Studying microbial genomes and observing cells in the lab often reveal new insights into their physiology, metabolism, and behaviour. Deciphering the function and evolution of cellular traits is fundamental for understanding an organism’s overall biology and ecological interactions.
The tricarboxylic acid (TCA) cycle is central to energy production and biosynthetic precursor synthesis in aerobic organisms. There are few known variations of a complete TCA cycle, with the common notion being that the enzymes involved have already evolved towards optimal performance. Here, we present evidence that an alternative TCA cycle, in which acetate:succinate CoA-transferase (ASCT) replaces the enzymatic step typically performed by succinyl-CoA synthetase (SCS), has arisen in diverse bacterial groups, including microbial symbionts of animals such as humans and insects.
Gut microbes play substantial roles in animal health and development. Honey bees and bumble bees possess a simple, yet unique, gut microbiota that has only recently been described, and is still poorly understood. My goal is to 1) Understand the natural history of these microbes (what are their functions? how did they evolve?) and 2) Establish the bee gut as a model system for microbiome research by developing genetic tools, genomic datasets, and culture collections.
As prolific pollinators of plants, bees are critical for sustaining both natural ecosystems and human agriculture. Research into the relationship with their symbiotic gut microbes may well uncover ways to improve health and aid conservation of these important insects.
Evolution of gut microbes
The genome of strain wkB8
Metabolism and interactions of S. alvi and G. apicola
FISH-labeled gut section, showing bacteria localization
a) S. alvi, and b) G. apicola. Bar, 200 nm
Dynamic microbiome evolution in social bees.
Kwong WK, Medina LA, Koch H, Sing KW, Soh EJY, Ascher JS, Jaffé R, and Moran NA
Science Advances. 2017. 3(3):e1600515.
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Honey bees, bumble bees, and stingless bees comprise a group of related social bees common throughout the world. Here, we conduct wide sampling across 4 continents and in doing so, reveal a dynamic evolutionary history behind the microbiota of these bees. We find multiple gains and losses of gut bacterial lineages, the presence of generalist as well as host-specific strains, and patterns of diversification driven, in part, by host ecology (for example, colony size). Different host species have distinct gut communities, largely independent of geography. These results suggest that gut microbes have diversified alongside bees for millions of years, possibly facilitated by their hosts’ social lifestyle.
Gut microbial communities can greatly affect host health by modulating the host’s immune system. We test whether this occurs in honey bees. Using transcriptomic and proteomic methods, we show that the native, non-pathogenic gut flora induces immune responses in the bee host. Such responses might be a host mechanism to regulate the microbiota, and could potentially benefit host health by priming the immune system against future pathogenic infections.
Genome-wide screen identifies host colonization determinants in a bacterial gut symbiont.
Powell JE*, Leonard SP*, Kwong WK*, Engel P, and Moran NA
Proceedings of the National Academy of Sciences of the United States of America. 2016. 113(48):13887–13892.
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The genes enabling a bacterium to colonize its host are poorly characterized for most symbiotic microbes. Here we used TnSeq, a powerful method coupling transposon mutagenesis with high-throughput DNA sequencing, to screen for these important genes across the entire genome of a major bee gut symbiont. We find that host colonization is dependent on genes mediating cell surface interactions (e.g., adhesion), metabolism under nutrient limitation, and responses to various stresses. This study also demonstrates the ability to genetically manipulate the bee gut microbiota, thus laying the groundwork for more targeted dissections of this system.
Metabolism of toxic sugars by strains of the bee gut symbiont Gilliamella apicola.
Zheng H, Nishida A, Kwong WK, Koch H, Engel P, Steele MI, and Moran NA
mBio. 2016. 7(6):e01326-16.
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We find that Gilliamella strains have different abilities to digest sugars in the bee diet, some of which can be toxic to the bee in high concentrations. We sequenced the genomes of 42 Gilliamella strains, and find that strains living within honey bees have more diverse carbohydrate degradation abilities than strains from bumble bees.
Here, we review the latest developments regarding the bee microbiome, with particular emphasis on comparing the gut bacteria of humans and honey bees. The composition and ontogeny of the bee microbiome, as well as its functions in pathogen defense and digestion, are summarized.
Apibacter adventoris gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from honey bees.
Kwong WK and Moran NA
International Journal of Systematic and Evolutionary Microbiology. 2016. 66:1323-1329.
We isolate and describe a new bacterium, Apibacter, that appears to be a core member of the gut microbiome of two honey bee species from Asia (the Eastern honey bee, Apis cerana, and the Giant honey bee, Apis dorsata).
Why are only certain bacteria found in association with a particular host? The process by which animal microbiotas become specialized is not well understood. Here, we briefly summarize the existing literature on this topic and outline how the bee gut can serve as a useful model for studying this phenomenon.
Genome sequences of Lactobacillus spp. strains wkB8 and wkB10, members of the ‘Firm-5’ clade, from honey bee guts.
Kwong WK, Mancenido AL, and Moran NA
Genome Announcements. 2014. 2(6) pii:e01176-14.
Lactobacillus are among the most common fermentative bacteria, found in or on many plants and animals, and used to produce foodstuffs (e.g. yogourt, cheese, alcohol). Honey bees have their own resident group of Lactobacillus, called the ‘Firm-5’ clade, which also happens to be an abundant member of gut microbial community. In this paper, we present the first complete genome of a ‘Firm-5’ strain, and sequence another divergent strain to draft status.
Genomics and host specialization of honey bee and bumble bee gut symbionts.
Kwong WK, Engel P, Koch H, and Moran NA
Proceedings of the National Academy of Sciences, USA. 2014. 111(31):11509-11514.
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Featured article, Commentary
Although the existence and identity of Snodgrassella alvi and Gilliamella apicola has now been established, we knew little about their basic biology and the relationship with their bee hosts. To learn more, we sequenced and analyzed the genomes of 3 strains of each species, comparing their gene contents and revealing their functional capabilities. Our metabolic network reconstruction indicated niche partitioning between S. alvi and G. apicola: by utilizing different resources, both symbionts can coexist in the gut. They may even form syntrophic (cross-feeding) interactions, enhancing each others’ growth. We identified numerous genes that are likely involved in the gut colonization process, such as adhesins and secretion systems. Colonization is host-specific: our in-vivo experiments showed that strains of S. alvi are only able to colonize honey bees or bumble bees, but not both. This suggests that bees have coevolved with their microbes over millions of years, to the point where their interactions have become highly specialized.
Here, we describe easy-to-follow protocols for 16S rDNA based microbial community profiling, fluorescent in-situ hybridization (FISH) imaging, and gut symbiont culturing. These techniques provide investigators with an established set of tools with which to begin study of the bee gut system.
Frischella perrara gen. nov., sp. nov., a gammaproteobacterium isolated from the gut of the honey bee, Apis mellifera.
Engel P, Kwong WK, and Moran NA
International Journal of Systematic and Evolutionary Microbiology. 2013. 63:3646-3651.
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Frischella perrara is another member of the unique bee gut microbiota, identified from 16S rDNA surveys, yet previously uncultivated. Here, we describe its challenging isolation, biochemical characterization, and phylogenetic placement (it is distantly related to Gilliamella, belonging to the Orbales order). This bacterium, which we name after Karl von Frisch, appears uniquely adapted to honey bees, and is absent from bumble bees. The genome of F. perrara was sequenced in a subsequent study.
Cultivation and characterization of the gut symbionts of honey bees and bumble bees: description of Snodgrassella alvi gen. nov., sp. nov., a member of the family Neisseriaceae of the Betaproteobacteria, and Gilliamella apicola gen. nov., sp. nov., a member of Orbaceae fam. nov., Orbales ord. nov., a sister taxon to the order ‘Enterobacteriales‘ of the Gammaproteobacteria.
Kwong WK and Moran NA
International Journal of Systematic and Evolutionary Microbiology. 2013. 63:2008-2018.
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Surveying novel environments using culture-based microbiology is inherently biased, since cultivation conditions greatly affect what types of microbes can be recovered. Culture-independent analysis, made possible by advances in DNA sequencing, allow for an unbiased view of bacterial community composition. In the case of the bee gut, two abundant bacteria were identified by 16S rDNA sequencing, but had not been cultured or described. Using a targeted approach, we were able to grow these novel gut symbionts in-vitro and describe their phenotypic properties. They constituted new species, for which the names Gilliamella apicola and Snodgrassella alvi are proposed. Through phylogenetic analysis, we also found that Gilliamella formed a deeply branching clade, sufficiently divergent from other described species to warrant classification in a new order, which we name Orbales.
Antibiotics have revolutionized medicine and agriculture, leading to lower mortality and greater productivity. However, bacteria have evolved resistance, and this problem is getting worse. Understanding the ecology of antibiotic resistance, by identifying reservoirs and transmission modes, is necessary for better management policies.
Wastewater, a major juncture in resistance ecology
The fos gene family
Long-term exposure to antibiotics has caused accumulation of resistance determinants in the gut microbiota of honey bees.
Tian B, Fadhil NH, Powell JE, Kwong WK, and Moran NA
mBio. 2012. 3(6):e00377-12.
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Issue cover, Commentary in mBio
The antibiotic tetracycline has been used by beekeepers for >50 years to combat foulbrood disease. We wondered how this might be affecting the normal bee gut microbiota. Sampling bees worldwide, we found more tetracycline resistance genes in gut bacteria from commercial & treated hives compared to wild & organic colonies. We also discovered high levels of tetracycline resistance in cultured bacteria from honey bees, but not wild bumble bees. Thus, human intervention, through pervasive antibiotic treatment, have selected for the build-up of resistance and altered the genetic makeup of the normal bee microbiome.
Complex integrons containing qnrB4-ampC (blaDHA-1) in plasmids of multidrug resistant Citrobacter freundii from wastewater.
Yim G*, Kwong W*, Davies J, and Miao V
Canadian Journal of Microbiology. 2012. 10.1139/cjm-2012-0576.
Quinolones are widely-used, powerful broad-spectrum antibiotics. Because they are synthetic compounds, transferable resistance to quinolones was unexpected; however, the recent discovery of qnr genes on plasmids proved that resistance to quinolones could indeed be acquired and transferred. Here, we find that Citrobacter, a wastewater bacterium, harbors a diversity of qnr-bearing, integron-carrying plasmids, thus supporting Citrobacter spp. as the source of the qnrB class of genes and giving insight into how these resistance genes have rapidly spread across the world.
Identification of a novel fosfomycin resistance gene (fosA2) in Enterobacter cloacae from the Salmon River, Canada.
Xu H, Miao V, Kwong W, Xia R, and Davies J
Letters in Applied Microbiology. 2011. 52(4):427-429.
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Fosfomycin is a broad-spectrum antibiotic used to treat urinary tract infections. We found a new gene, fosA2, which can confer high levels of resistance to fosfomycin. This gene was found in a river, showing that natural waterways may be reservoirs of diverse and novel resistance determinants.