SRR6033664 - Apis mellifera

Basic Information

Run: SRR6033664

Assay Type: WGS

Bioproject: PRJNA407112

Biosample: SAMN07634951

Bytes: 56304317

Center Name: COLUMBIA

Sequencing Information

Instrument: Illumina MiSeq

Library Layout: SINGLE

Library Selection: RANDOM PCR

Platform: ILLUMINA

Geographic Information

Country: USA

Continent: North America

Location Name: USA: California

Latitude/Longitude: 41.7928 N 124.1208 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.	0.46%	40.5
Burkholderia Host Order Match Host Species Match	RISB2389	Apis mellifera Order: Hymenoptera	None	0.54%	30.5
Pseudomonas sp. CIP-10 Species-level Match Host Order Match	RISB1564	Liometopum apiculatum Order: Hymenoptera	None	7.53%	22.5
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	0.46%	20.5
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	0.17%	19.1
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	0.17%	18.9
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	0.85%	17.7
Stenotrophomonas maltophilia Species-level Match Host Order Match	RISB2004	Trichogramma chilonis Order: Hymenoptera	could significantly increase both female count	1.60%	17.5
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	0.17%	17.5
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	7.53%	17.4
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.	7.10%	17.1
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)	7.53%	15.9
Snodgrassella alvi Species-level Match Host Order Match	RISB1947	Apis cerana Order: Hymenoptera	None	0.85%	15.9
Gilliamella apicola Species-level Match Host Order Match	RISB1945	Apis cerana Order: Hymenoptera	None	0.46%	15.5
Lactobacillus apis Species-level Match Host Order Match	RISB1556	Apis florea Order: Hymenoptera	None	0.12%	15.1
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.	1.41%	14.7
Klebsiella pneumoniae Species-level Match	RISB2459	Bombyx mori Order: Lepidoptera	degradation of cellulose, xylan, pectin and starch	7.10%	13.1
Klebsiella pneumoniae Species-level Match	RISB1994	Diatraea saccharalis Order: Lepidoptera	possess cellulose degrading activity	7.10%	12.8
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	3.04%	12.4
Spiroplasma Host Order Match	RISB0613	Lariophagus distinguendus Order: Hymenoptera	induces cytoplasmic incompatibility (CI)	1.41%	12.2
Burkholderia Host Order Match	RISB2149	Osmia bicornis Order: Hymenoptera	may be essential to support Osmia larvae in their nutrient uptake	0.54%	11.8
Spiroplasma Host Order Match	RISB0284	Formica Order: Hymenoptera	None	1.41%	11.4
Acinetobacter Host Order Match	RISB2000	Trichogramma chilonis Order: Hymenoptera	could significantly increase both female count	0.25%	11.2
Burkholderia Host Order Match	RISB2101	Formica exsecta Order: Hymenoptera	produce antibiotics	0.54%	10.9
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	3.04%	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	0.62%	10.6
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.	1.60%	10.6
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.	0.21%	10.2
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.	0.07%	10.1
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	0.62%	9.8
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	1.60%	9.3
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	0.21%	9.2
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)	0.62%	9.0
Escherichia coli Species-level Match	RISB2120	Galleria mellonella Order: Lepidoptera	mediate trans-generational immune priming	3.04%	8.9
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.	0.07%	8.6
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	0.07%	8.1
Corynebacterium sp. Z-1 Species-level Match	RISB0531	Helicoverpa armigera Order: Lepidoptera	Corynebacterium sp. 2-TD, mediates the toxicity of the 2-tridecanone to H. armigera	1.40%	8.1
Enterococcus faecalis Species-level Match	RISB0497	Cryptolestes ferrugineus Order: Coleoptera	bacteria can degrade malathion, pirimiphos-methyl, and deltamethrin and utilize these insecticides as the carbon source in vitro.	0.13%	7.7
Enterococcus faecalis Species-level Match	RISB1411	Bactrocera dorsalis Order: Diptera	female Bactrocera dorsalis fed Enterococcus faecalis and Klebsiella oxytoca enriched diets lived longer but had lower fecundity	0.13%	7.7
Enterococcus faecalis Species-level Match	RISB2042	Harpalus pensylvanicus Order: Coleoptera	E. faecalis facilitate seed consumption by H. pensylvanicus, possibly by contributing digestive enzymes to their host	0.13%	7.5
Salmonella enterica Species-level Match	RISB0413	Melanaphis sacchari Order: Hemiptera	None	2.27%	7.3
Bacillus cereus Species-level Match	RISB2237	Anticarsia gemmatalis Order: Lepidoptera	mitigation of the negative effects of proteinase inhibitors produced by the host plant	0.21%	6.9
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	0.08%	6.7
Staphylococcus epidermidis Species-level Match	RISB1070	Oryctes rhinoceros Order: Coleoptera	gut microbe	1.43%	6.7
Lactiplantibacillus plantarum Species-level Match	RISB0674	Drosophila melanogaster Order: Diptera	could effectively inhibit fungal spore germinations	0.19%	6.2
Streptococcus	RISB2625	Galleria mellonella Order: Lepidoptera	suppress bacteria ingested with food by producing bacteriocin and by releasing a lysozyme like enzyme	3.72%	5.7
Microbacterium sp. zg-Y818 Species-level Match	RISB2095	Aedes aegypti Order: Diptera	axenic larvae cannot develop	0.09%	5.7
Staphylococcus hominis Species-level Match	RISB1881	Aedes aegypti Order: Diptera	gut microbiome	0.17%	5.5
Staphylococcus hominis Species-level Match	RISB1071	Oryctes rhinoceros Order: Coleoptera	gut microbe	0.17%	5.4
Streptococcus	RISB2624	Reticulitermes flavipes Order: Blattodea	can be broken down into substances such as carbon dioxide, ammonia and acetic acid	3.72%	5.4
Lactiplantibacillus plantarum Species-level Match	RISB0608	Drosophila melanogaster Order: Diptera	None	0.19%	5.2
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.	0.25%	5.1
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)	0.25%	4.9
Streptococcus	RISB2604	Homona magnanima Order: Lepidoptera	influence the growth of Bacillus thuringiensis in the larvae	3.72%	4.9
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	0.05%	4.3
Micrococcus	RISB2276	Ostrinia nubilalis Order: Lepidoptera	extreme cellulolytic enzymes, at extreme (pH 12) conditions, exhibited cellulolytic properties	0.48%	2.4
Leuconostoc	RISB0812	Hypothenemus hampei Order: Coleoptera	might contribute to caffeine breakdown using the C-18 oxidation pathway	0.66%	2.1
Bradyrhizobium	RISB0135	Coccinella septempunctata Order: Coleoptera	be commonly found in plant roots and they all have nitrogen fixation abilities	0.44%	2.0
Halomonas	RISB1808	Monochamus galloprovincialis Order: Coleoptera	Have the ability for degradation of cellulose, proteins and starch	0.37%	1.7
Mycobacterium	RISB1156	Nicrophorus concolor Order: Coleoptera	produces Antimicrobial compounds	0.65%	1.3
Brevibacterium	RISB0464	Acrida cinerea Order: Orthoptera	correlated with the hemicellulose digestibility	0.33%	1.3
Komagataeibacter	RISB1883	Drosophila suzukii Order: Diptera	produce volatile substances that attract female D. suzukii	0.07%	1.2
Clostridium	RISB0028	Sesamia inferens Order: Lepidoptera	degrade Chlorpyrifos and Chlorantraniliprole in vitro	0.05%	1.1
Brevibacterium	RISB2359	Bombyx mori Order: Lepidoptera	producing lipase in a gut environment	0.33%	1.1
Aeromonas	RISB2456	Bombyx mori Order: Lepidoptera	able to utilize the CMcellulose and xylan	0.17%	1.0
Neisseria	RISB0512	Plutella xylostella Order: Lepidoptera	None	0.99%	1.0
Aeromonas	RISB2086	Aedes aegypti Order: Diptera	axenic larvae cannot develop	0.17%	0.7
Aeromonas	RISB1145	Tenebrio molitor Order: Coleoptera	degrading plastics	0.17%	0.5
Bombilactobacillus	RISB0617	Spodoptera frugiperda Order: Lepidoptera	degrade amygdalin	0.07%	0.4
Halomonas	RISB1374	Bemisia tabaci Order: Hemiptera	None	0.37%	0.4
Brevibacterium	RISB0897	Myzus persicae Order: Hemiptera	None	0.33%	0.3
Cupriavidus	RISB0694	Alydus tomentosus Order: Hemiptera	None	0.08%	0.1
Ralstonia	RISB0243	Spodoptera frugiperda Order: Lepidoptera	None	0.06%	0.1
Clostridium	RISB1959	Pyrrhocoridae Order: Hemiptera	None	0.05%	0.1
Selenomonas	RISB1305	Aphis gossypii Order: Hemiptera	None	0.04%	0.0