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Little AS, Younker IT, Schechter MS, Bernardino PN, Méheust R, Stemczynski J, Scorza K, Mullowney MW, Sharan D, Waligurski E, Smith R, Ramanswamy R, Leiter W, Moran D, McMillin M, Odenwald MA, Iavarone AT, Sidebottom AM, Sundararajan A, Pamer EG, Eren AM, Light SH. Dietary- and host-derived metabolites are used by diverse gut bacteria for anaerobic respiration. Nat Microbiol 2024; 9:55-69. [PMID: 38177297 PMCID: PMC11055453 DOI: 10.1038/s41564-023-01560-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 11/14/2023] [Indexed: 01/06/2024]
Abstract
Respiratory reductases enable microorganisms to use molecules present in anaerobic ecosystems as energy-generating respiratory electron acceptors. Here we identify three taxonomically distinct families of human gut bacteria (Burkholderiaceae, Eggerthellaceae and Erysipelotrichaceae) that encode large arsenals of tens to hundreds of respiratory-like reductases per genome. Screening species from each family (Sutterella wadsworthensis, Eggerthella lenta and Holdemania filiformis), we discover 22 metabolites used as respiratory electron acceptors in a species-specific manner. Identified reactions transform multiple classes of dietary- and host-derived metabolites, including bioactive molecules resveratrol and itaconate. Products of identified respiratory metabolisms highlight poorly characterized compounds, such as the itaconate-derived 2-methylsuccinate. Reductase substrate profiling defines enzyme-substrate pairs and reveals a complex picture of reductase evolution, providing evidence that reductases with specificities for related cinnamate substrates independently emerged at least four times. These studies thus establish an exceptionally versatile form of anaerobic respiration that directly links microbial energy metabolism to the gut metabolome.
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Affiliation(s)
- Alexander S Little
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Isaac T Younker
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Matthew S Schechter
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Paola Nol Bernardino
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Raphaël Méheust
- Génomique Métabolique, CEA, Genoscope, Institut François Jacob, Université d'Évry, Université Paris-Saclay, CNRS, Evry, France
| | - Joshua Stemczynski
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Kaylie Scorza
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | | | - Deepti Sharan
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Emily Waligurski
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Rita Smith
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | | | - William Leiter
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - David Moran
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Mary McMillin
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Matthew A Odenwald
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Section of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Anthony T Iavarone
- QB3/Chemistry Mass Spectrometry Facility, University of California, Berkeley, Berkeley, CA, USA
| | | | | | - Eric G Pamer
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
- Section of Infectious Diseases & Global Health, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - A Murat Eren
- Helmholtz Institute for Functional Marine Biodiversity, Oldenburg, Germany
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenbug, Germany
| | - Samuel H Light
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA.
- Department of Microbiology, University of Chicago, Chicago, IL, USA.
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2
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Bonmatí-Carrión MÁ, Rol MA. Melatonin as a Mediator of the Gut Microbiota-Host Interaction: Implications for Health and Disease. Antioxidants (Basel) 2023; 13:34. [PMID: 38247459 PMCID: PMC10812647 DOI: 10.3390/antiox13010034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 01/23/2024] Open
Abstract
In recent years, the role played by melatonin on the gut microbiota has gained increasingly greater attention. Additionally, the gut microbiota has been proposed as an alternative source of melatonin, suggesting that this antioxidant indoleamine could act as a sort of messenger between the gut microbiota and the host. This review analyses the available scientific literature about possible mechanisms involved in this mediating role, highlighting its antioxidant effects and influence on this interaction. In addition, we also review the available knowledge on the effects of melatonin on gut microbiota composition, as well as its ability to alleviate dysbiosis related to sleep deprivation or chronodisruptive conditions. The melatonin-gut microbiota relationship has also been discussed in terms of its role in the development of different disorders, from inflammatory or metabolic disorders to psychiatric and neurological conditions, also considering oxidative stress and the reactive oxygen species-scavenging properties of melatonin as the main factors mediating this relationship.
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Affiliation(s)
- María-Ángeles Bonmatí-Carrión
- Chronobiology Laboratory, Department of Physiology, College of Biology, Mare Nostrum Campus, University of Murcia, Instituto Universitario de Investigación en Envejecimiento, Instituto Murciano de Investigación Biosanitaria-Arrixaca, 30100 Murcia, Spain;
- Ciber Fragilidad y Envejecimiento Saludable (CIBERFES), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Maria-Angeles Rol
- Chronobiology Laboratory, Department of Physiology, College of Biology, Mare Nostrum Campus, University of Murcia, Instituto Universitario de Investigación en Envejecimiento, Instituto Murciano de Investigación Biosanitaria-Arrixaca, 30100 Murcia, Spain;
- Ciber Fragilidad y Envejecimiento Saludable (CIBERFES), Instituto de Salud Carlos III, 28029 Madrid, Spain
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3
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Heinken A, Hertel J, Acharya G, Ravcheev DA, Nyga M, Okpala OE, Hogan M, Magnúsdóttir S, Martinelli F, Nap B, Preciat G, Edirisinghe JN, Henry CS, Fleming RMT, Thiele I. Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine. Nat Biotechnol 2023; 41:1320-1331. [PMID: 36658342 PMCID: PMC10497413 DOI: 10.1038/s41587-022-01628-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 11/30/2022] [Indexed: 01/21/2023]
Abstract
The human microbiome influences the efficacy and safety of a wide variety of commonly prescribed drugs. Designing precision medicine approaches that incorporate microbial metabolism would require strain- and molecule-resolved, scalable computational modeling. Here, we extend our previous resource of genome-scale metabolic reconstructions of human gut microorganisms with a greatly expanded version. AGORA2 (assembly of gut organisms through reconstruction and analysis, version 2) accounts for 7,302 strains, includes strain-resolved drug degradation and biotransformation capabilities for 98 drugs, and was extensively curated based on comparative genomics and literature searches. The microbial reconstructions performed very well against three independently assembled experimental datasets with an accuracy of 0.72 to 0.84, surpassing other reconstruction resources and predicted known microbial drug transformations with an accuracy of 0.81. We demonstrate that AGORA2 enables personalized, strain-resolved modeling by predicting the drug conversion potential of the gut microbiomes from 616 patients with colorectal cancer and controls, which greatly varied between individuals and correlated with age, sex, body mass index and disease stages. AGORA2 serves as a knowledge base for the human microbiome and paves the way to personalized, predictive analysis of host-microbiome metabolic interactions.
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Affiliation(s)
- Almut Heinken
- School of Medicine, University of Galway, Galway, Ireland
- Ryan Institute, University of Galway, Galway, Ireland
- INSERM UMRS 1256, Nutrition, Genetics, and Environmental Risk Exposure (NGERE), University of Lorraine, Nancy, France
| | - Johannes Hertel
- School of Medicine, University of Galway, Galway, Ireland
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
| | - Geeta Acharya
- Integrated BioBank of Luxembourg, Dudelange, Luxembourg
| | - Dmitry A Ravcheev
- School of Medicine, University of Galway, Galway, Ireland
- Ryan Institute, University of Galway, Galway, Ireland
| | | | | | - Marcus Hogan
- School of Medicine, University of Galway, Galway, Ireland
- Ryan Institute, University of Galway, Galway, Ireland
| | - Stefanía Magnúsdóttir
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Filippo Martinelli
- School of Medicine, University of Galway, Galway, Ireland
- Ryan Institute, University of Galway, Galway, Ireland
| | - Bram Nap
- School of Medicine, University of Galway, Galway, Ireland
- Ryan Institute, University of Galway, Galway, Ireland
| | - German Preciat
- Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - Janaka N Edirisinghe
- Computation Institute, University of Chicago, Chicago, IL, USA
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, USA
| | - Christopher S Henry
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, USA
| | - Ronan M T Fleming
- School of Medicine, University of Galway, Galway, Ireland
- Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - Ines Thiele
- School of Medicine, University of Galway, Galway, Ireland.
- Ryan Institute, University of Galway, Galway, Ireland.
- Division of Microbiology, University of Galway, Galway, Ireland.
- APC Microbiome Ireland, Cork, Ireland.
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4
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Colella M, Charitos IA, Ballini A, Cafiero C, Topi S, Palmirotta R, Santacroce L. Microbiota revolution: How gut microbes regulate our lives. World J Gastroenterol 2023; 29:4368-4383. [PMID: 37576701 PMCID: PMC10415973 DOI: 10.3748/wjg.v29.i28.4368] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/16/2023] [Accepted: 07/10/2023] [Indexed: 07/26/2023] Open
Abstract
The human intestine is a natural environment ecosystem of a complex of diversified and dynamic microorganisms, determined through a process of competition and natural selection during life. Those intestinal microorganisms called microbiota and are involved in a variety of mechanisms of the organism, they interact with the host and therefore are in contact with the organs of the various systems. However, they play a crucial role in maintaining host homeostasis, also influencing its behaviour. Thus, microorganisms perform a series of biological functions important for human well-being. The host provides the microorganisms with the environment and nutrients, simultaneously drawing many benefits such as their contribution to metabolic, trophic, immunological, and other functions. For these reasons it has been reported that its quantitative and qualitative composition can play a protective or harmful role on the host health. Therefore, a dysbiosis can lead to an association of unfavourable factors which lead to a dysregulation of the physiological processes of homeostasis. Thus, it has pre-viously noted that the gut microbiota can participate in the pathogenesis of autoimmune diseases, chronic intestinal inflammation, diabetes mellitus, obesity and atherosclerosis, neurological disorders (e.g., neurological diseases, autism, etc.) colorectal cancer, and more.
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Affiliation(s)
- Marica Colella
- Interdisciplinary Department of Medicine, Section of Microbiology and Virology, University of Bari “Aldo Moro”, Bari 70124, Italy
| | - Ioannis Alexandros Charitos
- Maugeri Clinical Scientific Research Institutes (IRCCS) of Pavia - Division of Pneumology and Respiratory Rehabilitation, Scientific Institute of Bari, Bari 70124, Italy
| | - Andrea Ballini
- Department of Clinical and Experimental Medicine, University of Foggia, Foggia 71122, Italy
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Naples 80138, Italy
| | - Concetta Cafiero
- Area of Molecular Pathology, Anatomic Pathology Unit, Fabrizio Spaziani Hospital, Frosinone 03100, Italy
| | - Skender Topi
- Department of Clinical Disciplines, School of Technical Medical Sciences, University of Elbasan “A. Xhuvani”, Elbasan 3001, Albania
| | - Raffaele Palmirotta
- Interdisciplinary Department of Medicine, Section of Microbiology and Virology, University of Bari “Aldo Moro”, Bari 70124, Italy
| | - Luigi Santacroce
- Interdisciplinary Department of Medicine, Section of Microbiology and Virology, University of Bari “Aldo Moro”, Bari 70124, Italy
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5
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Comolli J, Walsh DI, Bobrow J, Lennartz CL, Guido NJ, Thorsen T. An in vitro platform for study of the human gut microbiome under an oxygen gradient. Biomed Microdevices 2023; 25:14. [PMID: 37014472 PMCID: PMC10073063 DOI: 10.1007/s10544-023-00653-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/05/2023] [Indexed: 04/05/2023]
Abstract
The complex, dynamic environment of the human lower gastrointestinal tract is colonized by hundreds of bacterial species that impact health and performance. Ex vivo study of the functional interactions between microbial community members in conditions representative of those in the gut is an ongoing challenge. We have developed an in vitro 40-plex platform that provides an oxygen gradient to support simultaneous maintenance of microaerobic and anaerobic microbes from the gut microbiome that can aid in rapid characterization of microbial interactions and direct comparison of individual microbiome samples. In this report, we demonstrate that the platform more closely maintained the microbial diversity and composition of human donor fecal microbiome samples than strict anaerobic conditions. The oxygen gradient established in the platform allowed the stratification and subsequent sampling of diverse microbial subpopulations that colonize microaerobic and anaerobic micro-environments. With the ability to run forty samples in parallel, the platform has the potential to be used as a rapid screening tool to understand how the gut microbiome responds to environmental perturbations such as toxic compound exposure, dietary changes, or pharmaceutical treatments.
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Affiliation(s)
- James Comolli
- Biological & Chemical Technologies Group, MIT Lincoln Laboratory, Lexington, MA, USA
| | - David I Walsh
- Biological & Chemical Technologies Group, MIT Lincoln Laboratory, Lexington, MA, USA
| | - Johanna Bobrow
- Biological & Chemical Technologies Group, MIT Lincoln Laboratory, Lexington, MA, USA
| | - Chelsea L Lennartz
- Biological & Chemical Technologies Group, MIT Lincoln Laboratory, Lexington, MA, USA
| | - Nicholas J Guido
- Biological & Chemical Technologies Group, MIT Lincoln Laboratory, Lexington, MA, USA
| | - Todd Thorsen
- Biological & Chemical Technologies Group, MIT Lincoln Laboratory, Lexington, MA, USA.
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6
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Rudolph SE, Longo BN, Tse MW, Houchin MR, Shokoufandeh MM, Chen Y, Kaplan DL. Crypt-Villus Scaffold Architecture for Bioengineering Functional Human Intestinal Epithelium. ACS Biomater Sci Eng 2022; 8:4942-4955. [PMID: 36191009 PMCID: PMC10379436 DOI: 10.1021/acsbiomaterials.2c00851] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Crypt-villus architecture in the small intestine is crucial for the structural integrity of the intestinal epithelium and maintenance of gut homeostasis. We utilized three-dimensional (3D) printing and inverse molding techniques to form three-dimensional (3D) spongy scaffold systems that resemble the intestinal crypt-villus microarchitecture. The scaffolds consist of silk fibroin protein with curved lumens with rows of protruding villi with invaginating crypts to generate the architecture. Intestinal cell (Caco-2, HT29-MTX) attachment and growth, as well as long-term culture support were demonstrated with cell polarization and tissue barrier properties compared to two-dimensional (2D) Transwell culture controls. Further, physiologically relevant oxygen gradients were generated in the 3D system. The various advantages of this system may be ascribed to the more physiologically relevant 3D environment, offering a system for the exploration of disease pathogenesis, host-microbiome interactions, and therapeutic discovery.
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Affiliation(s)
- Sara E Rudolph
- Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, Massachusetts 02155, United States
| | - Brooke N Longo
- Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, Massachusetts 02155, United States
| | - Megan W Tse
- Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, Massachusetts 02155, United States
| | - Megan R Houchin
- Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, Massachusetts 02155, United States
| | - Mina M Shokoufandeh
- Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, Massachusetts 02155, United States
| | - Ying Chen
- Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, Massachusetts 02155, United States
| | - David L Kaplan
- Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, Massachusetts 02155, United States
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7
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Thorgersen MP, Schut GJ, Poole FL, Haja DK, Putumbaka S, Mycroft HI, de Vries WJ, Adams MWW. Obligately aerobic human gut microbe expresses an oxygen resistant tungsten-containing oxidoreductase for detoxifying gut aldehydes. Front Microbiol 2022; 13:965625. [PMID: 36051760 PMCID: PMC9424855 DOI: 10.3389/fmicb.2022.965625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 07/26/2022] [Indexed: 11/13/2022] Open
Abstract
Brevibacillus massiliensis strain phR is an obligately aerobic microbe that was isolated from human feces. Here, we show that it readily takes up tungsten (W), a metal previously associated only with anaerobes. The W is incorporated into an oxidoreductase enzyme (BmWOR) that was purified from native biomass. BmWOR consists of a single 65 kDa subunit and contains a single W-pyranopterin cofactor and a single [4Fe-4S] cluster. It exhibited high aldehyde-oxidizing activity with very high affinities (apparent Km < 6 μM) for aldehydes common in the human gut and in cooked foods, including furfural, propionaldehyde, benzaldehyde and tolualdehyde, suggesting that BmWOR plays a key role in their detoxification. B. massiliensis converted added furfural to furoic acid when grown in the presence of W, but not in the presence of the analogous element molybdenum. B. massiliensis ferredoxin (BmFd) served as the electron acceptor (apparent Km < 5 μM) for BmWOR suggesting it is the physiological electron carrier. Genome analysis revealed a Fd-dependent rather than NADH-dependent Complex I, suggesting that WOR not only serves a detoxification role but its aldehyde substrates could also serve as a source of energy. BmWOR is the first tungstoenzyme and the first member of the WOR family to be obtained from a strictly aerobic microorganism. Remarkably, BmWOR oxidized furfural in the presence of air (21% O2, v/v) but only if BmFd was also present. BmWOR is the first characterized member of the Clade 83 WORs, which are predominantly found in extremely halophilic and aerobic archaea (Clade 83A), with many isolated from food sources, while the remaining bacterial members (Clade 83B) include both aerobes and anaerobes. The potential advantages for microbes found in foods and involved in human gut health that harbor O2-resistant WORs, including in Bacillus and Brevibacillus based-probiotics, are discussed.
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8
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Chen Y, Rudolph S, Longo BN, Pace F, Roh T, Condruti R, Gee M, Watnick P, Kaplan DL. Bioengineered 3D Tissue Model of Intestine Epithelium with Oxygen Gradients to Sustain Human Gut Microbiome. Adv Healthc Mater 2022; 11:e2200447. [PMID: 35686484 PMCID: PMC9388577 DOI: 10.1002/adhm.202200447] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 05/25/2022] [Indexed: 01/24/2023]
Abstract
The human gut microbiome is crucial to hosting physiology and health. Therefore, stable in vitro coculture of primary human intestinal cells with a microbiome community is essential for understanding intestinal disease progression and revealing novel therapeutic targets. Here, a three-dimensional scaffold system is presented to regenerate an in vitro human intestinal epithelium that recapitulates many functional characteristics of the native small intestines. The epithelium, derived from human intestinal enteroids, contains mature intestinal epithelial cells and possesses selectively permeable barrier functions. Importantly, by properly positioning the scaffolds cultured under normal atmospheric conditions, two physiologically relevant oxygen gradients, a proximal-to-distal oxygen gradient along the gastrointestinal (GI) tract, and a radial oxygen gradient across the epithelium, are distinguished in the tissues when the lumens are faced up and down in cultures, respectively. Furthermore, the presence of the low oxygen gradients supported the coculture of intestinal epithelium along with a complex living commensal gut microbiome (including obligate anaerobes) to simulate temporal microbiome dynamics in the native human gut. This unique silk scaffold platform may enable the exploration of microbiota-related mechanisms of disease pathogenesis and host-pathogen dynamics in infectious diseases including the potential to explore the human microbiome-gut-brain axis and potential novel microbiome-based therapeutics.
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Affiliation(s)
- Ying Chen
- Department of Biomedical Engineering, Tufts University, 4 Colby St, Medford, MA, 02155, USA,To whom correspondence may be addressed. ;
| | - Sara Rudolph
- Department of Biomedical Engineering, Tufts University, 4 Colby St, Medford, MA, 02155, USA
| | - Brooke N. Longo
- Department of Biomedical Engineering, Tufts University, 4 Colby St, Medford, MA, 02155, USA
| | - Fernanda Pace
- Division of Infectious Diseases, Boston Children’s Hospital, 300 Longwood Avenue, Boston, MA 02115, USA,Department of Pediatrics, Harvard Medical School, 25 Shattuck St, Boston, MA 02115, USA
| | - Terrence Roh
- Department of Biomedical Engineering, Tufts University, 4 Colby St, Medford, MA, 02155, USA
| | - Rebecca Condruti
- Department of Biomedical Engineering, Tufts University, 4 Colby St, Medford, MA, 02155, USA
| | - Michelle Gee
- Department of Biomedical Engineering, Tufts University, 4 Colby St, Medford, MA, 02155, USA
| | - Paula Watnick
- Division of Infectious Diseases, Boston Children’s Hospital, 300 Longwood Avenue, Boston, MA 02115, USA,Department of Pediatrics, Harvard Medical School, 25 Shattuck St, Boston, MA 02115, USA
| | - David L. Kaplan
- Department of Biomedical Engineering, Tufts University, 4 Colby St, Medford, MA, 02155, USA,Division of Infectious Diseases, Boston Children’s Hospital, 300 Longwood Avenue, Boston, MA 02115, USA,To whom correspondence may be addressed. ;
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9
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Panigrahi MK, Kaliaperumal V, Akella A, Venugopal G, Ramadass B. Mapping microbiome-redox spectrum and evaluating Microbial-Redox Index in chronic gastritis. Sci Rep 2022; 12:8450. [PMID: 35589904 PMCID: PMC9120160 DOI: 10.1038/s41598-022-12431-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 05/11/2022] [Indexed: 12/27/2022] Open
Abstract
Peptic ulcer disease (PUD) and chronic gastritis are prevalent in developing countries. The role of oxidative stress in the pathogenesis of gastrointestinal mucosal disorders is well recognized. In PUD, the gastric mucosa and its associated microbiome are subject to diet and stress-induced oxidative perturbations. Tissue redox potential (ORP) measurement can quantify oxidative stress, reflecting the balance between prooxidants and antioxidants. This study hypothesizes that the oxidative stress quantified by tissue ORP will be associated with characteristic changes in the mucosa-associated microbiome in PUD and gastritis. In addition, we propose using relative microbial abundance as a quantitative marker of mucosal health. Endoscopy was performed to obtain gastric mucosal biopsies from ten PUD and ten non-ulcer dyspepsia (NUD) patients. The tissue ORP was measured directly with a microelectrode using a biopsy specimen. A second specimen from an adjacent site was subjected to 16s rRNA gene sequencing. From the OTUs, the relative abundance of the microbial taxon in each of the samples was derived. We analyzed the genome of the predominant species for genes encoding the utilization of oxygen as an electron acceptor in respiration and for the presence of antioxidant defense mechanisms. The organisms were then grouped based on their established and inferred redox traits. Shannon diversity index and Species richness were calculated on rarefied data. The relative abundance of organisms that prefer high ORP over those that favor low ORP is conceived as the “Microbial Redox Index (MRI),” an indicator of mucosal health. In the gastric mucosa, aerobic species predominate and are more diverse than the anaerobes. The predominant aerobes are Helicobacter pylori and Sphingobacterium mizutaii. The abundance of these two species had an inverse correlation with the abundance of low ORP preferring anaerobes. Their relative abundance ratio (Microbial Redox Index) correlated with the tissue oxidation–reduction potential (ORP), a direct measure of oxidative stress. Correlation analysis also revealed that the abundance of all anaerobes inversely correlated with the dominant aerobic taxa. In addition, Shannon and Species richness diversity indices, the probable indicators of mucosal health, were negatively correlated with Microbial Redox Index. Using PUD as a prototype mucosal disease, this article describes a generalized approach to infer and quantify mucosal oxidative stress by analyzing the relative abundance of microorganisms that preferentially grow at the extremes of the tissue redox potential. This ratiometric Microbial Redox Index can also be assessed using simple qPCR without the need for sequencing. The approach described herein may be helpful as a widely applicable quantitative measure of mucosal health with prognostic and therapeutic implications.
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Affiliation(s)
- Manas Kumar Panigrahi
- Department of Gastroenterology, All India Institute of Medical Sciences, Bhubaneswar, India
| | - Venkatesh Kaliaperumal
- MYAS-NIN Department of Sports Science, ICMR-National Institute of Nutrition, Hyderabad, India
| | - Abhishek Akella
- Center of Excellence for Clinical Microbiome Research, All India Institute of Medical Sciences, Bhubaneswar, 751019, India
| | - Giriprasad Venugopal
- Center of Excellence for Clinical Microbiome Research, All India Institute of Medical Sciences, Bhubaneswar, 751019, India
| | - Balamurugan Ramadass
- Center of Excellence for Clinical Microbiome Research, All India Institute of Medical Sciences, Bhubaneswar, 751019, India. .,Department of Biochemistry, All India Institute of Medical Sciences, Bhubaneswar, India.
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10
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Newton K, Gonzalez E, Pitre FE, Brereton NJB. Microbial community origin and fate through a rural wastewater treatment plant. Environ Microbiol 2022; 24:2516-2542. [PMID: 35466495 DOI: 10.1111/1462-2920.16025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 04/20/2022] [Indexed: 11/29/2022]
Abstract
Conventional wastewater treatment relies on a complex microbiota; however, much of this community is still to be characterised. To better understand the origin, dynamics and fate of bacteria within a wastewater treatment plant: untreated primary wastewater, activated sludge, and post-treatment effluent were characterised. From 3,163 Exact Sequence Variants (ESVs), 860 were annotated to species-level. In primary wastewater, 28% of ESVs were putative bacterial species previously associated with humans, 14% with animals and 5% as common to the environment. Differential abundance analysis revealed significant relative reductions in ESVs from potentially humans-associated species from primary wastewater to activated sludge, and significant increases in ESVs from species associated with nutrient cycling. Between primary wastewater and effluent, 51% of ESVs from human-associated species did not significantly differ, and species such as Bacteroides massiliensis and Bacteroides dorei increased. These findings illustrate that activated sludge increased extracellular protease and urease-producing species, ammonia and nitrite oxidizers, denitrifiers and specific phosphorus accumulators. Although many human-associated species declined, some persisted in effluent, including strains of potential health or environmental concern. Species-level microbial assessment may be useful for understanding variation in wastewater treatment efficiency as well as for monitoring the release of microbes into surface water and the wider ecosystem. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Kymberly Newton
- Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, H1X 2B2, Canada
| | - Emmanuel Gonzalez
- Canadian Center for Computational Genomics, Department of Human Genetics, McGill University, Montréal, H3A 1A4, Canada
| | - Frederic E Pitre
- Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, H1X 2B2, Canada
| | - Nicholas J B Brereton
- Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, H1X 2B2, Canada
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11
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Saa P, Urrutia A, Silva-Andrade C, Martín AJ, Garrido D. Modeling approaches for probing cross-feeding interactions in the human gut microbiome. Comput Struct Biotechnol J 2021; 20:79-89. [PMID: 34976313 PMCID: PMC8685919 DOI: 10.1016/j.csbj.2021.12.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 12/03/2021] [Accepted: 12/04/2021] [Indexed: 12/16/2022] Open
Abstract
Microbial communities perform emergent activities that are essentially different from those carried by their individual members. The gut microbiome and its metabolites have a significant impact on the host, contributing to homeostasis or disease. Food molecules shape this community, being fermented through cross-feeding interactions of metabolites such as lactate, acetate, and amino acids, or products derived from macromolecule degradation. Mathematical and experimental approaches have been applied to understand and predict the interactions between microorganisms in complex communities such as the gut microbiota. Rational and mechanistic understanding of microbial interactions is essential to exploit their metabolic activities and identify keystone taxa and metabolites. The latter could be used in turn to modulate or replicate the metabolic behavior of the community in different contexts. This review aims to highlight recent experimental and modeling approaches for studying cross-feeding interactions within the gut microbiome. We focus on short-chain fatty acid production and fiber fermentation, which are fundamental processes in human health and disease. Special attention is paid to modeling approaches, particularly kinetic and genome-scale stoichiometric models of metabolism, to integrate experimental data under different diet and health conditions. Finally, we discuss limitations and challenges for the broad application of these modeling approaches and their experimental verification for improving our understanding of the mechanisms of microbial interactions.
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Affiliation(s)
- Pedro Saa
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
- Institute for Mathematical and Computational Engineering, Pontificia Universidad Católica de Chile, Vicuña Mackenna, 4860 Santiago, Chile
| | - Arles Urrutia
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Claudia Silva-Andrade
- Laboratorio de Biología de Redes, Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Alberto J. Martín
- Laboratorio de Biología de Redes, Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Daniel Garrido
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
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12
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The Emerging Scenario of the Gut-Brain Axis: The Therapeutic Actions of the New Actor Kefir against Neurodegenerative Diseases. Antioxidants (Basel) 2021; 10:antiox10111845. [PMID: 34829716 PMCID: PMC8614795 DOI: 10.3390/antiox10111845] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/14/2021] [Accepted: 11/17/2021] [Indexed: 12/18/2022] Open
Abstract
The fact that millions of people worldwide suffer from Alzheimer’s disease (AD) or Parkinson’s disease (PD), the two most prevalent neurodegenerative diseases (NDs), has been a permanent challenge to science. New tools were developed over the past two decades and were immediately incorporated into routines in many laboratories, but the most valuable scientific contribution was the “waking up” of the gut microbiota. Disturbances in the gut microbiota, such as an imbalance in the beneficial/pathogenic effects and a decrease in diversity, can result in the passage of undesired chemicals and cells to the systemic circulation. Recently, the potential effect of probiotics on restoring/preserving the microbiota was also evaluated regarding important metabolite and vitamin production, pathogen exclusion, immune system maturation, and intestinal mucosal barrier integrity. Therefore, the focus of the present review is to discuss the available data and conclude what has been accomplished over the past two decades. This perspective fosters program development of the next steps that are necessary to obtain confirmation through clinical trials on the magnitude of the effects of kefir in large samples.
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13
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Abstract
The disruption of gut microbiota homeostasis has been associated with numerous diseases and with a disproportionate inflammatory response, including overproduction of nitric oxide (NO) in the intestinal lumen. However, the influence of NO on the human gut microbiota has not been well characterized yet. We used in vitro fermentation systems inoculated with human fecal samples to monitor the effect of repetitive NO pulses on the gut microbiota. NO exposure increased the redox potential and modified the fermentation profile and gas production. The overall metabolome was modified, reflecting less strict anaerobic conditions and shifts in amino acid and nitrogen metabolism. NO exposure led to a microbial shift in diversity with a decrease in Clostridium leptum group and Faecalibacterium prausnitzii biomass and an increased abundance of the Dialister genus. Escherichia coli, Enterococcus faecalis, and Proteus mirabilis operational taxonomic unit abundance increased, and strains from those species isolated after NO stress showed resistance to high NO concentrations. As a whole, NO quickly changed microbial fermentations, functions, and composition in a pulse- and dose-dependent manner. NO could shift, over time, the trophic chain to conditions that are unfavorable for strict anaerobic microbial processes, implying that a prolonged or uncontrolled inflammation has detrimental and irreversible consequences on the human microbiome. IMPORTANCE Gut microbiota dysbiosis has been associated with inflammatory diseases. The human inflammatory response leads to an overproduction of nitric oxide (NO) in the gut. However, so far, the influence of NO on the human gut microbiota has not been characterized. In this study, we used in vitro fermentation systems with human fecal samples to understand the effect of NO on the microbiota: NO modified the microbial composition and its functionality. High NO concentration depleted the microbiota of beneficial butyrate-producing species and favored potentially deleterious species (E. coli, E. faecalis, and P. mirabilis), which we showed can sustain high NO concentrations. Our work shows that NO may participate in the vicious circle of inflammation, leading to detrimental and irreversible consequences on human health.
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14
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Broman E, Zilius M, Samuiloviene A, Vybernaite-Lubiene I, Politi T, Klawonn I, Voss M, Nascimento FJA, Bonaglia S. Active DNRA and denitrification in oxic hypereutrophic waters. WATER RESEARCH 2021; 194:116954. [PMID: 33667950 DOI: 10.1016/j.watres.2021.116954] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 02/17/2021] [Accepted: 02/18/2021] [Indexed: 06/12/2023]
Abstract
Since the start of synthetic fertilizer production more than a hundred years ago, the coastal ocean has been exposed to increasing nutrient loading, which has led to eutrophication and extensive algal blooms. Such hypereutrophic waters might harbor anaerobic nitrogen (N) cycling processes due to low-oxygen microniches associated with abundant organic particles, but studies on nitrate reduction in coastal pelagic environments are scarce. Here, we report on 15N isotope-labeling experiments, metagenome, and RT-qPCR data from a large hypereutrophic lagoon indicating that dissimilatory nitrate reduction to ammonium (DNRA) and denitrification were active processes, even though the bulk water was fully oxygenated (> 224 µM O2). DNRA in the bottom water corresponded to 83% of whole-ecosystem DNRA (water + sediment), while denitrification was predominant in the sediment. Microbial taxa important for DNRA according to the metagenomic data were dominated by Bacteroidetes (genus Parabacteroides) and Proteobacteria (genus Wolinella), while denitrification was mainly associated with proteobacterial genera Pseudomonas, Achromobacter, and Brucella. The metagenomic and microscopy data suggest that these anaerobic processes were likely occurring in low-oxygen microniches related to extensive growth of filamentous cyanobacteria, including diazotrophic Dolichospermum and non-diazotrophic Planktothrix. By summing the total nitrate fluxes through DNRA and denitrification, it results that DNRA retains approximately one fifth (19%) of the fixed N that goes through the nitrate pool. This is noteworthy as DNRA represents thus a very important recycling mechanism for fixed N, which sustains algal proliferation and leads to further enhancement of eutrophication in these endangered ecosystems.
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Affiliation(s)
- Elias Broman
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden; Baltic Sea Centre, Stockholm University, 106 91 Stockholm, Sweden.
| | - Mindaugas Zilius
- Marine Research Institute, Klaipeda University, 92294 Klaipeda, Lithuania
| | | | | | - Tobia Politi
- Marine Research Institute, Klaipeda University, 92294 Klaipeda, Lithuania
| | - Isabell Klawonn
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde, Seestr. 15, 18119 Rostock, Germany
| | - Maren Voss
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde, Seestr. 15, 18119 Rostock, Germany
| | - Francisco J A Nascimento
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden; Baltic Sea Centre, Stockholm University, 106 91 Stockholm, Sweden
| | - Stefano Bonaglia
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden; Marine Research Institute, Klaipeda University, 92294 Klaipeda, Lithuania; Department of Biology, University of Southern Denmark, 5230 Odense, Denmark; Department of Marine Sciences, University of Gothenburg, Box 461, 405 30 Gothenburg, Sweden.
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15
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Goyal S, Tsang DKL, Maisonneuve C, Girardin SE. Sending signals - The microbiota's contribution to intestinal epithelial homeostasis. Microbes Infect 2020; 23:104774. [PMID: 33189870 DOI: 10.1016/j.micinf.2020.10.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 10/31/2020] [Indexed: 12/18/2022]
Abstract
The intestine is inhabited by a diverse range of microorganisms, which requires the host to employ numerous barrier measures to prevent bacterial invasion. However, the intestinal microbiota additionally acts symbiotically with host cells to maintain epithelial barrier function, and perturbation to this interaction plays a pivotal role in intestinal pathogenesis. In this review, we highlight current findings of how the intestinal microbiota influences host intestinal epithelial cells. In particular, we review the roles of numerous microbial-derived products as well as mechanisms by which these microbial products influence the regulation of intestinal epithelial population dynamics and barrier function.
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Affiliation(s)
- Shawn Goyal
- Department of Laboratory Medicine and Pathobiology, Canada
| | - Derek K L Tsang
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | | | - Stephen E Girardin
- Department of Laboratory Medicine and Pathobiology, Canada; Department of Immunology, University of Toronto, Toronto, Ontario, Canada.
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16
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Bonfiglio G, Neroni B, Radocchia G, Marazzato M, Pantanella F, Schippa S. Insight into the Possible Use of the Predator Bdellovibrio bacteriovorus as a Probiotic. Nutrients 2020; 12:E2252. [PMID: 32731403 PMCID: PMC7468853 DOI: 10.3390/nu12082252] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/23/2020] [Accepted: 07/24/2020] [Indexed: 12/25/2022] Open
Abstract
The gut microbiota is a complex microbial ecosystem that coexists with the human organism in the intestinal tract. The members of this ecosystem live together in a balance between them and the host, contributing to its healthy state. Stress, aging, and antibiotic therapies are the principal factors affecting the gut microbiota composition, breaking the mutualistic relationship among microbes and resulting in the overgrowth of potential pathogens. This condition, called dysbiosis, has been linked to several chronic pathologies. In this review, we propose the use of the predator Bdellovibrio bacteriovorus as a possible probiotic to prevent or counteract dysbiotic outcomes and look at the findings of previous research.
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17
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Light SH, Méheust R, Ferrell JL, Cho J, Deng D, Agostoni M, Iavarone AT, Banfield JF, D’Orazio SEF, Portnoy DA. Extracellular electron transfer powers flavinylated extracellular reductases in Gram-positive bacteria. Proc Natl Acad Sci U S A 2019; 116:26892-26899. [PMID: 31818955 PMCID: PMC6936397 DOI: 10.1073/pnas.1915678116] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mineral-respiring bacteria use a process called extracellular electron transfer to route their respiratory electron transport chain to insoluble electron acceptors on the exterior of the cell. We recently characterized a flavin-based extracellular electron transfer system that is present in the foodborne pathogen Listeria monocytogenes, as well as many other Gram-positive bacteria, and which highlights a more generalized role for extracellular electron transfer in microbial metabolism. Here we identify a family of putative extracellular reductases that possess a conserved posttranslational flavinylation modification. Phylogenetic analyses suggest that divergent flavinylated extracellular reductase subfamilies possess distinct and often unidentified substrate specificities. We show that flavinylation of a member of the fumarate reductase subfamily allows this enzyme to receive electrons from the extracellular electron transfer system and support L. monocytogenes growth. We demonstrate that this represents a generalizable mechanism by finding that a L. monocytogenes strain engineered to express a flavinylated extracellular urocanate reductase uses urocanate by a related mechanism and to a similar effect. These studies thus identify an enzyme family that exploits a modular flavin-based electron transfer strategy to reduce distinct extracellular substrates and support a multifunctional view of the role of extracellular electron transfer activities in microbial physiology.
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Affiliation(s)
- Samuel H. Light
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Raphaël Méheust
- Department of Earth and Planetary Science, University of California, Berkeley, CA 94720
- Innovative Genomics Institute, Berkeley, CA 94704
| | - Jessica L. Ferrell
- Department of Microbiology, Immunology & Molecular Genetics, University of Kentucky, Lexington, KY 40536-0298
| | - Jooyoung Cho
- Department of Microbiology, Immunology & Molecular Genetics, University of Kentucky, Lexington, KY 40536-0298
| | - David Deng
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Marco Agostoni
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720
| | - Anthony T. Iavarone
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720
- QB3/Chemistry Mass Spectrometry Facility, University of California, Berkeley, CA 94720
| | - Jillian F. Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, CA 94720
- Innovative Genomics Institute, Berkeley, CA 94704
| | - Sarah E. F. D’Orazio
- Department of Microbiology, Immunology & Molecular Genetics, University of Kentucky, Lexington, KY 40536-0298
| | - Daniel A. Portnoy
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
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18
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Ravcheev DA, Moussu L, Smajic S, Thiele I. Comparative Genomic Analysis Reveals Novel Microcompartment-Associated Metabolic Pathways in the Human Gut Microbiome. Front Genet 2019; 10:636. [PMID: 31333721 PMCID: PMC6620236 DOI: 10.3389/fgene.2019.00636] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 06/18/2019] [Indexed: 12/16/2022] Open
Abstract
Bacterial microcompartments are self-assembling subcellular structures surrounded by a semipermeable protein shell and found only in bacteria, but not archaea or eukaryotes. The general functions of the bacterial microcompartments are to concentrate enzymes, metabolites, and cofactors for multistep pathways; maintain the cofactor ratio; protect the cell from toxic metabolic intermediates; and protect the encapsulated pathway from unwanted side reactions. The bacterial microcompartments were suggested to play a significant role in organisms of the human gut microbiome, especially for various pathogens. Here, we used a comparative genomics approach to analyze the bacterial microcompartments in 646 individual genomes of organisms commonly found in the human gut microbiome. The bacterial microcompartments were found in 150 (23.2%) analyzed genomes. These microcompartments include previously known ones for the utilization of ethanolamine, 1,2-propanediol, choline, and fucose/rhamnose. Moreover, we reconstructed two novel pathways associated with the bacterial microcompartments. These pathways are catabolic pathways for the utilization of 1-amino-2-propanol/1-amino-2-propanone and xanthine. Remarkably, the xanthine utilization pathway does not demonstrate similarity to previously known microcompartment-associated pathways. Thus, we describe a novel type of bacterial microcompartment.
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Affiliation(s)
- Dmitry A Ravcheev
- School of Medicine, National University of Ireland, Galway, University Road, Galway, Ireland.,Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Lubin Moussu
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Semra Smajic
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Ines Thiele
- School of Medicine, National University of Ireland, Galway, University Road, Galway, Ireland.,Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.,Discipline of Microbiology, School of Natural Sciences, National University of Ireland, Galway, University Road, Galway, Ireland
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19
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Heinken A, Ravcheev DA, Baldini F, Heirendt L, Fleming RMT, Thiele I. Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease. MICROBIOME 2019; 7:75. [PMID: 31092280 PMCID: PMC6521386 DOI: 10.1186/s40168-019-0689-3] [Citation(s) in RCA: 179] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 04/26/2019] [Indexed: 05/10/2023]
Abstract
BACKGROUND The human gut microbiome performs important functions in human health and disease. A classic example for host-gut microbial co-metabolism is host biosynthesis of primary bile acids and their subsequent deconjugation and transformation by the gut microbiome. To understand these system-level host-microbe interactions, a mechanistic, multi-scale computational systems biology approach that integrates the different types of omic data is needed. Here, we use a systematic workflow to computationally model bile acid metabolism in gut microbes and microbial communities. RESULTS Therefore, we first performed a comparative genomic analysis of bile acid deconjugation and biotransformation pathways in 693 human gut microbial genomes and expanded 232 curated genome-scale microbial metabolic reconstructions with the corresponding reactions (available at https://vmh.life ). We then predicted the bile acid biotransformation potential of each microbe and in combination with other microbes. We found that each microbe could produce maximally six of the 13 secondary bile acids in silico, while microbial pairs could produce up to 12 bile acids, suggesting bile acid biotransformation being a microbial community task. To investigate the metabolic potential of a given microbiome, publicly available metagenomics data from healthy Western individuals, as well as inflammatory bowel disease patients and healthy controls, were mapped onto the genomes of the reconstructed strains. We constructed for each individual a large-scale personalized microbial community model that takes into account strain-level abundances. Using flux balance analysis, we found considerable variation in the potential to deconjugate and transform primary bile acids between the gut microbiomes of healthy individuals. Moreover, the microbiomes of pediatric inflammatory bowel disease patients were significantly depleted in their bile acid production potential compared with that of controls. The contributions of each strain to overall bile acid production potential across individuals were found to be distinct between inflammatory bowel disease patients and controls. Finally, bottlenecks limiting secondary bile acid production potential were identified in each microbiome model. CONCLUSIONS This large-scale modeling approach provides a novel way of analyzing metagenomics data to accelerate our understanding of the metabolic interactions between the host and gut microbiomes in health and diseases states. Our models and tools are freely available to the scientific community.
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Affiliation(s)
- Almut Heinken
- School of Medicine, National University of Ireland, Galway, University Road, Galway, Ireland
| | - Dmitry A Ravcheev
- School of Medicine, National University of Ireland, Galway, University Road, Galway, Ireland
| | - Federico Baldini
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Laurent Heirendt
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Ronan M T Fleming
- Division of Analytical Biosciences, Leiden Academic Centre for Drug Research, Faculty of Science, University of Leiden, Leiden, The Netherlands
| | - Ines Thiele
- School of Medicine, National University of Ireland, Galway, University Road, Galway, Ireland.
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg.
- Discipline of Microbiology, School of Natural Sciences, National University of Ireland, Galway, University Road, Galway, Ireland.
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20
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Oxidative Stress and the Microbiota-Gut-Brain Axis. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2018; 2018:2406594. [PMID: 30622664 PMCID: PMC6304899 DOI: 10.1155/2018/2406594] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 11/04/2018] [Indexed: 12/27/2022]
Abstract
The gut-brain axis is increasingly recognized as an important pathway of communication and of physiological regulation, and gut microbiota seems to play a significant role in this mutual relationship. Oxidative stress is one of the most important pathogenic mechanisms for both neurodegenerative diseases, such as Alzheimer's or Parkinson's, and acute conditions, such as stroke or traumatic brain injury. A peculiar microbiota type might increase brain inflammation and reactive oxygen species levels and might favor abnormal aggregation of proteins. Reversely, brain lesions of various etiologies result in alteration of gut properties and microbiota. These recent hypotheses could open a door for new therapeutic approaches in various neurological diseases.
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21
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Prattichizzo F, Giuliani A, Mensà E, Sabbatinelli J, De Nigris V, Rippo MR, La Sala L, Procopio AD, Olivieri F, Ceriello A. Pleiotropic effects of metformin: Shaping the microbiome to manage type 2 diabetes and postpone ageing. Ageing Res Rev 2018; 48:87-98. [PMID: 30336272 DOI: 10.1016/j.arr.2018.10.003] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 09/13/2018] [Accepted: 10/10/2018] [Indexed: 02/06/2023]
Abstract
Metformin is the first-choice therapy to lower glycaemia and manage type 2 diabetes. Continuously emerging epidemiological data and experimental models are showing additional protective effects of metformin against a number of age-related diseases (ARDs), e.g., cardiovascular diseases and cancer. This evidence has prompted the design of a specific trial, i.e., the Targeting Aging with Metformin (TAME) trial, to test metformin as an anti-ageing molecule. However, a unifying or prevailing mechanism of action of metformin is still debated. Here, we summarize the epidemiological data linking metformin to ARD prevention. Then, we dissect the deeply studied mechanisms of action explaining its antihyperglycemic effect and the putative mechanisms supporting its anti-ageing properties, focusing on studies using clinically pertinent doses. We hypothesize that the molecular observations obtained in different models with metformin could be indirectly mediated by its effect on gut flora. Novel evidence suggests that metformin reshapes the human microbiota, promoting the growth of beneficial bacterial species and counteracting the expansion of detrimental bacterial species. In turn, this action would influence the balance between pro- and anti-inflammatory circulating factors, thereby promoting glycaemic control and healthy ageing. This framework may reconcile diverse observations, providing information for designing further studies to elucidate the complex interplay between metformin and the metabiome harboured in mammalian body compartments, thereby paving the way for innovative, bacterial-based therapeutics to manage type 2 diabetes and foster a longer healthspan.
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Affiliation(s)
| | - Angelica Giuliani
- Department of Clinical and Molecular Sciences, DISCLIMO, Università Politecnica delle Marche, Ancona, Italy
| | - Emanuela Mensà
- Department of Clinical and Molecular Sciences, DISCLIMO, Università Politecnica delle Marche, Ancona, Italy
| | - Jacopo Sabbatinelli
- Department of Clinical and Molecular Sciences, DISCLIMO, Università Politecnica delle Marche, Ancona, Italy
| | - Valeria De Nigris
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Maria Rita Rippo
- Department of Clinical and Molecular Sciences, DISCLIMO, Università Politecnica delle Marche, Ancona, Italy
| | | | - Antonio Domenico Procopio
- Department of Clinical and Molecular Sciences, DISCLIMO, Università Politecnica delle Marche, Ancona, Italy; Center of Clinical Pathology and Innovative Therapy, Italian National Research Centre on Aging, IRCCS INRCA, Ancona, Italy
| | - Fabiola Olivieri
- Department of Clinical and Molecular Sciences, DISCLIMO, Università Politecnica delle Marche, Ancona, Italy; Center of Clinical Pathology and Innovative Therapy, Italian National Research Centre on Aging, IRCCS INRCA, Ancona, Italy
| | - Antonio Ceriello
- IRCCS MultiMedica, Milan, Italy; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Spain
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22
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Reese AT, Cho EH, Klitzman B, Nichols SP, Wisniewski NA, Villa MM, Durand HK, Jiang S, Midani FS, Nimmagadda SN, O'Connell TM, Wright JP, Deshusses MA, David LA. Antibiotic-induced changes in the microbiota disrupt redox dynamics in the gut. eLife 2018; 7:35987. [PMID: 29916366 PMCID: PMC6008055 DOI: 10.7554/elife.35987] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 05/26/2018] [Indexed: 12/18/2022] Open
Abstract
How host and microbial factors combine to structure gut microbial communities remains incompletely understood. Redox potential is an important environmental feature affected by both host and microbial actions. We assessed how antibiotics, which can impact host and microbial function, change redox state and how this contributes to post-antibiotic succession. We showed gut redox potential increased within hours of an antibiotic dose in mice. Host and microbial functioning changed under treatment, but shifts in redox potentials could be attributed specifically to bacterial suppression in a host-free ex vivo human gut microbiota model. Redox dynamics were linked to blooms of the bacterial family Enterobacteriaceae. Ecological succession to pre-treatment composition was associated with recovery of gut redox, but also required dispersal from unaffected gut communities. As bacterial competition for electron acceptors can be a key ecological factor structuring gut communities, these results support the potential for manipulating gut microbiota through managing bacterial respiration. The gut is home to a large and diverse community of bacteria and other microbes, known as the gut microbiota. The makeup of this community is important for the health of both the host and its residents. For instance, many gut bacteria help to digest food or keep disease-causing bacteria in check. In return, the host provides them with nutrients. When this balance is disturbed, the host is exposed to risks such as infections. In particular, treatments with antibiotics that kill gut bacteria can lead to side effects like diarrhea, because the gut becomes recolonized with harmful bacteria including Clostridium difficile and Salmonella. Reese et al. have now investigated what happens to the gut environment after antibiotic treatment and how the gut microbiota recovers. Mice treated with broad-spectrum antibiotics showed an increase in the “redox potential” of their gut environment. Redox potential captures a number of measures of the chemical makeup of an environment, and provides an estimate for how efficiently some bacteria in that environment can grow. Some of the change in redox potential came from the host’s own immune system releasing chemicals as it reacted to the effects of the treatment. However, Reese et al. found that treating gut bacteria in an artificial gut – which has no immune system – also increased the redox potential. This experiment suggests that bacteria actively shape their chemical environment in the gut. After the treatment, bacteria that thrive under high redox potentials, which include some disease-causing species, recovered first and fastest. This, in turn, helped to bring redox potential back to how it was before the treatment. Although the gut’s chemical environment recovered, some bacterial species were wiped out by the antibiotic treatment. The microbiota only returned to its previous state when the treated mice were housed together with non-treated mice. This was expected because mice that live together commonly exchange microbes, for instance by eating each other’s feces, and the treated mice received new species to replenish their microbiota. These findings are important because they show that the chemical environment shapes and is shaped by the bacterial communities in the gut. Future research may investigate if altering redox potential in the gut could help to keep the microbiota healthier in infections and diseases of the digestive tract.
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Affiliation(s)
- Aspen T Reese
- Department of Biology, Duke University, Durham, United States.,Department of Molecular Genetics and Microbiology, Duke University, Durham, United States
| | - Eugenia H Cho
- Department of Bioengineering, University of Pennsylvania, Philadelphia, United States
| | - Bruce Klitzman
- Department of Surgery, Duke University Medical Center, Durham, United States
| | | | | | - Max M Villa
- Department of Molecular Genetics and Microbiology, Duke University, Durham, United States
| | - Heather K Durand
- Department of Molecular Genetics and Microbiology, Duke University, Durham, United States
| | - Sharon Jiang
- Department of Molecular Genetics and Microbiology, Duke University, Durham, United States
| | - Firas S Midani
- Program in Computational Biology and Bioinformatics, Duke University, Durham, United States
| | - Sai N Nimmagadda
- Department of Biomedical Engineering, Duke University, Durham, United States
| | - Thomas M O'Connell
- Department of Otolaryngology-Head and Neck Surgery, Indiana University School of Medicine, Indianapolis, United States
| | - Justin P Wright
- Department of Biology, Duke University, Durham, United States
| | - Marc A Deshusses
- Department of Civil and Environmental Engineering, Duke University, Durham, United States
| | - Lawrence A David
- Department of Molecular Genetics and Microbiology, Duke University, Durham, United States.,Program in Computational Biology and Bioinformatics, Duke University, Durham, United States.,Department of Biomedical Engineering, Duke University, Durham, United States.,Center for Genomic and Computational Biology, Duke University, Durham, United States
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23
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Fenn K, Strandwitz P, Stewart EJ, Dimise E, Rubin S, Gurubacharya S, Clardy J, Lewis K. Quinones are growth factors for the human gut microbiota. MICROBIOME 2017; 5:161. [PMID: 29262868 PMCID: PMC5738691 DOI: 10.1186/s40168-017-0380-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 12/04/2017] [Indexed: 05/19/2023]
Abstract
BACKGROUND The human gut microbiome has been linked to numerous components of health and disease. However, approximately 25% of the bacterial species in the gut remain uncultured, which limits our ability to properly understand, and exploit, the human microbiome. Previously, we found that growing environmental bacteria in situ in a diffusion chamber enables growth of uncultured species, suggesting the existence of growth factors in the natural environment not found in traditional cultivation media. One source of growth factors proved to be neighboring bacteria, and by using co-culture, we isolated previously uncultured organisms from the marine environment and identified siderophores as a major class of bacterial growth factors. Here, we employ similar co-culture techniques to grow bacteria from the human gut microbiome and identify novel growth factors. RESULTS By testing dependence of slow-growing colonies on faster-growing neighboring bacteria in a co-culture assay, eight taxonomically diverse pairs of bacteria were identified, in which an "induced" isolate formed a gradient of growth around a cultivatable "helper." This set included two novel species Faecalibacterium sp. KLE1255-belonging to the anti-inflammatory Faecalibacterium genus-and Sutterella sp. KLE1607. While multiple helper strains were identified, Escherichia coli was also capable of promoting growth of all induced isolates. Screening a knockout library of E. coli showed that a menaquinone biosynthesis pathway was required for growth induction of Faecalibacterium sp. KLE1255 and other induced isolates. Purified menaquinones induced growth of 7/8 of the isolated strains, quinone specificity profiles for individual bacteria were identified, and genome analysis suggests an incomplete menaquinone biosynthetic capability yet the presence of anaerobic terminal reductases in the induced strains, indicating an ability to respire anaerobically. CONCLUSIONS Our data show that menaquinones are a major class of growth factors for bacteria from the human gut microbiome. These organisms are taxonomically diverse, including members of the genus Faecalibacterium, Bacteroides, Bilophila, Gordonibacter, and Sutterella. This suggests that loss of quinone biosynthesis happened independently in many lineages of the human microbiota. Quinones can be used to improve existing bacterial growth media or modulate the human gut microbiota by encouraging the growth of important symbionts, such as Faecalibacterium species.
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Affiliation(s)
- Kathrin Fenn
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, 134 Mugar Hall, 360 Huntington Ave, Boston, MA 02115 USA
- Present address: Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115 USA
| | - Philip Strandwitz
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, 134 Mugar Hall, 360 Huntington Ave, Boston, MA 02115 USA
| | - Eric J. Stewart
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, 134 Mugar Hall, 360 Huntington Ave, Boston, MA 02115 USA
| | - Eric Dimise
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115 USA
| | - Sarah Rubin
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, 134 Mugar Hall, 360 Huntington Ave, Boston, MA 02115 USA
- Present address: Department of Molecular Genetics, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Shreya Gurubacharya
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, 134 Mugar Hall, 360 Huntington Ave, Boston, MA 02115 USA
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115 USA
| | - Kim Lewis
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, 134 Mugar Hall, 360 Huntington Ave, Boston, MA 02115 USA
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24
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Barton LL, Ritz NL, Fauque GD, Lin HC. Sulfur Cycling and the Intestinal Microbiome. Dig Dis Sci 2017; 62:2241-2257. [PMID: 28766244 DOI: 10.1007/s10620-017-4689-5] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 07/19/2017] [Indexed: 02/08/2023]
Abstract
In this review, we focus on the activities transpiring in the anaerobic segment of the sulfur cycle occurring in the gut environment where hydrogen sulfide is produced. While sulfate-reducing bacteria are considered as the principal agents for hydrogen sulfide production, the enzymatic desulfhydration of cysteine by heterotrophic bacteria also contributes to production of hydrogen sulfide. For sulfate-reducing bacteria respiration, molecular hydrogen and lactate are suitable as electron donors while sulfate functions as the terminal electron acceptor. Dietary components provide fiber and macromolecules that are degraded by bacterial enzymes to monomers, and these are fermented by intestinal bacteria with the production to molecular hydrogen which promotes the metabolic dominance by sulfate-reducing bacteria. Sulfate is also required by the sulfate-reducing bacteria, and this can be supplied by sulfate- and sulfonate-containing compounds that are hydrolyzed by intestinal bacterial with the release of sulfate. While hydrogen sulfide in the intestinal biosystem may be beneficial to bacteria by increasing resistance to antibiotics, and protecting them from reactive oxygen species, hydrogen sulfide at elevated concentrations may become toxic to the host.
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Affiliation(s)
- Larry L Barton
- Department of Biology, MSCO3 2020, University of New Mexico, Albuquerque, NM, 87131, USA.
| | - Nathaniel L Ritz
- New Mexico VA Health Care System, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Guy D Fauque
- CNRS, IRD, Mediterranean Institute of Oceanography (MIO) UM 110, Aix-Marseille Université, Université de Toulon, Campus de Luminy, Case 901, 13288, Marseille Cedex 09, France
| | - Henry C Lin
- New Mexico VA Health Care System, University of New Mexico, Albuquerque, NM, 87131, USA
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25
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Ravcheev DA, Thiele I. Comparative Genomic Analysis of the Human Gut Microbiome Reveals a Broad Distribution of Metabolic Pathways for the Degradation of Host-Synthetized Mucin Glycans and Utilization of Mucin-Derived Monosaccharides. Front Genet 2017; 8:111. [PMID: 28912798 PMCID: PMC5583593 DOI: 10.3389/fgene.2017.00111] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 08/11/2017] [Indexed: 12/27/2022] Open
Abstract
The colonic mucus layer is a dynamic and complex structure formed by secreted and transmembrane mucins, which are high-molecular-weight and heavily glycosylated proteins. Colonic mucus consists of a loose outer layer and a dense epithelium-attached layer. The outer layer is inhabited by various representatives of the human gut microbiota (HGM). Glycans of the colonic mucus can be used by the HGM as a source of carbon and energy when dietary fibers are not sufficiently available. Both commensals and pathogens can utilize mucin glycans. Commensals are mostly involved in the cleavage of glycans, while pathogens mostly utilize monosaccharides released by commensals. This HGM-derived degradation of the mucus layer increases pathogen susceptibility and causes many other health disorders. Here, we analyzed 397 individual HGM genomes to identify pathways for the cleavage of host-synthetized mucin glycans to monosaccharides as well as for the catabolism of the derived monosaccharides. Our key results are as follows: (i) Genes for the cleavage of mucin glycans were found in 86% of the analyzed genomes, which significantly higher than a previous estimation. (ii) Genes for the catabolism of derived monosaccharides were found in 89% of the analyzed genomes. (iii) Comparative genomic analysis identified four alternative forms of the monosaccharide-catabolizing enzymes and four alternative forms of monosaccharide transporters. (iv) Eighty-five percent of the analyzed genomes may be involved in potential feeding pathways for the monosaccharides derived from cleaved mucin glycans. (v) The analyzed genomes demonstrated different abilities to degrade known mucin glycans. Generally, the ability to degrade at least one type of mucin glycan was predicted for 81% of the analyzed genomes. (vi) Eighty-two percent of the analyzed genomes can form mutualistic pairs that are able to degrade mucin glycans and are not degradable by any of the paired organisms alone. Taken together, these findings provide further insight into the inter-microbial communications of the HGM as well as into host-HGM interactions.
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Affiliation(s)
- Dmitry A Ravcheev
- Luxembourg Centre for Systems Biomedicine, University of LuxembourgEsch-sur-Alzette, Luxembourg
| | - Ines Thiele
- Luxembourg Centre for Systems Biomedicine, University of LuxembourgEsch-sur-Alzette, Luxembourg
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26
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Fukuyama J, Rumker L, Sankaran K, Jeganathan P, Dethlefsen L, Relman DA, Holmes SP. Multidomain analyses of a longitudinal human microbiome intestinal cleanout perturbation experiment. PLoS Comput Biol 2017; 13:e1005706. [PMID: 28821012 PMCID: PMC5576755 DOI: 10.1371/journal.pcbi.1005706] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 08/30/2017] [Accepted: 07/27/2017] [Indexed: 12/29/2022] Open
Abstract
Our work focuses on the stability, resilience, and response to perturbation of the bacterial communities in the human gut. Informative flash flood-like disturbances that eliminate most gastrointestinal biomass can be induced using a clinically-relevant iso-osmotic agent. We designed and executed such a disturbance in human volunteers using a dense longitudinal sampling scheme extending before and after induced diarrhea. This experiment has enabled a careful multidomain analysis of a controlled perturbation of the human gut microbiota with a new level of resolution. These new longitudinal multidomain data were analyzed using recently developed statistical methods that demonstrate improvements over current practices. By imposing sparsity constraints we have enhanced the interpretability of the analyses and by employing a new adaptive generalized principal components analysis, incorporated modulated phylogenetic information and enhanced interpretation through scoring of the portions of the tree most influenced by the perturbation. Our analyses leverage the taxa-sample duality in the data to show how the gut microbiota recovers following this perturbation. Through a holistic approach that integrates phylogenetic, metagenomic and abundance information, we elucidate patterns of taxonomic and functional change that characterize the community recovery process across individuals. We provide complete code and illustrations of new sparse statistical methods for high-dimensional, longitudinal multidomain data that provide greater interpretability than existing methods.
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Affiliation(s)
- Julia Fukuyama
- Statistics Department, Stanford University, Stanford, California, USA
| | - Laurie Rumker
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, California, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Kris Sankaran
- Statistics Department, Stanford University, Stanford, California, USA
| | | | - Les Dethlefsen
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, California, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - David A. Relman
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, California, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
- Infectious Diseases Section, Veterans Affairs Palo Alto Health Care System, Palo Alto, California, USA
| | - Susan P. Holmes
- Statistics Department, Stanford University, Stanford, California, USA
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27
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Ethanolamine and Phosphatidylethanolamine: Partners in Health and Disease. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2017; 2017:4829180. [PMID: 28785375 PMCID: PMC5529665 DOI: 10.1155/2017/4829180] [Citation(s) in RCA: 193] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Accepted: 06/01/2017] [Indexed: 12/18/2022]
Abstract
Phosphatidylethanolamine (PE) is the second most abundant phospholipid in mammalian cells. PE comprises about 15–25% of the total lipid in mammalian cells; it is enriched in the inner leaflet of membranes, and it is especially abundant in the inner mitochondrial membrane. PE has quite remarkable activities: it is a lipid chaperone that assists in the folding of certain membrane proteins, it is required for the activity of several of the respiratory complexes, and it plays a key role in the initiation of autophagy. In this review, we focus on PE's roles in lipid-induced stress in the endoplasmic reticulum (ER), Parkinson's disease (PD), ferroptosis, and cancer.
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28
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Harel A, Häggblom MM, Falkowski PG, Yee N. Evolution of prokaryotic respiratory molybdoenzymes and the frequency of their genomic co-occurrence. FEMS Microbiol Ecol 2016; 92:fiw187. [DOI: 10.1093/femsec/fiw187] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2016] [Indexed: 02/03/2023] Open
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29
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Jameson E, Doxey AC, Airs R, Purdy KJ, Murrell JC, Chen Y. Metagenomic data-mining reveals contrasting microbial populations responsible for trimethylamine formation in human gut and marine ecosystems. Microb Genom 2016; 2:e000080. [PMID: 28785417 PMCID: PMC5537630 DOI: 10.1099/mgen.0.000080] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 07/19/2016] [Indexed: 01/20/2023] Open
Abstract
Existing metagenome datasets from many different environments contain untapped potential for understanding metabolic pathways and their biological impact. Our interest lies in the formation of trimethylamine (TMA), a key metabolite in both human health and climate change. Here, we focus on bacterial degradation pathways for choline, carnitine, glycine betaine and trimethylamine N-oxide (TMAO) to TMA in human gut and marine metagenomes. We found the TMAO reductase pathway was the most prevalent pathway in both environments. Proteobacteria were found to contribute the majority of the TMAO reductase pathway sequences, except in the stressed gut, where Actinobacteria dominated. Interestingly, in the human gut metagenomes, a high proportion of the Proteobacteria hits were accounted for by the genera Klebsiella and Escherichia. Furthermore Klebsiella and Escherichia harboured three of the four potential TMA-production pathways (choline, carnitine and TMAO), suggesting they have a key role in TMA cycling in the human gut. In addition to the intensive TMAO-TMA cycling in the marine environment, our data suggest that carnitine-to-TMA transformation plays an overlooked role in aerobic marine surface waters, whereas choline-to-TMA transformation is important in anaerobic marine sediments. Our study provides new insights into the potential key microbes and metabolic pathways for TMA formation in two contrasting environments.
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Affiliation(s)
- Eleanor Jameson
- School of Life Sciences, Gibbet Hill Campus, The University of Warwick, Coventry, CV4 7AL, UK
| | - Andrew C. Doxey
- Department of Biology, University of Waterloo, 200 University Ave. W, Waterloo, Ontario N2L 3G1, Canada
| | - Ruth Airs
- Plymouth Marine Laboratory, Prospect Pl, Plymouth PL1 3DH, UK
| | - Kevin J. Purdy
- School of Life Sciences, Gibbet Hill Campus, The University of Warwick, Coventry, CV4 7AL, UK
| | - J. Colin Murrell
- University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Yin Chen
- School of Life Sciences, Gibbet Hill Campus, The University of Warwick, Coventry, CV4 7AL, UK
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30
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Ravcheev DA, Thiele I. Genomic Analysis of the Human Gut Microbiome Suggests Novel Enzymes Involved in Quinone Biosynthesis. Front Microbiol 2016; 7:128. [PMID: 26904004 PMCID: PMC4746308 DOI: 10.3389/fmicb.2016.00128] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 01/25/2016] [Indexed: 02/06/2023] Open
Abstract
Ubiquinone and menaquinone are membrane lipid-soluble carriers of electrons that are essential for cellular respiration. Eukaryotic cells can synthesize ubiquinone but not menaquinone, whereas prokaryotes can synthesize both quinones. So far, most of the human gut microbiome (HGM) studies have been based on metagenomic analysis. Here, we applied an analysis of individual HGM genomes to the identification of ubiquinone and menaquinone biosynthetic pathways. In our opinion, the shift from metagenomics to analysis of individual genomes is a pivotal milestone in investigation of bacterial communities, including the HGM. The key results of this study are as follows. (i) The distribution of the canonical pathways in the HGM genomes was consistent with previous reports and with the distribution of the quinone-dependent reductases for electron acceptors. (ii) The comparative genomics analysis identified four alternative forms of the previously known enzymes for quinone biosynthesis. (iii) Genes for the previously unknown part of the futalosine pathway were identified, and the corresponding biochemical reactions were proposed. We discuss the remaining gaps in the menaquinone and ubiquinone pathways in some of the microbes, which indicate the existence of further alternate genes or routes. Together, these findings provide further insight into the biosynthesis of quinones in bacteria and the physiology of the HGM.
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Affiliation(s)
- Dmitry A Ravcheev
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg Esch-sur-Alzette, Luxembourg
| | - Ines Thiele
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg Esch-sur-Alzette, Luxembourg
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31
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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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