SRR12668538 - Tribolium castaneum

Basic Information

Run: SRR12668538

Assay Type: WGS

Bioproject: PRJNA663749

Biosample: SAMN16178277

Bytes: 63182995

Center Name: NATIONAL CENTER FOR BIOLOGICAL SCIENCES

Sequencing Information

Instrument: Illumina MiSeq

Library Layout: PAIRED

Library Selection: PCR

Platform: ILLUMINA

Quality Control Information

Filter Percentage: -

QC Average Length: -

Retained Reads: -

Geographic Information

Country: India

Continent: Asia

Location Name: India:Bangalore

Latitude/Longitude: 12.9716 N 77.5946 E

Sample Information

Host: Tribolium castaneum

Isolation: -

Biosample Model: Metagenome or environmental

Collection Date: 2017-08-12

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
Escherichia coli Species-level Match Host Order Match Host Species 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	2.53%	40.3
Enterococcus faecalis Species-level Match Host Order Match Host Species Match	RISB0374	Tribolium castaneum Order: Coleoptera	modulates host phosphine resistance by interfering with the redox system	2.12%	38.6
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	26.87%	30.6
Xanthomonas	RISB0217	Xylocopa appendiculata Order: Hymenoptera	strains biodegraded polyethylene terephthalate PET powder, broke it into its degradation products	26.87%	28.8
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.	2.12%	19.7
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	2.12%	19.5
Sphingobacterium sp. ML3W Species-level Match Host Order Match	RISB2227	Leptinotarsa decemlineata Order: Coleoptera	Colorado potato beetle (Leptinotarsa decemlineata) larvae exploit bacteria in their oral secretions to suppress antiherbivore defenses in tomato (Solanum lycopersicum)	0.21%	18.6
Sphingobacterium sp. R2 Species-level Match Host Order Match	RISB2227	Leptinotarsa decemlineata Order: Coleoptera	Colorado potato beetle (Leptinotarsa decemlineata) larvae exploit bacteria in their oral secretions to suppress antiherbivore defenses in tomato (Solanum lycopersicum)	0.19%	18.5
Pseudomonas aeruginosa Species-level Match Host Order Match	RISB0364	Pagiophloeus tsushimanus Order: Coleoptera	terpenoid-degrading: the highest degradation rates of D-camphor, linalool, and eucalyptol	1.28%	18.1
Morganella morganii Species-level Match Host Order Match	RISB1867	Costelytra zealandica Order: Coleoptera	Female beetles were previously shown to use phenol as their sex pheromone produced by symbiotic bacteria in the accessory or colleterial gland	0.09%	17.9
Morganella morganii Species-level Match Host Order Match	RISB1548	Costelytra zealandica Order: Coleoptera	symbionts residing in the colleterial glands produce phenol 1 as the female sex pheromone	0.09%	16.9
Morganella morganii Species-level Match Host Order Match	RISB1868	Costelytra zealandica Order: Coleoptera	produces phenol as the sex pheromone of the host from tyrosine in the colleterial gland	0.09%	16.8
Klebsiella pneumoniae Species-level Match Host Order Match	RISB1153	Tenebrio molitor Order: Coleoptera	degrading plastics	1.00%	16.4
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	11.18%	15.4
Staphylococcus epidermidis Species-level Match Host Order Match	RISB1070	Oryctes rhinoceros Order: Coleoptera	gut microbe	0.11%	15.3
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	0.16%	15.2
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	0.16%	14.5
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.	0.16%	14.2
Sodalis Host Order Match	RISB2035	Sitophilus oryzae Order: Coleoptera	endosymbiont dynamics parallels numerous transcriptional changes in weevil developing adults and affects several biological processes, including metabolism and development	0.16%	13.6
Sodalis Host Order Match	RISB2607	Sitophilus oryzae Order: Coleoptera	induces the specific differentiation of the bacteriocytes, increases mitochondrial oxidative phosphorylation through the supply of pantothenic acid and riboflavin	0.16%	13.4
Rhizobium Host Order Match	RISB0135	Coccinella septempunctata Order: Coleoptera	be commonly found in plant roots and they all have nitrogen fixation abilities	1.60%	13.2
Sodalis Host Order Match	RISB1718	Sitophilus zeamais Order: Coleoptera	we investigated the role of a quorum sensing（QS ） system in S. praecaptivus and found that it negatively regulates a potent insect-killing phenotype	0.16%	13.1
Bacillus Host Order Match	RISB1645	Osphranteria coerulescens Order: Coleoptera	The isolate has cellulolytic activity and can hydrolyze CMC, avicel, cellulose and sawdust with broad temperature and pH stability	0.20%	12.8
Bacillus Host Order Match	RISB0493	Sitophilus oryzae Order: Coleoptera	bacteria can degrade malathion, pirimiphos-methyl, and deltamethrin and utilize these insecticides as the carbon source in vitro.	0.20%	12.8
Clostridium	RISB0028	Sesamia inferens Order: Lepidoptera	degrade Chlorpyrifos and Chlorantraniliprole in vitro	11.18%	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	2.53%	11.9
Bacillus Host Order Match	RISB0805	Hypothenemus hampei Order: Coleoptera	might contribute to caffeine breakdown using the C-8 oxidation pathway	0.20%	11.6
Paenibacillus Host Order Match	RISB0813	Hypothenemus hampei Order: Coleoptera	might contribute to caffeine breakdown using the C-9 oxidation pathway	0.18%	11.6
Kosakonia Host Order Match	RISB0810	Hypothenemus hampei Order: Coleoptera	might contribute to caffeine breakdown using the C-16 oxidation pathway	0.11%	11.5
Clostridium	RISB1959	Pyrrhocoridae Order: Hemiptera	None	11.18%	11.2
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.	1.00%	11.0
Kosakonia Host Order Match	RISB1155	Tenebrio molitor Order: Coleoptera	degrading plastics	0.11%	10.5
Serratia symbiotica Species-level Match	RISB0576	Acyrthosiphon pisum Order: Hemiptera	process of regression from winged to wingless morph was inhibited by Serratia symbiotica. The existence of the symbiont did not affect the body mass and fecundity of adult aphids, but it increased the body weight of nymphs and temporally increased the quantity of a primary symbiont, Buchnera aphidicola	0.05%	10.1
Serratia symbiotica Species-level Match	RISB0179	Acyrthosiphon pisum Order: Hemiptera	harboring Serratia improved host aphid growth and fecundity but reduced longevity. Serratia defends aphids against P. japonica by impeding the predator's development and predation capacity, and modulating its foraging behavior	0.05%	9.6
Salmonella enterica Species-level Match	RISB0413	Melanaphis sacchari Order: Hemiptera	None	4.03%	9.0
Enterobacter ludwigii Species-level Match	RISB1543	Helicoverpa zea Order: Lepidoptera	two immunity-related genes glucose oxidase (GOX) and lysozyme (LYZ) were more highly expressed in both salivary glands and midguts compared with MgCl2 solution-treated caterpillars	0.32%	8.9
Serratia symbiotica Species-level Match	RISB1333	Adelges tsugae Order: Hemiptera	help to maintain aphid fitness during heat stress to varying degrees; the presence of facultative symbionts like S. symbiotica may protect the obligate symbiont Buchnera	0.05%	8.4
Escherichia coli Species-level Match	RISB2120	Galleria mellonella Order: Lepidoptera	mediate trans-generational immune priming	2.53%	8.4
Enterobacter ludwigii Species-level Match	RISB1223	Delia antiqua Order: Diptera	six bacteria protect larvae from infection with the entomopathogen Beauveria bassiana through symbiotic bacterium-derived organic acids	0.32%	8.0
Sphingomonas sp. NBWT7 Species-level Match	RISB0134	Spodoptera frugiperda Order: Lepidoptera	provide a protective effect to against chlorantraniliprole stress to S. frugiperda	1.03%	7.7
Sphingomonas sp. C3-2 Species-level Match	RISB0134	Spodoptera frugiperda Order: Lepidoptera	provide a protective effect to against chlorantraniliprole stress to S. frugiperda	0.47%	7.1
Klebsiella pneumoniae Species-level Match	RISB2459	Bombyx mori Order: Lepidoptera	degradation of cellulose, xylan, pectin and starch	1.00%	7.0
Candidatus Erwinia haradaeae Species-level Match	RISB1632	Lachninae Order: Hemiptera	None	1.72%	6.7
Enterobacter ludwigii Species-level Match	RISB1397	Delia antiqua Order: Diptera	suppressed Beauveria bassiana conidia germination and hyphal growth	0.32%	6.7
Methylobacterium sp. 17Sr1-1 Species-level Match	RISB2053	Atractomorpha sinensis Order: Orthoptera	associated with cellulolytic enzymes	0.19%	5.9
Chryseobacterium sp. JJR-5R Species-level Match	RISB2092	Aedes aegypti Order: Diptera	axenic larvae cannot develop	0.17%	5.7
Brevundimonas sp. Bb-A Species-level Match	RISB1703	Phlebotomus papatasi Order: Diptera	None	0.49%	5.5
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.	0.18%	5.2
Candidatus Karelsulcia muelleri Species-level Match	RISB1591	Philaenus spumarius Order: Hemiptera	None	0.09%	5.1
Streptococcus	RISB2625	Galleria mellonella Order: Lepidoptera	suppress bacteria ingested with food by producing bacteriocin and by releasing a lysozyme like enzyme	2.66%	4.7
Streptococcus	RISB2624	Reticulitermes flavipes Order: Blattodea	can be broken down into substances such as carbon dioxide, ammonia and acetic acid	2.66%	4.3
Streptococcus	RISB2604	Homona magnanima Order: Lepidoptera	influence the growth of Bacillus thuringiensis in the larvae	2.66%	3.9
Paenibacillus	RISB0774	Delia antiqua Order: Diptera	showed significant contact inhibition activity against fungal entomopathogen Fusarium moniliforme, Botryosphaeria dothidea and both Fusarium oxysporum respectively	0.18%	3.4
Massilia	RISB2151	Osmia bicornis Order: Hymenoptera	may be essential to support Osmia larvae in their nutrient uptake	0.76%	2.1
Nocardioides	RISB1914	Hyles euphorbiae Order: Lepidoptera	able to degrade alkaloids and/or latex	0.18%	0.9
Flavobacterium	RISB0659	Melanaphis bambusae Order: Hemiptera	None	0.38%	0.4
Ralstonia	RISB0243	Spodoptera frugiperda Order: Lepidoptera	None	0.11%	0.1