Limits...
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.


The microbiome composition in the gut of Chd1-/- and Chd1WT/WT flies is significantly different.(A) Principal Coordinate Analysis (PCoA) plot depicting β-diversity by jackknifed UniFrac distances (normalized, weighted UniFrac metric) based on 97% similarity OTU assignments. Chd1WT/WT and Chd1-/- replicates differ considerably for PC1, which explains 89.1% of the total variation. To estimate the statistical significance of the clustering a two-sample t-test based on distance matrices (distances within all replicates versus distances between all replicates) was performed (P = 4.709 e-5). (B) Rarefaction curves of 97% identity OTUs for Chd1WT/WT and Chd1-/- sample replicates show exhaustive sampling depth.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4836739&req=5

pone.0153476.g001: The microbiome composition in the gut of Chd1-/- and Chd1WT/WT flies is significantly different.(A) Principal Coordinate Analysis (PCoA) plot depicting β-diversity by jackknifed UniFrac distances (normalized, weighted UniFrac metric) based on 97% similarity OTU assignments. Chd1WT/WT and Chd1-/- replicates differ considerably for PC1, which explains 89.1% of the total variation. To estimate the statistical significance of the clustering a two-sample t-test based on distance matrices (distances within all replicates versus distances between all replicates) was performed (P = 4.709 e-5). (B) Rarefaction curves of 97% identity OTUs for Chd1WT/WT and Chd1-/- sample replicates show exhaustive sampling depth.

Mentions: To examine the composition of the intestinal microbiome of Chd1 flies, we performed deep sequencing of 16S rRNA gene amplicons of guts isolated from Chd1-/- and control flies (Chd1WT/WT), which carried a wild-type Chd1 rescue transgene in a Chd1-deficient genetic background [27]. We isolated genomic DNA from guts of 4 days old virgins for PCR amplification of the variable regions V1 and V2 of the bacterial 16S rRNA gene. Using the Ion PGM sequencing platform for deep sequencing, we obtained a total of 1,451,602 reads after quality filtering representing a mean 241,933 reads per replicate. The preprocessed sequences were clustered into operational taxonomic units (OTUs) using the SILVA database [31] as a reference with a sequence identity threshold of 97%. Principal Coordinate Analysis (PCoA) revealed clear separation between Chd1 mutant and wild-type replicates with PC1 explaining 89.1% of the overall variation (Fig 1A). This was confirmed by a two-sample t-test applied on the calculated distance matrix using QIIME (P = 4.709 e-5). Thus, the difference in bacterial community composition of Chd1 mutant and wild-type samples correlates with the genetic background of the host flies, whereas variability among replicates of the same genotype only accounts for a minimal portion of the total disparity.


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)

The microbiome composition in the gut of Chd1-/- and Chd1WT/WT flies is significantly different.(A) Principal Coordinate Analysis (PCoA) plot depicting β-diversity by jackknifed UniFrac distances (normalized, weighted UniFrac metric) based on 97% similarity OTU assignments. Chd1WT/WT and Chd1-/- replicates differ considerably for PC1, which explains 89.1% of the total variation. To estimate the statistical significance of the clustering a two-sample t-test based on distance matrices (distances within all replicates versus distances between all replicates) was performed (P = 4.709 e-5). (B) Rarefaction curves of 97% identity OTUs for Chd1WT/WT and Chd1-/- sample replicates show exhaustive sampling depth.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4836739&req=5

pone.0153476.g001: The microbiome composition in the gut of Chd1-/- and Chd1WT/WT flies is significantly different.(A) Principal Coordinate Analysis (PCoA) plot depicting β-diversity by jackknifed UniFrac distances (normalized, weighted UniFrac metric) based on 97% similarity OTU assignments. Chd1WT/WT and Chd1-/- replicates differ considerably for PC1, which explains 89.1% of the total variation. To estimate the statistical significance of the clustering a two-sample t-test based on distance matrices (distances within all replicates versus distances between all replicates) was performed (P = 4.709 e-5). (B) Rarefaction curves of 97% identity OTUs for Chd1WT/WT and Chd1-/- sample replicates show exhaustive sampling depth.
Mentions: To examine the composition of the intestinal microbiome of Chd1 flies, we performed deep sequencing of 16S rRNA gene amplicons of guts isolated from Chd1-/- and control flies (Chd1WT/WT), which carried a wild-type Chd1 rescue transgene in a Chd1-deficient genetic background [27]. We isolated genomic DNA from guts of 4 days old virgins for PCR amplification of the variable regions V1 and V2 of the bacterial 16S rRNA gene. Using the Ion PGM sequencing platform for deep sequencing, we obtained a total of 1,451,602 reads after quality filtering representing a mean 241,933 reads per replicate. The preprocessed sequences were clustered into operational taxonomic units (OTUs) using the SILVA database [31] as a reference with a sequence identity threshold of 97%. Principal Coordinate Analysis (PCoA) revealed clear separation between Chd1 mutant and wild-type replicates with PC1 explaining 89.1% of the overall variation (Fig 1A). This was confirmed by a two-sample t-test applied on the calculated distance matrix using QIIME (P = 4.709 e-5). Thus, the difference in bacterial community composition of Chd1 mutant and wild-type samples correlates with the genetic background of the host flies, whereas variability among replicates of the same genotype only accounts for a minimal portion of the total disparity.

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.