SRR6033683 - Apis mellifera

Basic Information

Run: SRR6033683

Assay Type: WGS

Bioproject: PRJNA407112

Biosample: SAMN07634945

Bytes: 88958674

Center Name: COLUMBIA

Sequencing Information

Instrument: Illumina MiSeq

Library Layout: SINGLE

Library Selection: RANDOM PCR

Platform: ILLUMINA

Quality Control Information

Filter Percentage: 0.0085

QC Average Length: 149

Retained Reads: -

Geographic Information

Country: Kenya

Continent: Africa

Location Name: Kenya: Kakamega

Latitude/Longitude: 0.2527 N 34.9232 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
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
Lactobacillus Host Order Match Host Species Match	RISB0475	Apis mellifera Order: Hymenoptera	A. kunkeei alleviated acetamiprid-induced symbiotic microbiota dysregulation and mortality in honeybees	0.20%	32.3
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	0.20%	32.0
Lactobacillus Host Order Match Host Species Match	RISB0615	Apis mellifera Order: Hymenoptera	Improve learning and memory performance	0.20%	31.0
Burkholderia Host Order Match Host Species Match	RISB2389	Apis mellifera Order: Hymenoptera	None	0.82%	30.8
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.	9.71%	19.7
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	0.09%	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	0.09%	18.8
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	0.66%	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	0.09%	17.4
Pseudomonas sp. CIP-10 Species-level Match Host Order Match	RISB1564	Liometopum apiculatum Order: Hymenoptera	None	1.48%	16.5
Stenotrophomonas maltophilia Species-level Match Host Order Match	RISB2004	Trichogramma chilonis Order: Hymenoptera	could significantly increase both female count	0.33%	16.3
Klebsiella pneumoniae Species-level Match	RISB2459	Bombyx mori Order: Lepidoptera	degradation of cellulose, xylan, pectin and starch	9.71%	15.7
Snodgrassella alvi Species-level Match Host Order Match	RISB1947	Apis cerana Order: Hymenoptera	None	0.66%	15.7
Klebsiella pneumoniae Species-level Match	RISB1994	Diatraea saccharalis Order: Lepidoptera	possess cellulose degrading activity	9.71%	15.4
Burkholderia Host Order Match	RISB2149	Osmia bicornis Order: Hymenoptera	may be essential to support Osmia larvae in their nutrient uptake	0.82%	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	2.80%	12.1
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	1.48%	11.3
Burkholderia Host Order Match	RISB2101	Formica exsecta Order: Hymenoptera	produce antibiotics	0.82%	11.2
Acinetobacter Host Order Match	RISB2000	Trichogramma chilonis Order: Hymenoptera	could significantly increase both female count	0.11%	11.0
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	2.80%	10.5
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.	0.18%	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	0.09%	10.1
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.	0.06%	10.1
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)	1.48%	9.8
Salmonella enterica Species-level Match	RISB0413	Melanaphis sacchari Order: Hemiptera	None	4.52%	9.5
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.	0.33%	9.3
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	0.09%	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	0.18%	9.2
Escherichia coli Species-level Match	RISB2120	Galleria mellonella Order: Lepidoptera	mediate trans-generational immune priming	2.80%	8.6
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.	0.06%	8.6
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)	0.09%	8.4
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	0.06%	8.1
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	0.33%	8.0
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.	0.32%	7.9
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	0.32%	7.9
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	0.32%	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	0.18%	6.9
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	0.23%	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	0.05%	6.6
Staphylococcus epidermidis Species-level Match	RISB1070	Oryctes rhinoceros Order: Coleoptera	gut microbe	0.89%	6.1
Lactiplantibacillus plantarum Species-level Match	RISB0674	Drosophila melanogaster Order: Diptera	could effectively inhibit fungal spore germinations	0.09%	6.1
Microbacterium sp. zg-Y818 Species-level Match	RISB2095	Aedes aegypti Order: Diptera	axenic larvae cannot develop	0.08%	5.6
Staphylococcus hominis Species-level Match	RISB1881	Aedes aegypti Order: Diptera	gut microbiome	0.15%	5.4
Staphylococcus hominis Species-level Match	RISB1071	Oryctes rhinoceros Order: Coleoptera	gut microbe	0.15%	5.4
Lactiplantibacillus plantarum Species-level Match	RISB0608	Drosophila melanogaster Order: Diptera	None	0.09%	5.1
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.	0.11%	5.0
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)	0.11%	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	0.06%	4.3
Streptococcus	RISB2625	Galleria mellonella Order: Lepidoptera	suppress bacteria ingested with food by producing bacteriocin and by releasing a lysozyme like enzyme	1.47%	3.5
Streptococcus	RISB2624	Reticulitermes flavipes Order: Blattodea	can be broken down into substances such as carbon dioxide, ammonia and acetic acid	1.47%	3.1
Streptococcus	RISB2604	Homona magnanima Order: Lepidoptera	influence the growth of Bacillus thuringiensis in the larvae	1.47%	2.7
Micrococcus	RISB2276	Ostrinia nubilalis Order: Lepidoptera	extreme cellulolytic enzymes, at extreme (pH 12) conditions, exhibited cellulolytic properties	0.59%	2.5
Bradyrhizobium	RISB0135	Coccinella septempunctata Order: Coleoptera	be commonly found in plant roots and they all have nitrogen fixation abilities	0.06%	1.6
Halomonas	RISB1808	Monochamus galloprovincialis Order: Coleoptera	Have the ability for degradation of cellulose, proteins and starch	0.07%	1.4
Clostridium	RISB0028	Sesamia inferens Order: Lepidoptera	degrade Chlorpyrifos and Chlorantraniliprole in vitro	0.06%	1.1
Aeromonas	RISB2456	Bombyx mori Order: Lepidoptera	able to utilize the CMcellulose and xylan	0.30%	1.1
Brevibacterium	RISB0464	Acrida cinerea Order: Orthoptera	correlated with the hemicellulose digestibility	0.07%	1.0
Mycobacterium	RISB1156	Nicrophorus concolor Order: Coleoptera	produces Antimicrobial compounds	0.30%	0.9
Neisseria	RISB0512	Plutella xylostella Order: Lepidoptera	None	0.93%	0.9
Aeromonas	RISB2086	Aedes aegypti Order: Diptera	axenic larvae cannot develop	0.30%	0.9
Brevibacterium	RISB2359	Bombyx mori Order: Lepidoptera	producing lipase in a gut environment	0.07%	0.8
Cupriavidus	RISB0694	Alydus tomentosus Order: Hemiptera	None	0.71%	0.7
Aeromonas	RISB1145	Tenebrio molitor Order: Coleoptera	degrading plastics	0.30%	0.7
Ralstonia	RISB0243	Spodoptera frugiperda Order: Lepidoptera	None	0.29%	0.3
Halomonas	RISB1374	Bemisia tabaci Order: Hemiptera	None	0.07%	0.1
Brevibacterium	RISB0897	Myzus persicae Order: Hemiptera	None	0.07%	0.1
Clostridium	RISB1959	Pyrrhocoridae Order: Hemiptera	None	0.06%	0.1