Spatial organization of a model 15-member human gut microbiota established in gnotobiotic mice

Proceedings of the National Academy of Sciences, Год журнала: 2017, Номер 114(43)

Опубликована: Окт. 9, 2017

Significance Spatial structure is postulated to have a powerful influence on establishing and sustaining the signaling metabolic exchanges that define relationships among members of gut microbiota host. However, information about community spatial limited. Simultaneous imaging components 15-member model human bacterial over range scales in gnotobiotic mice revealed colon better conceptualized as an incompletely mixed bioreactor, rather than having sharply stratified luminal mucosal compartments. Identifying host microbial factors constrain ability establish sizeable single or oligotaxon agglomerations should yield new insights how “micro”-scale mixing defines function.

Язык: Английский

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Bacterial Unculturability and the Formation of Intercellular Metabolic Networks

Trends in Microbiology, Год журнала: 2017, Номер 25(5), С. 349 - 361

Опубликована: Апрель 5, 2017

Язык: Английский

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Evolutionary limits to cooperation in microbial communities

Proceedings of the National Academy of Sciences, Год журнала: 2014, Номер 111(50), С. 17941 - 17946

Опубликована: Дек. 1, 2014

Microbes produce many compounds that are costly to a focal cell but promote the survival and reproduction of neighboring cells. This observation has led suggestion microbial strains species will commonly cooperate by exchanging compounds. Here, we examine this idea with an ecoevolutionary model where microbes make multiple secretions, which can be exchanged among genotypes. We show cooperation between genotypes only evolves under specific demographic regimes characterized intermediate genetic mixing. The key constraint on cooperative exchanges is loss autonomy: become reliant complementary may not reliably encountered. Moreover, form observe arises through mutual exploitation related cheating "Black Queen" evolution for single secretion. A major corollary reduces community productivity relative autonomous strain makes everything it needs. prediction finds support in recent work from synthetic communities. Overall, our suggests natural selection often limit communities that, when do occur, they inefficient solution group living.

Язык: Английский

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Advancing microbial sciences by individual-based modelling

Nature Reviews Microbiology, Год журнала: 2016, Номер 14(7), С. 461 - 471

Опубликована: Июнь 6, 2016

Язык: Английский

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Privatization of cooperative benefits stabilizes mutualistic cross-feeding interactions in spatially structured environments

The ISME Journal, Год журнала: 2015, Номер 10(6), С. 1413 - 1423

Опубликована: Дек. 1, 2015

Язык: Английский

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Ecological modelling approaches for predicting emergent properties in microbial communities

Nature Ecology & Evolution, Год журнала: 2022, Номер 6(7), С. 855 - 865

Опубликована: Май 16, 2022

Язык: Английский

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Killing by Type VI secretion drives genetic phase separation and correlates with increased cooperation

Nature Communications, Год журнала: 2017, Номер 8(1)

Опубликована: Фев. 6, 2017

Abstract By nature of their small size, dense growth and frequent need for extracellular metabolism, microbes face persistent public goods dilemmas. Genetic assortment is the only general solution stabilizing cooperation, but all known mechanisms structuring microbial populations depend on availability free space, an often unrealistic constraint. Here we describe a class self-organization that operates within densely packed bacterial populations. Through mathematical modelling experiments with Vibrio cholerae, show how killing adjacent competitors via Type VI secretion system (T6SS) precipitates phase separation ‘Model A’ universality order-disorder transition mediated by killing. We mathematically demonstrate T6SS-mediated should favour evolution empirically support this prediction using phylogenetic comparative analysis. This work illustrates twin role played T6SS, dealing death to local while simultaneously creating conditions potentially favouring cooperation kin.

Язык: Английский

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Resource limitation drives spatial organization in microbial groups

The ISME Journal, Год журнала: 2015, Номер 10(6), С. 1471 - 1482

Опубликована: Ноя. 27, 2015

Abstract Dense microbial groups such as bacterial biofilms commonly contain a diversity of cell types that define their functioning. However, we have limited understanding what maintains, or purges, this diversity. Theory suggests resource levels are key to and the spatial arrangement genotypes in groups, but need empirical tests. Here use theory experiments study effects nutrient level on spatio-genetic structuring colonies. Well-fed colonies maintain larger well-mixed areas, they also expand more rapidly compared with poorly-fed ones. Given enough space expand, therefore, well-fed lose separate over similar timescale poorly fed In sum, long there is some degree limitation, observe emergence structured communities. We conclude resource-driven central both pattern process diverse

Язык: Английский

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Spatial organization of bacterial populations in response to oxygen and carbon counter-gradients in pore networks

Nature Communications, Год журнала: 2018, Номер 9(1)

Опубликована: Фев. 16, 2018

Microbial activity in soil is spatially heterogeneous often forming spatial hotspots that contribute disproportionally to biogeochemical processes. Evidence suggests bacterial organization contributes the persistence of anoxic even unsaturated soils. Such processes are difficult observe situ at microscale, hence mechanisms and time scales relevant for remain largely qualitative. Here we develop an experimental platform based on glass-etched micrometric pore networks mimics resource gradients postulated aggregates fluorescently tagged aerobic facultative anaerobic bacteria. Two initially intermixed species, Pseudomonas putida veronii, segregate into preferential regions promoted by opposing carbon oxygen (such persistent coexistence not possible well-mixed cultures). The study provides quantitative visualization modeling within aggregate-like hotspots, a key step towards developing mechanistic representation community pores.

Язык: Английский

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The Classification and Evolution of Bacterial Cross-Feeding

Frontiers in Ecology and Evolution, Год журнала: 2019, Номер 7

Опубликована: Май 14, 2019

Bacterial feeding has evolved towards specific evolutionary niches and the sources of energy differ between species strains. Although bacteria fundamentally compete for nutrients, excreted products from one strain may be preferred source or a essential nutrients another strain. The large variability in preferences bacterial strains often provides complex cross-feeding relationships bacteria, particularly environments such as human lower gut, which impacts on host's digestion nutrition. amount information is available strains, it important to consider evolution cross-feeding. Adaptation environmental stimuli continuous process, thus understanding microbial interactions allows us determine resilience populations changes this environment, nutrient supply, how new might emerge future. In review, we provide framework terminology dividing into four forms that can used classification analysis dynamics. Under proposed framework, discuss origins factors spatial structure influence their emergence subsequent persistence. This review draws both theoretical experimental literature cross-disciplinary perspective different types

Язык: Английский

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