SRR6033675 - Apis mellifera

Basic Information

Run: SRR6033675

Assay Type: WGS

Bioproject: PRJNA407112

Biosample: SAMN07634924

Bytes: 41797751

Center Name: COLUMBIA

Sequencing Information

Instrument: Illumina MiSeq

Library Layout: SINGLE

Library Selection: RANDOM PCR

Platform: ILLUMINA

Geographic Information

Country: India

Continent: Asia

Location Name: India

Latitude/Longitude: 13.0712 N 77.5805 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 apicola Species-level Match 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.	5.21%	45.2
Bartonella Host Order Match Host Species Match	RISB1673	Apis mellifera Order: Hymenoptera	a gut symbiont of insects and that the adaptation to blood-feeding insects facilitated colonization of the mammalian bloodstream	0.08%	32.6
Burkholderia Host Order Match Host Species Match	RISB2389	Apis mellifera Order: Hymenoptera	None	0.81%	30.8
Pseudomonas sp. CIP-10 Species-level Match Host Order Match	RISB1564	Liometopum apiculatum Order: Hymenoptera	None	12.82%	27.8
Gilliamella apicola Species-level Match 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	5.21%	25.2
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	12.82%	22.6
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	5.21%	22.1
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)	12.82%	21.2
Gilliamella apicola Species-level Match Host Order Match	RISB1945	Apis cerana Order: Hymenoptera	None	5.21%	20.2
Snodgrassella alvi Species-level Match Host Order Match	RISB1947	Apis cerana Order: Hymenoptera	None	5.21%	20.2
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	0.92%	19.9
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	0.92%	19.6
Stenotrophomonas maltophilia Species-level Match Host Order Match	RISB2004	Trichogramma chilonis Order: Hymenoptera	could significantly increase both female count	3.19%	19.1
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	0.92%	18.3
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	7.78%	17.1
Corynebacterium Host Order Match	RISB1285	Aphidius colemani Order: Hymenoptera	Repelling parasitism	5.47%	15.9
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	7.78%	15.5
Lactobacillus apis Species-level Match Host Order Match	RISB1556	Apis florea Order: Hymenoptera	None	0.06%	15.1
Serratia symbiotica Species-level Match Host Order Match	RISB2331	Camponotus japonicus Order: Hymenoptera	None	0.03%	15.0
Spiroplasma Host Order Match	RISB1353	Cephus cinctus Order: Hymenoptera	The bacterium also encoded biosynthetic pathways for essential vitamins B2, B3, and B9. We identified putative Spiroplasma virulence genes: cardiolipin and chitinase.	0.71%	14.0
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
Escherichia coli Species-level Match	RISB2120	Galleria mellonella Order: Lepidoptera	mediate trans-generational immune priming	7.78%	13.6
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.	2.74%	12.7
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.	3.19%	12.2
Burkholderia Host Order Match	RISB2149	Osmia bicornis Order: Hymenoptera	may be essential to support Osmia larvae in their nutrient uptake	0.81%	12.1
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
Spiroplasma Host Order Match	RISB0613	Lariophagus distinguendus Order: Hymenoptera	induces cytoplasmic incompatibility (CI)	0.71%	11.5
Variovorax Host Order Match	RISB2153	Osmia bicornis Order: Hymenoptera	may be essential to support Osmia larvae in their nutrient uptake	0.04%	11.3
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.	1.32%	11.3
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	1.29%	11.3
Burkholderia Host Order Match	RISB2101	Formica exsecta Order: Hymenoptera	produce antibiotics	0.81%	11.2
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	3.19%	10.9
Providencia Host Order Match	RISB0984	Nasonia vitripennis Order: Hymenoptera	may highly associated with diapause	0.05%	10.8
Spiroplasma Host Order Match	RISB0284	Formica Order: Hymenoptera	None	0.71%	10.7
Yersinia Host Order Match	RISB0407	Anaphes nitens Order: Hymenoptera	None	0.61%	10.6
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	1.29%	10.5
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	1.32%	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	0.10%	10.1
Providencia Host Order Match	RISB1352	Nasonia vitripennis Order: Hymenoptera	None	0.05%	10.1
Serratia symbiotica Species-level Match	RISB0576	Acyrthosiphon pisum Order: Hemiptera	process of regression from winged to wingless morph was inhibited by Serratia symbiotica. The existence of the symbiont did not affect the body mass and fecundity of adult aphids, but it increased the body weight of nymphs and temporally increased the quantity of a primary symbiont, Buchnera aphidicola	0.03%	10.0
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	0.10%	9.9
Acinetobacter sp. ESL0695 Species-level Match	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)	0.13%	9.8
Acinetobacter sp. SCLZS86 Species-level Match	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)	0.04%	9.7
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)	1.29%	9.6
Serratia symbiotica Species-level Match	RISB0179	Acyrthosiphon pisum Order: Hemiptera	harboring Serratia improved host aphid growth and fecundity but reduced longevity. Serratia defends aphids against P. japonica by impeding the predator's development and predation capacity, and modulating its foraging behavior	0.03%	9.6
Salmonella enterica Species-level Match	RISB0413	Melanaphis sacchari Order: Hemiptera	None	4.11%	9.1
Acinetobacter sp. ESL0695 Species-level Match	RISB1978	Blattella germanica Order: Blattodea	gut microbiota contributes to production of VCAs that act as fecal aggregation agents and that cockroaches discriminate among the complex odors that emanate from a diverse microbial community	0.13%	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	0.10%	8.9
Klebsiella pneumoniae Species-level Match	RISB2459	Bombyx mori Order: Lepidoptera	degradation of cellulose, xylan, pectin and starch	2.74%	8.7
Klebsiella pneumoniae Species-level Match	RISB1994	Diatraea saccharalis Order: Lepidoptera	possess cellulose degrading activity	2.74%	8.5
Lactobacillus sp. IBH004 Species-level Match	RISB0292	Lymantria dispar asiatica Order: Lepidoptera	Beauveria bassiana infection-based assays showed that the mortality of non-axenic L. dispar asiatica larvae was significantly higher than that of axenic larvae at 72 h.	0.08%	8.4
Morganella morganii Species-level Match	RISB0772	Delia antiqua Order: Diptera	showed significant volatile inhibition activity against fungal entomopathogen Fusarium moniliforme, Botryosphaeria dothidea and both Fusarium oxysporum respectively	0.06%	8.3
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	1.47%	8.1
Bacillus cereus Species-level Match	RISB2237	Anticarsia gemmatalis Order: Lepidoptera	mitigation of the negative effects of proteinase inhibitors produced by the host plant	1.32%	8.0
Morganella morganii Species-level Match	RISB0008	Phormia regina Order: Diptera	deterred oviposition by female stable flies; The flies' oviposition decisions appear to be guided by bacteria-derived semiochemicals as the bacteria	0.06%	8.0
Morganella morganii Species-level Match	RISB1867	Costelytra zealandica Order: Coleoptera	Female beetles were previously shown to use phenol as their sex pheromone produced by symbiotic bacteria in the accessory or colleterial gland	0.06%	7.9
Corynebacterium	RISB0363	Pagiophloeus tsushimanus Order: Coleoptera	terpenoid-degrading: the highest degradation rates of D-camphor, linalool, and eucalyptol	5.47%	7.3
Corynebacterium	RISB0531	Helicoverpa armigera Order: Lepidoptera	Corynebacterium sp. 2-TD, mediates the toxicity of the 2-tridecanone to H. armigera	5.47%	7.1
Delftia lacustris Species-level Match	RISB1754	Spodoptera frugiperda Order: Lepidoptera	may influence the metabolization of pesticides in insects	0.48%	6.6
Delftia lacustris Species-level Match	RISB0657	Melanaphis bambusae Order: Hemiptera	None	0.48%	5.5
Bombilactobacillus bombi Species-level Match	RISB0617	Spodoptera frugiperda Order: Lepidoptera	degrade amygdalin	0.03%	5.4
Staphylococcus epidermidis Species-level Match	RISB1070	Oryctes rhinoceros Order: Coleoptera	gut microbe	0.10%	5.3
Staphylococcus hominis Species-level Match	RISB1881	Aedes aegypti Order: Diptera	gut microbiome	0.03%	5.3
Staphylococcus hominis Species-level Match	RISB1071	Oryctes rhinoceros Order: Coleoptera	gut microbe	0.03%	5.3
Sphingobium	RISB1837	Dendroctonus valens Order: Coleoptera	It can trongly degrade naringenin, and pinitol, the main soluble carbohydrate of P. tabuliformis, is retained in L. procerum-infected phloem and facilitate naringenin biodegradation by the microbiotas.	0.82%	4.8
Novosphingobium	RISB1837	Dendroctonus valens Order: Coleoptera	It can trongly degrade naringenin, and pinitol, the main soluble carbohydrate of P. tabuliformis, is retained in L. procerum-infected phloem and facilitate naringenin biodegradation by the microbiotas.	0.06%	4.1
Rhizobium	RISB0135	Coccinella septempunctata Order: Coleoptera	be commonly found in plant roots and they all have nitrogen fixation abilities	1.86%	3.4
Vibrio	RISB1810	Monochamus galloprovincialis Order: Coleoptera	Have the ability for degradation of cellulose, proteins and starch	2.07%	3.4
Streptococcus	RISB2625	Galleria mellonella Order: Lepidoptera	suppress bacteria ingested with food by producing bacteriocin and by releasing a lysozyme like enzyme	1.27%	3.3
Yersinia	RISB0492	Cimex hemipterus Order: Hemiptera	the disruption of the abundant Yersinia possibly could be related to the enhanced susceptibility towards the insecticides	0.61%	3.0
Streptococcus	RISB2624	Reticulitermes flavipes Order: Blattodea	can be broken down into substances such as carbon dioxide, ammonia and acetic acid	1.27%	2.9
Streptococcus	RISB2604	Homona magnanima Order: Lepidoptera	influence the growth of Bacillus thuringiensis in the larvae	1.27%	2.5
Halomonas	RISB1808	Monochamus galloprovincialis Order: Coleoptera	Have the ability for degradation of cellulose, proteins and starch	1.13%	2.5
Neisseria	RISB0512	Plutella xylostella Order: Lepidoptera	None	2.38%	2.4
Micrococcus	RISB2276	Ostrinia nubilalis Order: Lepidoptera	extreme cellulolytic enzymes, at extreme (pH 12) conditions, exhibited cellulolytic properties	0.41%	2.3
Blautia	RISB0091	Hyphantria cunea Order: Lepidoptera	enhance the compatibility of invasive pests to new hosts and enable more rapid adaptation to new habitats.	0.14%	2.3
Actinomyces	RISB1234	Hermetia illucens Order: Diptera	provides the tools for degrading of a broad range of substrates	0.09%	1.4
Dysgonomonas	RISB1235	Hermetia illucens Order: Diptera	provides the tools for degrading of a broad range of substrates	0.02%	1.3
Halomonas	RISB1374	Bemisia tabaci Order: Hemiptera	None	1.13%	1.1
Sphingobium	RISB1880	Aedes aegypti Order: Diptera	gut microbiome	0.82%	1.1
Providencia	RISB1001	Anastrepha obliqua Order: Diptera	improve the sexual competitiveness of males	0.05%	0.9
Aeromonas	RISB2456	Bombyx mori Order: Lepidoptera	able to utilize the CMcellulose and xylan	0.03%	0.9
Aeromonas	RISB2086	Aedes aegypti Order: Diptera	axenic larvae cannot develop	0.03%	0.6
Aeromonas	RISB1145	Tenebrio molitor Order: Coleoptera	degrading plastics	0.03%	0.4
Cupriavidus	RISB0694	Alydus tomentosus Order: Hemiptera	None	0.36%	0.4
Variovorax	RISB1712	Phlebotomus papatasi Order: Diptera	None	0.04%	0.0
Dysgonomonas	RISB1481	Brachinus elongatulus Order: Coleoptera	None	0.02%	0.0