CeMbio - The<i>Caenorhabditis elegans</i>Microbiome Resource

Dirksen, Philipp; Assié, Adrien; Zimmermann, Johannes; Zhang, Fan; Tietje, Adina-Malin; Marsh, Sarah Arnaud; Félix, Marie‐Anne; Shapira, Michael Y.; Kaleta, Christoph; Schulenburg, Hinrich; Samuel, Buck S.

doi:10.1534/g3.120.401309

Cited by 122 publications

(237 citation statements)

References 78 publications

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“…Previous studies have assessed the natural C. elegans microbiota [18] by isolating and cultivating nematodes in decaying organic matter, and have isolated native bacterial strains by grinding the naturally colonized worms [30][31][32]45]. We isolated new bacterial strains from worms with a similar protocol (CR collection, Methods) and also utilized the MYb collection from Dirksen et al [32,60] which contains some of the bacteria persistently found in the C. elegans gut. From these two collections, we selected a phylogenetically diverse set of bacterial isolates, spanning four different phyla, to study the colonization patterns of native bacteria (Fig.…”

Section: Three-species Microbiotas Are Predicted By Pairwise Outcomesmentioning

confidence: 99%

Interspecies bacterial competition regulates community assembly in the C. elegans intestine

et al. 2021

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From insects to mammals, a large variety of animals hold in their intestines complex bacterial communities that play an important role in health and disease. To further our understanding of how intestinal bacterial communities assemble and function, we study the C. elegans microbiota with a bottom-up approach by feeding this nematode with bacterial monocultures as well as mixtures of two to eight bacterial species. We find that bacteria colonizing well in monoculture do not always do well in co-cultures due to interspecies bacterial interactions. Moreover, as community diversity increases, the ability to colonize the worm gut in monoculture becomes less important than interspecies interactions for determining community assembly. To explore the role of host–microbe adaptation, we compare bacteria isolated from C. elegans intestines and non-native isolates, and we find that the success of colonization is determined more by a species’ taxonomy than by the isolation source. Lastly, by comparing the assembled microbiotas in two C. elegans mutants, we find that innate immunity via the p38 MAPK pathway decreases bacterial abundances yet has little influence on microbiota composition. These results highlight that bacterial interspecies interactions, more so than host–microbe adaptation or gut environmental filtering, play a dominant role in the assembly of the C. elegans microbiota.

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Section: Three-species Microbiotas Are Predicted By Pairwise Outcomesmentioning

confidence: 99%

Interspecies bacterial competition regulates community assembly in the C. elegans intestine

et al. 2021

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“…While we highlight mouse models above, many additional organisms serve as powerful laboratory systems to reveal insights into the relationship between the microbiome and host transcription. Studies conducted in zebrafish (Murdoch and Rawls 2019), C. elegans (Dirksen et al 2020;Yang et al 2019), and Drosophila melanogaster (Broderick et al 2014;Douglas 2018;Elya et al 2016) for example, all have revealed the impact of the microbiome on immunity, metabolism, and developmental gene regulation.…”

Section: Relationship Between Microbiome and Gene Expression In Modelmentioning

confidence: 99%

The relationship between the gut microbiome and host gene expression: a review

2020

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Despite the growing knowledge surrounding host–microbiome interactions, we are just beginning to understand how the gut microbiome influences—and is influenced by—host gene expression. Here, we review recent literature that intersects these two fields, summarizing themes across studies. Work in model organisms, human biopsies, and cell culture demonstrate that the gut microbiome is an important regulator of several host pathways relevant for disease, including immune development and energy metabolism, and vice versa. The gut microbiome remodels host chromatin, causes differential splicing, alters the epigenetic landscape, and directly interrupts host signaling cascades. Emerging techniques like single-cell RNA sequencing and organoid generation have the potential to refine our understanding of the relationship between the gut microbiome and host gene expression in the future. By intersecting microbiome and host gene expression, we gain a window into the physiological processes important for fostering the extensive cross-kingdom interactions and ultimately our health.

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“…We also sought to model the functional redundancy observed in natural communities by including several taxonomically related bacterial strains from distinct wild C. elegans strains or habitats (range of 2-22 strains). BIGbiome complements simplified microbiomes like the recently developed 12-member CeMbio community 20 as it reflects the extensive strain level microbial diversity found in C. elegans natural microbiomes while still remaining experimentally tractable.…”

Section: Resultsmentioning

confidence: 99%

Natural genetic variation drives microbiome selection in theCaenorhabditis elegansgut

Zhang

Weckhorst

Assié

et al. 2021

Preprint

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Host genetic landscapes can shape microbiome assembly in the animal gut by contributing to the establishment of distinct physiological environments. However, the genetic determinants contributing to the stability and variation of these microbiome types remain largely undefined. Here, we use the free-living nematode Caenorhabditis elegans to identify natural genetic variation among wild strains of C. elegans strains that drives assembly of distinct microbiomes. To achieve this, we first established a diverse model microbiome that represents the phylogenetic and functional diversity naturally found in the C. elegans microbiome. Using this community, we show that C. elegans utilizes immune, xenobiotic and metabolic signaling pathways to favor the assembly of different microbiome types. Variations in these pathways were associated with the enrichment for specific commensals, including the Alphaproteobacteria Ochrobactrum. Using RNAi and mutant strains, we showed that host selection for Ochrobactrum is mediated specifically by host insulin signaling pathways. Ochrobactrum recruitment is blunted in the absence of daf-2/IGFR and requires the insulin signaling transcription factors daf-16/FOXO and pqm-1/SALL2. Further, the ability of C. elegans to enrich for Ochrobactrum is correlated positively with host outcomes, as animals that develop faster are larger and have higher gut Ochrobactrum colonization as adults. These results highlight a new role for the highly conserved insulin signaling pathways in the regulation of microbiome composition in C. elegans.

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CeMbio - TheCaenorhabditis elegansMicrobiome Resource

Cited by 122 publications

References 78 publications

Interspecies bacterial competition regulates community assembly in the C. elegans intestine

Interspecies bacterial competition regulates community assembly in the C. elegans intestine

The relationship between the gut microbiome and host gene expression: a review

Natural genetic variation drives microbiome selection in theCaenorhabditis elegansgut

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