SRR6033665 - Apis mellifera

Basic Information

Run: SRR6033665

Assay Type: WGS

Bioproject: PRJNA407112

Biosample: SAMN07634930

Bytes: 55958099

Center Name: COLUMBIA

Sequencing Information

Instrument: Illumina MiSeq

Library Layout: SINGLE

Library Selection: RANDOM PCR

Platform: ILLUMINA

Geographic Information

Country: Nicaragua

Continent: North America

Location Name: Nicaragua

Latitude/Longitude: 12.1184 N 86.1224 W

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.	0.42%	40.4
Bifidobacterium asteroides Species-level Match Host Order Match Host Species Match	RISB0174	Apis mellifera 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	0.05%	40.1
Pseudomonas sp. CIP-10 Species-level Match Host Order Match	RISB1564	Liometopum apiculatum Order: Hymenoptera	None	16.95%	32.0
Burkholderia Host Order Match Host Species Match	RISB2389	Apis mellifera Order: Hymenoptera	None	0.04%	30.0
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	16.95%	26.8
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)	16.95%	25.3
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	0.42%	20.4
Bifidobacterium asteroides Species-level Match Host Order Match	RISB0175	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	0.05%	20.1
Stenotrophomonas maltophilia Species-level Match Host Order Match	RISB2004	Trichogramma chilonis Order: Hymenoptera	could significantly increase both female count	3.83%	19.8
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	0.57%	19.5
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	0.57%	19.3
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	1.94%	18.8
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	0.57%	17.9
Snodgrassella alvi Species-level Match Host Order Match	RISB1947	Apis cerana Order: Hymenoptera	None	1.94%	16.9
Lactobacillus apis Species-level Match Host Order Match	RISB1556	Apis florea Order: Hymenoptera	None	0.56%	15.6
Gilliamella apicola Species-level Match Host Order Match	RISB1945	Apis cerana Order: Hymenoptera	None	0.42%	15.4
Serratia symbiotica Species-level Match Host Order Match	RISB2331	Camponotus japonicus Order: Hymenoptera	None	0.04%	15.0
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	4.41%	13.7
Salmonella enterica Species-level Match	RISB0413	Melanaphis sacchari Order: Hemiptera	None	8.45%	13.5
Candidatus Blochmanniella Host Order Match	RISB2542	Camponotus Order: Hymenoptera	Blochmannia provide essential amino acids to its host,Camponotus floridanus, and that it may also play a role in nitrogen recycling via its functional urease	0.07%	13.2
Candidatus Blochmanniella Host Order Match	RISB1827	Camponotus floridanus Order: Hymenoptera	a modulation of immune gene expression which may facilitate tolerance towards the endosymbionts and thus may contribute to their transovarial transmission	0.07%	13.2
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.	3.83%	12.8
Candidatus Blochmanniella Host Order Match	RISB2448	Camponotus floridanus Order: Hymenoptera	nutritional contribution of the bacteria to host metabolism by production of essential amino acids and urease-mediated nitrogen recycling	0.07%	12.8
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	4.41%	12.1
Corynebacterium Host Order Match	RISB1285	Aphidius colemani Order: Hymenoptera	Repelling parasitism	1.73%	12.1
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.	1.67%	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	3.83%	11.5
Burkholderia Host Order Match	RISB2149	Osmia bicornis Order: Hymenoptera	may be essential to support Osmia larvae in their nutrient uptake	0.04%	11.3
Yersinia Host Order Match	RISB0407	Anaphes nitens Order: Hymenoptera	None	0.86%	10.9
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.	0.82%	10.8
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	0.64%	10.6
Burkholderia Host Order Match	RISB2101	Formica exsecta Order: Hymenoptera	produce antibiotics	0.04%	10.4
Lactococcus lactis Species-level Match	RISB0131	Ceratitis capitata Order: Diptera	The intestinal microbiota structure was significantly influenced by the probiotic treatment while still maintaining a stable core dominant community of Enterobacteriacea. The colony with these microbiome had the most improved potential functions in terms of gut microbes as well as the carbohydrates active enzymes most improved potential functions.	0.30%	10.3
Escherichia coli Species-level Match	RISB2120	Galleria mellonella Order: Lepidoptera	mediate trans-generational immune priming	4.41%	10.2
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	0.04%	10.0
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	0.03%	10.0
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	0.64%	9.9
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	0.82%	9.8
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	0.03%	9.8
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	0.04%	9.6
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)	0.64%	9.0
Lactococcus lactis Species-level Match	RISB0967	Oulema melanopus Order: Coleoptera	contribute to the decomposition of complex carbohydrates, fatty acids, or polysaccharides in the insect gut. It might also contribute to the improvement of nutrient availability.	0.30%	8.9
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	0.03%	8.8
Bifidobacterium asteroides Species-level Match	RISB0616	Spodoptera frugiperda Order: Lepidoptera	Strain wkB204 grew in the presence of amygdalin as the sole carbon source, suggesting that this strain degrades amygdalin and is not susceptible to the potential byproducts	0.05%	8.5
Candidatus Portiera aleyrodidarum Species-level Match	RISB1193	Bemisia tabaci Order: Hemiptera	synthesizing essential amino acid (e.g. tryptophan, leucine and L-Isoleucine), Bemisia tabaci provides vital nutritional support for growth, development and reproduction	0.03%	8.4
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.	0.04%	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	0.03%	8.3
Lactococcus lactis Species-level Match	RISB0113	Bactrocera dorsalis Order: Diptera	increase the resistance of B. dorsalis to β-cypermethrin by regulating cytochrome P450 (P450) enzymes and α-glutathione S-transferase (GST) activities	0.30%	8.3
Acinetobacter guillouiae Species-level Match	RISB0768	Delia antiqua Order: Diptera	showed significant volatile inhibition activity against fungal entomopathogen Fusarium moniliforme, Botryosphaeria dothidea and both Fusarium oxysporum respectively	0.02%	8.3
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	0.03%	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	0.03%	7.9
Klebsiella pneumoniae Species-level Match	RISB2459	Bombyx mori Order: Lepidoptera	degradation of cellulose, xylan, pectin and starch	1.67%	7.7
Bacillus cereus Species-level Match	RISB2237	Anticarsia gemmatalis Order: Lepidoptera	mitigation of the negative effects of proteinase inhibitors produced by the host plant	0.82%	7.5
Klebsiella pneumoniae Species-level Match	RISB1994	Diatraea saccharalis Order: Lepidoptera	possess cellulose degrading activity	1.67%	7.4
Candidatus Portiera aleyrodidarum Species-level Match	RISB2289	Bemisia tabaci Order: Hemiptera	encoding the capability to synthetize, or participate in the synthesis of, several amino acids and carotenoids,	0.03%	7.3
Candidatus Portiera aleyrodidarum Species-level Match	RISB1973	Bemisia tabaci Order: Hemiptera	a primary symbiont, which compensates for the deficient nutritional composition of its food sources	0.03%	7.0
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	0.06%	6.6
Staphylococcus epidermidis Species-level Match	RISB1070	Oryctes rhinoceros Order: Coleoptera	gut microbe	1.01%	6.2
Bombilactobacillus bombi Species-level Match	RISB0617	Spodoptera frugiperda Order: Lepidoptera	degrade amygdalin	0.04%	5.4
Bosea sp. ANAM02 Species-level Match	RISB1702	Phlebotomus papatasi Order: Diptera	None	0.13%	5.1
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	0.03%	5.0
Treponema	RISB2377	termite Order: Blattodea	when grown together, two termite-gut Treponema species influence each other's gene expression in a far more comprehensive and nuanced manner than might have been predicted based on the results of previous studies on the respective pure cultures	0.03%	4.9
Rahnella	RISB1623	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	0.05%	4.9
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.	0.03%	4.8
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	0.14%	4.4
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	0.03%	4.0
Citrobacter	RISB1503	Bactrocera dorsalis Order: Diptera	Pesticide-degrading bacteria were frequently detected from pesticide-resistant insects. Susceptible insects became resistant after inoculation of the pesticide-degrading symbiont	0.03%	3.6
Corynebacterium	RISB0363	Pagiophloeus tsushimanus Order: Coleoptera	terpenoid-degrading: the highest degradation rates of D-camphor, linalool, and eucalyptol	1.73%	3.5
Citrobacter	RISB0192	Hermetia illucens Order: Diptera	can directly promote the expression of two gene families related to intestinal protein metabolism: Hitryp serine protease trypsin family and Himtp metallopeptidase family	0.03%	3.4
Methylobacter	RISB1440	Lutzomyia evansi Order: Diptera	Methylobacterium can be important in several physiological and metabolic processes in Lu. evansi, which suggests that interactions could occur with Leishmania parasite	0.06%	3.4
Corynebacterium	RISB0531	Helicoverpa armigera Order: Lepidoptera	Corynebacterium sp. 2-TD, mediates the toxicity of the 2-tridecanone to H. armigera	1.73%	3.4
Yersinia	RISB0492	Cimex hemipterus Order: Hemiptera	the disruption of the abundant Yersinia possibly could be related to the enhanced susceptibility towards the insecticides	0.86%	3.3
Citrobacter	RISB0517	Leptinotarsa decemlineata Order: Coleoptera	affect the cellular and humoral immunity of the insect, increasing its susceptibility to Bacillus thuringiensis var. tenebrionis (morrisoni) (Bt)	0.03%	2.9
Streptococcus	RISB2625	Galleria mellonella Order: Lepidoptera	suppress bacteria ingested with food by producing bacteriocin and by releasing a lysozyme like enzyme	0.80%	2.8
Vibrio	RISB1810	Monochamus galloprovincialis Order: Coleoptera	Have the ability for degradation of cellulose, proteins and starch	1.37%	2.7
Streptococcus	RISB2624	Reticulitermes flavipes Order: Blattodea	can be broken down into substances such as carbon dioxide, ammonia and acetic acid	0.80%	2.4
Rhizobium	RISB0135	Coccinella septempunctata Order: Coleoptera	be commonly found in plant roots and they all have nitrogen fixation abilities	0.76%	2.3
Halomonas	RISB1808	Monochamus galloprovincialis Order: Coleoptera	Have the ability for degradation of cellulose, proteins and starch	0.93%	2.3
Rahnella	RISB1800	Dendroctonus valens Order: Coleoptera	could alleviate or compromise the antagonistic effects of fungi O. minus and L. procerum on RTB larval growth	0.05%	2.2
Rahnella	RISB0741	Dendroctonus ponderosae Order: Coleoptera	R. aquatilis decreased (−)-α-pinene (38%) and (+)-α-pinene (46%) by 40% and 45% (by GC-MS), respectively	0.05%	2.1
Micrococcus	RISB2276	Ostrinia nubilalis Order: Lepidoptera	extreme cellulolytic enzymes, at extreme (pH 12) conditions, exhibited cellulolytic properties	0.23%	2.1
Mycobacterium	RISB1156	Nicrophorus concolor Order: Coleoptera	produces Antimicrobial compounds	1.38%	2.0
Streptococcus	RISB2604	Homona magnanima Order: Lepidoptera	influence the growth of Bacillus thuringiensis in the larvae	0.80%	2.0
Actinomyces	RISB1234	Hermetia illucens Order: Diptera	provides the tools for degrading of a broad range of substrates	0.05%	1.3
Clostridium	RISB0028	Sesamia inferens Order: Lepidoptera	degrade Chlorpyrifos and Chlorantraniliprole in vitro	0.14%	1.2
Halomonas	RISB1374	Bemisia tabaci Order: Hemiptera	None	0.93%	0.9
Aeromonas	RISB2456	Bombyx mori Order: Lepidoptera	able to utilize the CMcellulose and xylan	0.04%	0.9
Methylobacter	RISB2053	Atractomorpha sinensis Order: Orthoptera	associated with cellulolytic enzymes	0.06%	0.8
Aeromonas	RISB2086	Aedes aegypti Order: Diptera	axenic larvae cannot develop	0.04%	0.6
Geobacillus	RISB1251	Potamobates horvathi Order: Hemiptera	None	0.59%	0.6
Methylobacter	RISB2340	Saturniidae Order: Lepidoptera	Nitrogen fixation	0.06%	0.4
Aeromonas	RISB1145	Tenebrio molitor Order: Coleoptera	degrading plastics	0.04%	0.4
Neisseria	RISB0512	Plutella xylostella Order: Lepidoptera	None	0.28%	0.3
Cupriavidus	RISB0694	Alydus tomentosus Order: Hemiptera	None	0.15%	0.2
Clostridium	RISB1959	Pyrrhocoridae Order: Hemiptera	None	0.14%	0.1
Treponema	RISB0169	Reticulitermes flaviceps Order: Blattodea	None	0.03%	0.0