Interrogation of Internal Workings in Microbial Community Assembly: Play a Game through a Behavioral Network?

Wang, Qian; Liu, Xinjuan; Jiang, Libo; Cao, Yige; Zhan, Xiang; Griffin, Christopher; Wu, Rongling

doi:10.1128/msystems.00550-19

Cited by 11 publications

(19 citation statements)

References 33 publications

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“…The host has the ability to modulate the development of microbial populations through a number of chemical compounds with antibiotic or anti-fungal properties 36 . Self-regulation of the different microbial communities is also true 37 . Thus, we notice in animals resistant to DCS an increase in 2,6-quinolediol 38 and Azelate 32 , while m-coumaric acid, i.e.…”

Section: Discussionmentioning

confidence: 99%

Evidence of a hormonal reshuffle in the cecal metabolome fingerprint of a strain of rats resistant to decompression sickness

Vallée

Dugrenot

Desruelle

et al. 2021

Sci Rep

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On one side, decompression sickness (DCS) with neurological disorders lead to a reshuffle of the fecal metabolome from rat caecum. On the other side, there is high inter-individual variability in terms of occurrence of DCS. One could wonder whether the fecal metabolome could be linked to the DCS-susceptibility. We decided to study male and female rats selected for their resistance to decompression sickness, and we hypothesize a strong impregnation concerning the fecal metabolome. The aim is to verify whether the rats resistant to the accident have a fecal metabolomic signature different from the stem generations sensitive to DCS. 39 DCS-resistant animals (21 females and 18 males), aged 14 weeks, were compared to 18 age-matched standard Wistar rats (10 females and 8 males), i.e., the same as those we used for the founding stock. Conventional and ChemRICH approaches helped the metabolomic interpretation of the 226 chemical compounds analyzed in the cecal content. Statistical analysis shows a panel of 81 compounds whose expression had changed following the selection of rats based on their resistance to DCS. 63 compounds are sex related. 39 are in common. This study shows the spectral fingerprint of the fecal metabolome from the caecum of a strain of rats resistant to decompression sickness. This study also confirms a difference linked to sex in the metabolome of non-selected rats, which disappear with selective breeding. Results suggest hormonal and energetic reshuffle, including steroids sugars or antibiotic compounds, whether in the host or in the microbial community.

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Section: Discussionmentioning

confidence: 99%

Evidence of a hormonal reshuffle in the cecal metabolome fingerprint of a strain of rats resistant to decompression sickness

Vallée

Dugrenot

Desruelle

et al. 2021

Sci Rep

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“…Several studies have identified highly interconnected ‘hub species’ in microbial networks that act as mediators between a host and its associated microbiome 15 , 32 . Yet, we are still unclear in which way microbes interact with each other to shape polymicrobial communities 33 . We know little about how microbiota members contribute to the establishment, stability, and resilience of microbial communities essential for the maintenance of plant health.…”

Section: Introductionmentioning

confidence: 99%

Network mapping of root–microbe interactions in Arabidopsis thaliana

Zhang

et al. 2021

npj Biofilms Microbiomes

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Understanding how plants interact with their colonizing microbiota to determine plant phenotypes is a fundamental question in modern plant science. Existing approaches for genome-wide association studies (GWAS) are often focused on the association analysis between host genes and the abundance of individual microbes, failing to characterize the genetic bases of microbial interactions that are thought to be important for microbiota structure, organization, and function. Here, we implement a behavioral model to quantify various patterns of microbe-microbe interactions, i.e., mutualism, antagonism, aggression, and altruism, and map host genes that modulate microbial networks constituted by these interaction types. We reanalyze a root-microbiome data involving 179 accessions of Arabidopsis thaliana and find that the four networks differ structurally in the pattern of bacterial-fungal interactions and microbiome complexity. We identify several fungus and bacterial hubs that play a central role in mediating microbial community assembly surrounding A. thaliana root systems. We detect 1142 significant host genetic variants throughout the plant genome and then implement Bayesian networks (BN) to reconstruct epistatic networks involving all significant SNPs, of which 91 are identified as hub QTLs. Results from gene annotation analysis suggest that most of the hub QTLs detected are in proximity to candidate genes, executing a variety of biological functions in plant growth and development, resilience against pathogens, root development, and abiotic stress resistance. This study provides a new gateway to understand how genetic variation in host plants influences microbial communities and our results could help improve crops by harnessing soil microbes.

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“…However, we found that competition between N-cycling groups may only explain a small part of the community change because N-cycling communities were only weakly correlated to each other. Instead, we propose that the heterogeneous response of individual probes is because of the different physiological responses bacteria and archaea evolve to cope with the environment and their interactions with other microbes [25]. Although not tested in this study, it is also possible that other microbes are competing with the Ncycling communities or that a bacterium that possesses a Ncycling gene may not necessarily utilize the gene, instead prioritizing the function of other genes.…”

Section: Discussionmentioning

confidence: 96%

The Diversity of Nitrogen-Cycling Microbial Genes in a Waste Stabilization Pond Reveals Changes over Space and Time that Is Uncoupled to Changing Nitrogen Chemistry

et al. 2020

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Nitrogen removal is an important process for wastewater ponds prior to effluent release. Bacteria and archaea can drive nitrogen removal if they possess the genes required to metabolize nitrogen. In the tropical savanna of northern Australia, we identified the previously unresolved microbial communities responsible for nitrogen cycling in a multi-pond wastewater stabilization system by measuring genomic DNA and cDNA for the following: nifH (nitrogen fixation); nosZ (denitrification); hzsA (anammox); archaeal AamoA and bacterial BamoA (ammonia oxidation); nxrB (nitrite oxidation); and nrfA (dissimilatory NO3 reduction to NH3). By collecting 160 DNA and 40 cDNA wastewater samples and measuring nitrogen (N)-cycling genes using a functional gene array, we found that genes from all steps of the N cycle were present and, except for nxrB, were also expressed. As expected, N-cycling communities showed daily, seasonal, and yearly shifts. However, contrary to our prediction, probes from most functional groups, excluding nosZ and AamoA, were different between ponds. Further, different genes that perform the same N-cycling role sometimes had different trends over space and time, resulting in only weak correlations between the different functional communities. Although N-cycling communities were correlated with wastewater nitrogen levels and physico-chemistry, the relationship was not strong enough to reliably predict the presence or diversity of N-cycling microbes. The complex and dynamic response of these genes to other functional groups and the changing physico-chemical environment provides insight into why altering wastewater pond conditions can result an abundance of some gene variants while others are lost.

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Interrogation of Internal Workings in Microbial Community Assembly: Play a Game through a Behavioral Network?

Cited by 11 publications

References 33 publications

Evidence of a hormonal reshuffle in the cecal metabolome fingerprint of a strain of rats resistant to decompression sickness

Evidence of a hormonal reshuffle in the cecal metabolome fingerprint of a strain of rats resistant to decompression sickness

Network mapping of root–microbe interactions in Arabidopsis thaliana

The Diversity of Nitrogen-Cycling Microbial Genes in a Waste Stabilization Pond Reveals Changes over Space and Time that Is Uncoupled to Changing Nitrogen Chemistry

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