SRR6033671 - Apis mellifera

Basic Information

Run: SRR6033671

Assay Type: WGS

Bioproject: PRJNA407112

Biosample: SAMN07634936

Bytes: 62209109

Center Name: COLUMBIA

Sequencing Information

Instrument: Illumina MiSeq

Library Layout: SINGLE

Library Selection: RANDOM PCR

Platform: ILLUMINA

Quality Control Information

Filter Percentage: 0.0061

QC Average Length: 148

Retained Reads: -

Geographic Information

Country: Panama

Continent: North America

Location Name: Panama

Latitude/Longitude: 9.1500 N 79.8500 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.	0.18%	40.2
Lactobacillus Host Order Match Host Species Match	RISB0475	Apis mellifera Order: Hymenoptera	A. kunkeei alleviated acetamiprid-induced symbiotic microbiota dysregulation and mortality in honeybees	0.55%	32.6
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	0.55%	32.4
Lactobacillus Host Order Match Host Species Match	RISB0615	Apis mellifera Order: Hymenoptera	Improve learning and memory performance	0.55%	31.3
Burkholderia Host Order Match Host Species Match	RISB2389	Apis mellifera Order: Hymenoptera	None	1.13%	31.1
Pseudomonas sp. CIP-10 Species-level Match Host Order Match	RISB1564	Liometopum apiculatum Order: Hymenoptera	None	9.25%	24.3
Stenotrophomonas maltophilia Species-level Match Host Order Match	RISB2004	Trichogramma chilonis Order: Hymenoptera	could significantly increase both female count	5.84%	21.8
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	0.18%	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	0.60%	19.6
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	0.60%	19.3
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	9.25%	19.1
Streptomyces sp. NBC_00250 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	0.04%	19.0
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	8.56%	18.6
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	8.56%	17.8
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)	9.25%	17.6
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	0.56%	17.4
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)	8.56%	16.9
Snodgrassella alvi Species-level Match Host Order Match	RISB1947	Apis cerana Order: Hymenoptera	None	0.56%	15.6
Gilliamella apicola Species-level Match Host Order Match	RISB1945	Apis cerana Order: Hymenoptera	None	0.18%	15.2
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.	5.84%	14.8
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	4.51%	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.	3.67%	13.7
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	5.84%	13.5
Streptococcus	RISB2625	Galleria mellonella Order: Lepidoptera	suppress bacteria ingested with food by producing bacteriocin and by releasing a lysozyme like enzyme	10.89%	12.9
Streptococcus	RISB2624	Reticulitermes flavipes Order: Blattodea	can be broken down into substances such as carbon dioxide, ammonia and acetic acid	10.89%	12.5
Burkholderia Host Order Match	RISB2149	Osmia bicornis Order: Hymenoptera	may be essential to support Osmia larvae in their nutrient uptake	1.13%	12.4
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	4.51%	12.2
Streptococcus	RISB2604	Homona magnanima Order: Lepidoptera	influence the growth of Bacillus thuringiensis in the larvae	10.89%	12.1
Acinetobacter Host Order Match	RISB2000	Trichogramma chilonis Order: Hymenoptera	could significantly increase both female count	0.97%	11.9
Burkholderia Host Order Match	RISB2101	Formica exsecta Order: Hymenoptera	produce antibiotics	1.13%	11.5
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.	1.20%	11.2
Escherichia coli Species-level Match	RISB2120	Galleria mellonella Order: Lepidoptera	mediate trans-generational immune priming	4.51%	10.3
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	1.20%	10.2
Klebsiella pneumoniae Species-level Match	RISB2459	Bombyx mori Order: Lepidoptera	degradation of cellulose, xylan, pectin and starch	3.67%	9.7
Klebsiella pneumoniae Species-level Match	RISB1994	Diatraea saccharalis Order: Lepidoptera	possess cellulose degrading activity	3.67%	9.4
Bacillus cereus Species-level Match	RISB2237	Anticarsia gemmatalis Order: Lepidoptera	mitigation of the negative effects of proteinase inhibitors produced by the host plant	1.20%	7.9
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.	0.03%	7.6
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	0.03%	7.6
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	0.03%	7.4
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	0.51%	7.2
Sphingomonas sp. NY01 Species-level Match	RISB0134	Spodoptera frugiperda Order: Lepidoptera	provide a protective effect to against chlorantraniliprole stress to S. frugiperda	0.10%	6.7
Sphingomonas sp. R1 Species-level Match	RISB0134	Spodoptera frugiperda Order: Lepidoptera	provide a protective effect to against chlorantraniliprole stress to S. frugiperda	0.07%	6.7
Salmonella enterica Species-level Match	RISB0413	Melanaphis sacchari Order: Hemiptera	None	1.70%	6.7
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
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.	0.97%	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)	0.97%	5.7
Staphylococcus epidermidis Species-level Match	RISB1070	Oryctes rhinoceros Order: Coleoptera	gut microbe	0.20%	5.4
Staphylococcus hominis Species-level Match	RISB1881	Aedes aegypti Order: Diptera	gut microbiome	0.04%	5.3
Staphylococcus hominis Species-level Match	RISB1071	Oryctes rhinoceros Order: Coleoptera	gut microbe	0.04%	5.3
Brevundimonas sp. PAMC22021 Species-level Match	RISB1703	Phlebotomus papatasi Order: Diptera	None	0.04%	5.0
Paenibacillus	RISB2195	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.	0.02%	5.0
Rhizobium	RISB0135	Coccinella septempunctata Order: Coleoptera	be commonly found in plant roots and they all have nitrogen fixation abilities	2.50%	4.1
Paenibacillus	RISB0774	Delia antiqua Order: Diptera	showed significant contact inhibition activity against fungal entomopathogen Fusarium moniliforme, Botryosphaeria dothidea and both Fusarium oxysporum respectively	0.02%	3.3
Actinomyces	RISB1234	Hermetia illucens Order: Diptera	provides the tools for degrading of a broad range of substrates	1.95%	3.2
Proteus	RISB0001	Leptinotarsa decemlineata Order: Coleoptera	produces toxic hydrogen cyanide (HCN) and a mandelonitrile-producing cyanoglucoside, amygdalin, which protect the insect from predation	0.13%	2.8
Proteus	RISB2315	Aedes aegypti Order: Diptera	upregulates AMP gene expression, resulting in suppression of DENV infection in the mosquito gut epithelium	0.13%	2.3
Halomonas	RISB1808	Monochamus galloprovincialis Order: Coleoptera	Have the ability for degradation of cellulose, proteins and starch	0.79%	2.1
Paenibacillus	RISB0813	Hypothenemus hampei Order: Coleoptera	might contribute to caffeine breakdown using the C-9 oxidation pathway	0.02%	1.4
Brevibacterium	RISB0464	Acrida cinerea Order: Orthoptera	correlated with the hemicellulose digestibility	0.45%	1.4
Vibrio	RISB1810	Monochamus galloprovincialis Order: Coleoptera	Have the ability for degradation of cellulose, proteins and starch	0.02%	1.3
Brevibacterium	RISB2359	Bombyx mori Order: Lepidoptera	producing lipase in a gut environment	0.45%	1.2
Proteus	RISB2460	Bombyx mori Order: Lepidoptera	degradation of cellulose, xylan, pectin and starch	0.13%	1.1
Aeromonas	RISB2456	Bombyx mori Order: Lepidoptera	able to utilize the CMcellulose and xylan	0.05%	0.9
Halomonas	RISB1374	Bemisia tabaci Order: Hemiptera	None	0.79%	0.8
Gordonia	RISB1912	Hyles euphorbiae Order: Lepidoptera	able to degrade alkaloids and/or latex	0.03%	0.8
Mycobacterium	RISB1156	Nicrophorus concolor Order: Coleoptera	produces Antimicrobial compounds	0.05%	0.7
Aeromonas	RISB2086	Aedes aegypti Order: Diptera	axenic larvae cannot develop	0.05%	0.6
Brevibacterium	RISB0897	Myzus persicae Order: Hemiptera	None	0.45%	0.5
Aeromonas	RISB1145	Tenebrio molitor Order: Coleoptera	degrading plastics	0.05%	0.4
Selenomonas	RISB1305	Aphis gossypii Order: Hemiptera	None	0.16%	0.2
Cupriavidus	RISB0694	Alydus tomentosus Order: Hemiptera	None	0.10%	0.1