Host genetic variation in mucosal immunity pathways influences the upper airway microbiome

Gilad, Yoav; Nicolae, Dan L.; Pinto, Jayant M.; Ober, Carole

doi:10.1101/062232

Cited by 13 publications

(15 citation statements)

References 74 publications

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“…Similar examples have been reported in other host–microbe interactions, for instance, in coral− Symbiodinium symbioses (e.g. Tonk et al ., ), in the foliar fungal communities of the balsam poplar ( Populus balsamifera ; Bálint et al ., ), and, recently, in the human upper airway microbiome (Igartua et al ., ). These results highlight the importance of considering host genotype‐by‐environment interactions when studying patterns of symbiont community shifts.…”

Section: Discussionmentioning

confidence: 97%

Environment and host identity structure communities of green algal symbionts in lichens

et al. 2017

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SummaryAn understanding of how biotic interactions shape species' distributions is central to predicting host-symbiont responses under climate change. Switches to locally adapted algae have been proposed to be an adaptive strategy of lichen-forming fungi to cope with environmental change. However, it is unclear how lichen photobionts respond to environmental gradients, and whether they play a role in determining the fungal host's upper and lower elevational limits.Deep-coverage Illumina DNA metabarcoding was used to track changes in the community composition of Trebouxia algae associated with two phylogenetically closely related, but ecologically divergent fungal hosts along a steep altitudinal gradient in the Mediterranean region.We detected the presence of multiple Trebouxia species in the majority of thalli. Both altitude and host genetic identity were strong predictors of photobiont community assembly in these two species. The predominantly clonally dispersing fungus showed stronger altitudinal structuring of photobiont communities than the sexually reproducing host. Elevation ranges of the host were not limited by the lack of compatible photobionts.Our study sheds light on the processes guiding the formation and distribution of specific fungal-algal combinations in the lichen symbiosis. The effect of environmental filtering acting on both symbiotic partners appears to shape the distribution of lichens.

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Section: Discussionmentioning

confidence: 97%

Environment and host identity structure communities of green algal symbionts in lichens

et al. 2017

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“…While phylum‐level CST grouping may be the most easily understandable, as segregation into CST was often influenced by the species most commonly observed, it does not provide clear resolution of lineage functional interactions or how specific bacterial lineages may act as keystone species shaping wound bacterial community properties. Clarity about emergent wound community properties can be developed with future studies that integrate metagenome functional analysis and interaction network‐based approaches . The integration of ecological analytical approaches will allow development of predictive models of community succession of wound microbiomes in response to specific treatments, which may lead to improvements in strategies for antibiotic therapy.…”

Section: Discussionmentioning

confidence: 99%

Temporal dynamics of relative abundances and bacterial succession in chronic wound communities

Tipton

Mathew

Wolcott³

et al. 2017

Wound Repair Regeneration

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Polymicrobial bacterial infection is an important factor contributing to wound chronicity. Consequently, clinicians frequently adopt a biofilm-based wound care approach, in which wounds are treated utilizing DNA sequencing information about microbial communities. While more successful than treatment not using community information, there is little information about temporal dynamics of wound communities and optimal approaches over the course of treatment. To characterize these dynamics, temporal analysis over three sampling points was conducted for 167 chronic wounds. Across sampling intervals, wound communities from the same patients changed in composition, and most commonly shared less than 50% of observed species. There was a significant relationship between community similarity and time between sampling. Classifying wounds into state types, we found that communities frequently transitioned from Pseudomonas or Staphylococcus dominated, into a highly variable state type. Although low abundance microbial species are typically disregarded due to uncertainty of biological importance, we found that 80% of wound microbiomes included common or dominant species at subsequent time points that were in low abundance in earlier samples. Moreover, these species were often those known to frequently infect wounds. Results document compositional shifts through the course of treatment and suggest that routine consideration of low abundance species may improve biofilm-based wound care. Moreover, findings indicate that integrating ecological modeling to understand wound microbiome succession may lead to more informed therapy.

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“…Because a larger number of GWAS have been performed on the human and mouse microbiome, these models offer a glimpse of the advantages and challenges that await plant biologists as the library of microbiome‐associated variants grows. GWAS has successfully identified over 200 SNPs associated with variation in human microbiome composition (Knights et al ., ; Blekhman et al ., ; Davenport et al ., ; Bonder et al ., ; Goodrich et al ., ; Turpin et al ., ; Wang et al ., ; Demmitt et al ., ; Igartua et al ., ; Kolde et al ., ; Rothschild et al ., ), and a few genomic regions associated with microbiome composition in mice (Org et al ., ). The majority of these associations are with the relative abundances of individual bacterial families or genera, although some studies report associations with overall community composition or species richness (Wang et al ., ).…”

Section: Previous Workmentioning

confidence: 99%

Genome‐wide association studies on the phyllosphere microbiome: Embracing complexity in host–microbe interactions

et al. 2019

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Summary Environmental sequencing shows that plants harbor complex communities of microbes that vary across environments. However, many approaches for mapping plant genetic variation to microbe‐related traits were developed in the relatively simple context of binary host–microbe interactions under controlled conditions. Recent advances in sequencing and statistics make genome‐wide association studies (GWAS) an increasingly promising approach for identifying the plant genetic variation associated with microbes in a community context. This review discusses early efforts on GWAS of the plant phyllosphere microbiome and the outlook for future studies based on human microbiome GWAS. A workflow for GWAS of the phyllosphere microbiome is then presented, with particular attention to how perspectives on the mechanisms, evolution and environmental dependence of plant–microbe interactions will influence the choice of traits to be mapped.

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Host genetic variation in mucosal immunity pathways influences the upper airway microbiome

Cited by 13 publications

References 74 publications

Environment and host identity structure communities of green algal symbionts in lichens

Environment and host identity structure communities of green algal symbionts in lichens

Temporal dynamics of relative abundances and bacterial succession in chronic wound communities

Genome‐wide association studies on the phyllosphere microbiome: Embracing complexity in host–microbe interactions

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