SRR6033657 - Apis mellifera

Basic Information

Run: SRR6033657

Assay Type: WGS

Bioproject: PRJNA407112

Biosample: SAMN07634938

Bytes: 67903819

Center Name: COLUMBIA

Sequencing Information

Instrument: Illumina MiSeq

Library Layout: SINGLE

Library Selection: RANDOM PCR

Platform: ILLUMINA

Geographic Information

Country: Switzerland

Continent: Europe

Location Name: Switzerland

Latitude/Longitude: 46.5197 N 6.6323 E

Sample Information

Host: Apis mellifera

Isolation: Whole body homogenate

Biosample Model: Metagenome or environmental

Collection Date: 2015-08-01

Taxonomic Classification

Potential Symbionts

About Potential Symbionts

This table shows potential symbiont identified in the metagenome sample. Matches are scored based on:

Relative abundance in the sample
Species-level matches with known symbionts
Host insect order matches with reference records
Completeness and richness of functional records

Note: only the three highest scoring comparison records were retained for each symbiont species or genus in the sample

Based on our current records database, this section aims to identify potential functional symbionts in this metagenome sample, with scoring based on:

Relative abundance in sample
Species-level matches with known symbionts
Host insect order matches
Functional record completeness

Note: Showing top 3 highest scoring records for each species/genus

Symbiont Name	Record	Host Species	Function	Abundance	Score Score Composition: Symbiont Abundance Species match bonus Host match bonus Function richness Higher scores indicate stronger symbiotic relationship potential
Gilliamella Host Order Match Host Species Match	RISB0102	Apis mellifera Order: Hymenoptera	Gilliamella apicola carries the gene for the desaturase FADS2, which is able to metabolize polyunsaturated fatty acids from pollen and synthesize endocannabinoid, a lipogenic neuroactive substance, thereby modulating reward learning and memory in honeybees.	0.78%	35.8
Lactobacillus Host Order Match Host Species Match	RISB0475	Apis mellifera Order: Hymenoptera	A. kunkeei alleviated acetamiprid-induced symbiotic microbiota dysregulation and mortality in honeybees	0.60%	32.7
Lactobacillus Host Order Match Host Species Match	RISB0368	Apis mellifera Order: Hymenoptera	increased bee survival after S. marcescens infection, inhibited its proliferation in the gut	0.60%	32.4
Lactobacillus Host Order Match Host Species Match	RISB0615	Apis mellifera Order: Hymenoptera	Improve learning and memory performance	0.60%	31.4
Burkholderia Host Order Match Host Species Match	RISB2389	Apis mellifera Order: Hymenoptera	None	0.16%	30.2
Pseudomonas sp. CIP-10 Species-level Match Host Order Match	RISB1564	Liometopum apiculatum Order: Hymenoptera	None	15.13%	30.1
Pseudomonas sp. CIP-10 Species-level Match	RISB1622	Dendroctonus valens Order: Coleoptera	volatiles from predominant bacteria regulate the consumption sequence of carbon sources d-pinitol and d-glucose in the fungal symbiont Leptographium procerum, and appear to alleviate the antagonistic effect from the fungus against RTB larvae	15.13%	25.0
Streptomyces sp. T12 Species-level Match Host Order Match	RISB0943	Polybia plebeja Order: Hymenoptera	this bacterium produces antimicrobial compounds that are active against Hirsutella citriformis, a natural fungal enemy of its host, and the human pathogens Staphylococcus aureus and Candida albicans	5.76%	24.7
Streptomyces sp. T12 Species-level Match Host Order Match	RISB2334	Sirex noctilio Order: Hymenoptera	degrading woody substrates and that such degradation may assist in nutrient acquisition by S. noctilio, thus contributing to its ability to be established in forested habitats worldwide	5.76%	24.5
Pseudomonas sp. CIP-10 Species-level Match	RISB2224	Leptinotarsa decemlineata Order: Coleoptera	Colorado potato beetle (Leptinotarsa decemlineata) larvae exploit bacteria in their oral secretions to suppress antiherbivore defenses in tomato (Solanum lycopersicum)	15.13%	23.5
Streptomyces sp. T12 Species-level Match Host Order Match	RISB1134	mud dauber wasp Order: Hymenoptera	secondary metabolites derived from a Streptomyces sp. displayed significant inhibitory activity against hexokinase II	5.76%	23.1
Stenotrophomonas maltophilia Species-level Match Host Order Match	RISB2004	Trichogramma chilonis Order: Hymenoptera	could significantly increase both female count	3.93%	19.9
Corynebacterium Host Order Match	RISB1285	Aphidius colemani Order: Hymenoptera	Repelling parasitism	7.36%	17.8
Snodgrassella alvi Species-level Match Host Order Match	RISB1423	Bombus spp. Order: Hymenoptera	The bumble bee microbiome slightly increases survivorship when the host is exposed to selenate	0.13%	17.0
Enterobacter sp. T2 Species-level Match	RISB0893	Bactrocera dorsalis Order: Diptera	be beneficial, with some quality control indices, such as adult size, pupal weight, survival rate under stress and nutritionally rich conditions, and mating competitiveness, being significantly increased, while slight nonsignificant increases in emergence rate and flight ability were observed	6.40%	16.4
Gilliamella Host Order Match	RISB0177	Apis cerana Order: Hymenoptera	Bifidobacterium provides complementary demethylation service to promote Gilliamella growth on methylated homogalacturonan, an enriched polysaccharide of pectin. In exchange, Gilliamella shares digestive products with Bifidobacterium, through which a positive interaction is established	0.78%	15.8
Enterobacter sp. T2 Species-level Match	RISB1338	Ceratitis capitata Order: Diptera	Enterobacter sp. AA26 dry biomass can fully replace the brewer’s yeast as a protein source in medfly larval diet without any effect on the productivity and the biological quality of reared medfly of VIENNA 8 GSS	6.40%	15.6
Snodgrassella alvi Species-level Match Host Order Match	RISB1947	Apis cerana Order: Hymenoptera	None	0.13%	15.1
Enterobacter sp. T2 Species-level Match	RISB2221	Leptinotarsa decemlineata Order: Coleoptera	Colorado potato beetle (Leptinotarsa decemlineata) larvae exploit bacteria in their oral secretions to suppress antiherbivore defenses in tomato (Solanum lycopersicum)	6.40%	14.7
Xanthomonas Host Order Match	RISB0498	Xylocopa appendiculata Order: Hymenoptera	Xanthomonas strain from Japanese carpenter bee is effective PU-degradable bacterium and is able to use polyacryl-based PU as a nutritional source, as well as other types of PS-PU and PE-PU	0.02%	13.8
Klebsiella pneumoniae Species-level Match	RISB2185	Scirpophaga incertulas Order: Lepidoptera	The ability of these arthropods to feed on wood, foliage and detritus is likely to involve catalysis by different types of cellulases/hemicellulases that are secreted by gut microbiota to digest the structural and recalcitrant lignocellulosic residues in their foods.	3.34%	13.3
Stenotrophomonas maltophilia Species-level Match	RISB1122	Bombyx mori Order: Lepidoptera	facilitate host resistance against organophosphate insecticides, provides essential amino acids that increase host fitness and allow the larvae to better tolerate the toxic effects of the insecticide.	3.93%	12.9
Xanthomonas Host Order Match	RISB0217	Xylocopa appendiculata Order: Hymenoptera	strains biodegraded polyethylene terephthalate PET powder, broke it into its degradation products	0.02%	12.0
Acinetobacter Host Order Match	RISB2000	Trichogramma chilonis Order: Hymenoptera	could significantly increase both female count	0.96%	11.9
Bacillus cereus Species-level Match	RISB2161	Termitidae Order: Blattodea	The ability of these arthropods to feed on wood, foliage and detritus is likely to involve catalysis by different types of cellulases/hemicellulases that are secreted by gut microbiota to digest the structural and recalcitrant lignocellulosic residues in their foods.	1.69%	11.7
Stenotrophomonas maltophilia Species-level Match	RISB1227	Delia antiqua Order: Diptera	six bacteria protect larvae from infection with the entomopathogen Beauveria bassiana through symbiotic bacterium-derived organic acids	3.93%	11.6
Burkholderia Host Order Match	RISB2149	Osmia bicornis Order: Hymenoptera	may be essential to support Osmia larvae in their nutrient uptake	0.16%	11.5
Streptococcus	RISB2625	Galleria mellonella Order: Lepidoptera	suppress bacteria ingested with food by producing bacteriocin and by releasing a lysozyme like enzyme	9.44%	11.5
Streptococcus	RISB2624	Reticulitermes flavipes Order: Blattodea	can be broken down into substances such as carbon dioxide, ammonia and acetic acid	9.44%	11.1
Gilliamella Host Order Match	RISB1945	Apis cerana Order: Hymenoptera	None	0.78%	10.8
Bacillus cereus Species-level Match	RISB2489	Anticarsia gemmatalis Order: Lepidoptera	allow the adaptation of this insect to plants rich in protease inhibitors, minimizing the potentially harmful consequences of protease inhibitors from some of this insect host plants, such as soybean	1.69%	10.7
Streptococcus	RISB2604	Homona magnanima Order: Lepidoptera	influence the growth of Bacillus thuringiensis in the larvae	9.44%	10.6
Burkholderia Host Order Match	RISB2101	Formica exsecta Order: Hymenoptera	produce antibiotics	0.16%	10.5
Bacillus subtilis Species-level Match	RISB0481	Bombyx mori Order: Lepidoptera	B. subtilis can generate a variety of primary and secondary metabolites, such as B vitamins and antimicrobial compounds, to provide micronutrients and enhance the pathogen resistance of their insect host; The antimicrobial compounds secreted by B. subtilis were the primary driving force for the reconstruction of intestinal microbiota	0.46%	10.5
Listeria monocytogenes Species-level Match	RISB2308	Drosophila melanogaster Order: Diptera	L. monocytogenes infection disrupts host energy metabolism by depleting energy stores (triglycerides and glycogen) and reducing metabolic pathway activity (beta-oxidation and glycolysis). The infection affects antioxidant defense by reducing uric acid levels and alters amino acid metabolism. These metabolic changes are accompanied by melanization, potentially linked to decreased tyrosine levels.	0.27%	10.3
Buchnera aphidicola Species-level Match	RISB0236	Acyrthosiphon pisum Order: Hemiptera	Buchnera the nutritional endosymbiont of A. pisum is located inside of bacteriocytes and requires aspartate from the aphid host, because it cannot make it de novo. Further Buchnera needs aspartate for the biosynthesis of the essential amino acids lysine and threonine, which the aphid and Buchnera require for survival	0.01%	10.0
Escherichia coli Species-level Match	RISB1339	Manduca sexta Order: Lepidoptera	modulate immunity-related gene expression in the infected F0 larvae, and also in their offspring, triggered immune responses in the infected host associated with shifts in both DNA methylation and histone acetylation	0.62%	9.9
Buchnera aphidicola Species-level Match	RISB2485	Macrosiphum euphorbiae Order: Hemiptera	symbiont expression patterns differ between aphid clones with differing levels of virulence, and are influenced by the aphids' host plant. Potentially, symbionts may contribute to differential adaptation of aphids to host plant resistance	0.01%	9.8
Klebsiella pneumoniae Species-level Match	RISB2459	Bombyx mori Order: Lepidoptera	degradation of cellulose, xylan, pectin and starch	3.34%	9.3
Corynebacterium	RISB0363	Pagiophloeus tsushimanus Order: Coleoptera	terpenoid-degrading: the highest degradation rates of D-camphor, linalool, and eucalyptol	7.36%	9.1
Klebsiella pneumoniae Species-level Match	RISB1994	Diatraea saccharalis Order: Lepidoptera	possess cellulose degrading activity	3.34%	9.1
Corynebacterium	RISB0531	Helicoverpa armigera Order: Lepidoptera	Corynebacterium sp. 2-TD, mediates the toxicity of the 2-tridecanone to H. armigera	7.36%	9.0
Buchnera aphidicola Species-level Match	RISB0685	Acyrthosiphon pisum Order: Hemiptera	It supplies the host with vitamins and essential amino acids, such as arginine and methionine that aphids cannot synthesize or derive insufficiently from their diet, the phloem sap of plants	0.01%	8.8
Escherichia coli Species-level Match	RISB0128	Tribolium castaneum Order: Coleoptera	may produce 4,8-dimethyldecanal (DMD) production that is strongly associated with attraction to females and host pheromone communication	0.62%	8.3
Staphylococcus hominis Species-level Match	RISB1881	Aedes aegypti Order: Diptera	gut microbiome	2.22%	7.5
Staphylococcus hominis Species-level Match	RISB1071	Oryctes rhinoceros Order: Coleoptera	gut microbe	2.22%	7.4
Frischella perrara Species-level Match	RISB2028	Diceroprocta semicincta Order: Hemiptera	causes the formation of a scab-like structure on the gut epithelium of its host	0.53%	7.1
Salmonella enterica Species-level Match	RISB0413	Melanaphis sacchari Order: Hemiptera	None	1.71%	6.7
Escherichia coli Species-level Match	RISB2120	Galleria mellonella Order: Lepidoptera	mediate trans-generational immune priming	0.62%	6.4
Staphylococcus epidermidis Species-level Match	RISB1070	Oryctes rhinoceros Order: Coleoptera	gut microbe	0.94%	6.2
Acinetobacter	RISB0140	Nilaparvata lugens Order: Hemiptera	Acinetobacter can effectively degrade cellulose and harmful substances such as polystyrene and phenol.It can help the short-winged BPH to improve its detoxification ability in harsh environments and adapt to environmental changes at any time.	0.96%	5.8
Acinetobacter	RISB0730	Curculio chinensis Order: Coleoptera	Acinetobacter sp. in C. chinensis enriched after treating with saponin, and when incubating bacteria with saponin for 72 h, saponin content significantly decreased from 4.054 to 1.867 mg/mL (by 16S rRNA metagenome sequencing and HPLC)	0.96%	5.6
Bombilactobacillus bombi Species-level Match	RISB0617	Spodoptera frugiperda Order: Lepidoptera	degrade amygdalin	0.09%	5.4
Enterococcus	RISB0728	Cnaphalocrocis medinalis Order: Lepidoptera	The core dominant Enterococcus species possessed complete pathways of 14 carbohydrates metabolism, 11 amino acids biosynthesis, and two vitamins synthesize, implied to contribute an essential role to the nutrition intake and development of C. medinalis	0.11%	5.1
Enterococcus	RISB0476	Spodoptera litura Order: Lepidoptera	The ingestion of bacteria negatively affected the development and nutritional physiology of insect. The bacteria after successful establishment started degrading the gut wall and invaded the haemocoel thereby causing the death of the host.	0.11%	4.9
Vibrio	RISB1810	Monochamus galloprovincialis Order: Coleoptera	Have the ability for degradation of cellulose, proteins and starch	3.38%	4.7
Clostridium	RISB2301	Pyrrhocoris apterus Order: Hemiptera	could play an important role for the insect by degrading complex dietary components, providing nutrient supplementation, or detoxifying noxious chemicals (e.g. cyclopropenoic fatty acids or gossypol) in the diet	0.08%	4.3
Enterococcus	RISB2493	Anticarsia gemmatalis Order: Lepidoptera	allow the adaptation of this insect to plants rich in protease inhibitors, minimizing the potentially harmful consequences of protease inhibitors from some of this insect host plants, such as soybean	0.11%	4.1
Ignatzschineria	RISB0562	Chrysomya megacephala Order: Diptera	Ignatzschineria indica is a Gram-negative bacterium commonly associated with maggot infestation and myiasis, a probable marker for myiasis diagnosis	0.04%	3.0
Micrococcus	RISB2276	Ostrinia nubilalis Order: Lepidoptera	extreme cellulolytic enzymes, at extreme (pH 12) conditions, exhibited cellulolytic properties	0.68%	2.6
Halomonas	RISB1808	Monochamus galloprovincialis Order: Coleoptera	Have the ability for degradation of cellulose, proteins and starch	0.33%	1.7
Bradyrhizobium	RISB0135	Coccinella septempunctata Order: Coleoptera	be commonly found in plant roots and they all have nitrogen fixation abilities	0.04%	1.6
Clostridium	RISB0028	Sesamia inferens Order: Lepidoptera	degrade Chlorpyrifos and Chlorantraniliprole in vitro	0.08%	1.1
Gordonia	RISB1912	Hyles euphorbiae Order: Lepidoptera	able to degrade alkaloids and/or latex	0.11%	0.9
Halomonas	RISB1374	Bemisia tabaci Order: Hemiptera	None	0.33%	0.3
Neisseria	RISB0512	Plutella xylostella Order: Lepidoptera	None	0.25%	0.3
Cupriavidus	RISB0694	Alydus tomentosus Order: Hemiptera	None	0.09%	0.1
Clostridium	RISB1959	Pyrrhocoridae Order: Hemiptera	None	0.08%	0.1