SRR6033673 - Apis mellifera

Basic Information

Run: SRR6033673

Assay Type: WGS

Bioproject: PRJNA407112

Biosample: SAMN07634928

Bytes: 59122114

Center Name: COLUMBIA

Sequencing Information

Instrument: Illumina MiSeq

Library Layout: SINGLE

Library Selection: RANDOM PCR

Platform: ILLUMINA

Geographic Information

Country: Kenya

Continent: Africa

Location Name: Kenya: Mbita

Latitude/Longitude: 0.4354 S 34.2144 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.	1.46%	41.5
Bifidobacterium 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	0.11%	35.1
Lactobacillus Host Order Match Host Species Match	RISB0475	Apis mellifera Order: Hymenoptera	A. kunkeei alleviated acetamiprid-induced symbiotic microbiota dysregulation and mortality in honeybees	0.38%	32.4
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	0.38%	32.2
Lactobacillus Host Order Match Host Species Match	RISB0615	Apis mellifera Order: Hymenoptera	Improve learning and memory performance	0.38%	31.2
Pseudomonas aeruginosa Species-level Match	RISB0364	Pagiophloeus tsushimanus Order: Coleoptera	terpenoid-degrading: the highest degradation rates of D-camphor, linalool, and eucalyptol	24.21%	31.0
Burkholderia Host Order Match Host Species Match	RISB2389	Apis mellifera Order: Hymenoptera	None	0.06%	30.1
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	1.46%	21.5
Pseudomonas sp. CIP-10 Species-level Match Host Order Match	RISB1564	Liometopum apiculatum Order: Hymenoptera	None	5.48%	20.5
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.	10.03%	20.0
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	0.44%	19.4
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	2.41%	19.3
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	0.44%	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	0.44%	17.8
Snodgrassella alvi Species-level Match Host Order Match	RISB1947	Apis cerana Order: Hymenoptera	None	2.41%	17.4
Stenotrophomonas maltophilia Species-level Match Host Order Match	RISB2004	Trichogramma chilonis Order: Hymenoptera	could significantly increase both female count	1.01%	16.9
Gilliamella apicola Species-level Match Host Order Match	RISB1945	Apis cerana Order: Hymenoptera	None	1.46%	16.5
Klebsiella pneumoniae Species-level Match	RISB2459	Bombyx mori Order: Lepidoptera	degradation of cellulose, xylan, pectin and starch	10.03%	16.0
Klebsiella pneumoniae Species-level Match	RISB1994	Diatraea saccharalis Order: Lepidoptera	possess cellulose degrading activity	10.03%	15.8
Pseudomonas sp. FP833 Species-level Match Host Order Match	RISB1564	Liometopum apiculatum Order: Hymenoptera	None	0.71%	15.7
Corynebacterium Host Order Match	RISB1285	Aphidius colemani Order: Hymenoptera	Repelling parasitism	4.87%	15.3
Bifidobacterium 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	0.11%	15.1
Serratia symbiotica Species-level Match Host Order Match	RISB2331	Camponotus japonicus Order: Hymenoptera	None	0.05%	15.1
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	0.18%	13.9
Xanthomonas Host Order Match	RISB0217	Xylocopa appendiculata Order: Hymenoptera	strains biodegraded polyethylene terephthalate PET powder, broke it into its degradation products	0.18%	12.1
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	2.17%	11.5
Diaphorobacter Host Order Match	RISB2150	Osmia bicornis Order: Hymenoptera	may be essential to support Osmia larvae in their nutrient uptake	0.13%	11.4
Salmonella enterica Species-level Match	RISB0413	Melanaphis sacchari Order: Hemiptera	None	6.38%	11.4
Burkholderia Host Order Match	RISB2149	Osmia bicornis Order: Hymenoptera	may be essential to support Osmia larvae in their nutrient uptake	0.06%	11.4
Yersinia Host Order Match	RISB0407	Anaphes nitens Order: Hymenoptera	None	0.61%	10.6
Burkholderia Host Order Match	RISB2101	Formica exsecta Order: Hymenoptera	produce antibiotics	0.06%	10.4
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.	0.19%	10.2
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	0.17%	10.2
Bifidobacterium Host Order Match	RISB1944	Apis cerana Order: Hymenoptera	None	0.11%	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	0.05%	10.1
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	0.05%	10.1
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.	1.01%	10.0
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	2.17%	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	0.05%	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	0.05%	9.6
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	0.17%	9.4
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	0.19%	9.2
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	0.05%	8.9
Acinetobacter pittii Species-level Match	RISB1977	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	0.02%	8.8
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	1.01%	8.7
Enterobacter ludwigii Species-level Match	RISB1543	Helicoverpa zea Order: Lepidoptera	two immunity-related genes glucose oxidase (GOX) and lysozyme (LYZ) were more highly expressed in both salivary glands and midguts compared with MgCl2 solution-treated caterpillars	0.05%	8.7
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
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
Escherichia coli Species-level Match	RISB2120	Galleria mellonella Order: Lepidoptera	mediate trans-generational immune priming	2.17%	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	0.03%	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
Carnobacterium maltaromaticum Species-level Match	RISB1693	Plutella xylostella Order: Lepidoptera	play an important role in the breakdown of plant cell walls, detoxification of plant phenolics, and synthesis of amino acids.	0.19%	7.7
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
Bacillus cereus Species-level Match	RISB2237	Anticarsia gemmatalis Order: Lepidoptera	mitigation of the negative effects of proteinase inhibitors produced by the host plant	0.19%	6.9
Carnobacterium maltaromaticum Species-level Match	RISB1692	Plutella xylostella Order: Lepidoptera	participate in the synthesis of host lacking amino acids histidine and threonine	0.19%	6.8
Corynebacterium	RISB0363	Pagiophloeus tsushimanus Order: Coleoptera	terpenoid-degrading: the highest degradation rates of D-camphor, linalool, and eucalyptol	4.87%	6.7
Corynebacterium	RISB0531	Helicoverpa armigera Order: Lepidoptera	Corynebacterium sp. 2-TD, mediates the toxicity of the 2-tridecanone to H. armigera	4.87%	6.5
Erwinia sp. Ejp617 Species-level Match	RISB0808	Hypothenemus hampei Order: Coleoptera	might contribute to caffeine breakdown using the C-12 oxidation pathway	0.09%	6.5
Lactiplantibacillus plantarum Species-level Match	RISB0674	Drosophila melanogaster Order: Diptera	could effectively inhibit fungal spore germinations	0.19%	6.2
Candidatus Riesia pediculicola Species-level Match	RISB2452	Pediculus humanus humanus Order: Phthiraptera	supplement body lice nutritionally deficient blood diet	0.02%	6.1
Carnobacterium maltaromaticum Species-level Match	RISB1691	Plutella xylostella Order: Lepidoptera	activity of cellulose and hemicellulose	0.19%	6.0
Lactococcus	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.	0.75%	5.8
Erwinia sp. Ejp617 Species-level Match	RISB1986	Bombyx mori Order: Lepidoptera	producing cellulase and amylase	0.09%	5.7
Staphylococcus epidermidis Species-level Match	RISB1070	Oryctes rhinoceros Order: Coleoptera	gut microbe	0.34%	5.6
Lactiplantibacillus plantarum Species-level Match	RISB0608	Drosophila melanogaster Order: Diptera	None	0.19%	5.2
Lactococcus	RISB2305	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	0.75%	5.0
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	0.01%	4.8
Lactococcus	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.	0.75%	4.3
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
Halomonas	RISB1808	Monochamus galloprovincialis Order: Coleoptera	Have the ability for degradation of cellulose, proteins and starch	1.28%	2.6
Rhizobium	RISB0135	Coccinella septempunctata Order: Coleoptera	be commonly found in plant roots and they all have nitrogen fixation abilities	1.02%	2.6
Streptococcus	RISB2625	Galleria mellonella Order: Lepidoptera	suppress bacteria ingested with food by producing bacteriocin and by releasing a lysozyme like enzyme	0.41%	2.4
Rahnella	RISB1800	Dendroctonus valens Order: Coleoptera	could alleviate or compromise the antagonistic effects of fungi O. minus and L. procerum on RTB larval growth	0.01%	2.2
Sphingomonas	RISB0420	Aphis gossypii Order: Hemiptera	Sphingomonas could mediate A. gossypii resistance to imidacloprid by hydroxylation and nitroreduction	0.08%	2.1
Micrococcus	RISB2276	Ostrinia nubilalis Order: Lepidoptera	extreme cellulolytic enzymes, at extreme (pH 12) conditions, exhibited cellulolytic properties	0.22%	2.1
Rahnella	RISB0741	Dendroctonus ponderosae Order: Coleoptera	R. aquatilis decreased (−)-α-pinene (38%) and (+)-α-pinene (46%) by 40% and 45% (by GC-MS), respectively	0.01%	2.1
Streptococcus	RISB2624	Reticulitermes flavipes Order: Blattodea	can be broken down into substances such as carbon dioxide, ammonia and acetic acid	0.41%	2.1
Vibrio	RISB1810	Monochamus galloprovincialis Order: Coleoptera	Have the ability for degradation of cellulose, proteins and starch	0.70%	2.0
Sphingomonas	RISB1307	Aphis gossypii Order: Hemiptera	have been previously described in associations with phloem-feeding insects, in low abundances	0.08%	1.9
Sphingomonas	RISB0134	Spodoptera frugiperda Order: Lepidoptera	provide a protective effect to against chlorantraniliprole stress to S. frugiperda	0.08%	1.7
Streptococcus	RISB2604	Homona magnanima Order: Lepidoptera	influence the growth of Bacillus thuringiensis in the larvae	0.41%	1.6
Actinomyces	RISB1234	Hermetia illucens Order: Diptera	provides the tools for degrading of a broad range of substrates	0.24%	1.5
Dysgonomonas	RISB1235	Hermetia illucens Order: Diptera	provides the tools for degrading of a broad range of substrates	0.03%	1.3
Halomonas	RISB1374	Bemisia tabaci Order: Hemiptera	None	1.28%	1.3
Aeromonas	RISB2456	Bombyx mori Order: Lepidoptera	able to utilize the CMcellulose and xylan	0.07%	0.9
Gordonia	RISB1912	Hyles euphorbiae Order: Lepidoptera	able to degrade alkaloids and/or latex	0.05%	0.8
Aeromonas	RISB2086	Aedes aegypti Order: Diptera	axenic larvae cannot develop	0.07%	0.6
Cupriavidus	RISB0694	Alydus tomentosus Order: Hemiptera	None	0.52%	0.5
Aeromonas	RISB1145	Tenebrio molitor Order: Coleoptera	degrading plastics	0.07%	0.4
Diaphorobacter	RISB1062	Oryctes rhinoceros Order: Coleoptera	gut microbe	0.13%	0.4
Neisseria	RISB0512	Plutella xylostella Order: Lepidoptera	None	0.17%	0.2
Dysgonomonas	RISB1481	Brachinus elongatulus Order: Coleoptera	None	0.03%	0.0