Phenotypic responses to interspecies competition and commensalism in a naturally-derived microbial co-culture
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ABSTRACT:
PROVIDER: PRJNA406985 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6031200.fastq.gz | Fastqsanger.gz | |||
| SRR6031210.fastq.gz | Fastqsanger.gz | |||
| SRR6031220.fastq.gz | Fastqsanger.gz | |||
| SRR6031230.fastq.gz | Fastqsanger.gz | |||
| SRR6031240.fastq.gz | Fastqsanger.gz |
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Project description:The fundamental question of whether different microbial species will co-exist or compete in a given environment depends on context, composition and environmental constraints. Model microbial systems can yield some general principles related to this question. In this study we employed a naturally occurring co-culture composed of heterotrophic bacteria, Halomonas sp. HL-48 and Marinobacter sp. HL-58, to ask two fundamental scientific questions: 1) how do the phenotypes of two naturally co-existing species respond to partnership as compared to axenic growth? and 2) how do growth and molecular phenotypes of these species change with respect to competitive and commensal interactions? We hypothesized - and confirmed - that co-cultivation under glucose as the sole carbon source would result in competitive interactions. Similarly, when glucose was swapped with xylose, the interactions became commensal because Marinobacter HL-58 was supported by metabolites derived from Halomonas HL-48. Each species responded to partnership by changing both its growth and molecular phenotype as assayed via batch growth kinetics and global transcriptomics. These phenotypic responses depended on nutrient availability and so the environment ultimately controlled how they responded to each other. This simplified model community revealed that microbial interactions are context-specific and different environmental conditions dictate how interspecies partnerships will unfold.
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Project description:we develop an interspecies pluripotent stem cell (PSC) co-culture strategy and uncover a previously unknown mode of cell competition. Interspecies PSC competition occurs during primed but not naive pluripotency, and between evolutionarily distant species. We identified genes related to NF-κB signaling pathways, among others, were upregulated in loser cells and genetic inactivation of RELA, a core component of canonical NF-κB pathway, could overcome interspecies PSC competition. We further showed that an upstream regulator of the NF-κB signaling, MYD88 innate immune signal transduction adaptor, was also involved in promoting loser PSC elimination. Suppressing interspecies PSC competition via genetic perturbation of MYD88 or P65 improved engraftment of human cells in early post-implantation mouse embryos. Our study discovers a new paradigm of cell competition and paves the way for studying evolutionarily conserved cell competition mechanisms during early mammalian development. Strategies developed here to overcome interspecies PSC competition may facilitate interspecies organogenesis between evolutionary distant species, including humans.
2020-12-31 | GSE142394 | GEO
Project description:Testing of response of hetertrophic partners (Halomonas sp. HL-48 and Marinobacter sp. HL-58) to both axenic and co-culture growth using both glucose and xylose
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Project description:Cell competition as a barrier for interspecies chimerism between evolutionary distant species
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Project description:Among ~5,000,000 fungal species on Earth, Candida albicans is exceptional in its lifelong association with humans, where it exists either as a benign component of the gastrointestinal microbiome or as an invasive pathogen. Although it is generally assumed that invasiveness results from a breakdown of host immunity , it is also possible that specific fungal programs control the transition between these divergent lifestyles. Here, we report that exposure of C. albicans to the mammalian gut triggers a developmental switch, driven by the Wor1 transcription factor, to a commensal cell type. Wor1 has been thought to occur only in unique genetic backgrounds, but we show that WOR1 expression is triggered when wild-type cells are propagated in a murine gastrointestinal infection model. Similar to Wor1’s role in a white-opaque switch for mating, WOR1 overexpression within the host induces a novel switch affecting cell and colony morphology and conferring commensal fitness. However, these hyperfit GUT (Gastrointestinally-IndUced Transition) cells lack the functional hallmarks of opaque cells, which they resemble morphologically, whereas bona fide opaque cells are defective for commensalism. Instead, the GUT cell transcriptome is optimized for the environment of the distal mammalian digestive tract. The GUT cell type switch illuminates how a single organism can utilize distinct genetic programs to transition between commensalism and invasive tissue pathogenesis Candida albicans strains including the Wild type strain (SN425), WOR1OE -White (a/a, SN1044), WOR1OE -GUT (a/a, SN1045), White (a/a, SN966) and Opaque (a/a, SN967) were grown at room temperature in SC medium supplemented with 100ug/ml adenine; 2-4 biological replicates were performed per strain. RNA was prepared from these strains and samples were hybridized on custom Agilent C. albicans ORF arrays (15,000 spots/array, 70-mer probes).
2013-07-28 | E-GEOD-43972 | biostudies-arrayexpress
Project description:Among ~5,000,000 fungal species on Earth, Candida albicans is exceptional in its lifelong association with humans, where it exists either as a benign component of the gastrointestinal microbiome or as an invasive pathogen. Although it is generally assumed that invasiveness results from a breakdown of host immunity , it is also possible that specific fungal programs control the transition between these divergent lifestyles. Here, we report that exposure of C. albicans to the mammalian gut triggers a developmental switch, driven by the Wor1 transcription factor, to a commensal cell type. Wor1 has been thought to occur only in unique genetic backgrounds, but we show that WOR1 expression is triggered when wild-type cells are propagated in a murine gastrointestinal infection model. Similar to Wor1’s role in a white-opaque switch for mating, WOR1 overexpression within the host induces a novel switch affecting cell and colony morphology and conferring commensal fitness. However, these hyperfit GUT (Gastrointestinally-IndUced Transition) cells lack the functional hallmarks of opaque cells, which they resemble morphologically, whereas bona fide opaque cells are defective for commensalism. Instead, the GUT cell transcriptome is optimized for the environment of the distal mammalian digestive tract. The GUT cell type switch illuminates how a single organism can utilize distinct genetic programs to transition between commensalism and invasive tissue pathogenesis
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Project description:MreCD are required for correct cell shape, biofilm architecture and interspecies competition in Streptococcus mutans
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Project description:In present, interspecies cloning and interspecies-pregnancy were studied for endangered species rescue. However, the low implantation and survival ratio, spontaneous abortion, and unknown reason embryos absorption are the common and difficult problems of interspecies-pregnancy. In order to discover the mechanism of interspecies-pregnant failure and find ways to overcome the xeon-pregnant obstacles, we chosen the rat embryos pregnant in mouse uterus as a interspecies-pregnancy model. Three groups were set, mouse embryos to mouse recipients (MM) as control group, rat embryos to mouse recipients (RM), and rat and mouse embryos to mouse recipients together (RMM) as experiment groups. The former studies showed that rat embryos live no longer than day 7 of mouse pregnancy (D7). Our results showed that rat embryos survived to D7, and still existed to day 9 of mouse pregnancy (D9) in RM group. Surprisingly, the rat embryos survived to day 13 of the mouse gestation (D13) in RMM group. Microarray analysis was used to detect the global-gene expression profile changes of the whole implantation sites among the three groups at D7 and D9. By this way, we screened out the genes promoting the implanted rat embryos development in a mouse uterus which helped the rat embryos survive to D13 in RMM group compared with RM group, and the genes hindering the rat embryos development in a mouse uterus which prevented rat embryos living longer than D7 in RM group and D13 in RMM group compared with MM group. These findings provide insights into the mechanism of interspecies pregnant failure and new idea for interspecies pregnant studies. Experiment Overall Design: microarray was use to screen the genes among the day 7 and day 9 implantation sites of rat embryos implantation sites in a mouse uterus between rat embryos transfer to mouse recipients and rat embryos transfer to mouse recipients with mouse embryos. The mouse day7 and day 9 embryos implantation sites were use as control. Experiment Overall Design: totally 6 samples were analyzed, each samples two replications (one of them had three replications).
2008-06-12 | E-GEOD-4002 | biostudies-arrayexpress
Project description:Periods of social instability can elicit adaptive phenotypic plasticity to promote success in future competition. However, the underlying molecular mechanisms have primarily been studied in captive and lab-reared animals, leaving uncertainty as to how natural competition among free-living animals affects gene activity. Here, we experimentally generated social competition among wild, cavity-nesting female birds (tree swallows, Tachycineta bicolor). After territorial settlement, we reduced the availability of key breeding resources (i.e., nest boxes), generating heightened competition; within 24 hr we reversed the manipulation, causing aggressive interactions to subside. We sampled females during the peak of competition and 48hr after it ended, along with date-matched controls. We measured transcriptomic and epigenomic responses to competition in two socially relevant brain regions (hypothalamus and ventromedial telencephalon). Gene network analyses suggest that processes related to energy mobilization and social aggression (e.g., dopamine synthesis) were upregulated during competition, the latter of which persisted 2 days after competition had ended. Cellular maintenance processes were also downregulated after competition. Competition additionally altered methylation patterns, particularly in pathways related to hormonal signaling, which appeared transcriptionally poised to respond to future competition . Thus, experimental competition among free-living animals shifts gene expression in ways that may facilitate the demands of competition at the expense of self-maintenance. Further, some of these effects persisted after competition ended, demonstrating the potential for epigenetic biological embedding of the social environment in ways that could “prime” individuals for success in future social instability.
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