Extensive intra-phylotype diversity in lactobacilli and bifidobacteria from the honeybee gut

Abstract

BackgroundIn the honeybee Apis mellifera, the bacterial gut community is consistently colonized by eight distinct phylotypes of bacteria. Managed bee colonies are of considerable economic interest and it is therefore important to elucidate the diversity and role of this microbiota in the honeybee. In this study, we have sequenced the genomes of eleven strains of lactobacilli and bifidobacteria isolated from the honey crop of the honeybee A. mellifera.ResultsSingle gene phylogenies confirmed that the isolated strains represent the diversity of lactobacilli and bifidobacteria in the gut, as previously identified by 16S rRNA gene sequencing. Core genome phylogenies of the lactobacilli and bifidobacteria further indicated extensive divergence between strains classified as the same phylotype. Phylotype-specific protein families included unique surface proteins. Within phylotypes, we found a remarkably high level of gene content diversity. Carbohydrate metabolism and transport functions contributed up to 45% of the accessory genes, with some genomes having a higher content of genes encoding phosphotransferase systems for the uptake of carbohydrates than any previously sequenced genome. These genes were often located in highly variable genomic segments that also contained genes for enzymes involved in the degradation and modification of sugar residues. Strain-specific gene clusters for the biosynthesis of exopolysaccharides were identified in two phylotypes. The dynamics of these segments contrasted with low recombination frequencies and conserved gene order structures for the core genes. Hits for CRISPR spacers were almost exclusively found within phylotypes, suggesting that the phylotypes are associated with distinct phage populations.ConclusionsThe honeybee gut microbiota has been described as consisting of a modest number of phylotypes; however, the genomes sequenced in the current study demonstrated a very high level of gene content diversity within all three described phylotypes of lactobacilli and bifidobacteria, particularly in terms of metabolic functions and surface structures, where many features were strain-specific. Together, these results indicate niche differentiation within phylotypes, suggesting that the honeybee gut microbiota is more complex than previously thought.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1476-6) contains supplementary material, which is available to authorized users.

Microorganisms in Honey

“…This access has been carried out mainly by sequencing the coding region of the 16S subunit of the bacterial ribosome [53,121,130], both from genomic DNA from microorganisms growing on selective media as Man-Rogosa-Sharpe agar, Sabouraud dextrose agar, and Candida agar [117,120,131,132], such as process-independent culture as specific PCR [68], denaturing gradient gel electrophoresis [124,125], mixed and deep 16S sequencing [49,128], pyrosequencing [53,116,121], and clone library [115,118,120,122]. While culturedependent methods are ideal for quantification of microorganisms and phenotypic testing, culture-independent methods generally have greater coverage in relation to the amount of different species accessed and are ideal for fingerprinting studies, and the identification of these species may be performed by real-time PCR analysis [49,68,125,128].…”

“…These methods, although they have different principles, were able to distinguish similarly the narrow niche of bacterial species and the diversity of strains present in these matrices [120]. In some works, the complete genome [132,133] or metagenome [114,115] of the narrow range of species of microorganisms is accessed, enabling the search for specific functions of these bacteria for beehives by gene annotation, PCR screening [114], and Post-Light TM ion semiconductor sequencing [127]. Fluorescent in situ hybridization microscopy has also been used to characterize distribution and abundance of specific phyla across the life cycle and among gut organs [68].…”

“…Several microorganisms present in the honey and in the gut of honeybees have antagonistic effects on honeybees and human pathogens, especially of Bacillus genus [123,134], lactic acid bacteria as Lactobacillus [71,121,124,[130][131][132]135], Enterococcus [130], Bifidobacteria [116,132,[136][137][138], and Acetobacteraceae [117,121,133]. These same microorganisms can be accessed for other purposes, such as its potential as fermenters [116,130,133] or probiotics [116].…”

Bartonella apis sp. nov., a honey bee gut symbiont of the class Alphaproteobacteria

“…In other environments, these bacteria have so far not been detected, which suggests specific adaptation to the gut of social bees. Genome sequencing projects have provided the first insights into the functional capabilities of the bee gut bacteria (Ellegaard et al, 2015;Engel et al, 2012;Kwong et al, 2014a, b). Furthermore, cultures of most community members have been established and species names proposed, such as Snodgrassella alvi (Betaproteobacteria), Gilliamella apicola and Frischella perrara (Gammaproteobacteria), Bifidobacterium asteroides (Actinobacteria) and Lactobacillus apis and Lactobacillus mellis (Firmicutes) (Engel et al, 2013;Killer et al, 2014;Olofsson et al, 2014).…”

Effect of water and resource availability on ant feeding preferences: a field experiment on the Mediterranean ant Crematogaster scutellaris

“…Genomic analyses and recent functional experimental studies suggest that this core microbial community is involved in a range of key functions including nutrition and health (Engel et al 2012;Kwong et al 2014;Engel et al 2014;Lee et al 2015;Ellegaard et al 2015;Engel et al 2015;Raymann et al 2017;Zheng et al 2017;Kešnerová et al 2017). Specifically, the gut community of worker honey bees is dominated by nine bacterial species clusters that make up 95-98% of the community (Jeyaprakash et al 2003;Babendreier et al 2006;Martinson et al 2011;Moran et al 2012;Sabree et al 2012;CorbyHarris et al 2014;Kwong et al 2017).…”