Modelling spatial patterns in host-associated microbial communities
Matti O. Ruuskanen,Matti O. Ruuskanen,Guilhem Sommeria-Klein,Aki S. Havulinna,Teemu J. Niiranen,Teemu J. Niiranen,Teemu J. Niiranen,Leo Lahti +7 more
TLDR
In this article, the authors overview known factors affecting the composition of microbiota across diverse host types and at different scales, with a focus on the human gut as one of the most actively studied microbiota.Abstract:
Microbial communities exhibit spatial structure at different scales, due to constant interactions with their environment and dispersal limitation. While this spatial structure is often considered in studies focusing on free-living environmental communities, it has received less attention in the context of host-associated microbial communities or microbiota. The wider adoption of methods accounting for spatial variation in these communities will help to address open questions in basic microbial ecology as well as realize the full potential of microbiome-aided medicine. Here, we first overview known factors affecting the composition of microbiota across diverse host types and at different scales, with a focus on the human gut as one of the most actively studied microbiota. We outline a number of topical open questions in the field related to spatial variation and patterns. We then review the existing methodology for the spatial modelling of microbiota. We suggest that methodology from related fields, such as systems biology and macro-organismal ecology, could be adapted to obtain more accurate models of spatial structure. We further posit that methodological developments in the spatial modelling and analysis of microbiota could in turn broadly benefit theoretical and applied ecology and contribute to the development of novel industrial and clinical applications.read more
Citations
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Gut Microbiome Composition Is Predictive of Incident Type 2 Diabetes in a Population Cohort of 5,572 Finnish Adults
TL;DR: In this paper , the authors examined associations between gut microbiome composition and incident type 2 diabetes using multivariable-adjusted Cox regression models, and observed robust species-level taxonomic features predictive of incident Type 2 diabetes over long-term follow-up.
Journal ArticleDOI
Disentangling Diet- and Medium-Associated Microbes in Shaping Daphnia Gut Microbiome.
TL;DR: In this article, two Daphnia magna genotypes (genotype-1 and genotype-2) were respectively inoculated with three different inoculums: medium microbial inoculum, diet-associated microbial immunulum, and medium and diet-mixed microbial immunology.
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An experimental test of disease resistance function in the skin-associated bacterial communities of three tropical amphibian species.
Myra C. Hughey,Eria A. Rebollar,Reid N. Harris,Roberto Ibáñez,Stephen Loftus,Leanna L House,Kevin P. C. Minbiole,Molly C. Bletz,Daniel Medina,William C. Shoemaker,Meredith C. Swartwout,Lisa K. Belden +11 more
TL;DR: The findings indicate that microbially-mediated pathogen resistance is a complex trait that can vary within and across host species, and suggest that symbiont communities that have experienced prior selection for defensive microbes may be less likely to be disturbed by pathogen exposure.
Journal ArticleDOI
Towards standardized and reproducible research in skin microbiomes
Matti O. Ruuskanen,Deepti Vats,Renuka Potbhare,Ameeta RaviKumar,Eveliina Munukka,Richa Ashma,Leo Lahti +6 more
TL;DR: Application of standardized practices in the study of skin microbial communities could help to understand their complex structures, functional capacities, and health associations and increase the reproducibility of the research.
Journal ArticleDOI
PlanktoScope: Affordable Modular Quantitative Imaging Platform for Citizen Oceanography
Thibaut Pollina,Adam G. Larson,Fabien Lombard,Hongquan Li,D. Le Guen,Sébastien Colin,Colomban de Vargas,Manu Prakash +7 more
TL;DR: The PlanktoScope as discussed by the authors is a modular hardware/software open-source strategy for building a versatile, re-configurable imaging platform that can be adapted to a number of applications in aquatic biology and ecology.
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