Limits...
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.

Show MeSH

Related in: MedlinePlus

Plot of pyrosequencing samples in the 2-D nMDS space based on inter-sample UniFrac distances (A).Minimum stress after 999 iterations is 0.05. The cluster of samples in the lower-left quadrate (ones without labels) is expanded in the top right corner (B).
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4359114&req=5

pone.0118566.g004: Plot of pyrosequencing samples in the 2-D nMDS space based on inter-sample UniFrac distances (A).Minimum stress after 999 iterations is 0.05. The cluster of samples in the lower-left quadrate (ones without labels) is expanded in the top right corner (B).

Mentions: Based on the UniFrac “all environments together” test, there was an overall significant difference among the pyrosequencing samples, a difference that was based on a combination of their community composition and the phylogenetic distances among the OTUs within the communities (P ≤ 0.01, after correcting for multiple comparisons). This difference was primarily driven by pyrosequencing samples “FRATERNUS_FL”, “USSURENSIS” and “CONVEXUS” (Table 5). The distinctiveness of these microbial communities was supported by NMDS and jackknife hierarchical clustering (Fig. 4 and S5 Fig.). The sample “CONVEXUS” was dominated by three bacterial OTUs, all of which were either absent or present at very low abundance in other pyrosequencing samples. These three OTUs included two closely related taxa belonging to the order of Lactobacillales (relative abundance = 50.3% and 37.5%, respectively) and one belonging to Oceanospirillales (11.2%) (Fig. 2, S4 Fig.). The sample “USSURENSIS” was dominated by a member of Lactobacillales (relative abundance = 99.3%), which occurred in significant abundance in only one other pyrosequencing sample (“TERRESTRIS_ARG”). The third highly distinctive pyrosequencing sample was “FRATERNUS_FL”. It contained two principal OTUs, belonging to Flavobacteriales (76.2%) and Enterobacteriales (17.1%), respectively. Both of these OTUs occurred in significant abundance in only 1–2 other gut bacterial communities (Fig. 2, S4 Fig.). The communities of five pyrosequencing samples (“TERRESTRIS_FR”, “IMPATIENS_GA”, “PENSYLVANICUS_FL”, “PENSYLVANICUS_NC”, and “ATRATUS”) were highly similar; they were all dominated (relative abundance > 94%) by an OTU whose representative sequence (HUSOE0I01A3N3V) closely matched that of S. alvi (see Gut bacterial taxa).


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)

Plot of pyrosequencing samples in the 2-D nMDS space based on inter-sample UniFrac distances (A).Minimum stress after 999 iterations is 0.05. The cluster of samples in the lower-left quadrate (ones without labels) is expanded in the top right corner (B).
© Copyright Policy
Related In: Results  -  Collection

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

pone.0118566.g004: Plot of pyrosequencing samples in the 2-D nMDS space based on inter-sample UniFrac distances (A).Minimum stress after 999 iterations is 0.05. The cluster of samples in the lower-left quadrate (ones without labels) is expanded in the top right corner (B).
Mentions: Based on the UniFrac “all environments together” test, there was an overall significant difference among the pyrosequencing samples, a difference that was based on a combination of their community composition and the phylogenetic distances among the OTUs within the communities (P ≤ 0.01, after correcting for multiple comparisons). This difference was primarily driven by pyrosequencing samples “FRATERNUS_FL”, “USSURENSIS” and “CONVEXUS” (Table 5). The distinctiveness of these microbial communities was supported by NMDS and jackknife hierarchical clustering (Fig. 4 and S5 Fig.). The sample “CONVEXUS” was dominated by three bacterial OTUs, all of which were either absent or present at very low abundance in other pyrosequencing samples. These three OTUs included two closely related taxa belonging to the order of Lactobacillales (relative abundance = 50.3% and 37.5%, respectively) and one belonging to Oceanospirillales (11.2%) (Fig. 2, S4 Fig.). The sample “USSURENSIS” was dominated by a member of Lactobacillales (relative abundance = 99.3%), which occurred in significant abundance in only one other pyrosequencing sample (“TERRESTRIS_ARG”). The third highly distinctive pyrosequencing sample was “FRATERNUS_FL”. It contained two principal OTUs, belonging to Flavobacteriales (76.2%) and Enterobacteriales (17.1%), respectively. Both of these OTUs occurred in significant abundance in only 1–2 other gut bacterial communities (Fig. 2, S4 Fig.). The communities of five pyrosequencing samples (“TERRESTRIS_FR”, “IMPATIENS_GA”, “PENSYLVANICUS_FL”, “PENSYLVANICUS_NC”, and “ATRATUS”) were highly similar; they were all dominated (relative abundance > 94%) by an OTU whose representative sequence (HUSOE0I01A3N3V) closely matched that of S. alvi (see Gut bacterial taxa).

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