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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.


Related in: MedlinePlus

Age-related changes of bacterial load and species distribution in Chd1 mutant and wild-type flies.(A) Flies of the indicated ages were surface-sterilized and homogenates were plated on Ace agar (left panel) to select for Acetobacteraceae or on MRS agar (right panel) to select for Lactobacillaceae. CFUs per fly were calculated and mean values from four biological replicates ±SEM were plotted. (B) Semiquantitative PCR was used to determine the relative amounts of Acetobacter “A” and Pseudomonas “P” species in guts of flies of the indicated ages. Band intensities were quantified and P/A ratios were calculated. Mean values ±SEM of three biological replicates are shown.
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pone.0153476.g003: Age-related changes of bacterial load and species distribution in Chd1 mutant and wild-type flies.(A) Flies of the indicated ages were surface-sterilized and homogenates were plated on Ace agar (left panel) to select for Acetobacteraceae or on MRS agar (right panel) to select for Lactobacillaceae. CFUs per fly were calculated and mean values from four biological replicates ±SEM were plotted. (B) Semiquantitative PCR was used to determine the relative amounts of Acetobacter “A” and Pseudomonas “P” species in guts of flies of the indicated ages. Band intensities were quantified and P/A ratios were calculated. Mean values ±SEM of three biological replicates are shown.

Mentions: To determine if differences in gut microbiome composition and titre between Chd1-/- and Chd1WT/WT flies persist during adult life, we employed PCR- and bacterial plating assays. Since our deep sequencing results showed that the majority of bacteria in both Chd1 mutant and control strains belongs to the Acetobacteraceae family, we plated Drosophila homogenates on the Ace medium semiselective for Acetobacteraceae [21] for estimation of bacterial numbers. Moreover, we used plating on MRS agar under microaerophil conditions to assay Lactobacillus load. In good agreement with earlier reports [17–19,21,42], bacterial titres increased with age in Chd1WT/WT flies but reached a plateau around 14 days of age. Chd1 mutant guts exhibited considerably higher Acetobacter titres at the earlier time points tested (4, 7, 10 days), while titres were roughly equal in mutant and control flies at days 14 and 21 (Fig 3A, left panel). Particularly on day 7, bacterial load was almost two orders of magnitude higher in Chd1-/- flies compared to Chd1WT/WT suggesting rapid accumulation of Acetobacteraceae in younger mutant flies. By contrast, Lactobacilli showed lower representation in younger Chd1 mutant flies compared to rescued control flies with progressively decreasing titres until day 10 of age. At days 14 and 21, Chd1 mutant and wild-type flies had again similar Lactobacillus levels (Fig 3A, right panel). These results confirm our results from the deep sequencing experiments (performed with 4 day old flies) that the loss of Chd1 correlates with an accumulation of Acetobacter and a decrease of Lactobacillus species in Drosophila.


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)

Age-related changes of bacterial load and species distribution in Chd1 mutant and wild-type flies.(A) Flies of the indicated ages were surface-sterilized and homogenates were plated on Ace agar (left panel) to select for Acetobacteraceae or on MRS agar (right panel) to select for Lactobacillaceae. CFUs per fly were calculated and mean values from four biological replicates ±SEM were plotted. (B) Semiquantitative PCR was used to determine the relative amounts of Acetobacter “A” and Pseudomonas “P” species in guts of flies of the indicated ages. Band intensities were quantified and P/A ratios were calculated. Mean values ±SEM of three biological replicates are shown.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0153476.g003: Age-related changes of bacterial load and species distribution in Chd1 mutant and wild-type flies.(A) Flies of the indicated ages were surface-sterilized and homogenates were plated on Ace agar (left panel) to select for Acetobacteraceae or on MRS agar (right panel) to select for Lactobacillaceae. CFUs per fly were calculated and mean values from four biological replicates ±SEM were plotted. (B) Semiquantitative PCR was used to determine the relative amounts of Acetobacter “A” and Pseudomonas “P” species in guts of flies of the indicated ages. Band intensities were quantified and P/A ratios were calculated. Mean values ±SEM of three biological replicates are shown.
Mentions: To determine if differences in gut microbiome composition and titre between Chd1-/- and Chd1WT/WT flies persist during adult life, we employed PCR- and bacterial plating assays. Since our deep sequencing results showed that the majority of bacteria in both Chd1 mutant and control strains belongs to the Acetobacteraceae family, we plated Drosophila homogenates on the Ace medium semiselective for Acetobacteraceae [21] for estimation of bacterial numbers. Moreover, we used plating on MRS agar under microaerophil conditions to assay Lactobacillus load. In good agreement with earlier reports [17–19,21,42], bacterial titres increased with age in Chd1WT/WT flies but reached a plateau around 14 days of age. Chd1 mutant guts exhibited considerably higher Acetobacter titres at the earlier time points tested (4, 7, 10 days), while titres were roughly equal in mutant and control flies at days 14 and 21 (Fig 3A, left panel). Particularly on day 7, bacterial load was almost two orders of magnitude higher in Chd1-/- flies compared to Chd1WT/WT suggesting rapid accumulation of Acetobacteraceae in younger mutant flies. By contrast, Lactobacilli showed lower representation in younger Chd1 mutant flies compared to rescued control flies with progressively decreasing titres until day 10 of age. At days 14 and 21, Chd1 mutant and wild-type flies had again similar Lactobacillus levels (Fig 3A, right panel). These results confirm our results from the deep sequencing experiments (performed with 4 day old flies) that the loss of Chd1 correlates with an accumulation of Acetobacter and a decrease of Lactobacillus species in Drosophila.

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.


Related in: MedlinePlus