Biology subjects

Ellegaard, K. M.

Publications and source records attributed to Ellegaard, K. M..

7 recordsLinked to original sources

bioRxiv2024

SARS-CoV-2 sequencing artifacts associated with targeted PCR enrichment and read mapping

Protocols and pipelines for SARS-CoV-2 genome sequencing were rapidly established when the COVID-19 outbreak was declared a pandemic. The most widely used approach for sequencing SARS-CoV-2 includes targeted enrichment by PCR, followed by shotgun sequencing and reference-based genome assembly. As the continued surveillance of SARS-CoV-2 worldwide is transitioning towards a lower level of intensity, it is timely to re-visit the sequencing protocols and pipelines established during the acute phase of the pandemic. In the current study, we have investigated the impact of primer scheme and reference genome choice by sequencing samples with multiple primer schemes (Artic V3, V4.1 and V5.3.2) and re-processing reads with multiple reference genomes. We have also analysed the temporal development in ambiguous base calls during the emergence of the BA.2.86.x variant. We found that the primers used for targeted enrichment can result in recurrent ambiguous base calls, which can accumulate rapidly in response to the emergence of a new variant. We also found examples of consistent base calling errors, associated with PCR artifacts and amplicon drop-out. Similarly, misalignments and partially mapped reads on the reference genome resulted in ambiguous base calls, as well as defining mutations being omitted from the assembly. These findings highlight some key limitations of using targeted enrichment by PCR and reference-based genome assembly for sequencing SARS-CoV-2, and the importance of continuously monitoring and updating primer schemes and bioinformatic pipelines.

bioinformatics↗

bioRxiv2022

Turnover of strain-level diversity modulates functional traits in the honeybee gut microbiome between nurses and foragers

Strain-level diversity is widespread among bacterial species and can expand the functional potential of natural microbial communities. However, to what extent communities undergo consistent shifts in strain composition in response to environmental/host changes is less well understood. Here, we used shotgun metagenomics to compare the gut microbiota of two behavioral states of the Western honeybee (Apis mellifera), namely nurse and forager bees. While their gut microbiota is composed of the same bacterial species, we detected consistent changes in strain-level composition between nurses and foragers. Single nucleotide variant profiles of predominant bacterial species clustered by behavioral state. Moreover, we identified strain-specific gene content related to nutrient utilization, vitamin biosynthesis, and cell-cell interactions specifically associated with the two behavioral states. Our findings show that strain-level diversity in host-associated communities can undergo consistent changes in response to host behavioral changes modulating the functional potential of the community.

microbiology↗

bioRxiv2022

Deep divergence and genomic diversification of gut symbionts of neotropical stingless bees

Social bees harbor conserved gut microbiota that may have been acquired in a common ancestor of social bees and subsequently co-diversified with their hosts. However, most of this knowledge is based on studies on the gut microbiota of honey bees and bumble bees. Much less is known about the gut microbiota of the third and most diverse group of social bees, the stingless bees. Specifically, the absence of genomic data from their microbiota presents an important knowledge gap in understanding the evolution and functional diversity of the social bee microbiota. Here we combined community profiling with culturing and genome sequencing of gut bacteria from six neotropical stingless bee species from Brazil. Phylogenomic analyses show that most stingless bee gut isolates form deep-branching sister clades of core members of the honey bee and bumble bee gut microbiota with conserved functional capabilities, confirming the common ancestry and ecology of their microbiota. However, our bacterial phylogenies were not congruent with those of the host indicating that the evolution of the social bee gut microbiota was not driven by strict co-diversification, but included host switches and independent symbiont gain and losses. Finally, as reported for the honey bee and bumble bee microbiota, we find substantial genomic divergence among strains of stingless bee gut bacteria suggesting adaptation to different host species and glycan niches. Our study offers first insights into the genomic diversity of the stingless bee microbiota, and highlights the need for broader samplings to understand the evolution of the social bee gut microbiota. ImportanceStingless bees are the most diverse group of the corbiculate bees and represent important pollinator species throughout the tropics and subtropics. They harbor specialized microbial communities in their gut that are related to those found in honey bees and bumble bees and that are likely important for bee health. Few bacteria have been cultured from the gut of stingless bees which has prevented characterization of their genomic diversity and functional potential. Here, we established cultures of major community members of the gut microbiota of six stingless bee species and sequenced their genomes. We find that most stingless bee isolates belong to novel bacterial species distantly related to those found in honey bees and bumble bees and encoding similar functional capabilities. Our study offers a new perspective on the evolution of the social bee gut microbiota and presents the basis to characterize the symbiotic relationships between gut bacteria and stingless bees.

microbiology↗

bioRxiv2020

Vast differences in strain-level diversity in the gut microbiota of two closely related honey bee species

Most bacterial species encompass strains with vastly different gene content. Strain diversity in microbial communities is therefore considered to be of functional importance. Yet, little is known about the extent to which related microbial communities differ in diversity at this level and which underlying mechanisms may constrain and maintain strain-level diversity. Here, we used shotgun metagenomics to characterize and compare the gut microbiota of two honey bee species, Apis mellifera and Apis cerana, which have diverged about 6 mio years ago. While both host species are colonized by largely overlapping bacterial 16S rRNA phylotypes, we find that their communities are highly host-specific when analyzed with genomic resolution. Despite their similar ecology, A. mellifera displayed a much higher extent of strain-level diversity and functional gene content in the microbiota than A. cerana, per colony and per individual bee. In particular, the gene repertoire for polysaccharide degradation was massively expanded in the microbiota of A. mellifera relative to A. cerana. Bee management practices, divergent ecological adaptation, or habitat size may have contributed to the observed differences in microbiota composition of these two key pollinator species. Our results illustrate that the gut microbiota of closely related animal hosts can differ vastly in genomic diversity despite sharing similar levels of diversity at the 16S rRNA gene. This is likely to have consequences for gut microbiota functioning and host-symbiont interactions, highlighting the need for metagenomic studies to understand the ecology and evolution of microbial communities.

microbiology↗

bioRxiv2019

Acetobacteraceae in the honey bee gut comprise two distant clades with diverging metabolism and ecological niches

Various bacteria of the family Acetobacteraceae are associated with the gut environment of insects. Honey bees harbor two distinct Acetobacteraceae in their gut, Alpha2.1 and Alpha2.2. While Alpha2.1 seems to be a gut specialist, Alpha2.2 is also found in the diet (e.g. royal jelly), the hypopharyngeal glands, and the larvae of honey bees. Here, we combined amplicon and genome sequencing to better understand functional differences associated with the ecology of Alpha2.1 and Alpha2.2. We find that the two phylotypes are differentially distributed along the worker and queen bee gut. Phylogenetic analysis shows that Alpha2.2 is nested within the acetic acid bacteria and consists of two separate sub-lineages, whereas Alpha2.1 belongs to a basal lineage with an unusual GC content for Acetobacteraceae. Gene content analysis revealed major differences in the central carbon and respiratory metabolism between the two phylotypes. While Alpha2.2 encodes two periplasmic dehydrogenases to carry out oxidative fermentation, Alpha2.1 lacks this capability, but instead harbors a diverse set of cytoplasmic dehydrogenases. These differences are accompanied by the loss of the TCA cycle in Alpha2.2, but not in Alpha2.1. We speculate that Alpha2.2 has specialized for fast-resource utilization through incomplete carbohydrate oxidation, giving it an advantage in sugar-rich environments such as royal jelly. On the contrary, the broader metabolic range of Alpha2.1 may provide an advantage in the worker bee hindgut, where competition with other bacteria and flexibility in resource utilization may be relevant for persistence. Our results show that bacteria belonging to the same family may utilize vastly different strategies to colonize niches associated with the animal gut.

genomics↗

bioRxiv2018

Genomic changes underlying host specialization in the bee gut symbiont Lactobacillus Firm5

Bacteria that engage in longstanding associations with particular hosts are expected to evolve host-specific adaptations that limit their capacity to thrive in other environments. Consistent with this, many gut symbionts seem to have a limited host range, based on community profiling and phylogenomics. However, few studies have experimentally investigated host specialization of gut symbionts and underlying mechanisms have largely remained elusive. Here, we studied host specialization of a dominant gut symbiont of social bees, Lactobacillus Firm5. We show that Firm5 strains isolated from honey bees and bumble bees separate into deep-branching phylogenetic lineages. Despite their divergent evolution, colonization experiments show that bumble bee strains are capable of colonizing the honey bee gut. However, they were less successful than honey bee strains, and competition with honey bee strains completely abolished their colonization, whereas honey bee strains were able to coexist. This suggests that both host selection and interbacterial competition play important roles for host specialization. Using comparative genomics of 27 Firm5 isolates, we identified candidate genomic changes underlying host specialization. We found that honey bee strains harbored a larger and more diverse gene pool of carbohydrate-related functions than bumble bee strains. As dietary-derived carbohydrates are the main energy source for strains of the Firm5 phylotype, the metabolic flexibility of honey bee strains may give these bacteria a competitive advantage over bumble bee strains in colonizing the gut niche and hence contribute to host specialization.

microbiology↗

bioRxiv2017

Disentangling metabolic functions of bacteria in the honey bee gut

It is presently unclear how much individual community members contribute to the overall metabolic output of a gut microbiota. To address this question, we used the honey bee, which harbors a relatively simple and remarkably conserved gut microbiota with striking parallels to the mammalian system and importance for bee health. Using untargeted metabolomics, we profiled metabolic changes in gnotobiotic bees that were colonized with the complete microbiota reconstituted from cultured strains. We then determined the contribution of individual community members in mono-colonized bees, and recapitulated our findings using in vitro cultures. Our results show that the honey bee gut microbiota utilizes a wide range of pollen-derived substrates including flavonoids and outer pollen wall components, suggesting a key role for degradation of recalcitrant secondary plant metabolites and pollen digestion. In turn, multiple species were responsible for the accumulation of organic acids and polyphenol degradation products, and a specific gut symbiont, Bifidobacterium asteroides, stimulated the production of host hormones known to impact bee development. While we found evidence for cross-feeding interactions, [~]80% of the identified metabolic changes were also observed in mono-colonized bees with Lactobacilli being responsible for the largest share of the metabolic output. These results suggest that bacteria in the honey bee gut colonize largely independent metabolic niches, which may be a general characteristic of gut microbiomes. Our study reveals diverse metabolic functions of gut bacteria that are likely to contribute to bee health, and provide fundamental insights into how metabolic functions are partitioned within gut communities.\n\nAuthor summaryHoney bees are important pollinators that harbor a simple gut microbiota with striking parallels to the mammalian system. This makes them relevant models to study gut microbiota functions and its impact on host health. We applied untargeted metabolomics to characterize metabolic changes induced by the gut microbiota, and to characterize contributions of the major community members. We find that the gut microbiota digests recalcitrant substrates derived from the bees pollen-diet. Most metabolic changes could be explained by the activity of individual community members suggesting substrate specificity and independent metabolic niches. Our study provides novel insights into the functional understanding of the bee gut microbiota and provides a framework for applying untargeted metabolomics to disentangle metabolic functions of gut bacteria.

microbiology↗