Project description:Background: Germ-free or axenic organisms are valuable tools for studying immunity, digestion, and development in different hosts. Although most of these studies have been conducted on mice, recently, germ-free invertebrate models (e.g. Drosophila and Apis) are used due to their easy husbandry, low cost for production, maintenance and the high number of individuals per generation they produce. However, a limitation of using these insects is the simple bacterial community present in their guts. The gut of the American cockroach Periplaneta americana displays a complex gut bacterial community composed of hundreds of species. Using P. americana, we developed a germ-free omnivorous invertebrate model to investigate how gut bacteria stimulate and shape normal gut development and metabolism. To determine if the insect host is directly affected by the presence of specific members of their bacterial community, gnotobiotic cockroaches were generated by inoculating a set of various P. americana gut-endemic Gram-negative (Bacteroidetes; n=11) and Gram-positive (Firmicutes; n=2) bacterial strains into germ-free insects. Additionally, we were able to recover the ‘normal’ bacterial-induced gut phenotype by co-housing germ-free cockroaches with wildtype P. americana to produce gut-bacteria conventionalized insects. Changes in gene expression profiles from two distinct regions (midgut and hindgut) of P. americana guts were quantified by RNA-Seq analysis of the germfree, gnotobiotic and conventionalized insects. Basic transcriptomics description: High-resolution transcriptome profiling of germ-free, gnotobiotic, and conventionalized treated P. americana midgut and hindguts. Ca. 43 million reads were obtained for each treatment. A de-novo assembly of all sequence reads was performed by Trinity assembler. Transcriptome assembly yielded 369,082 gene models and 554,155 isoforms. After running Trinotate pipeline, 65,047 (12 %) these transcripts matched an annotated product in at least one of the reference databases used (Uniprot, pfam, KEGG, COG). Additionally, 1,008 putative bacterial genes were annotated in the P. americana genome and ultimately excluded from these analyses. After bacteria decontamination, 553,147 assembled isoforms were used for transcript quantification and differential expression analysis using the DESeq2 pipeline. DESeq2 analysis detected 6,730 and 3,958 differentially expressed transcripts among the germ-free, gnotobiotic and conventionalized treatments in P. americana hindgut and midgut, respectively.

Project description:Genome scale metabolic model of Drosophila gut microbe Acetobacter fabarum Abstract - An important goal for many nutrition-based microbiome studies is to identify the metabolic function of microbes in complex microbial communities and their impact on host physiology. This research can be confounded by poorly understood effects of community composition and host diet on the metabolic traits of individual taxa. Here, we investigated these multiway interactions by constructing and analyzing metabolic models comprising every combination of five bacterial members of the Drosophila gut microbiome (from single taxa to the five-member community of Acetobacter and Lactobacillus species) under three nutrient regimes. We show that the metabolic function of Drosophila gut bacteria is dynamic, influenced by community composition, and responsive to dietary modulation. Furthermore, we show that ecological interactions such as competition and mutualism identified from the growth patterns of gut bacteria are underlain by a diversity of metabolic interactions, and show that the bacteria tend to compete for amino acids and B vitamins more frequently than for carbon sources. Our results reveal that, in addition to fermentation products such as acetate, intermediates of the tricarboxylic acid (TCA) cycle, including 2-oxoglutarate and succinate, are produced at high flux and cross-fed between bacterial taxa, suggesting important roles for TCA cycle intermediates in modulating Drosophila gut microbe interactions and the potential to influence host traits. These metabolic models provide specific predictions of the patterns of ecological and metabolic interactions among gut bacteria under different nutrient regimes, with potentially important consequences for overall community metabolic function and nutritional interactions with the host.IMPORTANCE Drosophila is an important model for microbiome research partly because of the low complexity of its mostly culturable gut microbiota. Our current understanding of how Drosophila interacts with its gut microbes and how these interactions influence host traits derives almost entirely from empirical studies that focus on individual microbial taxa or classes of metabolites. These studies have failed to capture fully the complexity of metabolic interactions that occur between host and microbe. To overcome this limitation, we reconstructed and analyzed 31 metabolic models for every combination of the five principal bacterial taxa in the gut microbiome of Drosophila This revealed that metabolic interactions between Drosophila gut bacterial taxa are highly dynamic and influenced by cooccurring bacteria and nutrient availability. Our results generate testable hypotheses about among-microbe ecological interactions in the Drosophila gut and the diversity of metabolites available to influence host traits.

Dataset Information

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets