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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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Consensus Bayesian inference tree showing phylogenetic relationships of representative sequences of 74 bacterial OTUs, and their classifications at the level of Class (classification bootstrap confidence in parenthesis).The IDs of the OTUs are abbreviated by only keeping their unique, last five characters (e.g., HUSOE0I01A9P4E to A9P4E). The tree was inferred by combining these sequences with 274 16S rRNA sequences from [42], followed by dropping the latter sequences from the tree using the drop.tip function found in the R package “ape”. Thickened branches indicate posterior probabilities of 90% or higher; stars signify sequences that have classification-phylogeny incompatibility. See S1 Fig. for classifications of the OTUs at various taxonomic levels. See S2 Fig. for the full trees that include sequences from [42].
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pone.0118566.g001: Consensus Bayesian inference tree showing phylogenetic relationships of representative sequences of 74 bacterial OTUs, and their classifications at the level of Class (classification bootstrap confidence in parenthesis).The IDs of the OTUs are abbreviated by only keeping their unique, last five characters (e.g., HUSOE0I01A9P4E to A9P4E). The tree was inferred by combining these sequences with 274 16S rRNA sequences from [42], followed by dropping the latter sequences from the tree using the drop.tip function found in the R package “ape”. Thickened branches indicate posterior probabilities of 90% or higher; stars signify sequences that have classification-phylogeny incompatibility. See S1 Fig. for classifications of the OTUs at various taxonomic levels. See S2 Fig. for the full trees that include sequences from [42].

Mentions: Concordance between the taxonomy assigned to sequences and their placement in the bacterial phylogeny was strong, as sequences possessing the same taxonomic classifications generally clustered together in the tree (Fig. 1, S1 Fig. and S2 Fig.). This was especially true for the full-length sequences from a previous work [42], where there were no classification-phylogeny mismatches at any taxonomic level, except for one case (at the Family level) in which a sequence assigned to Anaplasmataceae was phylogenetically nested within Rickettsiaceae, a sister Family within the same Order, Rickettsiales (S2 Fig.). Sequences assigned to Family-level bacterial phylotypes commonly found in honey bees were found in expected positions in the phylogeny. For example, sequences assigned to alpha-2.2 were found within Rhodospirillales, and those assigned to beta were found within Neisseriales (S1 Fig.). Of the 74 bacterial OTUs we delimited, representative sequences from only six (6.1%) showed classification-phylogeny mismatches, indicating that the short sequences made it more difficult to conduct classification and/or phylogeny placement (Fig. 1). These six sequences received relatively low bootstrap confidence scores from the naïve Bayesian classifier (at the Class level, average = 74.5%). Sequences belonging to OTUs with mismatches constitute a small portion of the total pool (0.24%) and thus have negligible effects on downstream analysis (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)

Consensus Bayesian inference tree showing phylogenetic relationships of representative sequences of 74 bacterial OTUs, and their classifications at the level of Class (classification bootstrap confidence in parenthesis).The IDs of the OTUs are abbreviated by only keeping their unique, last five characters (e.g., HUSOE0I01A9P4E to A9P4E). The tree was inferred by combining these sequences with 274 16S rRNA sequences from [42], followed by dropping the latter sequences from the tree using the drop.tip function found in the R package “ape”. Thickened branches indicate posterior probabilities of 90% or higher; stars signify sequences that have classification-phylogeny incompatibility. See S1 Fig. for classifications of the OTUs at various taxonomic levels. See S2 Fig. for the full trees that include sequences from [42].
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4359114&req=5

pone.0118566.g001: Consensus Bayesian inference tree showing phylogenetic relationships of representative sequences of 74 bacterial OTUs, and their classifications at the level of Class (classification bootstrap confidence in parenthesis).The IDs of the OTUs are abbreviated by only keeping their unique, last five characters (e.g., HUSOE0I01A9P4E to A9P4E). The tree was inferred by combining these sequences with 274 16S rRNA sequences from [42], followed by dropping the latter sequences from the tree using the drop.tip function found in the R package “ape”. Thickened branches indicate posterior probabilities of 90% or higher; stars signify sequences that have classification-phylogeny incompatibility. See S1 Fig. for classifications of the OTUs at various taxonomic levels. See S2 Fig. for the full trees that include sequences from [42].
Mentions: Concordance between the taxonomy assigned to sequences and their placement in the bacterial phylogeny was strong, as sequences possessing the same taxonomic classifications generally clustered together in the tree (Fig. 1, S1 Fig. and S2 Fig.). This was especially true for the full-length sequences from a previous work [42], where there were no classification-phylogeny mismatches at any taxonomic level, except for one case (at the Family level) in which a sequence assigned to Anaplasmataceae was phylogenetically nested within Rickettsiaceae, a sister Family within the same Order, Rickettsiales (S2 Fig.). Sequences assigned to Family-level bacterial phylotypes commonly found in honey bees were found in expected positions in the phylogeny. For example, sequences assigned to alpha-2.2 were found within Rhodospirillales, and those assigned to beta were found within Neisseriales (S1 Fig.). Of the 74 bacterial OTUs we delimited, representative sequences from only six (6.1%) showed classification-phylogeny mismatches, indicating that the short sequences made it more difficult to conduct classification and/or phylogeny placement (Fig. 1). These six sequences received relatively low bootstrap confidence scores from the naïve Bayesian classifier (at the Class level, average = 74.5%). Sequences belonging to OTUs with mismatches constitute a small portion of the total pool (0.24%) and thus have negligible effects on downstream analysis (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