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Deep sequencing and ecological characterization of gut microbial communities of diverse bumble bee species.

Lim HC, Chu CC, Seufferheld MJ, Cameron SA - PLoS ONE (2015)

Bottom Line: The most abundant and prevalent (occurring in 92% of the samples) bacterial OTU, based on 16S rRNA sequences, closely matched that of the previously described Betaproteobacteria species Snodgrassella alvi.Bacteria that were first described in bee-related external environments dominated a number of gut bacterial communities, suggesting that they are not strictly dependent on the internal gut environment.Using light and fluorescent microscopy, we demonstrated that the gut bacteria form a biofilm on the internal epithelial surface of the ileum, corroborating results obtained from Apis mellifera.

View Article: PubMed Central - PubMed

Affiliation: Department of Entomology, University of Illinois, Urbana, IL, 61801, United States of America.

ABSTRACT
Gut bacterial communities of bumble bees are correlated with defense against pathogens. Further understanding this host-microbe association is vitally important as bumble bees are currently experiencing global population declines, potentially due in part to emergent diseases. In this study, we used pyrosequencing and community fingerprinting (ARISA) to characterize the gut microbial communities of nine bumble species from across the Bombus phylogeny. Overall, we delimited 74 bacterial taxa (operational taxonomic units or OTUs) belonging to Betaproteobacteria, Gammaproteobacteria, Bacilli, Actinobacteria, Flavobacteria and Alphaproteobacteria. Each bacterial community was taxonomically simple, containing an average of 1.9 common (relative abundance per sample > 5%) bacterial OTUs. The most abundant and prevalent (occurring in 92% of the samples) bacterial OTU, based on 16S rRNA sequences, closely matched that of the previously described Betaproteobacteria species Snodgrassella alvi. Bacteria that were first described in bee-related external environments dominated a number of gut bacterial communities, suggesting that they are not strictly dependent on the internal gut environment. The ARISA data showed a correlation between bacterial community structures and the geographic locations where the bees were sampled, suggesting that at least a subset of the bacterial species may be transmitted environmentally. Using light and fluorescent microscopy, we demonstrated that the gut bacteria form a biofilm on the internal epithelial surface of the ileum, corroborating results obtained from Apis mellifera.

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Heatmap showing relative abundance of each bacterial OTU (rows) in each of the pyrosequencing sample (columns).On the left is a cladogram showing phylogenetic relationships of the OTUs (tip labels = representative sequence ID). The IDs of the OTUs are abbreviated by only keeping their unique, last five characters (e.g., HUSOE0I01BDDRB to BDDRB). On the right are classifications of the OTUs at two taxonomic levels, if available. For clarity, only labels for OTUs with relative abundance > 10% are shown. Atop the heatmap, a cladogram indicates phylogenetic relationships of the bee species investigated. The bars at the bottom of the graph indicate the phylogenetic clade in which each bee species falls. MD = Mendacibombus (subgenus). See S4 Fig. for fully labeled tips.
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pone.0118566.g002: Heatmap showing relative abundance of each bacterial OTU (rows) in each of the pyrosequencing sample (columns).On the left is a cladogram showing phylogenetic relationships of the OTUs (tip labels = representative sequence ID). The IDs of the OTUs are abbreviated by only keeping their unique, last five characters (e.g., HUSOE0I01BDDRB to BDDRB). On the right are classifications of the OTUs at two taxonomic levels, if available. For clarity, only labels for OTUs with relative abundance > 10% are shown. Atop the heatmap, a cladogram indicates phylogenetic relationships of the bee species investigated. The bars at the bottom of the graph indicate the phylogenetic clade in which each bee species falls. MD = Mendacibombus (subgenus). See S4 Fig. for fully labeled tips.

Mentions: For each pyrosequencing sample, we obtained 1,296 to 12,408 high-quality reads representing seven to 19 bacterial OTUs (Table 3). Sample-based rarefaction analysis showed that OTU richness curves largely plateaued. On the other hand, inter-sample rarefaction indicated that more bacterial OTUs are likely to be found with additional pyrosequencing samples (S3 Fig.). Three pyrosequencing samples, “IMPATIENS_MI”, “PENSYLVANICUS_FL” and “TERRESTRIS_FR”, had the highest estimated bacterial richness (10.4–11.9) when sequencing depth was normalized to that of “BOHEMICUS” (n = 1,296), the sample with the smallest number of reads (Table 3). While each pyrosequencing sample contained several OTUs (range: 7–19), many of the OTUs were rare (Fig. 2, S4 Fig.). In any particular sample, the maximum number of OTUs with relative abundance above 1% was five (average = 2.54 ± 1.20 [standard deviation, SE]) while the average number of OTUs with relative abundance above 5% was 1.92 ± 0.95 (S1 Table).


Deep sequencing and ecological characterization of gut microbial communities of diverse bumble bee species.

Lim HC, Chu CC, Seufferheld MJ, Cameron SA - PLoS ONE (2015)

Heatmap showing relative abundance of each bacterial OTU (rows) in each of the pyrosequencing sample (columns).On the left is a cladogram showing phylogenetic relationships of the OTUs (tip labels = representative sequence ID). The IDs of the OTUs are abbreviated by only keeping their unique, last five characters (e.g., HUSOE0I01BDDRB to BDDRB). On the right are classifications of the OTUs at two taxonomic levels, if available. For clarity, only labels for OTUs with relative abundance > 10% are shown. Atop the heatmap, a cladogram indicates phylogenetic relationships of the bee species investigated. The bars at the bottom of the graph indicate the phylogenetic clade in which each bee species falls. MD = Mendacibombus (subgenus). See S4 Fig. for fully labeled tips.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4359114&req=5

pone.0118566.g002: Heatmap showing relative abundance of each bacterial OTU (rows) in each of the pyrosequencing sample (columns).On the left is a cladogram showing phylogenetic relationships of the OTUs (tip labels = representative sequence ID). The IDs of the OTUs are abbreviated by only keeping their unique, last five characters (e.g., HUSOE0I01BDDRB to BDDRB). On the right are classifications of the OTUs at two taxonomic levels, if available. For clarity, only labels for OTUs with relative abundance > 10% are shown. Atop the heatmap, a cladogram indicates phylogenetic relationships of the bee species investigated. The bars at the bottom of the graph indicate the phylogenetic clade in which each bee species falls. MD = Mendacibombus (subgenus). See S4 Fig. for fully labeled tips.
Mentions: For each pyrosequencing sample, we obtained 1,296 to 12,408 high-quality reads representing seven to 19 bacterial OTUs (Table 3). Sample-based rarefaction analysis showed that OTU richness curves largely plateaued. On the other hand, inter-sample rarefaction indicated that more bacterial OTUs are likely to be found with additional pyrosequencing samples (S3 Fig.). Three pyrosequencing samples, “IMPATIENS_MI”, “PENSYLVANICUS_FL” and “TERRESTRIS_FR”, had the highest estimated bacterial richness (10.4–11.9) when sequencing depth was normalized to that of “BOHEMICUS” (n = 1,296), the sample with the smallest number of reads (Table 3). While each pyrosequencing sample contained several OTUs (range: 7–19), many of the OTUs were rare (Fig. 2, S4 Fig.). In any particular sample, the maximum number of OTUs with relative abundance above 1% was five (average = 2.54 ± 1.20 [standard deviation, SE]) while the average number of OTUs with relative abundance above 5% was 1.92 ± 0.95 (S1 Table).

Bottom Line: The most abundant and prevalent (occurring in 92% of the samples) bacterial OTU, based on 16S rRNA sequences, closely matched that of the previously described Betaproteobacteria species Snodgrassella alvi.Bacteria that were first described in bee-related external environments dominated a number of gut bacterial communities, suggesting that they are not strictly dependent on the internal gut environment.Using light and fluorescent microscopy, we demonstrated that the gut bacteria form a biofilm on the internal epithelial surface of the ileum, corroborating results obtained from Apis mellifera.

View Article: PubMed Central - PubMed

Affiliation: Department of Entomology, University of Illinois, Urbana, IL, 61801, United States of America.

ABSTRACT
Gut bacterial communities of bumble bees are correlated with defense against pathogens. Further understanding this host-microbe association is vitally important as bumble bees are currently experiencing global population declines, potentially due in part to emergent diseases. In this study, we used pyrosequencing and community fingerprinting (ARISA) to characterize the gut microbial communities of nine bumble species from across the Bombus phylogeny. Overall, we delimited 74 bacterial taxa (operational taxonomic units or OTUs) belonging to Betaproteobacteria, Gammaproteobacteria, Bacilli, Actinobacteria, Flavobacteria and Alphaproteobacteria. Each bacterial community was taxonomically simple, containing an average of 1.9 common (relative abundance per sample > 5%) bacterial OTUs. The most abundant and prevalent (occurring in 92% of the samples) bacterial OTU, based on 16S rRNA sequences, closely matched that of the previously described Betaproteobacteria species Snodgrassella alvi. Bacteria that were first described in bee-related external environments dominated a number of gut bacterial communities, suggesting that they are not strictly dependent on the internal gut environment. The ARISA data showed a correlation between bacterial community structures and the geographic locations where the bees were sampled, suggesting that at least a subset of the bacterial species may be transmitted environmentally. Using light and fluorescent microscopy, we demonstrated that the gut bacteria form a biofilm on the internal epithelial surface of the ileum, corroborating results obtained from Apis mellifera.

Show MeSH
Related in: MedlinePlus