Cross-biome comparison of microbial association networks

Faust, Karoline; Lima‐Mendez, Gipsi; Lerat, Jean-Sébastien; Sathirapongsasuti, J. Fah; Knight, Rob; Huttenhower, Curtis; Lenaerts, Tom; Raes, Jeroen

doi:10.3389/fmicb.2015.01200

Cited by 155 publications

(128 citation statements)

References 70 publications

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“…Putative biotic interactions have been inferred from observational metagenomic studies, where positive or negative associations between microbial taxa are used as a proxy for positive or negative interactions (49–51). This approach can be confounded by the structure of relative abundance data of most metagenomic studies and by shared niche preferences of noninteracting organisms (52).…”

Section: Discussionmentioning

confidence: 99%

Biotic Interactions Shape the Ecological Distributions of Staphylococcus Species

Kastman

Kamelamela

Norville

et al. 2016

mBio

110

131

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Many metagenomic sequencing studies have observed the presence of closely related bacterial species or genotypes in the same microbiome. Previous attempts to explain these patterns of microdiversity have focused on the abiotic environment, but few have considered how biotic interactions could drive patterns of microbiome diversity. We dissected the patterns, processes, and mechanisms shaping the ecological distributions of three closely related Staphylococcus species in cheese rind biofilms. Paradoxically, the most abundant species (S. equorum) is the slowest colonizer and weakest competitor based on growth and competition assays in the laboratory. Through in vitro community reconstructions, we determined that biotic interactions with neighboring fungi help resolve this paradox. Species-specific stimulation of the poor competitor by fungi of the genus Scopulariopsis allows S. equorum to dominate communities in vitro as it does in situ. Results of comparative genomic and transcriptomic experiments indicate that iron utilization pathways, including a homolog of the S. aureus staphyloferrin B siderophore operon pathway, are potential molecular mechanisms underlying Staphylococcus-Scopulariopsis interactions. Our integrated approach demonstrates that fungi can structure the ecological distributions of closely related bacterial species, and the data highlight the importance of bacterium-fungus interactions in attempts to design and manipulate microbiomes.

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Section: Discussionmentioning

confidence: 99%

Biotic Interactions Shape the Ecological Distributions of Staphylococcus Species

Kastman

Kamelamela

Norville

et al. 2016

mBio

110

131

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“…6 Embeddedness of fungal OTUs with different distribution patterns in the communities in 1-year-old litter. Distributions of the network clustering coefficients are given for the OTUs of each distribution group according to Faust et al (2015). Colours code OTUs with distribution patterns as specified in Fig.…”

Section: Methodological Constraintsmentioning

confidence: 99%

“…To compare community structures between living and decaying leaves the dataset derived from 8 discs was used (Table S7). Network inference was adapted from Faust et al (2015), considering OTUs with a minimum occurrence in at least 3 samples from the respective plot. The obtained networks were visualized and processed as undirected networks in Cytoscape version 3.3.0 (Shannon et al 2003), with only positive edges being considered for the analyses.…”

Section: Statistical Analyses and Guild Delimitationmentioning

confidence: 99%

Transient leaf endophytes are the most active fungi in 1-year-old beech leaf litter

et al. 2017

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The ecological significance of fungi occurring asymptomatically inside living plant leaves is poorly understood. Given the broad saprotrophic potential of many endophytic fungi, we hypothesized that they persist in decaying litter for an extended period of time after leaf abscission. Fungal assemblages were assessed by highthroughput sequencing in autumn leaves of beech (Fagus sylvatica) and in the corresponding leaf litter in 388 samples from 22 beech forest plots in three widely distant regions of Germany. A considerable proportion of the leafendophytic fungi was also found in 1-year-old litter. Cooccurrence networks revealed that the fungi formed unstructured assemblages inside the living leaves, rather than well-structured communities. Previously endophytic fungi constituted an integral part of the fungal litter community and were by far the most active fungi in 1-year-old litter. We therefore consider these endophytic occurrences to represent transient stages. Composition of the aboveground microbiome appears therefore to be closely connected to the process of litter decomposition. Considering the respective linked fungal habitat will facilitate predicting nutrient and carbon cycling and storage in forest ecosystems as well as elucidating the ecology of leaf microbiomes.

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“…Host-associated microbiome networks (across several body sites and constructed with positive and negative interactions) showed higher connectedness (and network density) than soil networks (Faust et al 2015).…”

Section: Connectancementioning

confidence: 94%

“…Also, hostassociated networks contained more positive edges than soil microbial communities (Faust et al 2015;Friedman and Alm 2012) Invasion resistance arises in strongly interacting species-rich model competition communities (Case 1990) Transitive (hierarchical) competitive interactions are less stable than intransitive (cyclical) networks of competitive interactions (Petraitis 1979).…”

Section: Distribution Of Positive and Competitive Interactionsmentioning

confidence: 99%

Invasions of Host-Associated Microbiome Networks

Murall

Abbate

Touzel

et al. 2017

Networks of Invasion: Empirical Evidence and Case Studies

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International audienceThe study of biological invasions of ecological systems has much to offer research on within–host (WH) systems, particularly for understanding infections and developing therapies using biological agents. Thanks to the ground-work established in other fields, such as community ecology and evolutionary biology, and to modern methods of measurement and quantification, the study of microbiomes has quickly become a field at the forefront of modern systems biology. Investigations of host-associated microbiomes (e.g. for studying human health) are often centred on measuring and explaining the structure, functions and stability of these communities. This momentum promises to rapidly advance our understanding of ecological networks and their stability, resilience and resistance to invasions. However, intrinsic properties of host-associated microbiomes that differ from those of free-living systems present challenges to the development of a WH invasion ecology framework. The elucidation of principles underlying the invasibility of WH networks will ultimately help in the development of medical applications and help shape our understanding of human health and disease

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Cross-biome comparison of microbial association networks

Cited by 155 publications

References 70 publications

Biotic Interactions Shape the Ecological Distributions of Staphylococcus Species

Biotic Interactions Shape the Ecological Distributions of Staphylococcus Species

Transient leaf endophytes are the most active fungi in 1-year-old beech leaf litter

Invasions of Host-Associated Microbiome Networks

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