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Impact of the Chromatin Remodeling Factor CHD1 on Gut Microbiome Composition of Drosophila melanogaster.

Sebald J, Willi M, Schoberleitner I, Krogsdam A, Orth-Höller D, Trajanoski Z, Lusser A - PLoS ONE (2016)

Bottom Line: Using high-throughput sequencing of 16S rRNA gene amplicons, we found that Chd1 deletion mutant flies exhibit significantly reduced microbial diversity compared to rescued control strains.Finally, diet supplementation experiments with Lactobacillus plantarum revealed that, in contrast to wild-type flies, Chd1 mutant flies were unable to maintain higher L. plantarum titres over time.Collectively, these data provide evidence that loss of the chromatin remodeler CHD1 has a major impact on the gut microbiome of Drosophila melanogaster.

View Article: PubMed Central - PubMed

Affiliation: Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria.

ABSTRACT
The composition of the intestinal microbiota of Drosophila has been studied in some detail in recent years. Environmental, developmental and host-specific genetic factors influence microbiome composition in the fly. Our previous work has indicated that intestinal bacterial load can be affected by chromatin-targeted regulatory mechanisms. Here we studied a potential role of the conserved chromatin assembly and remodeling factor CHD1 in the shaping of the gut microbiome in Drosophila melanogaster. Using high-throughput sequencing of 16S rRNA gene amplicons, we found that Chd1 deletion mutant flies exhibit significantly reduced microbial diversity compared to rescued control strains. Specifically, although Acetobacteraceae dominated the microbiota of both Chd1 wild-type and mutant guts, Chd1 mutants were virtually monoassociated with this bacterial family, whereas in control flies other bacterial taxa constituted ~20% of the microbiome. We further show age-linked differences in microbial load and microbiota composition between Chd1 mutant and control flies. Finally, diet supplementation experiments with Lactobacillus plantarum revealed that, in contrast to wild-type flies, Chd1 mutant flies were unable to maintain higher L. plantarum titres over time. Collectively, these data provide evidence that loss of the chromatin remodeler CHD1 has a major impact on the gut microbiome of Drosophila melanogaster.

No MeSH data available.


Loss of CHD1 causes decreased species diversity in the gut microbiome.(A) Relative abundance of bacterial families (97% similarity threshold) determined by 16S rDNA sequencing in Chd1WT/WT and Chd1-/- samples. Families present at levels less than 1.5% were summarized as “others“. (B) Heatmap of the 25 most abundant 97% identity OTUs within Chd1WT/WT and Chd1-/- guts. OTU classification down to the lowest level possible is shown. Color bars denote the relative abundance (log10 values) of each OTU within the respective sample. OTUs are clustered according to their average relative abundance. (C) Heatmap showing the abundance of Acetobacter and Lactobacillus species in Chd1WT/WT and Chd1-/- samples identified by alignment of sequencing reads to all respective sequences in the SILVA database at an identity threshold of 99%. All OTUs with fewer than 10 counts, were excluded. Color bars denote the relative abundance (log10 values) of each species within the respective sample.
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pone.0153476.g002: Loss of CHD1 causes decreased species diversity in the gut microbiome.(A) Relative abundance of bacterial families (97% similarity threshold) determined by 16S rDNA sequencing in Chd1WT/WT and Chd1-/- samples. Families present at levels less than 1.5% were summarized as “others“. (B) Heatmap of the 25 most abundant 97% identity OTUs within Chd1WT/WT and Chd1-/- guts. OTU classification down to the lowest level possible is shown. Color bars denote the relative abundance (log10 values) of each OTU within the respective sample. OTUs are clustered according to their average relative abundance. (C) Heatmap showing the abundance of Acetobacter and Lactobacillus species in Chd1WT/WT and Chd1-/- samples identified by alignment of sequencing reads to all respective sequences in the SILVA database at an identity threshold of 99%. All OTUs with fewer than 10 counts, were excluded. Color bars denote the relative abundance (log10 values) of each species within the respective sample.

Mentions: Investigation of the bacterial taxa associated with the gut of Chd1 mutant and wild-type flies revealed that at the phylum level, Proteobacteria accounted for more than 97% of total reads across all samples, whereas Firmicutes, which have been shown to normally be the second dominating phylum in adult flies [10,13], were strikingly underrepresented in our analysis. On the family level, the bacterial community associated with Chd1WT/WT guts was dominated by Acetobacteraceae, while Pseudomonadaceae, Enterobacteriaceae, Comamonadaceae and Staphylococcaceae together comprised ~19% of the microbiota. By contrast, these families were nearly absent (0.5%) in Chd1-mutant flies. Likewise, Lactobacillaceae, accounted for only 0.3% within the bacterial community of wild-type and 0.2% of that of mutant flies (Fig 2A, S3 Fig, Table 2). All of these families have been reported to be associated with Drosophila before [11]. The relative proportion of detected bacterial families changed only slightly when the above-described different filtering parameters were applied (S3 Fig, Table 2). We next performed cluster analysis of the 25 most abundant OTUs (classification down to the lowest level possible) across both samples. Consistent with the taxa summary (Fig 2A), OTUs assigned to the Pseudomonadaceae, Enterobacteriaceae, Comamonadaceae or Staphylococcaceae families grouped into the two clusters with the lowest relative abundance, whereas Acetobacteraceae dominated the two high abundance OTU clusters (Fig 2B). The differences between Chd1 mutant and wild-type samples were most pronounced in the two low abundance clusters, whereas the variations in the Acetobacter-dominated clusters were minor.


Impact of the Chromatin Remodeling Factor CHD1 on Gut Microbiome Composition of Drosophila melanogaster.

Sebald J, Willi M, Schoberleitner I, Krogsdam A, Orth-Höller D, Trajanoski Z, Lusser A - PLoS ONE (2016)

Loss of CHD1 causes decreased species diversity in the gut microbiome.(A) Relative abundance of bacterial families (97% similarity threshold) determined by 16S rDNA sequencing in Chd1WT/WT and Chd1-/- samples. Families present at levels less than 1.5% were summarized as “others“. (B) Heatmap of the 25 most abundant 97% identity OTUs within Chd1WT/WT and Chd1-/- guts. OTU classification down to the lowest level possible is shown. Color bars denote the relative abundance (log10 values) of each OTU within the respective sample. OTUs are clustered according to their average relative abundance. (C) Heatmap showing the abundance of Acetobacter and Lactobacillus species in Chd1WT/WT and Chd1-/- samples identified by alignment of sequencing reads to all respective sequences in the SILVA database at an identity threshold of 99%. All OTUs with fewer than 10 counts, were excluded. Color bars denote the relative abundance (log10 values) of each species within the respective sample.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4836739&req=5

pone.0153476.g002: Loss of CHD1 causes decreased species diversity in the gut microbiome.(A) Relative abundance of bacterial families (97% similarity threshold) determined by 16S rDNA sequencing in Chd1WT/WT and Chd1-/- samples. Families present at levels less than 1.5% were summarized as “others“. (B) Heatmap of the 25 most abundant 97% identity OTUs within Chd1WT/WT and Chd1-/- guts. OTU classification down to the lowest level possible is shown. Color bars denote the relative abundance (log10 values) of each OTU within the respective sample. OTUs are clustered according to their average relative abundance. (C) Heatmap showing the abundance of Acetobacter and Lactobacillus species in Chd1WT/WT and Chd1-/- samples identified by alignment of sequencing reads to all respective sequences in the SILVA database at an identity threshold of 99%. All OTUs with fewer than 10 counts, were excluded. Color bars denote the relative abundance (log10 values) of each species within the respective sample.
Mentions: Investigation of the bacterial taxa associated with the gut of Chd1 mutant and wild-type flies revealed that at the phylum level, Proteobacteria accounted for more than 97% of total reads across all samples, whereas Firmicutes, which have been shown to normally be the second dominating phylum in adult flies [10,13], were strikingly underrepresented in our analysis. On the family level, the bacterial community associated with Chd1WT/WT guts was dominated by Acetobacteraceae, while Pseudomonadaceae, Enterobacteriaceae, Comamonadaceae and Staphylococcaceae together comprised ~19% of the microbiota. By contrast, these families were nearly absent (0.5%) in Chd1-mutant flies. Likewise, Lactobacillaceae, accounted for only 0.3% within the bacterial community of wild-type and 0.2% of that of mutant flies (Fig 2A, S3 Fig, Table 2). All of these families have been reported to be associated with Drosophila before [11]. The relative proportion of detected bacterial families changed only slightly when the above-described different filtering parameters were applied (S3 Fig, Table 2). We next performed cluster analysis of the 25 most abundant OTUs (classification down to the lowest level possible) across both samples. Consistent with the taxa summary (Fig 2A), OTUs assigned to the Pseudomonadaceae, Enterobacteriaceae, Comamonadaceae or Staphylococcaceae families grouped into the two clusters with the lowest relative abundance, whereas Acetobacteraceae dominated the two high abundance OTU clusters (Fig 2B). The differences between Chd1 mutant and wild-type samples were most pronounced in the two low abundance clusters, whereas the variations in the Acetobacter-dominated clusters were minor.

Bottom Line: Using high-throughput sequencing of 16S rRNA gene amplicons, we found that Chd1 deletion mutant flies exhibit significantly reduced microbial diversity compared to rescued control strains.Finally, diet supplementation experiments with Lactobacillus plantarum revealed that, in contrast to wild-type flies, Chd1 mutant flies were unable to maintain higher L. plantarum titres over time.Collectively, these data provide evidence that loss of the chromatin remodeler CHD1 has a major impact on the gut microbiome of Drosophila melanogaster.

View Article: PubMed Central - PubMed

Affiliation: Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria.

ABSTRACT
The composition of the intestinal microbiota of Drosophila has been studied in some detail in recent years. Environmental, developmental and host-specific genetic factors influence microbiome composition in the fly. Our previous work has indicated that intestinal bacterial load can be affected by chromatin-targeted regulatory mechanisms. Here we studied a potential role of the conserved chromatin assembly and remodeling factor CHD1 in the shaping of the gut microbiome in Drosophila melanogaster. Using high-throughput sequencing of 16S rRNA gene amplicons, we found that Chd1 deletion mutant flies exhibit significantly reduced microbial diversity compared to rescued control strains. Specifically, although Acetobacteraceae dominated the microbiota of both Chd1 wild-type and mutant guts, Chd1 mutants were virtually monoassociated with this bacterial family, whereas in control flies other bacterial taxa constituted ~20% of the microbiome. We further show age-linked differences in microbial load and microbiota composition between Chd1 mutant and control flies. Finally, diet supplementation experiments with Lactobacillus plantarum revealed that, in contrast to wild-type flies, Chd1 mutant flies were unable to maintain higher L. plantarum titres over time. Collectively, these data provide evidence that loss of the chromatin remodeler CHD1 has a major impact on the gut microbiome of Drosophila melanogaster.

No MeSH data available.