Microbial Community Design: Methods, Applications, And
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The Gut Microbiota and Inflammation
International Journal of Environmental Research and Public Health Review The Gut Microbiota and Inflammation: An Overview 1, 2 1, 1, , Zahraa Al Bander *, Marloes Dekker Nitert , Aya Mousa y and Negar Naderpoor * y 1 Monash Centre for Health Research and Implementation, School of Public Health and Preventive Medicine, Monash University, Melbourne 3168, Australia; [email protected] 2 School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane 4072, Australia; [email protected] * Correspondence: [email protected] (Z.A.B.); [email protected] (N.N.); Tel.: +61-38-572-2896 (N.N.) These authors contributed equally to this work. y Received: 10 September 2020; Accepted: 15 October 2020; Published: 19 October 2020 Abstract: The gut microbiota encompasses a diverse community of bacteria that carry out various functions influencing the overall health of the host. These comprise nutrient metabolism, immune system regulation and natural defence against infection. The presence of certain bacteria is associated with inflammatory molecules that may bring about inflammation in various body tissues. Inflammation underlies many chronic multisystem conditions including obesity, atherosclerosis, type 2 diabetes mellitus and inflammatory bowel disease. Inflammation may be triggered by structural components of the bacteria which can result in a cascade of inflammatory pathways involving interleukins and other cytokines. Similarly, by-products of metabolic processes in bacteria, including some short-chain fatty acids, can play a role in inhibiting inflammatory processes. In this review, we aimed to provide an overview of the relationship between the gut microbiota and inflammatory molecules and to highlight relevant knowledge gaps in this field. -
Human Microbiome: Your Body Is an Ecosystem
Human Microbiome: Your Body Is an Ecosystem This StepRead is based on an article provided by the American Museum of Natural History. What Is an Ecosystem? An ecosystem is a community of living things. The living things in an ecosystem interact with each other and with the non-living things around them. One example of an ecosystem is a forest. Every forest has a mix of living things, like plants and animals, and non-living things, like air, sunlight, rocks, and water. The mix of living and non-living things in each forest is unique. It is different from the mix of living and non-living things in any other ecosystem. You Are an Ecosystem The human body is also an ecosystem. There are trillions tiny organisms living in and on it. These organisms are known as microbes and include bacteria, viruses, and fungi. There are more of them living on just your skin right now than there are people on Earth. And there are a thousand times more than that in your gut! All the microbes in and on the human body form communities. The human body is an ecosystem. It is home to trillions of microbes. These communities are part of the ecosystem of the human Photo Credit: Gaby D’Alessandro/AMNH body. Together, all of these communities are known as the human microbiome. No two human microbiomes are the same. Because of this, you are a unique ecosystem. There is no other ecosystem like your body. Humans & Microbes Microbes have been around for more than 3.5 billion years. -
Structure and Function of the Global Ocean Microbiome
Structure and function of the global ocean microbiome Shinichi Sunagawa, Luis Pedro Coelho, Samuel Chaffron, Jens Roat Kultima, Karine Labadie, Guillem Salazar, Bardya Djahanschiri, Georg Zeller, Daniel R. Mende, Adriana Alberti, et al. To cite this version: Shinichi Sunagawa, Luis Pedro Coelho, Samuel Chaffron, Jens Roat Kultima, Karine Labadie, et al.. Structure and function of the global ocean microbiome. Science, American Association for the Advancement of Science, 2015, 348 (6237), pp.1261359. 10.1126/science.1261359. hal-01233742 HAL Id: hal-01233742 https://hal.archives-ouvertes.fr/hal-01233742 Submitted on 14 Apr 2021 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Revised Manuscript: Confidential 29 January 2015 Colors used throughout the revision of pre -edited manuscript Edits by Science editor in blue Edits by the A uthors in green Title: Structure and Function of the Global Ocean Microbiome Authors: Shinichi S unagawa 1,†,* , Luis Pedro Coelho 1,† , Samuel Chaffron 2,3,4,† , Jens Roat Kultima 1, Karine Labadie 5, Guillem Salazar 6, Bardya Djahanschiri 1, Georg Zeller 1, Daniel R. Mende 1, Adriana Alberti 5, Francisco M. Cornejo -Castillo 6, Paul I. Costea 1, Corinne Cruaud 5, Fr ancesco d'Ovidio 7, Stefan Engelen 5, Isabel Ferrera 6, Josep M. -
The Human Gut Microbiota: a Dynamic Interplay with the Host from Birth to Senescence Settled During Childhood
Review nature publishing group The human gut microbiota: a dynamic interplay with the host from birth to senescence settled during childhood Lorenza Putignani1, Federica Del Chierico2, Andrea Petrucca2,3, Pamela Vernocchi2,4 and Bruno Dallapiccola5 The microbiota “organ” is the central bioreactor of the gastroin- producing immunological memory (2). Indeed, the intestinal testinal tract, populated by a total of 1014 bacteria and charac- epithelium at the interface between microbiota and lymphoid terized by a genomic content (microbiome), which represents tissue plays a crucial role in the mucosa immune response more than 100 times the human genome. The microbiota (2). The IS ability to coevolve with the microbiota during the plays an important role in child health by acting as a barrier perinatal life allows the host and the microbiota to coexist in a against pathogens and their invasion with a highly dynamic relationship of mutual benefit, which consists in dispensing, in modality, exerting metabolic multistep functions and stimu- a highly coordinated way, specific immune responses toward lating the development of the host immune system, through the biomass of foreign antigens, and in discriminating false well-organized programming, which influences all of the alarms triggered by benign antigens (2). The failure to obtain growth and aging processes. The advent of “omics” technolo- or maintain this complex homeostasis has a negative impact gies (genomics, proteomics, metabolomics), characterized by on the intestinal and systemic health (2). Once the balance complex technological platforms and advanced analytical and fails, the “disturbance” causes the disease, triggering an abnor- computational procedures, has opened new avenues to the mal inflammatory response as it happens, for example, for the knowledge of the gut microbiota ecosystem, clarifying some inflammatory bowel diseases in newborns (2). -
Corals and Sponges Under the Light of the Holobiont Concept: How Microbiomes Underpin Our Understanding of Marine Ecosystems
fmars-08-698853 August 11, 2021 Time: 11:16 # 1 REVIEW published: 16 August 2021 doi: 10.3389/fmars.2021.698853 Corals and Sponges Under the Light of the Holobiont Concept: How Microbiomes Underpin Our Understanding of Marine Ecosystems Chloé Stévenne*†, Maud Micha*†, Jean-Christophe Plumier and Stéphane Roberty InBioS – Animal Physiology and Ecophysiology, Department of Biology, Ecology & Evolution, University of Liège, Liège, Belgium In the past 20 years, a new concept has slowly emerged and expanded to various domains of marine biology research: the holobiont. A holobiont describes the consortium formed by a eukaryotic host and its associated microorganisms including Edited by: bacteria, archaea, protists, microalgae, fungi, and viruses. From coral reefs to the Viola Liebich, deep-sea, symbiotic relationships and host–microbiome interactions are omnipresent Bremen Society for Natural Sciences, and central to the health of marine ecosystems. Studying marine organisms under Germany the light of the holobiont is a new paradigm that impacts many aspects of marine Reviewed by: Carlotta Nonnis Marzano, sciences. This approach is an innovative way of understanding the complex functioning University of Bari Aldo Moro, Italy of marine organisms, their evolution, their ecological roles within their ecosystems, and Maria Pia Miglietta, Texas A&M University at Galveston, their adaptation to face environmental changes. This review offers a broad insight into United States key concepts of holobiont studies and into the current knowledge of marine model *Correspondence: holobionts. Firstly, the history of the holobiont concept and the expansion of its use Chloé Stévenne from evolutionary sciences to other fields of marine biology will be discussed. -
In 1683 a Dutchman, Antonie Van Leeuwenhoek, Having Developed
How do we benefit from the microorganisms that live within us? In 1683 a Dutchman, Antonie van Leeuwenhoek, having developed microscopes many times more powerful than any before, examined the white matter from his teeth and observed, ‘the number of animals in the scruff of a man’s teeth are so many that I believe they exceed the number of men in a kingdom.’ After his death in 1723, no other scientists were able to see these ‘animalcules’ without the impressive magnification unique to Leeuwenhoek’s microscopes (bequeathed to, and promptly 2,3 lost by, the Royal Society) leaving his discovery to be dismissed for almost 150 years . Microbes only reclaimed the scientific spotlight 1860s when Louis Pasteur proved they could cause disease. However, this was the genesis of ‘germ theory,’ which indiscriminately cast all our resident bacteria as malicious invaders, and ensured that the microorganisms living within our bodies became known only as enemies to our health. Since then, modern medicine has focused on the war against microbes - through sanitation, antiseptics, and the miraculous development of antibiotics. The idea that these supposed “enemies” could actually be good for us only emerged this century, gaining prominence when the Human Microbiome Project in 2007 - a 5 year program to sequence the genomes of microbial populations of 300 healthy Americans - helped to unveil the myriad ways our resident bacteria benefit us. Our body’s flora has frequently been described as an entire organ. It harbours a diverse community of intricately connected microbes in a precarious state of symbiosis. In exchange for a favourable habitat, these microbes fulfil many functions we can’t perform ourselves: helping to metabolise otherwise indigestible compounds, regulating our immune response, and even influencing brain activity. -
Recent Developments in the Study of Plant Microbiomes
microorganisms Review Recent Developments in the Study of Plant Microbiomes Bernard R. Glick 1 and Elisa Gamalero 2,* 1 Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada; [email protected] 2 Dipartimento di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale “A. Avogadro”, Viale Teresa Michel, 11, 15121 Alessandria, Italy * Correspondence: [email protected] Abstract: To date, an understanding of how plant growth-promoting bacteria facilitate plant growth has been primarily based on studies of individual bacteria interacting with plants under different conditions. More recently, it has become clear that specific soil microorganisms interact with one another in consortia with the collective being responsible for the positive effects on plant growth. Different plants attract different cross-sections of the bacteria and fungi in the soil, initially based on the composition of the unique root exudates from each plant. Thus, plants mostly attract those microorganisms that are beneficial to plants and exclude those that are potentially pathogenic. Beneficial bacterial consortia not only help to promote plant growth, these consortia also protect plants from a wide range of direct and indirect environmental stresses. Moreover, it is currently possible to engineer plant seeds to contain desired bacterial strains and thereby benefit the next generation of plants. In this way, it may no longer be necessary to deliver beneficial microbiota to each individual growing plant. As we develop a better understanding of beneficial bacterial microbiomes, it may become possible to develop synthetic microbiomes where compatible bacteria work together to facilitate plant growth under a wide range of natural conditions. Keywords: soil bacteria; plant growth-promoting bacteria; PGPB; seed microbiomes; root micro- Citation: Glick, B.R.; Gamalero, E. -
Principles for Designing Synthetic Microbial Communities
Available online at www.sciencedirect.com ScienceDirect Principles for designing synthetic microbial communities 1,2 1,2 1 Nathan I Johns , Tomasz Blazejewski , Antonio LC Gomes 1,3 and Harris H Wang Advances in synthetic biology to build microbes with defined applications that involve complex substrates may require and controllable properties are enabling new approaches to the use of multiple pathways and processes, which may be design and program multispecies communities. This emerging difficult or impossible to execute efficiently using single field of synthetic ecology will be important for many areas of strains. These and other complex applications may be biotechnology, bioenergy and bioremediation. This endeavor best tackled by cohorts of different microbes, each pro- draws upon knowledge from synthetic biology, systems grammed with specialized sub-functions that synergize biology, microbial ecology and evolution. Fully realizing the towards an overall population-level function. This fact is potential of this discipline requires the development of new evident in natural systems where single species do not strategies to control the intercellular interactions, occupy all niches in an environment, but rather multiple spatiotemporal coordination, robustness, stability and species coexist and perform complementary roles, creat- biocontainment of synthetic microbial communities. Here, we ing intricate ecological networks [4]. review recent experimental, analytical and computational advances to study and build multi-species microbial With a greater understanding of natural microbial inter- communities with defined functions and behavior for various actions, dynamics, and ecology, we are poised to expand applications. We also highlight outstanding challenges and microbial engineering to mixed consortia in order to future directions to advance this field. -
Involvement of Gut Microbiome in Human Health and Disease
Liang et al. Gut Pathog (2018) 10:3 https://doi.org/10.1186/s13099-018-0230-4 Gut Pathogens REVIEW Open Access Involvement of gut microbiome in human health and disease: brief overview, knowledge gaps and research opportunities Dachao Liang1†, Ross Ka‑Kit Leung2*†, Wenda Guan2 and William W. Au3,4 Abstract The commensal, symbiotic, and pathogenic microbial community which resides inside our body and on our skin (the human microbiome) can perturb host energy metabolism and immunity, and thus signifcantly infuence develop‑ ment of a variety of human diseases. Therefore, the feld has attracted unprecedented attention in the last decade. Although a large amount of data has been generated, there are still many unanswered questions and no universal agreements on how microbiome afects human health have been agreed upon. Consequently, this review was writ‑ ten to provide an updated overview of the rapidly expanding feld, with a focus on revealing knowledge gaps and research opportunities. Specifcally, the review covered animal physiology, optimal microbiome standard, health inter‑ vention by manipulating microbiome, knowledge base building by text mining, microbiota community structure and its implications in human diseases and health monitoring by analyzing microbiome in the blood. The review should enhance interest in conducting novel microbiota investigations that will further improve health and therapy. Keywords: Microbiome, High throughput sequencing, Metagenomics, Human disease causation What is microbiome? collection of bacteria or their genomes, unless otherwise Microorganisms often live in the form of a community. specifed. Furthermore, they can live in close association with com- Microbiome can be found throughout the human plex organisms, such as plants and humans, by establish- body, ranging from the skin to the gut, and to previously ing commensal, ammensal, mutualistic, parasitic and/or considered as sterile environments such as the blood pathogenic relationships with their hosts. -
Holobionts As Units of Selection and a Model of Their Population Dynamics and Evolution
Biological Theory https://doi.org/10.1007/s13752-017-0287-1 ORIGINAL ARTICLE Holobionts as Units of Selection and a Model of Their Population Dynamics and Evolution Joan Roughgarden1,6 · Scott F. Gilbert2 · Eugene Rosenberg3 · Ilana Zilber‑Rosenberg4 · Elisabeth A. Lloyd5 Received: 15 January 2017 / Accepted: 5 September 2017 © Konrad Lorenz Institute for Evolution and Cognition Research 2017 Abstract Holobionts, consisting of a host and diverse microbial symbionts, function as distinct biological entities anatomically, metabolically, immunologically, and developmentally. Symbionts can be transmitted from parent to offspring by a variety of vertical and horizontal methods. Holobionts can be considered levels of selection in evolution because they are well- defined interactors, replicators/reproducers, and manifestors of adaptation. An initial mathematical model is presented to help understand how holobionts evolve. The model offered combines the processes of horizontal symbiont transfer, within-host symbiont proliferation, vertical symbiont transmission, and holobiont selection. The model offers equations for the popula- tion dynamics and evolution of holobionts whose hologenomes differ in gene copy number, not in allelic or loci identity. The model may readily be extended to include variation among holobionts in the gene identities of both symbionts and host. Keywords Holobiont · Holobiont model · Hologenome · Level of selection · Microbiome · Microbiota · Symbiont Introduction also provides a model for the evolution of a holobiont that combines microbe and host population processes. This article discusses the concept of a holobiont—an ani- Following Lederberg and McCray (2001), a microbiome mal or plant host together with all the microbes living on or refers to an “ecological community of commensal, symbi- in it, exosymbionts and endosymbionts, respectively. -
Host-Microbiota Interactions: from Holobiont Theory to Analysis Jean-Christophe Simon1* , Julian R
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Online Research @ Cardiff Simon et al. Microbiome (2019) 7:5 https://doi.org/10.1186/s40168-019-0619-4 COMMENTARY Open Access Host-microbiota interactions: from holobiont theory to analysis Jean-Christophe Simon1* , Julian R. Marchesi2,3, Christophe Mougel1 and Marc-André Selosse4,5 Abstract In the recent years, the holobiont concept has emerged as a theoretical and experimental framework to study the interactions between hosts and their associated microbial communities in all types of ecosystems. The spread of this concept in many branches of biology results from the fairly recent realization of the ubiquitous nature of host- associated microbes and their central role in host biology, ecology, and evolution. Through this special series “Host-microbiota interactions: from holobiont theory to analysis,” we wanted to promote this field of research which has considerable implications for human health, food production, and ecosystem protection. In this preface, we highlight a collection of articles selected for this special issue that show, use, or debate the concept of holobiont to approach taxonomically and ecologically diverse organisms, from humans and plants to sponges and insects. We also identify some theoretical and methodological challenges and propose directions for future research on holobionts. Keywords: Host-microbiota interactions, Holobiont, Hologenome, Metagenomics, Symbiosis Background the National Center for Scientific Research (CNRS), the It is becoming increasingly clear that the development, National Institute for Agricultural Research (INRA), growth, and health (in one word, all functions) of and the National Museum of Natural History (MNHN). -
A Community Perspective on the Concept of Marine Holobionts: Current Status, Challenges, and Future Directions
A community perspective on the concept of marine holobionts: current status, challenges, and future directions Simon M. Dittami1, Enrique Arboleda2, Jean-Christophe Auguet3, Arite Bigalke4, Enora Briand5, Paco Cárdenas6, Ulisse Cardini7, Johan Decelle8, Aschwin H. Engelen9, Damien Eveillard10, Claire M.M. Gachon11, Sarah M. Griffiths12, Tilmann Harder13, Ehsan Kayal2, Elena Kazamia14, Francois¸ H. Lallier15, Mónica Medina16, Ezequiel M. Marzinelli17,18,19, Teresa Maria Morganti20, Laura Núñez Pons21, Soizic Prado22, José Pintado23, Mahasweta Saha24,25, Marc-André Selosse26,27, Derek Skillings28, Willem Stock29, Shinichi Sunagawa30, Eve Toulza31, Alexey Vorobev32, Catherine Leblanc1 and Fabrice Not15 1 Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France 2 FR2424, Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France 3 MARBEC, Université de Montpellier, CNRS, IFREMER, IRD, Montpellier, France 4 Institute for Inorganic and Analytical Chemistry, Bioorganic Analytics, Friedrich-Schiller-Universität Jena, Jena, Germany 5 Laboratoire Phycotoxines, Ifremer, Nantes, France 6 Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden 7 Integrative Marine Ecology Dept, Stazione Zoologica Anton Dohrn, Napoli, Italy 8 Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRA, Grenoble, France 9 CCMAR, Universidade do Algarve, Faro, Portugal 10 Laboratoire des Sciences Numériques de Nantes (LS2N), Université