SRR19201381 - Rhyzopertha dominica

Basic Information

Run: SRR19201381

Assay Type: WGS

Bioproject: PRJNA836854

Biosample: SAMN28175367

Bytes: 3775815408

Center Name: JOHANNES GUTENBERG-UNIVERSITY MAINZ

Sequencing Information

Instrument: Illumina HiSeq 2500

Library Layout: PAIRED

Library Selection: RANDOM

Platform: ILLUMINA

Geographic Information

Country: Germany

Continent: Europe

Location Name: Germany: Berlin

Latitude/Longitude: -

Sample Information

Host: Rhyzopertha dominica

Isolation: beetle abdomen

Biosample Model: Metagenome or environmental

Collection Date: 2014

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
Streptomyces sp. SUK 48 Species-level Match Host Order Match	RISB0777	Copris tripartitus Order: Coleoptera	contribute brood ball hygiene by inhibiting fungal parasites in the environment	15.33%	31.9
Klebsiella pneumoniae Species-level Match Host Order Match	RISB1153	Tenebrio molitor Order: Coleoptera	degrading plastics	15.85%	31.2
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.	15.85%	25.9
Streptomyces sp. SUK 48 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	15.33%	24.3
Streptomyces sp. SUK 48 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	15.33%	24.0
Escherichia coli Species-level Match Host Order 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	6.24%	24.0
Pseudomonas sp. CIP-10 Species-level Match Host Order 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	2.94%	22.8
Klebsiella pneumoniae Species-level Match	RISB2459	Bombyx mori Order: Lepidoptera	degradation of cellulose, xylan, pectin and starch	15.85%	21.9
Pseudomonas sp. CIP-10 Species-level Match Host Order 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)	2.94%	21.3
Bacillus cereus Species-level Match Host Order Match	RISB1056	Oryctes rhinoceros Order: Coleoptera	provide symbiotic digestive functions to Oryctes	5.02%	21.0
Bacillus cereus Species-level Match Host Order Match	RISB1778	Lissorhoptrus oryzophilus Order: Coleoptera	might be promising paratransgenesis candidates	5.02%	20.9
Stenotrophomonas sp. 610A2 Species-level Match Host Order Match	RISB0325	Pharaxonotha floridana Order: Coleoptera	suggesting the occurrence of an unprecedented desferrioxamine-like biosynthetic pathway,including desferrioxamine B, which may help tolerating diets rich in azoxyglycosides, BMAA, and other cycad toxins, including a possible role for bacterial siderophores	0.08%	20.1
Stenotrophomonas maltophilia Species-level Match Host Order Match	RISB0139	Tenebrio molitor Order: Coleoptera	correlated with polyvinyl chloride PVC degradation	3.46%	19.5
Pseudomonas sp. CIP-10 Species-level Match Host Order Match	RISB0815	Hypothenemus hampei Order: Coleoptera	might contribute to caffeine breakdown using the C-15 oxidation pathway	2.94%	19.4
Erwinia sp. E602 Species-level Match Host Order Match	RISB0808	Hypothenemus hampei Order: Coleoptera	might contribute to caffeine breakdown using the C-12 oxidation pathway	2.27%	18.7
Stenotrophomonas sp. 610A2 Species-level Match Host Order Match	RISB2228	Leptinotarsa decemlineata Order: Coleoptera	Colorado potato beetle (Leptinotarsa decemlineata) larvae exploit bacteria in their oral secretions to suppress antiherbivore defenses in tomato (Solanum lycopersicum)	0.08%	18.4
Enterococcus faecalis Species-level Match Host Order Match	RISB0497	Cryptolestes ferrugineus Order: Coleoptera	bacteria can degrade malathion, pirimiphos-methyl, and deltamethrin and utilize these insecticides as the carbon source in vitro.	0.19%	17.8
Enterococcus faecalis Species-level Match Host Order Match	RISB2042	Harpalus pensylvanicus Order: Coleoptera	E. faecalis facilitate seed consumption by H. pensylvanicus, possibly by contributing digestive enzymes to their host	0.19%	17.5
Acinetobacter Host Order 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)	2.37%	17.1
Paenibacillus sp. DCT19 Species-level Match Host Order Match	RISB0813	Hypothenemus hampei Order: Coleoptera	might contribute to caffeine breakdown using the C-9 oxidation pathway	0.29%	16.7
Enterococcus faecalis Species-level Match Host Order Match	RISB0374	Tribolium castaneum Order: Coleoptera	modulates host phosphine resistance by interfering with the redox system	0.19%	16.6
Exiguobacterium sp. N4-1P Species-level Match Host Order Match	RISB1152	Tenebrio molitor Order: Coleoptera	degrading plastics	0.92%	16.3
Vibrio Host Order Match	RISB1810	Monochamus galloprovincialis Order: Coleoptera	Have the ability for degradation of cellulose, proteins and starch	4.86%	16.2
Staphylococcus Host Order Match	RISB0945	Callosobruchus maculatus Order: Coleoptera	The strain encodes complete biosynthetic pathways for the production of B vitamins and amino acids, including tyrosine; A carbohydrate-active enzyme search revealed that the genome codes for a number of digestive enzymes, reflecting the nutritional ecology of C. maculatus	1.18%	16.2
Burkholderia Host Order Match	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	0.95%	16.0
Acinetobacter Host Order Match	RISB1356	Callosobruchus maculatus Order: Coleoptera	These bacterial phyla may allow the adults C. maculatus to survive on DDVP treated grains, thereby making it inappropriate to control the beetle populations in the field.	2.37%	15.8
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	6.24%	15.6
Pantoea agglomerans Species-level Match Host Order Match	RISB1858	Lissorhoptrus oryzophilus Order: Coleoptera	None	0.31%	15.3
Burkholderia Host Order Match	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	0.95%	15.3
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.	5.02%	15.0
Burkholderia Host Order Match	RISB1836	Dendroctonus valens Order: Coleoptera	It can trongly degrade naringenin, and pinitol, the main soluble carbohydrate of P. tabuliformis, is retained in L. procerum-infected phloem and facilitate naringenin biodegradation by the microbiotas.	0.95%	15.0
Acinetobacter Host Order Match	RISB0520	Leptinotarsa decemlineata Order: Coleoptera	inhibited the expression of genes associated with the JA-mediated defense signaling pathway and SGA biosynthesis	2.37%	14.6
Wolbachia Host Order Match	RISB1452	Octodonta nipae Order: Coleoptera	Wolbachia harbored dominantly in a female than the male adult, while, no significant differences were observed between male and female body parts and tissues	0.89%	14.0
Staphylococcus Host Order Match	RISB0946	Callosobruchus maculatus Order: Coleoptera	The strain encodes complete biosynthetic pathways for the production of B vitamins and amino acids, including tyrosine	1.18%	13.5
Wolbachia Host Order Match	RISB2107	Sitophilus zeamais Order: Coleoptera	Wolbachia directly favored weevil fertility and exhibited only mild indirect effects, usually enhancing the SZPE effect	0.89%	13.3
Wolbachia Host Order Match	RISB1282	Ips sp. Order: Coleoptera	inducing cytoplasmic incompatibility, resulting in reproductive distortions and hence	0.89%	12.6
Escherichia coli Species-level Match	RISB2120	Galleria mellonella Order: Lepidoptera	mediate trans-generational immune priming	6.24%	12.1
Corynebacterium Host Order Match	RISB0363	Pagiophloeus tsushimanus Order: Coleoptera	terpenoid-degrading: the highest degradation rates of D-camphor, linalool, and eucalyptol	0.23%	12.0
Halomonas Host Order Match	RISB1808	Monochamus galloprovincialis Order: Coleoptera	Have the ability for degradation of cellulose, proteins and starch	0.10%	11.4
Staphylococcus Host Order Match	RISB1070	Oryctes rhinoceros Order: Coleoptera	gut microbe	1.18%	11.4
Mycobacterium Host Order Match	RISB1156	Nicrophorus concolor Order: Coleoptera	produces Antimicrobial compounds	0.75%	11.4
Aeromonas Host Order Match	RISB1145	Tenebrio molitor Order: Coleoptera	degrading plastics	0.08%	10.4
Pantoea agglomerans Species-level Match	RISB2197	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.	0.31%	10.3
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	0.12%	10.1
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	0.12%	9.9
Clostridium sp. AWRP Species-level Match	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	0.38%	9.6
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	0.12%	8.9
Blattabacterium cuenoti Species-level Match	RISB0133	Panesthiinae Order: Blattodea	enables hosts to subsist on a nutrient-poor diet; endosymbiont genome erosions are associated with repeated host transitions to an underground life	0.80%	8.7
Exiguobacterium sp. N4-1P Species-level Match	RISB0007	Phormia regina Order: Diptera	prompted oviposition by flies; The flies' oviposition decisions appear to be guided by bacteria-derived semiochemicals as the bacteria	0.92%	8.6
Paenibacillus sp. DCT19 Species-level Match	RISB0774	Delia antiqua Order: Diptera	showed significant contact inhibition activity against fungal entomopathogen Fusarium moniliforme, Botryosphaeria dothidea and both Fusarium oxysporum respectively	0.29%	8.6
Spiroplasma ixodetis Species-level Match	RISB0842	Dactylopius coccus Order: Hemiptera	use the T4SS to interact with the Dactylopius cells, which show a strong interaction and molecular signaling in the symbiosis	0.77%	8.3
Erwinia sp. E602 Species-level Match	RISB1986	Bombyx mori Order: Lepidoptera	producing cellulase and amylase	2.27%	7.9
Psychrobacter sp. M13 Species-level Match	RISB1773	Calliphoridae Order: Diptera	it shows physiological adaptation to survival in warmer temperatures and has been previously associated with food spoilage	0.09%	7.5
Pantoea agglomerans Species-level Match	RISB2579	Schistocerca gregaria Order: Orthoptera	produces an antifungal and antibacterial molecule serving as antimicrobial defense against gut pathogens	0.31%	7.4
Blattabacterium cuenoti Species-level Match	RISB0518	Cryptocercus punctulatus Order: Blattodea	collaborative arginine biosynthesis	0.80%	6.5
Blattabacterium cuenoti Species-level Match	RISB0093	Blattella germanica Order: Blattodea	obligate endosymbiont	0.80%	6.2
Lactiplantibacillus plantarum Species-level Match	RISB0674	Drosophila melanogaster Order: Diptera	could effectively inhibit fungal spore germinations	0.18%	6.2
Paenibacillus sp. DCT19 Species-level Match	RISB2098	Aedes aegypti Order: Diptera	axenic larvae cannot develop	0.29%	5.9
Microbacterium sp. XT11 Species-level Match	RISB2095	Aedes aegypti Order: Diptera	axenic larvae cannot develop	0.25%	5.8
Salmonella enterica Species-level Match	RISB0413	Melanaphis sacchari Order: Hemiptera	None	0.76%	5.8
Candidatus Karelsulcia muelleri Species-level Match	RISB1591	Philaenus spumarius Order: Hemiptera	None	0.44%	5.4
Lactiplantibacillus plantarum Species-level Match	RISB0608	Drosophila melanogaster Order: Diptera	None	0.18%	5.2
Arsenophonus	RISB1047	Aphis gossypii Order: Hemiptera	secondary symbiont reduction led to reduction of the total life span and intrinsic rate of natural increase as well as appearance of the deformed dead offspring. H. defensa and Arsenophonus contributed to the fitness of A. gossypii by enhancing its performance, but not through parasitoid resistance.	0.15%	5.2
Arsenophonus	RISB1300	Aphis gossypii Order: Hemiptera	Arsenophonus sp. can have different effects on its hosts, including obligate mutualism in blood-sucking insects, improving the performance of whiteflies, or through facultative mutualism by protecting psyllids against parasitoid attacks.	0.15%	4.9
Arsenophonus	RISB1334	Ommatissus lybicus Order: Hemiptera	the removal of Arsenophonus increased the developmental time of the immature stages and reduced the values of different life-history parameters including nymphal survival rate and adult longevity in the host	0.15%	4.3
Mammaliicoccus	RISB0075	Bombyx mori Order: Lepidoptera	could produce a secreted chitinolytic lysozyme (termed Msp1) to damage fungal cell walls，completely inhibit the spore germination of fungal entomopathogens Metarhizium robertsii and Beauveria bassiana	0.12%	4.1
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	0.19%	4.0
Liberibacter	RISB2310	Bactericerca cockerelli Order: Hemiptera	manipulate plant signaling and defensive responses, suppress accumulation of defense transcripts like JA and SA	0.07%	2.3
Xanthomonas	RISB0217	Xylocopa appendiculata Order: Hymenoptera	strains biodegraded polyethylene terephthalate PET powder, broke it into its degradation products	0.19%	2.1
Corynebacterium	RISB0531	Helicoverpa armigera Order: Lepidoptera	Corynebacterium sp. 2-TD, mediates the toxicity of the 2-tridecanone to H. armigera	0.23%	1.9
Liberibacter	RISB2524	Bactericera cockerelli Order: Hemiptera	Reduced expression of plant defensive gene in tomato probably for psyllid success	0.07%	1.7
Massilia	RISB2151	Osmia bicornis Order: Hymenoptera	may be essential to support Osmia larvae in their nutrient uptake	0.10%	1.4
Corynebacterium	RISB2360	Bombyx mori Order: Lepidoptera	producing lipase in a gut environment	0.23%	1.0
Liberibacter	RISB2333	Cacopsylla pyri Order: Hemiptera	behaves as an endophyte rather than a pathogen	0.07%	1.0
Aeromonas	RISB2456	Bombyx mori Order: Lepidoptera	able to utilize the CMcellulose and xylan	0.08%	0.9
Curtobacterium	RISB1910	Hyles euphorbiae Order: Lepidoptera	able to degrade alkaloids and/or latex	0.13%	0.9
Aeromonas	RISB2086	Aedes aegypti Order: Diptera	axenic larvae cannot develop	0.08%	0.6
Flavobacterium	RISB0659	Melanaphis bambusae Order: Hemiptera	None	0.51%	0.5
Achromobacter	RISB1869	Aedes aegypti Order: Diptera	gut microbiome	0.12%	0.4
Curtobacterium	RISB0900	Myzus persicae Order: Hemiptera	None	0.13%	0.1
Neisseria	RISB0512	Plutella xylostella Order: Lepidoptera	None	0.13%	0.1
Achromobacter	RISB0383	Aphis gossypii Order: Hemiptera	None	0.12%	0.1
Halomonas	RISB1374	Bemisia tabaci Order: Hemiptera	None	0.10%	0.1