The Experts below are selected from a list of 166548 Experts worldwide ranked by ideXlab platform

Rob Knight - One of the best experts on this subject based on the ideXlab platform.

  • seasonal variation of postmortem Microbial Communities
    Forensic Science Medicine and Pathology, 2015
    Co-Authors: David O Carter, Jessica L Metcalf, Alexander Bibat, Rob Knight
    Abstract:

    Body-associated microbes were recently shown to change significantly during decomposition, undergoing an ecological succession in experimental conditions using rodent and swine models. We investigated Microbial succession in soils associated with swine carcasses under experimental field conditions in summer and winter. We demonstrate that these postmortem Microbial Communities change in a specific, reproducible fashion, and that soil microbes represent a significant component of the postmortem Microbial community, contrary to widespread belief in forensic science. However, the effects of decomposition on soil Microbial Communities were different in summer and winter. We suggest that the Microbial ecological succession will be useful in medicolegal death investigation; however, observations in winter might not be applicable to summer, which indicates a need for a greater understanding of the seasonality of decomposition.

  • Lake Microbial Communities are resilient after a whole-ecosystem disturbance
    The ISME Journal, 2012
    Co-Authors: Ashley Shade, Noah Fierer, Rob Knight, Jordan S Read, Nicholas D Youngblut, Timothy K Kratz, Noah R Lottig, Eric E Roden, Emily H Stanley, Jesse Stombaugh
    Abstract:

    Disturbances act as powerful structuring forces on ecosystems. To ask whether environmental Microbial Communities have capacity to recover after a large disturbance event, we conducted a whole-ecosystem manipulation, during which we imposed an intense disturbance on freshwater Microbial Communities by artificially mixing a temperate lake during peak summer thermal stratification. We employed environmental sensors and water chemistry analyses to evaluate the physical and chemical responses of the lake, and bar-coded 16S ribosomal RNA gene pyrosequencing and automated ribosomal intergenic spacer analysis (ARISA) to assess the bacterial community responses. The artificial mixing increased mean lake temperature from 14 to 20 °C for seven weeks after mixing ended, and exposed the microorganisms to very different environmental conditions, including increased hypolimnion oxygen and increased epilimnion carbon dioxide concentrations. Though overall ecosystem conditions remained altered (with hypolimnion temperatures elevated from 6 to 20 °C), bacterial Communities returned to their pre-manipulation state as some environmental conditions, such as oxygen concentration, recovered. Recovery to pre-disturbance community composition and diversity was observed within 7 (epilimnion) and 11 (hypolimnion) days after mixing. Our results suggest that some Microbial Communities have capacity to recover after a major disturbance.

Orkun S Soyer - One of the best experts on this subject based on the ideXlab platform.

  • synthetic Microbial Communities
    Current Opinion in Microbiology, 2014
    Co-Authors: Tobias Groskopf, Orkun S Soyer
    Abstract:

    While natural Microbial Communities are composed of a mix of microbes with often unknown functions, the construction of synthetic Microbial Communities allows for the generation of defined systems with reduced complexity. Used in a top-down approach, synthetic Communities serve as model systems to ask questions about the performance and stability of Microbial Communities. In a second, bottom-up approach, synthetic Microbial Communities are used to study which conditions are necessary to generate interaction patterns like symbiosis or competition, and how higher order community structure can emerge from these. Besides their obvious value as model systems to understand the structure, function and evolution of Microbial Communities as complex dynamical systems, synthetic Communities can also open up new avenues for biotechnological applications.

Daniel Sellers - One of the best experts on this subject based on the ideXlab platform.

  • massively parallel screening of synthetic Microbial Communities
    Proceedings of the National Academy of Sciences of the United States of America, 2019
    Co-Authors: Jared Kehe, Anthony Kulesa, Anthony Ortiz, Cheri M Ackerman, Sri Gowtham Thakku, Daniel Sellers
    Abstract:

    Microbial Communities have numerous potential applications in biotechnology, agriculture, and medicine. Nevertheless, the limited accuracy with which we can predict interspecies interactions and environmental dependencies hinders efforts to rationally engineer beneficial consortia. Empirical screening is a complementary approach wherein synthetic Communities are combinatorially constructed and assayed in high throughput. However, assembling many combinations of microbes is logistically complex and difficult to achieve on a timescale commensurate with Microbial growth. Here, we introduce the kChip, a droplets-based platform that performs rapid, massively parallel, bottom-up construction and screening of synthetic Microbial Communities. We first show that the kChip enables phenotypic characterization of microbes across environmental conditions. Next, in a screen of ∼100,000 multispecies Communities comprising up to 19 soil isolates, we identified sets that promote the growth of the model plant symbiont Herbaspirillum frisingense in a manner robust to carbon source variation and the presence of additional species. Broadly, kChip screening can identify multispecies consortia possessing any optically assayable function, including facilitation of biocontrol agents, suppression of pathogens, degradation of recalcitrant substrates, and robustness of these functions to perturbation, with many applications across basic and applied Microbial ecology.

Yong Wang - One of the best experts on this subject based on the ideXlab platform.

  • pyrosequencing reveals highly diverse and species specific Microbial Communities in sponges from the red sea
    The ISME Journal, 2011
    Co-Authors: Yong Wang, Jiangke Yang, Feras F Lafi, Abdulaziz M Alsuwailem, Peiyuan Qian
    Abstract:

    Marine sponges are associated with a remarkable array of microorganisms. Using a tag pyrosequencing technology, this study was the first to investigate in depth the Microbial Communities associated with three Red Sea sponges, Hyrtios erectus, Stylissa carteri and Xestospongia testudinaria. We revealed highly diverse sponge-associated bacterial Communities with up to 1000 Microbial operational taxonomic units (OTUs) and richness estimates of up to 2000 species. Altogether, 26 bacterial phyla were detected from the Red Sea sponges, 11 of which were absent from the surrounding sea water and 4 were recorded in sponges for the first time. Up to 100 OTUs with richness estimates of up to 300 archaeal species were revealed from a single sponge species. This is by far the highest archaeal diversity ever recorded for sponges. A non-negligible proportion of unclassified reads was observed in sponges. Our results demonstrated that the sponge-associated Microbial Communities remained highly consistent in the same sponge species from different locations, although they varied at different degrees among different sponge species. A significant proportion of the tag sequences from the sponges could be assigned to one of the sponge-specific clusters previously defined. In addition, the sponge-associated Microbial Communities were consistently divergent from those present in the surrounding sea water. Our results suggest that the Red Sea sponges possess highly sponge-specific or even sponge-species-specific Microbial Communities that are resistant to environmental disturbance, and much of their Microbial diversity remains to be explored.

Marco Tulio Angulo - One of the best experts on this subject based on the ideXlab platform.

  • A theoretical framework for controlling complex Microbial Communities
    Nature Communications, 2019
    Co-Authors: Marco Tulio Angulo, Claude H. Moog, Yang Yu Liu
    Abstract:

    Microbes form complex Communities that perform critical roles for the integrity of their environment or the well-being of their hosts. Controlling these Microbial Communities can help us restore natural ecosystems and maintain healthy human microbiota. However, the lack of an efficient and systematic control framework has limited our ability to manipulate these Microbial Communities. Here we fill this gap by developing a control framework based on the new notion of structural accessibility. Our framework uses the ecological network of the community to identify minimum sets of its driver species, manipulation of which allows controlling the whole community. We numerically validate our control framework on large Communities, and then we demonstrate its application for controlling the gut microbiota of gnotobiotic mice infected with Clostridium difficile and the core microbiota of the sea sponge Ircinia oros. Our results provide a systematic pipeline to efficiently drive complex Microbial Communities towards desired states.Controlling Microbial Communities could help restore ecosystems and maintain healthy microbiota. Here, the authors introduce the notion of structural accessibility and develop a framework to identify minimal sets of driver species, manipulation of which could allow control of a Microbial community.

  • mapping the ecological networks of Microbial Communities
    Nature Communications, 2017
    Co-Authors: Marco Tulio Angulo, Yandong Xiao, Jonathan Friedman, Matthew K Waldor, Scott T Weiss
    Abstract:

    Mapping the ecological networks of Microbial Communities is a necessary step toward understanding their assembly rules and predicting their temporal behavior. However, existing methods require assuming a particular population dynamics model, which is not known a priori. Moreover, those methods require fitting longitudinal abundance data, which are often not informative enough for reliable inference. To overcome these limitations, here we develop a new method based on steady-state abundance data. Our method can infer the network topology and inter-taxa interaction types without assuming any particular population dynamics model. Additionally, when the population dynamics is assumed to follow the classic Generalized Lotka–Volterra model, our method can infer the inter-taxa interaction strengths and intrinsic growth rates. We systematically validate our method using simulated data, and then apply it to four experimental data sets. Our method represents a key step towards reliable modeling of complex, real-world Microbial Communities, such as the human gut microbiota.

  • Controlling Microbial Communities: a theoretical framework
    bioRxiv, 2017
    Co-Authors: Marco Tulio Angulo, Claude H. Moog
    Abstract:

    Microbial Communities perform key functions for the host they associate with or the environment they reside in. Our ability to control those Microbial Communities is crucial for maintaining or even enhancing the well-being of their host or environment. But this potential has not been fully harvested due to the lack of a systematic method to control those complex Microbial Communities. Here we introduce a theoretical framework to rigorously address this challenge, based on the new notion of structural accessibility. This framework allows the identification of minimal sets of “driver species” through which we can achieve feasible control of the entire community. We apply our framework to control the core microbiota of a sea sponge and the gut microbiota of gnotobiotic mice infected with C. difficile. This control-theoretical framework fundamentally enhances our ability to effectively manage and control complex Microbial Communities, such as the human gut microbiota. In particular, the concept of driver species of a Microbial community holds translational promise in the design of probiotic cocktails for various diseases associated with disrupted microbiota.