics, Boston University, 24 Cummington Mall, Boston, MA, 02215, USA
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79
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Co-Culture with Bifidobacterium catenulatum Improves the Growth, Gut Colonization, and Butyrate Production of Faecalibacterium prausnitzii: In Vitro and In Vivo Studies. Microorganisms 2020; 8:microorganisms8050788. [PMID: 32466189 PMCID: PMC7285360 DOI: 10.3390/microorganisms8050788] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 05/22/2020] [Accepted: 05/23/2020] [Indexed: 12/19/2022] Open
Abstract
Faecalibacterium prausnitzii is a major commensal bacterium in the human gut. It produces short-chain fatty acids that promote intestinal health. However, the bacterium is extremely oxygen-sensitive, making it difficult to develop as a probiotic. To facilitate practical application of F. prausnitzii, we investigated factors that affect its growth and mammalian gut colonization. We evaluated cross-feeding interactions between F. prausnitzii and seven Bifidobacterium strains, and the anti-inflammatory properties of bacterial metabolites produced in co-culture, in vitro and in vivo. Co-culture of F. prausnitzii and Bifidobacterium catenulatum, with fructooligosaccharides as an energy source, resulted in the greatest viable cell-count and butyrate production increases. Further, the co-culture supernatant reduced the amount of proinflammatory cytokines produced by HT-29 cells and RAW 264.7 macrophages, an effect that was similar to that of butyrate. Furthermore, feeding mice both Faecalibacterium and Bifidobacterium enhanced F. prausnitzii gut colonization. Finally, feeding the co-culture supernatant decreased interleukin 8 levels in the colon and increased butyrate levels in the cecum in the dextran sodium sulfate-induced colitis mouse model. These observations indicate that the Faecalibacterium-Bifidobacterium co-culture exerts an anti-inflammatory effect by promoting F. prausnitzii survival and short-chain fatty acid production, with possible implications for the treatment of inflammatory bowel disease.
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80
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Cheng CC, Duar RM, Lin X, Perez-Munoz ME, Tollenaar S, Oh JH, van Pijkeren JP, Li F, van Sinderen D, Gänzle MG, Walter J. Ecological Importance of Cross-Feeding of the Intermediate Metabolite 1,2-Propanediol between Bacterial Gut Symbionts. Appl Environ Microbiol 2020; 86:e00190-20. [PMID: 32276972 PMCID: PMC7237793 DOI: 10.1128/aem.00190-20] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 03/27/2020] [Indexed: 12/20/2022] Open
Abstract
Cross-feeding based on the metabolite 1,2-propanediol has been proposed to have an important role in the establishment of trophic interactions among gut symbionts, but its ecological importance has not been empirically established. Here, we show that in vitro growth of Lactobacillus reuteri (syn. Limosilactobacillus reuteri) ATCC PTA 6475 is enhanced through 1,2-propanediol produced by Bifidobacterium breve UCC2003 and Escherichia coli MG1655 from the metabolization of fucose and rhamnose, respectively. Work with isogenic mutants showed that the trophic interaction is dependent on the pduCDE operon in L. reuteri, which encodes the ability to use 1,2-propanediol, and the l-fucose permease (fucP) gene in B. breve, which is required for 1,2-propanediol formation from fucose. Experiments in gnotobiotic mice revealed that, although the pduCDE operon bestows a fitness burden on L. reuteri ATCC PTA 6475 in the mouse digestive tract, the ecological performance of the strain was enhanced in the presence of B. breve UCC2003 and the mucus-degrading species Bifidobacterium bifidum The use of the respective pduCDE and fucP mutants of L. reuteri and B. breve in the mouse experiments indicated that the trophic interaction was specifically based on 1,2-propanediol. Overall, our work established the ecological importance of cross-feeding relationships based on 1,2-propanediol for the fitness of a bacterial symbiont in the vertebrate gut.IMPORTANCE Through experiments in gnotobiotic mice that employed isogenic mutants of bacterial strains that produce (Bifidobacterium breve) and utilize (Lactobacillus reuteri) 1,2-propanediol, this study provides mechanistic insight into the ecological ramifications of a trophic interaction between gut symbionts. The findings improve our understanding on how cross-feeding influences the competitive fitness of L. reuteri in the vertebrate gut and revealed a putative selective force that shaped the evolution of the species. The findings are relevant since they provide a basis to design rational microbial-based strategies to modulate gut ecosystems, which could employ mixtures of bacterial strains that establish trophic interactions or a personalized approach based on the ability of a resident microbiota to provide resources for the incoming microbe.
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Affiliation(s)
| | - Rebbeca M Duar
- Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Canada
- Evolve BioSystems, Inc., Davis, California, USA
| | - Xiaoxi Lin
- Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Canada
| | - Maria Elisa Perez-Munoz
- Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Canada
| | - Stephanie Tollenaar
- Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Canada
| | - Jee-Hwan Oh
- Department of Food Science, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | | | - Fuyong Li
- Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Canada
| | - Douwe van Sinderen
- School of Microbiology and APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Michael G Gänzle
- Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Canada
| | - Jens Walter
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
- Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Canada
- Department of Food Science, University of Wisconsin-Madison, Madison, Wisconsin, USA
- School of Microbiology and APC Microbiome Institute, University College Cork, Cork, Ireland
- Department of Medicine, University College Cork, Cork, Ireland
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81
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Mutualistic cross-feeding in microbial systems generates bistability via an Allee effect. Sci Rep 2020; 10:7763. [PMID: 32385386 PMCID: PMC7210978 DOI: 10.1038/s41598-020-63772-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 04/03/2020] [Indexed: 11/16/2022] Open
Abstract
In microbial ecosystems, species not only compete for common resources but may also display mutualistic interactions as a result from metabolic cross-feeding. Such mutualism can lead to bistability. Depending on the initial population sizes, species will either survive or go extinct. Various phenomenological models have been suggested to describe bistability in mutualistic systems. However, these models do not account for interaction mediators such as nutrients. In contrast, nutrient-explicit models do not provide an intuitive understanding of what causes bistability. Here, we reduce a theoretical nutrient-explicit model of two mutualistic cross-feeders in a chemostat, uncovering an explicit relation to a growth model with an Allee effect. We show that the dilution rate in the chemostat leads to bistability by turning a weak Allee effect into a strong Allee effect. This happens as long as there is more production than consumption of cross-fed nutrients. Thanks to the explicit relationship of the reduced model with the underlying experimental parameters, these results allow to predict the biological conditions that sustain or prevent the survival of mutualistic species.
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82
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Metabolic Heterogeneity and Cross-Feeding in Bacterial Multicellular Systems. Trends Microbiol 2020; 28:732-743. [PMID: 32781027 DOI: 10.1016/j.tim.2020.03.008] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 03/25/2020] [Indexed: 01/19/2023]
Abstract
Cells in assemblages differentiate and perform distinct roles. Though many pathways of differentiation are understood at the molecular level in multicellular eukaryotes, the elucidation of similar processes in bacterial assemblages is recent and ongoing. Here, we discuss examples of bacterial differentiation, focusing on cases in which distinct metabolisms coexist and those that exhibit cross-feeding, with one subpopulation producing substrates that are metabolized by a second subpopulation. We describe several studies of single-species systems, then segue to studies of multispecies metabolic heterogeneity and cross-feeding in the clinical setting. Many of the studies described exemplify the application of new techniques and modeling approaches that provide insights into metabolic interactions relevant for bacterial growth outside the laboratory.
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83
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Payling L, Fraser K, Loveday S, Sims I, Roy N, McNabb W. The effects of carbohydrate structure on the composition and functionality of the human gut microbiota. Trends Food Sci Technol 2020. [DOI: 10.1016/j.tifs.2020.01.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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84
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Neff AS. Technical and Theoretic Limitations of the Experimental Evidence Supporting a Gut Bacterial Etiology in Mental Illness. Clin Ther 2020; 42:e74-e81. [PMID: 32115244 DOI: 10.1016/j.clinthera.2020.02.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 02/03/2020] [Accepted: 02/04/2020] [Indexed: 02/06/2023]
Abstract
The impact of gut bacteria on the brain and behavior has become the subject of intense research. The brain is sensitive to biochemical and physiologic changes in the body, for example, changes in blood oxygenation or nutritional status. The collection of microorganisms residing within the digestive tract (the gut microbiome) is increasingly considered a major contributor to human physiology. These 2 considerations have led to the hypothesis that human psychology, including complex constructs like emotion and mental illness, could be influenced by the composition or function of gut bacteria. Five lines of evidence have been used to support the concept, including human correlational research, probiotic supplementation, antibiotic use, germ-free animal research, and fecal transplantation. Results from these experiments do not provide substantial support for the theory that complex human psychology is under the influence of gut bacteria. Placebo-controlled interventional research in humans, in particular fecal microbiota transplantation, will be required before a stronger conclusion can be reached.
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Affiliation(s)
- Andrew Steven Neff
- Department of Psychiatry and Behavioral Neurosciences, Wayne State University School of Medicine, Detroit, MI, USA; Department of Psychology and Behavioral Sciences, Rochester University, Rochester Hills, MI, USA.
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85
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Lawson MAE, O'Neill IJ, Kujawska M, Gowrinadh Javvadi S, Wijeyesekera A, Flegg Z, Chalklen L, Hall LJ. Breast milk-derived human milk oligosaccharides promote Bifidobacterium interactions within a single ecosystem. THE ISME JOURNAL 2020; 14:635-648. [PMID: 31740752 PMCID: PMC6976680 DOI: 10.1038/s41396-019-0553-2] [Citation(s) in RCA: 205] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 10/28/2019] [Accepted: 11/01/2019] [Indexed: 12/12/2022]
Abstract
Diet-microbe interactions play an important role in modulating the early-life microbiota, with Bifidobacterium strains and species dominating the gut of breast-fed infants. Here, we sought to explore how infant diet drives distinct bifidobacterial community composition and dynamics within individual infant ecosystems. Genomic characterisation of 19 strains isolated from breast-fed infants revealed a diverse genomic architecture enriched in carbohydrate metabolism genes, which was distinct to each strain, but collectively formed a pangenome across infants. Presence of gene clusters implicated in digestion of human milk oligosaccharides (HMOs) varied between species, with growth studies indicating that within single infants there were differences in the ability to utilise 2'FL and LNnT HMOs between strains. Cross-feeding experiments were performed with HMO degraders and non-HMO users (using spent or 'conditioned' media and direct co-culture). Further 1H-NMR analysis identified fucose, galactose, acetate, and N-acetylglucosamine as key by-products of HMO metabolism; as demonstrated by modest growth of non-HMO users on spend media from HMO metabolism. These experiments indicate how HMO metabolism permits the sharing of resources to maximise nutrient consumption from the diet and highlights the cooperative nature of bifidobacterial strains and their role as 'foundation' species in the infant ecosystem. The intra- and inter-infant bifidobacterial community behaviour may contribute to the diversity and dominance of Bifidobacterium in early life and suggests avenues for future development of new diet and microbiota-based therapies to promote infant health.
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Affiliation(s)
- Melissa A E Lawson
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- Lydia Becker Institute for Immunology and Inflammation & Wellcome Trust Centre for Cell Matrix Research, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Ian J O'Neill
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- APC Microbiome Ireland, University College Cork, Biosciences Building, Cork, Ireland
| | - Magdalena Kujawska
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | | | - Anisha Wijeyesekera
- Department of Food & Nutritional Sciences, University of Reading, Reading, UK
| | - Zak Flegg
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Lisa Chalklen
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Lindsay J Hall
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK.
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86
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Developing a Microbial Consortium for Enhanced Metabolite Production from Simulated Food Waste. FERMENTATION-BASEL 2019. [DOI: 10.3390/fermentation5040098] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Food waste disposal and transportation of commodity chemicals to the point-of-need are substantial challenges in military environments. Here, we propose addressing these challenges via the design of a microbial consortium for the fermentation of food waste to hydrogen. First, we simulated the exchange metabolic fluxes of monocultures and pairwise co-cultures using genome-scale metabolic models on a food waste proxy. We identified that one of the top hydrogen producing co-cultures comprised Clostridium beijerinckii NCIMB 8052 and Yokenella regensburgei ATCC 43003. A consortium of these two strains produced a similar amount of hydrogen gas and increased butyrate compared to the C. beijerinckii monoculture, when grown on an artificial garbage slurry. Increased butyrate production in the consortium can be attributed to cross-feeding of lactate produced by Y. regensburgei. Moreover, exogenous lactate promotes the growth of C. beijerinckii with or without a limited amount of glucose. Increasing the scale of the consortium fermentation proved challenging, as two distinct attempts to scale-up the enhanced butyrate production resulted in different metabolic profiles than observed in smaller scale fermentations. Though the genome-scale metabolic model simulations provided a useful starting point for the design of microbial consortia to generate value-added products from waste materials, further model refinements based on experimental results are required for more robust predictions.
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