SRR3499636 - Negative control

Basic Information

Run: SRR3499636

Assay Type: WGS

Bioproject: PRJNA321195

Biosample: SAMN04978006

Bytes: 187464965

Center Name: BSRI

Sequencing Information

Instrument: Illumina MiSeq

Library Layout: PAIRED

Library Selection: RANDOM

Platform: ILLUMINA

Geographic Information

Country: USA

Continent: North America

Location Name: USA: Pennsylvania

Latitude/Longitude: 40.38002840 N 76.02538062 W

Sample Information

Host: Negative control

Isolation: mushroom farm

Biosample Model: Metagenome or environmental

Collection Date: 2016-01-01

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
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	2.71%	12.5
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.	2.18%	12.2
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	2.83%	12.2
Delftia	RISB0083	Osmia cornifrons Order: Hymenoptera	be known to exhibit antibiotic activity, suggesting their potential protective role against pathogens	10.09%	12.1
Delftia	RISB0806	Hypothenemus hampei Order: Coleoptera	might contribute to caffeine breakdown using the C-19 oxidation pathway	10.09%	11.5
Delftia	RISB1754	Spodoptera frugiperda Order: Lepidoptera	may influence the metabolization of pesticides in insects	10.09%	11.2
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)	2.71%	11.1
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	2.83%	10.6
Bacillus thuringiensis Species-level Match	RISB2177	Armadillidae Order: Isopoda	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.	0.52%	10.5
Pseudomonas sp. FP833 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	0.39%	10.2
Bacillus thuringiensis Species-level Match	RISB0109	Tuta absoluta Order: Lepidoptera	Individual exposure of B. thuringiensis isolates to P. absoluta revealed high susceptibility of the pest and could potentially be used to develop effective, safe and affordable microbial pesticides for the management of P. absoluta.	0.52%	10.2
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.	0.13%	10.1
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	0.04%	10.0
Acinetobacter sp. SCLZS86 Species-level Match	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)	0.23%	9.9
Streptomyces sp. ICC1 Species-level 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	0.87%	9.8
Acinetobacter sp. SWBY1 Species-level Match	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)	0.06%	9.7
Acinetobacter sp. WCHA45 Species-level Match	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)	0.03%	9.7
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.	0.65%	9.7
Streptomyces sp. ICC1 Species-level 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	0.87%	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	0.04%	9.3
Streptomyces sp. ICC4 Species-level 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	0.16%	9.1
Klebsiella michiganensis Species-level Match	RISB1052	Bactrocera dorsalis Order: Diptera	K. michiganensis BD177 has the strain-specific ability to provide three essential amino acids (phenylalanine, tryptophan and methionine) and two vitamins B (folate and riboflavin) to B. dorsalis	0.10%	9.0
Escherichia coli Species-level Match	RISB2120	Galleria mellonella Order: Lepidoptera	mediate trans-generational immune priming	2.83%	8.7
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)	0.04%	8.4
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	0.65%	8.4
Klebsiella pneumoniae Species-level Match	RISB2459	Bombyx mori Order: Lepidoptera	degradation of cellulose, xylan, pectin and starch	2.18%	8.2
Citrobacter freundii complex sp. CFNIH2 Species-level Match	RISB0517	Leptinotarsa decemlineata Order: Coleoptera	affect the cellular and humoral immunity of the insect, increasing its susceptibility to Bacillus thuringiensis var. tenebrionis (morrisoni) (Bt)	0.07%	8.0
Citrobacter freundii complex sp. CFNIH2 Species-level Match	RISB0127	Tribolium castaneum Order: Coleoptera	may produce 4,8-dimethyldecanal (DMD) production that is strongly associated with attraction to females and host pheromone communication	0.07%	7.8
Citrobacter freundii complex sp. CFNIH2 Species-level Match	RISB1221	Delia antiqua Order: Diptera	six bacteria protect larvae from infection with the entomopathogen Beauveria bassiana through symbiotic bacterium-derived organic acids	0.07%	7.8
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.	0.05%	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	0.05%	7.6
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.	0.03%	7.5
Psychrobacter sp. P2G3 Species-level Match	RISB1773	Calliphoridae Order: Diptera	it shows physiological adaptation to survival in warmer temperatures and has been previously associated with food spoilage	0.02%	7.5
Stenotrophomonas maltophilia Species-level Match	RISB1141	Hermetia illucens Order: Diptera	enhance the insect growth performance when reared on an unbalanced nutritionally poor diet	0.65%	7.5
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	0.05%	7.4
Burkholderia	RISB1172	Lagria villosa Order: Coleoptera	process a cryptic gene cluster that codes for the biosynthesis of a novel antifungal polyketide with a glutarimide pharmacophore, which led to the discovery of the gladiofungins as previously-overlooked components of the antimicrobial armory of the beetle symbiont	2.08%	7.1
Leclercia adecarboxylata Species-level Match	RISB1757	Spodoptera frugiperda Order: Lepidoptera	degradation of lambda-cyhalothrin, deltamethrin, chlorpyrifos ethyl, lufenuron and spinosyn	0.03%	6.9
Serratia proteamaculans Species-level Match	RISB1846	Dendroctonus adjunctus Order: Coleoptera	display strong cellulolytic activity and process a single endoglucanase encoding gene	0.06%	6.8
Carnobacterium maltaromaticum Species-level Match	RISB1692	Plutella xylostella Order: Lepidoptera	participate in the synthesis of host lacking amino acids histidine and threonine	0.03%	6.6
Burkholderia	RISB1729	Lagria hirta Order: Coleoptera	the symbionts inhibit the growth of antagonistic fungi on the eggs of the insect host, indicating that the Lagria-associated Burkholderia have evolved from plant pathogenic ancestors into insect defensive mutualists	2.08%	6.4
Burkholderia	RISB0402	Riptortus pedestris Order: Hemiptera	symbiont colonization induces the development of the midgut crypts via finely regulating the enterocyte cell cycles, enabling it to stably and abundantly colonize the generated spacious crypts of the bean bug host	2.08%	6.3
Leclercia adecarboxylata Species-level Match	RISB1758	Spodoptera frugiperda Order: Lepidoptera	may influence the metabolization of pesticides in insects	0.03%	6.2
Salmonella enterica Species-level Match	RISB0413	Melanaphis sacchari Order: Hemiptera	None	0.93%	5.9
Carnobacterium maltaromaticum Species-level Match	RISB1691	Plutella xylostella Order: Lepidoptera	activity of cellulose and hemicellulose	0.03%	5.8
Comamonas testosteroni Species-level Match	RISB1875	Aedes aegypti Order: Diptera	gut microbiome	0.07%	5.4
Staphylococcus epidermidis Species-level Match	RISB1070	Oryctes rhinoceros Order: Coleoptera	gut microbe	0.06%	5.3
Serratia grimesii Species-level Match	RISB0405	Anaphes nitens Order: Hymenoptera	None	0.06%	5.1
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.	0.06%	5.1
Thauera sp. K11 Species-level Match	RISB1711	Phlebotomus papatasi Order: Diptera	None	0.05%	5.1
Bifidobacterium	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	0.03%	5.0
Agrobacterium tumefaciens Species-level Match	RISB0650	Melanaphis bambusae Order: Hemiptera	None	0.02%	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	0.03%	4.9
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	0.06%	4.3
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	0.02%	4.2
Xanthomonas	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	0.02%	3.8
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.	0.06%	3.6
Bifidobacterium	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	0.03%	3.5
Methylobacterium	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	0.10%	3.4
Ralstonia	RISB0243	Spodoptera frugiperda Order: Lepidoptera	None	2.84%	2.8
Variovorax	RISB2153	Osmia bicornis Order: Hymenoptera	may be essential to support Osmia larvae in their nutrient uptake	1.40%	2.7
Yersinia	RISB0492	Cimex hemipterus Order: Hemiptera	the disruption of the abundant Yersinia possibly could be related to the enhanced susceptibility towards the insecticides	0.28%	2.7
Bradyrhizobium	RISB0135	Coccinella septempunctata Order: Coleoptera	be commonly found in plant roots and they all have nitrogen fixation abilities	1.09%	2.7
Bartonella	RISB1673	Apis mellifera Order: Hymenoptera	a gut symbiont of insects and that the adaptation to blood-feeding insects facilitated colonization of the mammalian bloodstream	0.01%	2.6
Streptococcus	RISB2625	Galleria mellonella Order: Lepidoptera	suppress bacteria ingested with food by producing bacteriocin and by releasing a lysozyme like enzyme	0.43%	2.5
Bacteroides	RISB0256	Leptocybe invasa Order: Hymenoptera	Differences in Male-Killing Rickettsia Bacteria between Lineages of the Invasive Gall-Causing Pest Leptocybe invasa	0.08%	2.4
Liberibacter	RISB2310	Bactericerca cockerelli Order: Hemiptera	manipulate plant signaling and defensive responses, suppress accumulation of defense transcripts like JA and SA	0.02%	2.3
Corynebacterium	RISB0363	Pagiophloeus tsushimanus Order: Coleoptera	terpenoid-degrading: the highest degradation rates of D-camphor, linalool, and eucalyptol	0.50%	2.3
Diaphorobacter	RISB2150	Osmia bicornis Order: Hymenoptera	may be essential to support Osmia larvae in their nutrient uptake	0.93%	2.2
Rahnella	RISB1800	Dendroctonus valens Order: Coleoptera	could alleviate or compromise the antagonistic effects of fungi O. minus and L. procerum on RTB larval growth	0.03%	2.2
Bacteroides	RISB0090	Hyphantria cunea Order: Lepidoptera	enhance the compatibility of invasive pests to new hosts and enable more rapid adaptation to new habitats.	0.08%	2.2
Corynebacterium	RISB0531	Helicoverpa armigera Order: Lepidoptera	Corynebacterium sp. 2-TD, mediates the toxicity of the 2-tridecanone to H. armigera	0.50%	2.2
Bacteroides	RISB1183	Oryzaephilus surinamensis Order: Coleoptera	supplement precursors for the cuticle synthesis and thereby enhance desiccation resistance of its host	0.08%	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	0.03%	2.1
Sphingomonas	RISB0420	Aphis gossypii Order: Hemiptera	Sphingomonas could mediate A. gossypii resistance to imidacloprid by hydroxylation and nitroreduction	0.09%	2.1
Streptococcus	RISB2624	Reticulitermes flavipes Order: Blattodea	can be broken down into substances such as carbon dioxide, ammonia and acetic acid	0.43%	2.1
Xanthomonas	RISB0217	Xylocopa appendiculata Order: Hymenoptera	strains biodegraded polyethylene terephthalate PET powder, broke it into its degradation products	0.02%	2.0
Sphingomonas	RISB1307	Aphis gossypii Order: Hemiptera	have been previously described in associations with phloem-feeding insects, in low abundances	0.09%	2.0
Sphingomonas	RISB0134	Spodoptera frugiperda Order: Lepidoptera	provide a protective effect to against chlorantraniliprole stress to S. frugiperda	0.09%	1.7
Liberibacter	RISB2524	Bactericera cockerelli Order: Hemiptera	Reduced expression of plant defensive gene in tomato probably for psyllid success	0.02%	1.6
Streptococcus	RISB2604	Homona magnanima Order: Lepidoptera	influence the growth of Bacillus thuringiensis in the larvae	0.43%	1.6
Massilia	RISB2151	Osmia bicornis Order: Hymenoptera	may be essential to support Osmia larvae in their nutrient uptake	0.20%	1.5
Variovorax	RISB1712	Phlebotomus papatasi Order: Diptera	None	1.40%	1.4
Duganella	RISB2152	Osmia bicornis Order: Hymenoptera	may be essential to support Osmia larvae in their nutrient uptake	0.10%	1.4
Halomonas	RISB1808	Monochamus galloprovincialis Order: Coleoptera	Have the ability for degradation of cellulose, proteins and starch	0.03%	1.4
Corynebacterium	RISB2360	Bombyx mori Order: Lepidoptera	producing lipase in a gut environment	0.50%	1.3
Komagataeibacter	RISB1883	Drosophila suzukii Order: Diptera	produce volatile substances that attract female D. suzukii	0.07%	1.2
Diaphorobacter	RISB1062	Oryctes rhinoceros Order: Coleoptera	gut microbe	0.93%	1.2
Clostridium	RISB0028	Sesamia inferens Order: Lepidoptera	degrade Chlorpyrifos and Chlorantraniliprole in vitro	0.02%	1.1
Liberibacter	RISB2333	Cacopsylla pyri Order: Hemiptera	behaves as an endophyte rather than a pathogen	0.02%	0.9
Aeromonas	RISB2456	Bombyx mori Order: Lepidoptera	able to utilize the CMcellulose and xylan	0.03%	0.9
Curtobacterium	RISB1910	Hyles euphorbiae Order: Lepidoptera	able to degrade alkaloids and/or latex	0.08%	0.8
Methylobacterium	RISB2053	Atractomorpha sinensis Order: Orthoptera	associated with cellulolytic enzymes	0.10%	0.8
Cupriavidus	RISB0694	Alydus tomentosus Order: Hemiptera	None	0.68%	0.7
Chryseobacterium	RISB2092	Aedes aegypti Order: Diptera	axenic larvae cannot develop	0.06%	0.6
Aeromonas	RISB2086	Aedes aegypti Order: Diptera	axenic larvae cannot develop	0.03%	0.6
Methylobacterium	RISB2340	Saturniidae Order: Lepidoptera	Nitrogen fixation	0.10%	0.4
Aeromonas	RISB1145	Tenebrio molitor Order: Coleoptera	degrading plastics	0.03%	0.4
Chryseobacterium	RISB1874	Aedes aegypti Order: Diptera	gut microbiome	0.06%	0.3
Achromobacter	RISB1869	Aedes aegypti Order: Diptera	gut microbiome	0.06%	0.3
Yersinia	RISB0407	Anaphes nitens Order: Hymenoptera	None	0.28%	0.3
Neisseria	RISB0512	Plutella xylostella Order: Lepidoptera	None	0.25%	0.3
Curtobacterium	RISB0900	Myzus persicae Order: Hemiptera	None	0.08%	0.1
Chryseobacterium	RISB0015	Aedes aegypti Order: Diptera	None	0.06%	0.1
Achromobacter	RISB0383	Aphis gossypii Order: Hemiptera	None	0.06%	0.1
Bifidobacterium	RISB1944	Apis cerana Order: Hymenoptera	None	0.03%	0.0
Halomonas	RISB1374	Bemisia tabaci Order: Hemiptera	None	0.03%	0.0
Paraburkholderia	RISB0125	Physopelta gutta Order: Hemiptera	None	0.03%	0.0
Clostridium	RISB1959	Pyrrhocoridae Order: Hemiptera	None	0.02%	0.0