Relevant bibliographies by topics / Host-microbiome interaction

Academic literature on the topic 'Host-microbiome interaction'

Author: Grafiati
Published: 10 December 2022
Last updated: 28 January 2023

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Journal articles on the topic "Host-microbiome interaction"

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Kelly, Paul. "Nutrition, intestinal defence and the microbiome." Proceedings of the Nutrition Society 69, no. 2 (March 5, 2010): 261–68. http://dx.doi.org/10.1017/s0029665110000108.

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The interaction between nutrition and infection was the subject of important work by several groups in the 1960s. The explosion of knowledge in immunology, including innate immunity, has led to increased understanding of the impact of nutrition on host defence, but much more work needs to be done in this area. In the last decade an increasing volume of work has opened up the previously obscure world of human endogenous flora. This work suggests that the microbiome, the total genetic pool of the microbiota, contributes to the already complex interaction between nutrition and infectious disease. The established concept that nutritional status, host defence and infection all impact on each other now has to be expanded into a multiple interaction, with the microbiota interacting with all three other elements. There is good evidence that the microbiome programmes host defence and drives a metabolome that impacts on energy balance, and indeed on some micronutrients. In turn, host defence shapes the microbiome, and nutritional status, particularly micronutrient status, helps determine several elements of host defence. While interventions in this area are in their infancy, the understanding of interactions that already have an enormous impact on global health is now at a threshold. The present review explores the evidence for these interactions with a view to putting potential interventions into the context of a conceptual framework.
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Loskutov, S. I., S. N. Proshin, and D. S. Ryabukhin. "Evolutionary aspects of gastrointestinal tract microbiome-host interaction underlying gastrointestinal barrier integrity." Russian Journal of Infection and Immunity 12, no. 5 (November 16, 2022): 819–26. http://dx.doi.org/10.15789/2220-7619-eao-1633.

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In the host sustenance and homeostasis, the microbiome is a key component in the functional system. Throughout ontogenetic development, microbiome including that of the gastrointestinal tract (GIT) is the vital factor that ensures not only host functioning, but also its interaction with environment. To uncover the mechanisms underlying GIT microbiome showing a decisive influence on host organism, a systematic approach is needed, because diverse microorganisms are predominantly localized in different parts of the GIT. Recently, a new interdisciplinary direction of science, nanobioinformatics that has been extensively developed considers gene networks as the major object of study representing a coordinated group of genes that functionally account for formation and phenotypic disclosure of various host traits. Here, an important place should be provided to the genetically determined level of the gastrointestinal tract microbiome, its interaction at the level of the host food systems. There have been increasing evidence indicating that the microbiome is directly involved in the pathogenesis of host diseases showing a multi-layered interaction with host metabolic and immune systems. At the same time, the microbial community is unevenly distributed throughout the gastrointestinal tract, and its different portions are variously active while interacting with the host immune system. The architecture of interaction between the microbiome and host cells is extremely complex, and the interaction of individual cells, at the same time, varies greatly. Bacteria colonizing the crypts of the small intestine regulate enterocyte proliferation by affecting DNA replication and gene expression, while bacteria at the tip of the intestinal villi mediate gene expression responsible for metabolism and immune response. Enterocytes and Paneth cells, in turn, regulate the vital activity of the community of microorganisms through the production of polysaccharides (carbohydrates) and antibacterial factors on their surface. Thus, the integrity of the gastrointestinal barrier (GIB) is maintained, which protects the body from infections and inflammation, while violation of its integrity leads to a number of diseases. It has been shown that depending on the dominance of certain types of bacteria the microbiome can maintain or disrupt GIB integrity. The structural and functional GIB integrity is important for body homeostasis. To date, at least 50 proteins have been characterized as being involved in the structural and functional integrability of tight junctions between gastrointestinal tract epithelial cells. The current review comprehensively discusses such issues and presents original research carried out at various facilities of translational biomedicine.
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Weersma, Rinse K., Alexandra Zhernakova, and Jingyuan Fu. "Interaction between drugs and the gut microbiome." Gut 69, no. 8 (May 14, 2020): 1510–19. http://dx.doi.org/10.1136/gutjnl-2019-320204.

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The human gut microbiome is a complex ecosystem that can mediate the interaction of the human host with their environment. The interaction between gut microbes and commonly used non-antibiotic drugs is complex and bidirectional: gut microbiome composition can be influenced by drugs, but, vice versa, the gut microbiome can also influence an individual’s response to a drug by enzymatically transforming the drug’s structure and altering its bioavailability, bioactivity or toxicity (pharmacomicrobiomics). The gut microbiome can also indirectly impact an individual’s response to immunotherapy in cancer treatment. In this review we discuss the bidirectional interactions between microbes and drugs, describe the changes in gut microbiota induced by commonly used non-antibiotic drugs, and their potential clinical consequences and summarise how the microbiome impacts drug effectiveness and its role in immunotherapy. Understanding how the microbiome metabolises drugs and reduces treatment efficacy will unlock the possibility of modulating the gut microbiome to improve treatment.
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Li, Yue-Han, Yuan-You Yang, Zhi-Gang Wang, and Zhuo Chen. "Emerging Function of Ecotype-Specific Splicing in the Recruitment of Commensal Microbiome." International Journal of Molecular Sciences 23, no. 9 (April 27, 2022): 4860. http://dx.doi.org/10.3390/ijms23094860.

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In recent years, host–microbiome interactions in both animals and plants has emerged as a novel research area for studying the relationship between host organisms and their commensal microbial communities. The fitness advantages of this mutualistic interaction can be found in both plant hosts and their associated microbiome, however, the driving forces mediating this beneficial interaction are poorly understood. Alternative splicing (AS), a pivotal post-transcriptional mechanism, has been demonstrated to play a crucial role in plant development and stress responses among diverse plant ecotypes. This natural variation of plants also has an impact on their commensal microbiome. In this article, we review the current progress of plant natural variation on their microbiome community, and discuss knowledge gaps between AS regulation of plants in response to their intimately related microbiota. Through the impact of this article, an avenue could be established to study the biological mechanism of naturally varied splicing isoforms on plant-associated microbiome assembly.
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Taschuk, Ryan, and Philip J. Griebel. "Commensal microbiome effects on mucosal immune system development in the ruminant gastrointestinal tract." Animal Health Research Reviews 13, no. 1 (June 2012): 129–41. http://dx.doi.org/10.1017/s1466252312000096.

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AbstractCommensal microflora play many roles within the mammalian gastrointestinal tract (GIT) that benefit host physiology by way of direct or indirect interactions with mucosal surfaces. Commensal flora comprises members across all microbial phyla, although predominantly bacterial, with population dynamics varying with host species, genotype, and environmental factors. Little is known, however, about the complex mechanisms regulating host–commensal interactions that underlie this mutually beneficial relationship and how alterations in the microbiome may influence host development and susceptibility to infection. Research into the gut microbiome has intensified as it becomes increasingly evident that symbiont–host interactions have a significant impact on mucosal immunity and health. Furthermore, evidence that microbial populations vary significantly throughout the GIT suggest that regional differences in the microbiome may also influence immune function within distinct compartments of the GIT. Postpartum colonization of the GIT has been shown to have a direct effect on mucosal immune system development, but information is limited regarding regional effects of the microbiome on the development, activation, and maturation of the mucosal immune system. This review discusses factors influencing the colonization and establishment of the microbiome throughout the GIT of newborn calves and the evidence that regional differences in the microbiome influence mucosal immune system development and maturation. The implications of this complex interaction are also discussed in terms of possible effects on responses to enteric pathogens and vaccines.
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Karaduta, Oleg, Zeljko Dvanajscak, and Boris Zybailov. "Metaproteomics—An Advantageous Option in Studies of Host-Microbiota Interaction." Microorganisms 9, no. 5 (April 30, 2021): 980. http://dx.doi.org/10.3390/microorganisms9050980.

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Gut microbiome contributes to host health by maintaining homeostasis, increasing digestive efficiency, and facilitating the development of the immune system. Manipulating gut microbiota is being recognized as a therapeutic target to manage various chronic diseases. The therapeutic manipulation of the intestinal microbiome is achieved through diet modification, the administration of prebiotics, probiotics, or antibiotics, and more recently, fecal microbiome transplantation (FMT). In this opinion paper, we give a perspective on the current status of application of multi-omics technologies in the analysis of host-microbiota interactions. The aim of this paper was to highlight the strengths of metaproteomics, which integrates with and often relies on other approaches.
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Brinker, Pina, Michael C. Fontaine, Leo W. Beukeboom, and Joana Falcao Salles. "Host, Symbionts, and the Microbiome: The Missing Tripartite Interaction." Trends in Microbiology 27, no. 6 (June 2019): 480–88. http://dx.doi.org/10.1016/j.tim.2019.02.002.

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Chimenti, Maria Sole, Carlo Perricone, Lucia Novelli, Francesco Caso, Luisa Costa, Dimitrios Bogdanos, Paola Conigliaro, et al. "Interaction between microbiome and host genetics in psoriatic arthritis." Autoimmunity Reviews 17, no. 3 (March 2018): 276–83. http://dx.doi.org/10.1016/j.autrev.2018.01.002.

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Pinker, Elisha, and Timur Tuganbaev. "Microbiome Composition and Circadian Rhythm Disruption Alters Epithelial Barrier Integrity." Columbia Undergraduate Science Journal 15 (May 24, 2021): 6–15. http://dx.doi.org/10.52214/cusj.v15i1.7408.

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The intestine is home to one of the most complex ecological communities, termed the human gut microbiome. The gut microbiome modulates a wide range of human diseases from diabetes to neurological disorders to cancer. Separating the host and the gut microbiome is the epithelial barrier. The intestinal epithelium serves as an adaptive interaction hub between the host and microbiome that plays an important role in deciding the outcome of host-microbiome interactions. Regulation of epithelial barrier permeability to ions, nutrients and microbiome metabolites is known to be a tightly controlled process on the host side. However, whether the microbiome community also affects epithelial permeability remains unclear. Here, we show that alterations in microbiota composition by treatment with antibiotics selectively targeting specific members of the microbiome community impacts the permeability of the intestine. Additionally, modulating the microbiome through other methods such as altering diet composition shows changes in permeability of the epithelial barrier. As daily feeding rhythm entrains diurnal fluctuations in microbiome, we have set out to measure epithelial barrier permeability throw out the clock. We have discovered that the permeability of the intestinal epithelial barrier exhibits circadian rhythms in mice. Disruption of these rhythms, through jet-lag or genetic deficiencies in circadian machinery, consequently alters epithelial barrier integrity. Together, these findings provide evidence that disruptions in circadian rhythms as well as alterations in microbiome composition have direct consequences in intestinal permeability, and that microbiome might serve as a tool in regulating epithelium permeability.
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Shine, Emilee E., and Jason M. Crawford. "Molecules from the Microbiome." Annual Review of Biochemistry 90, no. 1 (June 20, 2021): 789–815. http://dx.doi.org/10.1146/annurev-biochem-080320-115307.

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The human microbiome encodes a second genome that dwarfs the genetic capacity of the host. Microbiota-derived small molecules can directly target human cells and their receptors or indirectly modulate host responses through functional interactions with other microbes in their ecological niche. Their biochemical complexity has profound implications for nutrition, immune system development, disease progression, and drug metabolism, as well as the variation in these processes that exists between individuals. While the species composition of the human microbiome has been deeply explored, detailed mechanistic studies linking specific microbial molecules to host phenotypes are still nascent. In this review, we discuss challenges in decoding these interaction networks, which require interdisciplinary approaches that combine chemical biology, microbiology, immunology, genetics, analytical chemistry, bioinformatics, and synthetic biology. We highlight important classes of microbiota-derived small molecules and notable examples. An understanding of these molecular mechanisms is central to realizing the potential of precision microbiome editing in health, disease, and therapeutic responses.
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Dissertations / Theses on the topic "Host-microbiome interaction"

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Tamarelle, Jeanne. "Composition et dynamique du microbiote vaginal : facteurs associés et rôle dans l’infection par Chlamydia trachomatis The vaginal microbiota and its association with human papillomavirus, Chlamydia trachomatis, Neisseria gonorrhoeae and Mycoplasma genitalium infections: a systematic review and meta-analysis Vaginal microbiota composition and association with prevalent Chlamydia trachomatis infection: a cross- sectional study of young women attending a STI clinic in France Nonoptimal Vaginal Microbiota After Azithromycin Treatment for Chlamydia trachomatis Infection." Thesis, Université Paris-Saclay (ComUE), 2019. http://www.theses.fr/2019SACLV097.

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Chlamydia trachomatis (CT) est une bactérie sexuellement transmissible responsable d’infections génitales hautes pouvant conduire à une infertilité tubaire ou à des grossesses extra-utérines. C’est l’infection sexuellement transmissible la plus fréquente dans le monde, y compris en France. Les données épidémiologiques indiquent que l’incidence de cette infection est en augmentation malgré les mesures de contrôle mises en place, ce qui motive la révision des recommandations actuelles de dépistage de l’infection à CT. Le microbiote vaginal pourrait jouer un rôle majeur dans la prévention des IST via la compétition écologique et la production de métabolites, dont l’acide lactique. Le microbiote vaginal correspond à un équilibre dynamique fragile et susceptible d’être modifié par un ensemble d’expositions, parmi lesquelles les pratiques sexuelles et d’hygiène intime, l’exposition aux antibiotiques mais aussi la présence de pathogènes. L’objectif général de cette thèse est d’étudier ce triangle d’associations entre expositions, microbiote vaginal et infection par CT, à travers l’étude de la composition et de la dynamique du microbiote vaginal. Nous avons cherché à répondre aux questions suivantes : existe-t-il des marqueurs de l’infection par CT au niveau du microbiote vaginal ? La composition et la structure du microbiote vaginal sont-elles modifiées par l’infection par CT et la prise d’antibiotiques ? Quels sont les expositions associées à des perturbations du microbiote vaginal ? Une première étape a consisté à réaliser un état de l’art et d'estimer l’association entre microbiote vaginal et infection par CT dans la littérature, ainsi que pour trois autres IST d’importance clinique, et à évaluer le rôle de plusieurs facteurs dans l’hétérogénéité des mesures d’association observées. Dans un second temps, nous avons estimé cette association en s'appuyant sur la caractérisation moléculaire du microbiote vaginal, dans deux études en France et aux Etats-Unis. Nous avons montré qu’il y avait une surreprésentation des communautés bactériennes dominées par Lactobacillus iners (CST III) et de celles dépourvues de Lactobacillus spp. (CST IV) chez les femmes infectées par CT. En étudiant l’évolution du microbiote vaginal dans l’étude américaine, après traitement par azithromycine et clairance de CT, nous avons montré que le microbiote vaginal ne parvenait pas à évoluer vers un état optimal. Ce résultat laisse supposer qu’il persiste après traitement un risque vis-à-vis des réinfections. Enfin, dans deux études longitudinales à échantillonnage fréquent aux Etats-Unis, nous avons étudié les expositions associées à l’incidence et à la clairance d’un CST IV. Nous avons montré que lorsque le microbiote vaginal n’était pas dominé par L. iners, les facteurs associés à l’incidence d’un CST IV et à sa clairance étaient essentiellement les menstruations, tandis que chez les femmes dont le microbiote vaginal est dominé par L. iners, les menstruations mais aussi l’usage de lubrifiant, les douches vaginales, l’origine ethnique, l’âge et les rapports sexuels non protégés étaient associés à l’incidence d’un CST IV ou à sa clairance. Ainsi, ce travail de thèse a permis d'une part de confirmer l’association entre microbiote vaginal dépourvu de Lactobacillus et infection par CT en population en s'appuyant sur le séquençage génomique, et d'autre part de distinguer l’espèce L. iners des autres espèces de Lactobacillus et d’évaluer le risque associé au CST III. En permettant une meilleure compréhension de l’histoire naturelle de CT et des dynamiques du microbiote vaginal, nous espérons proposer des pistes pour améliorer les stratégies de contrôle de l’infection par CT et d’autres IST. Le potentiel innovant du projet réside dans l’usage de méthodes moléculaires nous permettant d’affiner notre approche de la santé en intégrant la prédisposition individuelle aux infections sexuellement transmissibles, ainsi ouvrant la voie vers la médecine personnalisée
Chlamydia trachomatis (CT) is a sexually transmitted bacteria responsible for cervicitis, urethritis, and pelvic inflammatory diseases leading to subsequent tubal infertility and ectopic pregnancies. It is the most frequent sexually transmitted infection worldwide, including in France. Epidemiological data indicate that the incidence rate is increasing despite the implementation of control measures, which motivates the revision of current screening strategies. The vaginal microbiota could play a major role in preventing sexually transmitted infections through ecological competition and metabolites, such as lactic acid production. The vaginal microbiota corresponds to a fine-tuned equilibrium likely to be modified by exposures such as sexual practices, hygiene practices, antibiotics but also presence of pathogens. The overall objective of this thesis is to study the association in this triangle composed of external exposures, vaginal microbiota and CT infection, through the study of the vaginal microbiota composition and dynamics. We aimed at answering these questions: are there biomarkers of CT infection in the vaginal microbiota? Are the vaginal microbiota composition and structure modified by CT infection and antibiotic consumption? What are the exposures associated with perturbations of the vaginal microbiota? To answer these questions, the first step consisted of a state of the art to estimate the association between vaginal microbiota and CT infection in the literature, as well as three other clinically relevant sexually transmitted infections, and to evaluate the role of several factors in the observed heterogeneity between studies. In a second step, we estimated this association using molecular characterization of the vaginal microbiota in two studies in France and in the United States. We showed that Lactobacillus iners-dominated communities (CST III) and Lactobacillus-deprived communities (CST IV) were over-represented among CT-positive women. By studying the vaginal microbiota after azithromycin treatment and CT clearance in the American study, we showed that the vaginal microbiota did not evolve towards an optimal state, suggesting that women may stay at risk of CT reinfections. Finally, in two longitudinal studies using frequent sampling in the United States, we studied exposures associated with incidence and clearance of a CST IV. We showed that when the vaginal microbiota was not dominated by L. iners, menses was the main factor associated with incidence and clearance of a CST IV, while for women whose vaginal microbiota is dominated by L. iners, menses but also lubricant use, douching, ethnic origins, age and condomless vaginal sex were associated with CST IV incidence and/or clearance. Therefore, this thesis allowed on the one hand to confirm the association between Lactobacillus-deprived vaginal microbiota and CT infection using genome sequencing, and on the other hand to single out L. iners from other Lactobacillus spp. and to evaluated the risk associated with CST III. By enabling a better understanding of the natural history of CT and of the vaginal microbiota dynamics, we hope to contribute to improving strategies for the control of CT infection and other STIs. The innovative potential of the project lies in the use of molecular methods, which allows refining of our approach of health management by integrating individual predisposition to sexually transmitted infections, thus paving the way for personalized medicine
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Sieksmeyer, Thorben [Verfasser]. "Host-microbiome-pathogen interactions in cockroaches / Thorben Sieksmeyer." Berlin : Freie Universität Berlin, 2021. http://d-nb.info/1231276096/34.

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Jacob, Staffan. "Microbiome, communication and reproduction : host-microbiome interactions and parent-offspring communication in birds." Toulouse 3, 2013. http://www.theses.fr/2013TOU30166.

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Les interactions entre les hôtes et leur microbiome sont probablement responsables de l'évolution de divers traits d'histoire de vie des hôtes. Pourtant, des approches expérimentales supportant cette hypothèse manquent encore. Dans cette thèse, nous avons étudié expérimentalement les effets du microbiome sur les coûts de la reproduction, le développement des jeunes, la communication et les défenses antimicrobiennes chez la mésange charbonnière (Parus major). Tout d'abord, nous montrons que le microbiome est impliqué dans la production par l'hôte des dommages oxydants inhérents à l'investissement dans la reproduction. Deuxièmement, nous avons trouvé que les femelles ajustent leur investissement en caroténoïdes dans leurs œufs en fonction de leur microbiome, et que l'exposition microbienne affecte la croissance des jeunes et leur condition à l'envol. Troisièmement, nous résultats suggèrent que les microorganismes ne dégradent pas la coloration du plumage chez des oiseaux sauvages, mais que l'exposition à des microorganismes lors de la reproduction influence l'investissement dans de nouvelles plumes durant la mue suivante. Finalement, nous avons montré que les mésanges modifient leur investissement dans leur glande uropygienne, un organe externe impliqué dans la régulation des microorganismes du plumage, en fonction de leur microbiome. Cette stratégie antimicrobienne qui diffère entre sexes pourrait alors permettre de réguler le microbiome du plumage. Nos résultats fournissent donc la première démonstration expérimentale de l'hypothèse stipulant que le microbiome joue un rôle dans l'évolution de traits d'histoire de vie des hôtes
Host-microbiome interactions have been pointed out to be potentially responsible for the evolution of numerous life history traits throughout the animal kingdom. However, experimental approaches are still lacking to support this hypothesis. In this thesis, we experimentally investigated the effects of the microbiome on the costs of reproduction, nestling development, communication and antimicrobial defences in Great tits (Parus major). Firstly, we showed that the microbiome mediated host oxidative damages inherent to investment in reproduction. Secondly, we found that females adjusted their investment of carotenoids in eggs depending on their microbiome, and that microbial exposure affected nestling growth and condition at fledging. Thirdly, our results suggest that microorganisms did not degrade feather colouration in wild birds, but microbial exposure during reproduction affected investment in new feathers during the following moult. Finally, we found that birds modified their investment in the uropygial gland, an external organ involved in the regulation of feather microbial communities, according to their microbiome. This antimicrobial strategy that differs between sexes could thus allowed regulation of feather microbiome. Our results consequently provide the first experimental evidence for the hypothesis that the microbiome plays a role in the evolution of host life history traits
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Alvarez, Contreras Carlos Alberto. "HOST-MICROBIOME INTERACTIONS AND REGULATION OF THE IMMUNE SYSTEM." Case Western Reserve University School of Graduate Studies / OhioLINK, 2021. http://rave.ohiolink.edu/etdc/view?acc_num=case1600446008947681.

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Mestdagh, Renaud. "Role of gut microbiome-host metabolic interactions in metabolic diseases." Thesis, Imperial College London, 2012. http://hdl.handle.net/10044/1/10003.

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The metabolic phenotype of any complex organism is dependent on a complex series of host and gut microbial gene (microbiome) interactions with diet. The microbiome itself can be affected by environmental factors such as stress, exposure to xenobiotics, lifestyle, and alterations in the mammalian-microbial-metabolic axis are associated with changes in disease factors. To understand further the impact of the commensal microbiota on the host metabolism, germ-free (GF) animals, inoculated with individual bacterial strains or complex microbiota, and conventional mice were characterised using 1H NMR spectroscopy and UPLC-MS-based metabolic profiling approaches, and by recording the physiological and immunological parameters. Higher systemic level of (D)-3-hydroxybutyrate and lower levels of circulating VLDL were observed in GF compared to conventional animals, indicating that the absence of gut microbiota stimulated lipolysis while it inhibited hepatic lipogenesis. Subsequently, the best inoculation procedure was obtained by inoculating single bacterial strains into individual animals followed by allowing the animals to exchange their microbes. Metabolic fingerprints showed that a 9 bacteria community is more able to regulate lipoprotein and circulating lipid levels compared to a 3 bacteria community. The origin of the inocula (mouse or human) impacts differently on the host metabolism since humanised mice were strongly disturbed (higher plasma triglyceride level) and displayed metabolic profiles similar to GF mice. Conversely, mouse-associated animals were physiologically, immunologically and metabolically similar to conventional animals. Finally, metabolic profiles and gut microbiota composition were statistically regressed and helped to identify specific bacteria, such as Ruminococcus lactaris and Faecalibacterium prausnitzii, and their putative role in the host homeostasis. To conclude, these results confirmed the influence of gut microbes on the host physiology and metabolism. This PhD thesis provides new insights into the role of gut bacteria to understand the microbial-related mechanisms that participate in the host lipid metabolism, potentially leading to development of obesity.
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Ibrahim, Khalid Subhi. "Biochemical interactions between the gut microbiome and host in obesity/type II diabetes." Thesis, Glasgow Caledonian University, 2017. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.743906.

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Boulange, Claire. "Metabonomic investigations of the mammalian host-gut microbiome interactions in obesity and metabolic diseases." Thesis, Imperial College London, 2013. http://hdl.handle.net/10044/1/24727.

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Obesity is known to contribute to the risk of developing type 2 diabetes mellitus, non-alcoholic fatty liver diseases, cancer, osteoarthritis and cardiovascular diseases. Obesity results from an imbalance between energy intake and energy expenditure but its aetiology is complex and not completely understood. Genetic and environmental factors, (high calorie diet, lack of physical activity) strongly influence the onset of obesity and metabolic diseases. Modifications of gut microbial-host metabolic interactions by dietary interventions also contribute to obesity and are associated with metabolic disturbances. Noticeably, some obese individuals seem protected from the development of metabolic diseases which highlight individual predispositions to obesity associated metabolic disturbances. It is therefore important to underpin the molecular mechanisms linked to obesity and the role of gut microbiota in the degradation of a healthy phenotype in an appropriate biological model. 1H nuclear magnetic spectroscopy and mass spectrometry analysis were employed to measure the abundant metabolites in C57BL/6 mouse urine, feces, and plasma. Metabolic profiles of mice subjected to dietary interventions were compared using multivariate statistics. Alterations of gut microbial ecosystem by dietary interventions were also assessed by 16s rRNA pyrosequencing of mouse fecal microbiota. When given a high fat diet, the obesity prone and obesity resistant mice showed differences in leucine catabolism and tricarboxylic cycle. This may indicate specific regulations of mitochondrial oxidative pathways during diet induced obesity (DIO), influencing obesity development and metabolic disturbances. Possible roles of gut microbiota in the regulation of mitochondrial oxidative pathways were also envisaged. Gut microbial remodelling by the supplementation of different prebiotic blends (galactosyl-oligosaccharides, fructosyl-oligosaccharides and inulin or galactosyl-oligosaccharides and cow milk oligosaccharides) during a high fat challenge also decreased obesity and low grade inflammation and affect mouse metabolism. Decreased gut bacterial amino acids fermentation by prebiotic supplementation may contribute to the improvement of mouse physiology during DIO.
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Desai, Prerak T. "Molecular Interactions of Salmonella with the Host Epithelium in Presence of Commensals." DigitalCommons@USU, 2011. https://digitalcommons.usu.edu/etd/1059.

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Food-borne infections are a major source of mortality and morbidity. Salmonella causes the highest number of Food-borne bacterial infections in the US. This work contributes towards developing strategies to control Salmonella by (a) defining receptors used by Salmonella to adhere to and invade the host epithelium; (b) developing a host receptor based rapid detection method for the pathogen in food matrix; (C) and defining mechanisms of how probiotics can help alleviate Salmonella-induced cell death in the host epithelium. We developed a cell-cell crosslinking method to discover host-microbe receptors, and discovered three new receptor-ligand interactions. Interaction of Salmonella Ef-Tu with Hsp90 from epithelial cells mediated adhesion, while interaction of Salmonella Ef-Tu with two host proteins that negatively regulate membrane ruffling (myosin phosphatase and alpha catenin) mediated adhesion and invasion. We also showed the role of host ganglioside GM1 in mediating invasion of epithelial cells by Salmonella. Further we exploited pathogen affinity for immobilized gangliosides to concentrate them out of solution and from complex food matrices for detection by qPCR. A sensitivity of 4 CFU/ml (3 hours) in samples without competing microflora was achieved. Samples with competing microflora had a sensitivity of 40,000 CFU/ml. Next we screened several probiotic strains for pathogen exclusion potential and found that Bifidobacterium longum subspp. infantis showed the highest potential for Salmonella enterica subspp. enterica ser. Typhimurium exclusion in a caco-2 cell culture model. B. infantis shared its binding specificity to ganglioside GM1 with S. ser. Typhimurium. Further, B. infantis completely inhibited Salmonella-induced caspase 8 and caspase 9 activity in intestinal epithelial cells. B. infantis also reduced the basal caspase 9 and caspase 3/7 activity in epithelial cells in absence of the pathogen. Western blots and gene expression profiling of epithelial cells revealed that the decreased caspase activation was concomitant with increased phosphorylation of pro-survival protein kinase Akt, increased expression of caspase inhibiting protein cIAP, and decreased expression of genes involved in mitochondrion organization, biogenesis and reactive oxygen species metabolic processes. Hence, B. infantis exerted its protective effects by repression of mitochondrial cell death pathway which was induced in the presence of S. ser. Typhimurium.
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Yoo, Christopher Charles. "Investigating the Role of Trimeric Autotransporter Adhesins in Fusobacterium nucleatum Pathogenesis." Thesis, Virginia Tech, 2019. http://hdl.handle.net/10919/101683.

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Fusobacterium nucleatum is a Gram-negative bacterium that serves as a bridging organism in polymicrobial biofilms within the oral cavity. Although the bacterium is abundant in healthy gingival tissue, recent studies have found that F. nucleatum is associated with a wide-spectrum of human diseases which include periodontal disease, preterm birth, endocarditis, colorectal cancer, and pancreatic cancer. Previous studies of F. nucleatum virulence have uncovered two surface adhesins, Fap2 and FadA, that interact with the surface of human cells; however, the study of new virulence factors was previously limited as there was no gene deletion system available to functionally analyze F. nucleatum proteins. Interestingly, F. nucleatum has a diverse landscape of structurally unique surface adhesins called Type 5c secreted trimeric autotransporter adhesins (TAAs), which are a family of proteins that are historically known for their contributions to bacterial pathogenesis. This dissertation encompasses the use of recombinant protein expression systems and newly developed gene deletion technology to provide a foundational understanding of the contribution of Type 5c secreted proteins in F. nucleatum pathogenesis. Our results show that the presence of TAAs on the surface of F. nucleatum contribute to the bacterium's ability to bind and invade human cells, establishing the need to characterize other F. nucleatum surface proteins. Additionally, our studies analyzed the proinflammatory landscape induced by F. nucleatum through the identification of specific cytokines that are being secreted during in vitro infections of human cells. Cytokine signaling is a critical aspect of the host cell immune response as it promotes the recruitment of immune cells to the site of infection for efficient clearance of bacterial pathogens. While it has been well established that F. nucleatum modulates the secretion of IL-8, our studies identified that the bacterium also promotes the secretion of CXCL1, which is an important signaling protein that promotes tumor metastases. Overall, the work provided in this dissertation has delivered the initial characterization of TAAs in F. nucleatum virulence, a framework for future studies of Type 5c secreted proteins in Fusobacterium pathogenesis, and the role of Fap2 and FadA in promoting pro-inflammatory and pro-metastatic signaling from colorectal cancer cells.
Master of Science in Life Sciences
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Harrison, Christy Anne, and Christy Anne Harrison. "The Role of Dysfunctional Na+/H+ Exchange in the Development of Dysbiosis and Subsequent Colitis." Diss., The University of Arizona, 2017. http://hdl.handle.net/10150/625602.

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The last half-century has seen a dramatic and alarming rise in the incidence of autoimmune disease in industrialized nations too rapid to be accounted for by genetics alone. Among those, Inflammatory Bowel Disease (IBD) has risen from a western disease affecting industrialized populations to an emerging global threat affecting diverse populations around the world. IBD is a complex disease that combines genetic susceptibility and environmental exposure, but one aspect appears to be clear: the involvement of the gut microbiome. Current thought holds that IBD is an autoimmune attack on commensal microbiota, causing extensive collateral damage to the host intestinal tissues in the process. However, it has remained unclear in the field whether the changes observed in the IBD microbiome are causative in nature or whether the microbiome is responding to already-underway inflammatory processes within the host. This dissertation investigates one host factor in particular with regard to the microbiome and the development of inflammation: sodium-hydrogen exchange at the brush border, mediated by sodium hydrogen exchanger 3 (NHE3). NHE3 is inhibited during active IBD, but its loss in knockout animals is also enough to promote spontaneous colitis in a microbiome-dependent fashion. This dissertation investigates the specific contribution of the microbiome in NHE3 knockout animals to determine whether loss of NHE3 may be mediating the onset of colitis through pro-inflammatory changes in the microbiome. Our results suggest that the microbiome fostered in an NHE3-deficient environment may accelerate the onset and severity of experimental colitis, though likely in concert with additional host factors.
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Books on the topic "Host-microbiome interaction"

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Singh, Ravindra Pal, Ramesh Kothari, Prakash G. Koringa, and Satya Prakash Singh, eds. Understanding Host-Microbiome Interactions - An Omics Approach. Singapore: Springer Singapore, 2017. http://dx.doi.org/10.1007/978-981-10-5050-3.

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Sun, Jun, and Pradeep K. Dudeja, eds. Mechanisms Underlying Host-Microbiome Interactions in Pathophysiology of Human Diseases. Boston, MA: Springer US, 2018. http://dx.doi.org/10.1007/978-1-4939-7534-1.

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Amaresan, N., A. Sankaranarayanan, D. Dhanasekaran, Dhiraj Paul, and Yogesh S. Shouche. Microbiome-Host Interactions. Taylor & Francis Group, 2021.

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Amaresan, N., A. Sankaranarayanan, D. Dhanasekaran, Dhiraj Paul, and Yogesh S. Shouche. Microbiome-Host Interactions. Taylor & Francis Group, 2021.

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Microbiome-Host Interactions. Taylor & Francis Group, 2021.

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Amaresan, N., A. Sankaranarayanan, D. Dhanasekaran, Dhiraj Paul, and Yogesh S. Shouche. Microbiome-Host Interactions. Taylor & Francis Group, 2021.

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Amaresan, N., A. Sankaranarayanan, D. Dhanasekaran, Dhiraj Paul, and Yogesh S. Shouche. Microbiome-Host Interactions. Taylor & Francis Group, 2021.

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Singh, Ravindra Pal, Ramesh Kothari, Prakash G. Koringa, and Satya Prakash Singh. Understanding Host-Microbiome Interactions - An Omics Approach: Omics of Host-Microbiome Association. Springer, 2018.

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Singh, Ravindra Pal, Ramesh Kothari, Prakash G. Koringa, and Satya Prakash Singh. Understanding Host-Microbiome Interactions - An Omics Approach: Omics of Host-Microbiome Association. Springer, 2017.

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Sun, Jun, and Pradeep K. Dudeja. Mechanisms Underlying Host-Microbiome Interactions in Pathophysiology of Human Diseases. Springer, 2018.

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Book chapters on the topic "Host-microbiome interaction"

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Roat, Chetana, and Meenu Saraf. "Unravelling the Interaction of Plant and Their Phyllosphere Microbiome." In Understanding Host-Microbiome Interactions - An Omics Approach, 157–72. Singapore: Springer Singapore, 2017. http://dx.doi.org/10.1007/978-981-10-5050-3_10.

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Dangar, Kruti G., Nirali M. Raiyani, Rupal D. Pandya, and Satya P. Singh. "Uncultivated Lineages and Host–Microbe Interaction in Saline Environment." In Understanding Host-Microbiome Interactions - An Omics Approach, 13–28. Singapore: Springer Singapore, 2017. http://dx.doi.org/10.1007/978-981-10-5050-3_2.

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Islam, Ekramul, and Kiron Bhakat. "Insights into the Structure, Function, and Dynamics of Rice Root and Rhizosphere-Associated Microbiome." In Microbiome-Host Interactions, 249–58. First edition. | Boca Raton : CRC Press, 2021.: CRC Press, 2021. http://dx.doi.org/10.1201/9781003037521-19.

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Resende Maldonado, Rafael, Ana Lúcia Alves Caram, Daniela Soares de Oliveira, Eliana Setsuko Kamimura, Mônica Roberta Mazalli, and Elizama Aguiar-Oliveira. "The Role of Probiotics and Prebiotics in the Composition of the Gut Microbiota and Their Influence on Inflammatory Bowel Disease, Obesity, and Diabetes." In Microbiome-Host Interactions, 113–28. First edition. | Boca Raton : CRC Press, 2021.: CRC Press, 2021. http://dx.doi.org/10.1201/9781003037521-10.

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Cundell, Diana R., and Manuela Tripepi. "Role of Dysregulation of the Human Oral and Gastrointestinal Microbiome in Chronic Inflammatory Disease." In Microbiome-Host Interactions, 157–78. First edition. | Boca Raton : CRC Press, 2021.: CRC Press, 2021. http://dx.doi.org/10.1201/9781003037521-12.

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Kalaiselvi, S., and A. Panneerselvam. "Growth Promotion Utility of the Plant Microbiome." In Microbiome-Host Interactions, 307–19. First edition. | Boca Raton : CRC Press, 2021.: CRC Press, 2021. http://dx.doi.org/10.1201/9781003037521-23.

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Mudgil, D. "Microbiome of Speleothems – Secondary Mineral Deposits." In Microbiome-Host Interactions, 323–31. First edition. | Boca Raton : CRC Press, 2021.: CRC Press, 2021. http://dx.doi.org/10.1201/9781003037521-24.

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Sarkar, Priyanka. "Biostatistics Including Multivariate Analysis Commonly Used for Microbiome Analysis/Study." In Microbiome-Host Interactions, 47–55. First edition. | Boca Raton : CRC Press, 2021.: CRC Press, 2021. http://dx.doi.org/10.1201/9781003037521-5.

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Haleem Khan, Ahmed Abdul. "Role of the Mycobiome in Agroecosystems." In Microbiome-Host Interactions, 275–93. First edition. | Boca Raton : CRC Press, 2021.: CRC Press, 2021. http://dx.doi.org/10.1201/9781003037521-21.

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Gowrishankar, Shanmugaraj, Arumugam Kamaladevi, and Shunmugiah Karutha Pandian. "Structure and Functional Role of Microbiome Associated with Specific Organs of Healthy Individuals." In Microbiome-Host Interactions, 59–68. First edition. | Boca Raton : CRC Press, 2021.: CRC Press, 2021. http://dx.doi.org/10.1201/9781003037521-6.

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Conference papers on the topic "Host-microbiome interaction"

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Fangmann, D., C. Knappe, A. Zietzsch, DM Schulte, K. Türk, A. Franke, and M. Laudes. "Bile acids as possible mediators of microbiome-host interaction." In Diabetes Kongress 2018 – 53. Jahrestagung der DDG. Georg Thieme Verlag KG, 2018. http://dx.doi.org/10.1055/s-0038-1641766.

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Elinav, Eran. "Abstract IA02: Host microbiome interactions in health and disease." In Abstracts: AACR Special Conference on the Microbiome, Viruses, and Cancer; February 21-24, 2020; Orlando, FL. American Association for Cancer Research, 2020. http://dx.doi.org/10.1158/1538-7445.mvc2020-ia02.

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WILSON, IAN A. "STRUCTURAL BASIS FOR HOST/COMMENSAL-MICROBE INTERACTIONS IN THE HUMAN DISTAL GUT MICROBIOME." In 23rd International Solvay Conference on Chemistry. WORLD SCIENTIFIC, 2014. http://dx.doi.org/10.1142/9789814603836_0017.

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Sazal, Musfiqur. "Signed Causal Bayesian Networks for Microbiomes." In LatinX in AI at Neural Information Processing Systems Conference 2019. Journal of LatinX in AI Research, 2019. http://dx.doi.org/10.52591/lxai2019120815.

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Inferring causality is the process of connecting causes with effects. Identifying even a single causal relationship from data is more valuable than observing dozens of correlations in a data set. Microbe-microbe and host-microbe interactions play a vital role in both health and disease. In this study, we investigate how to learn a causal structure from data from microbiome studies and its potential interpretation about events and processes in the microbial community under study. We report evidence that causal structure can extract colonization patterns even though the analysis only uses data with no temporal information
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Reports on the topic "Host-microbiome interaction"

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Matthew, Gray. Data from "Winter is Coming – Temperature Affects Immune Defenses and Susceptibility to Batrachochytrium salamandrivorans". University of Tennessee, Knoxville Libraries, January 2021. http://dx.doi.org/10.7290/t7sallfxxe.

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Environmental temperature is a key factor driving various biological processes, including immune defenses and host-pathogen interactions. Here, we evaluated the effects of environmental temperature on the pathogenicity of the emerging fungus, Batrachochytrium salamandrivorans (Bsal), using controlled laboratory experiments, and measured components of host immune defense to identify regulating mechanisms. We found that adult and juvenile Notophthalmus viridescens died faster due to Bsal chytridiomycosis at 14 ºC than at 6 and 22 ºC. Pathogen replication rates, total available proteins on the skin, and microbiome composition likely drove these relationships. Temperature-dependent skin microbiome composition in our laboratory experiments matched seasonal trends in wild N. viridescens, adding validity to these results. We also found that hydrophobic peptide production after two months post-exposure to Bsal was reduced in infected animals compared to controls, perhaps due to peptide release earlier in infection or impaired granular gland function in diseased animals. Using our temperature-dependent infection results, we performed a geographic analysis that suggested that N. viridescens populations in the northeastern United States and southeastern Canada are at greatest risk for Bsal invasion. Our results indicate that environmental temperature will play a key role in the epidemiology of Bsal and provide evidence that temperature manipulations may be a viable Bsal management strategy.
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Gottlieb, Yuval, Bradley Mullens, and Richard Stouthamer. investigation of the role of bacterial symbionts in regulating the biology and vector competence of Culicoides vectors of animal viruses. United States Department of Agriculture, June 2015. http://dx.doi.org/10.32747/2015.7699865.bard.

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Symbiotic bacteria have been shown to influence host reproduction and defense against biotic and abiotic stressors, and this relates to possible development of a symbiont-based control strategy. This project was based on the hypothesis that symbionts have a significant impact on Culicoides fitness and vector competence for animal viruses. The original objectives in our proposal were: 1. Molecular identification and localization of the newly-discovered symbiotic bacteria within C. imicola and C. schultzei in Israel and C. sonorensis in California. 2. Determination of the prevalence of symbiotic bacteria within different vector Culicoides populations. 3. Documentation of specific symbiont effects on vector reproduction and defense: 3a) test for cytoplasmic incompatibility in Cardinium-infected species; 3b) experimentally evaluate the role of the symbiont on infection or parasitism by key Culicoides natural enemies (iridescent virus and mermithid nematode). 4. Testing the role(s) of the symbionts in possible protection against infection of vector Culicoides by BTV. According to preliminary findings and difficulties in performing experimental procedures performed in other insect symbiosis systems where insect host cultures are easily maintained, we modified the last two objectives as follows: Obj. 3, we tested how symbionts affected general fitness of Israeli Culicoides species, and thoroughly described and evaluated the correlation between American Culicoides and their bacterial communities in the field. We also tried alternative methods to test symbiont-Culicoides interactions and launched studies to characterize low-temperature stress tolerances of the main US vector, which may be related to symbionts. Obj. 4, we tested the correlation between EHDV (instead of BTV) aquisition and Cardinium infection. Culicoides-bornearboviral diseases are emerging or re-emerging worldwide, causing direct and indirect economic losses as well as reduction in animal welfare. One novel strategy to reduce insects’ vectorial capacity is by manipulating specific symbionts to affect vector fitness or performance of the disease agent within. Little was known on the bacterial tenants occupying various Culicoides species, and thus, this project was initiated with the above aims. During this project, we were able to describe the symbiont Cardinium and whole bacterial communities in Israeli and American Culicoides species respectively. We showed that Cardinium infection prevalence is determined by land surface temperature, and this may be important to the larval stage. We also showed no patent significant effect of Cardinium on adult fitness parameters. We showed that the bacterial community in C. sonorensis varies significantly with the host’s developmental stage, but it varies little across multiple wastewater pond environments. This may indicate some specific biological interactions and allowed us to describe a “core microbiome” for C. sonorensis. The final set of analyses that include habitat sample is currently done, in order to separate the more intimately-associated bacteria from those inhabiting the gut contents or cuticle surface (which also could be important). We were also able to carefully study other biological aspects of Culicoides and were able to discriminate two species in C. schultzei group in Israel, and to investigate low temperature tolerances of C. sonorensis that may be related to symbionts. Scientific implications include the establishment of bacterial identification and interactions in Culicoides (our work is cited in other bacteria-Culicoides studies), the development molecular identification of C. schultzei group, and the detailed description of the microbiome of the immature and matched adult stages of C. sonorensis. Agricultural implications include understanding of intrinsic factors that govern Culicoides biology and population regulation, which may be relevant for vector control or reduction in pathogen transmission. Being able to precisely identify Culicoides species is central to understanding Culicoides borne disease epidemiology.
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Crowley, David E., Dror Minz, and Yitzhak Hadar. Shaping Plant Beneficial Rhizosphere Communities. United States Department of Agriculture, July 2013. http://dx.doi.org/10.32747/2013.7594387.bard.

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PGPR bacteria include taxonomically diverse bacterial species that function for improving plant mineral nutrition, stress tolerance, and disease suppression. A number of PGPR are being developed and commercialized as soil and seed inoculants, but to date, their interactions with resident bacterial populations are still poorly understood, and-almost nothing is known about the effects of soil management practices on their population size and activities. To this end, the original objectives of this research project were: 1) To examine microbial community interactions with plant-growth-promoting rhizobacteria (PGPR) and their plant hosts. 2) To explore the factors that affect PGPR population size and activity on plant root surfaces. In our original proposal, we initially prqposed the use oflow-resolution methods mainly involving the use of PCR-DGGE and PLFA profiles of community structure. However, early in the project we recognized that the methods for studying soil microbial communities were undergoing an exponential leap forward to much more high resolution methods using high-throughput sequencing. The application of these methods for studies on rhizosphere ecology thus became a central theme in these research project. Other related research by the US team focused on identifying PGPR bacterial strains and examining their effective population si~es that are required to enhance plant growth and on developing a simulation model that examines the process of root colonization. As summarized in the following report, we characterized the rhizosphere microbiome of four host plant species to determine the impact of the host (host signature effect) on resident versus active communities. Results of our studies showed a distinct plant host specific signature among wheat, maize, tomato and cucumber, based on the following three parameters: (I) each plant promoted the activity of a unique suite of soil bacterial populations; (2) significant variations were observed in the number and the degree of dominance of active populations; and (3)the level of contribution of active (rRNA-based) populations to the resident (DNA-based) community profiles. In the rhizoplane of all four plants a significant reduction of diversity was observed, relative to the bulk soil. Moreover, an increase in DNA-RNA correspondence indicated higher representation of active bacterial populations in the residing rhizoplane community. This research demonstrates that the host plant determines the bacterial community composition in its immediate vicinity, especially with respect to the active populations. Based on the studies from the US team, we suggest that the effective population size PGPR should be maintained at approximately 105 cells per gram of rhizosphere soil in the zone of elongation to obtain plant growth promotion effects, but emphasize that it is critical to also consider differences in the activity based on DNA-RNA correspondence. The results ofthis research provide fundamental new insight into the composition ofthe bacterial communities associated with plant roots, and the factors that affect their abundance and activity on root surfaces. Virtually all PGPR are multifunctional and may be expected to have diverse levels of activity with respect to production of plant growth hormones (regulation of root growth and architecture), suppression of stress ethylene (increased tolerance to drought and salinity), production of siderophores and antibiotics (disease suppression), and solubilization of phosphorus. The application of transcriptome methods pioneered in our research will ultimately lead to better understanding of how management practices such as use of compost and soil inoculants can be used to improve plant yields, stress tolerance, and disease resistance. As we look to the future, the use of metagenomic techniques combined with quantitative methods including microarrays, and quantitative peR methods that target specific genes should allow us to better classify, monitor, and manage the plant rhizosphere to improve crop yields in agricultural ecosystems. In addition, expression of several genes in rhizospheres of both cucumber and whet roots were identified, including mostly housekeeping genes. Denitrification, chemotaxis and motility genes were preferentially expressed in wheat while in cucumber roots bacterial genes involved in catalase, a large set of polysaccharide degradation and assimilatory sulfate reduction genes were preferentially expressed.
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