Biofilms: an emergent form of bacterial life

Nature Reviews Microbiology, Год журнала: 2016, Номер 14(9), С. 563 - 575

Опубликована: Авг. 11, 2016

Язык: Английский

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The ecology of the microbiome: Networks, competition, and stability

Science, Год журнала: 2015, Номер 350(6261), С. 663 - 666

Опубликована: Ноя. 5, 2015

What makes the gut microbiome stable? Classically, we think of our as stable, benign, and cooperative. Recent experimental work is beginning to unpick essential functions that can be attributed stable microbiota humans. To able manipulate improve health, need understand community structure composition models quantify predict stability. Coyte et al. applied concepts tools from ecology assembly. Independently developed converged on a surprising answer: A high diversity species likely coexist stably when system dominated by competitive, rather than cooperative, interactions. Science , this issue p. 663

Язык: Английский

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Feed Your Friends: Do Plant Exudates Shape the Root Microbiome?

Trends in Plant Science, Год журнала: 2017, Номер 23(1), С. 25 - 41

Опубликована: Окт. 17, 2017

Язык: Английский

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Deciphering microbial interactions and detecting keystone species with co-occurrence networks

Frontiers in Microbiology, Год журнала: 2014, Номер 5

Опубликована: Май 20, 2014

Co-occurrence networks produced from microbial survey sequencing data are frequently used to identify interactions between community members. While this approach has potential reveal ecological processes, it been insufficiently validated due the technical limitations inherent in studying complex ecosystems. Here, we simulate multi-species communities with known interaction patterns using generalized Lotka-Volterra dynamics, construct co-occurrence networks, and evaluate how well underlying interactions, experimental parameters can affect network inference interpretation. We find that recapitulate under certain conditions, but they lose interpretability when effects of habitat filtering become significant. demonstrate suffer local hot spots spurious correlation neighborhood "hub" species engage many interactions. also topological features associated keystone networks. This study provides a substantiated framework guide environmental microbiologists construction interpretation datasets.

Язык: Английский

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Spatial structure, cooperation and competition in biofilms

Nature Reviews Microbiology, Год журнала: 2016, Номер 14(9), С. 589 - 600

Опубликована: Июль 25, 2016

Язык: Английский

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Emergent simplicity in microbial community assembly

Science, Год журнала: 2018, Номер 361(6401), С. 469 - 474

Опубликована: Авг. 3, 2018

Interchanging species of similar function Under natural conditions, bacteria form mixed, interacting communities. Understanding how such communities assemble and stabilize is important in a range contexts, from biotechnological applications to what happens our guts. Goldford et al. sampled the microbial soil plants containing hundreds thousands sequence variants. The organisms were passaged after culture low concentrations single carbon sources cross-fed with each other's metabolites; then, resulting sequenced using 16S ribosomal RNA, outcomes modeled mathematically. mix that survived under steady conditions converged reproducibly reflect experimentally imposed rather than initially inoculated—although at coarse phylogenetic levels, taxonomic patterns persisted. Science , this issue p. 469

Язык: Английский

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Bacterial siderophores in community and host interactions

Nature Reviews Microbiology, Год журнала: 2019, Номер 18(3), С. 152 - 163

Опубликована: Ноя. 20, 2019

Язык: Английский

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Metabolic dependencies drive species co-occurrence in diverse microbial communities

Proceedings of the National Academy of Sciences, Год журнала: 2015, Номер 112(20), С. 6449 - 6454

Опубликована: Май 4, 2015

Microbial communities populate most environments on earth and play a critical role in ecology human health. Their composition is thought to be largely shaped by interspecies competition for the available resources, but cooperative interactions, such as metabolite exchanges, have also been implicated community assembly. The prevalence of metabolic interactions microbial communities, however, has remained unknown. Here, we systematically survey, using genome-scale modeling approach, extent resource exchanges over 800 communities. We find that, despite marked at level whole assemblies, harbor metabolically interdependent groups that recur across diverse habitats. By enumerating flux-balanced these co-occurring subcommunities predict likely exchanged metabolites, amino acids sugars, can promote group survival under nutritionally challenging conditions. Our results highlight dependencies major driver species co-occurrence hint recurring modules architecture.

Язык: Английский

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Challenges in microbial ecology: building predictive understanding of community function and dynamics

The ISME Journal, Год журнала: 2016, Номер 10(11), С. 2557 - 2568

Опубликована: Март 29, 2016

Abstract The importance of microbial communities (MCs) cannot be overstated. MCs underpin the biogeochemical cycles earth’s soil, oceans and atmosphere, perform ecosystem functions that impact plants, animals humans. Yet our ability to predict manage function these highly complex, dynamically changing is limited. Building predictive models link MC composition a key emerging challenge in ecology. Here, we argue addressing this requires close coordination experimental data collection method development with mathematical model building. We discuss specific examples where model–experiment integration has already resulted important insights into structure. also highlight research questions still demand better experiments models. such needed achieve significant progress understanding dynamics function, make practical suggestions as how could achieved.

Язык: Английский

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Bacterial Communities: Interactions to Scale

Frontiers in Microbiology, Год журнала: 2016, Номер 7

Опубликована: Авг. 8, 2016

In the environment, bacteria live in complex multispecies communities. These communities span scale from small, multicellular aggregates to billions or trillions of cells within gastrointestinal tract animals. The dynamics bacterial are determined by pairwise interactions that occur between different species community. Though a few at time, outcomes these interchanges have ramifications ripple through many orders magnitude, and ultimately affect macroscopic world including health host organisms. this review we cover how competition influences structures We also emphasize methods insights garnered culture-dependent interaction studies, metagenomic analyses, modeling experiments. Finally, argue integration multiple approaches will be instrumental future understanding underlying

Язык: Английский

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