SRR12668516 - Tribolium castaneum

Basic Information

Run: SRR12668516

Assay Type: WGS

Bioproject: PRJNA663749

Biosample: SAMN16178317

Bytes: 145985214

Center Name: NATIONAL CENTER FOR BIOLOGICAL SCIENCES

Sequencing Information

Instrument: Illumina MiSeq

Library Layout: PAIRED

Library Selection: PCR

Platform: ILLUMINA

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	7.10%	44.8
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	3.04%	39.5
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	19.13%	22.9
Xanthomonas	RISB0217	Xylocopa appendiculata Order: Hymenoptera	strains biodegraded polyethylene terephthalate PET powder, broke it into its degradation products	19.13%	21.1
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.	3.04%	20.6
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	3.04%	20.4
Serratia liquefaciens Species-level Match Host Order Match	RISB1624	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	0.05%	19.9
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	1.20%	18.0
Serratia liquefaciens Species-level Match Host Order Match	RISB1801	Dendroctonus valens Order: Coleoptera	could alleviate or compromise the antagonistic effects of fungi O. minus and L. procerum on RTB larval growth	0.05%	17.2
Klebsiella pneumoniae Species-level Match Host Order Match	RISB1153	Tenebrio molitor Order: Coleoptera	degrading plastics	1.48%	16.8
Bacillus cereus Species-level Match Host Order Match	RISB1056	Oryctes rhinoceros Order: Coleoptera	provide symbiotic digestive functions to Oryctes	0.54%	16.5
Bacillus cereus Species-level Match Host Order Match	RISB1778	Lissorhoptrus oryzophilus Order: Coleoptera	might be promising paratransgenesis candidates	0.54%	16.5
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	7.10%	16.4
Stenotrophomonas maltophilia Species-level Match Host Order Match	RISB0139	Tenebrio molitor Order: Coleoptera	correlated with polyvinyl chloride PVC degradation	0.07%	16.1
Staphylococcus epidermidis Species-level Match Host Order Match	RISB1070	Oryctes rhinoceros Order: Coleoptera	gut microbe	0.07%	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	0.13%	15.1
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	0.13%	14.4
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.	0.13%	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	0.29%	13.7
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	0.29%	13.5
Corynebacterium Host Order Match	RISB0363	Pagiophloeus tsushimanus Order: Coleoptera	terpenoid-degrading: the highest degradation rates of D-camphor, linalool, and eucalyptol	1.74%	13.5
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	0.29%	13.3
Escherichia coli Species-level Match	RISB2120	Galleria mellonella Order: Lepidoptera	mediate trans-generational immune priming	7.10%	12.9
Bacteroides Host Order Match	RISB1183	Oryzaephilus surinamensis Order: Coleoptera	supplement precursors for the cuticle synthesis and thereby enhance desiccation resistance of its host	0.44%	12.5
Vibrio Host Order Match	RISB1810	Monochamus galloprovincialis Order: Coleoptera	Have the ability for degradation of cellulose, proteins and starch	0.39%	11.7
Kosakonia Host Order Match	RISB0810	Hypothenemus hampei Order: Coleoptera	might contribute to caffeine breakdown using the C-16 oxidation pathway	0.11%	11.5
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.	1.48%	11.5
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.	1.26%	11.3
Aeromonas Host Order Match	RISB1145	Tenebrio molitor Order: Coleoptera	degrading plastics	0.21%	10.6
Kosakonia Host Order Match	RISB1155	Tenebrio molitor Order: Coleoptera	degrading plastics	0.11%	10.5
Salmonella enterica Species-level Match	RISB0413	Melanaphis sacchari Order: Hemiptera	None	5.41%	10.4
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	0.21%	10.2
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	0.79%	9.4
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.	0.07%	9.1
Acinetobacter pittii Species-level Match	RISB1977	Blattella germanica Order: Blattodea	gut microbiota contributes to production of VCAs that act as fecal aggregation agents and that cockroaches discriminate among the complex odors that emanate from a diverse microbial community	0.06%	8.9
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	0.79%	8.5
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	0.07%	7.8
Klebsiella pneumoniae Species-level Match	RISB2459	Bombyx mori Order: Lepidoptera	degradation of cellulose, xylan, pectin and starch	1.48%	7.5
Enterobacter ludwigii Species-level Match	RISB1397	Delia antiqua Order: Diptera	suppressed Beauveria bassiana conidia germination and hyphal growth	0.79%	7.1
Streptococcus	RISB2625	Galleria mellonella Order: Lepidoptera	suppress bacteria ingested with food by producing bacteriocin and by releasing a lysozyme like enzyme	3.85%	5.9
Streptococcus	RISB2624	Reticulitermes flavipes Order: Blattodea	can be broken down into substances such as carbon dioxide, ammonia and acetic acid	3.85%	5.5
Brevundimonas sp. Bb-A Species-level Match	RISB1703	Phlebotomus papatasi Order: Diptera	None	0.44%	5.4
Candidatus Erwinia haradaeae Species-level Match	RISB1632	Lachninae Order: Hemiptera	None	0.26%	5.3
Lactobacillus	RISB1866	Drosophila melanogaster Order: Diptera	The bacterial cells may thus be able to ameliorate the pH of the acidic region, by the release of weak bases.Additionally, the bacteria have a complex relationship with physiological processes which may affect ionic homeostasis in the gut, such as nutrition and immune function	0.20%	5.2
Candidatus Steffania adelgidicola Species-level Match	RISB2278	Adelges nordmannianae/piceae Order: Hemiptera	None	0.07%	5.1
Candidatus Karelsulcia muelleri Species-level Match	RISB1591	Philaenus spumarius Order: Hemiptera	None	0.06%	5.1
Streptococcus	RISB2604	Homona magnanima Order: Lepidoptera	influence the growth of Bacillus thuringiensis in the larvae	3.85%	5.1
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	1.42%	4.8
Lactobacillus	RISB0292	Lymantria dispar asiatica Order: Lepidoptera	Beauveria bassiana infection-based assays showed that the mortality of non-axenic L. dispar asiatica larvae was significantly higher than that of axenic larvae at 72 h.	0.20%	3.6
Corynebacterium	RISB0531	Helicoverpa armigera Order: Lepidoptera	Corynebacterium sp. 2-TD, mediates the toxicity of the 2-tridecanone to H. armigera	1.74%	3.4
Lactobacillus	RISB0715	Spodoptera frugiperda Order: Lepidoptera	Have the function of nutrient absorption, energy metabolism, the plant’s secondary metabolites degradation, insect immunity regulation, and so on	0.20%	3.1
Yersinia	RISB0492	Cimex hemipterus Order: Hemiptera	the disruption of the abundant Yersinia possibly could be related to the enhanced susceptibility towards the insecticides	0.61%	3.0
Bacteroides	RISB0256	Leptocybe invasa Order: Hymenoptera	Differences in Male-Killing Rickettsia Bacteria between Lineages of the Invasive Gall-Causing Pest Leptocybe invasa	0.44%	2.7
Bacteroides	RISB0090	Hyphantria cunea Order: Lepidoptera	enhance the compatibility of invasive pests to new hosts and enable more rapid adaptation to new habitats.	0.44%	2.6
Corynebacterium	RISB2360	Bombyx mori Order: Lepidoptera	producing lipase in a gut environment	1.74%	2.5
Methylobacterium	RISB2053	Atractomorpha sinensis Order: Orthoptera	associated with cellulolytic enzymes	1.42%	2.1
Candidatus Zinderia	RISB2451	Clastoptera arizonana Order: Hemiptera	Zinderia had gene homologs for the production of tryptophan, methionine, and histidine	0.07%	1.8
Methylobacterium	RISB2340	Saturniidae Order: Lepidoptera	Nitrogen fixation	1.42%	1.8
Glutamicibacter	RISB0606	Phthorimaea operculella Order: Lepidoptera	could degrade the major toxic α-solanine and α-chaconine in potatoes	0.10%	1.5
Brevibacterium	RISB0464	Acrida cinerea Order: Orthoptera	correlated with the hemicellulose digestibility	0.11%	1.1
Aeromonas	RISB2456	Bombyx mori Order: Lepidoptera	able to utilize the CMcellulose and xylan	0.21%	1.0
Brevibacterium	RISB2359	Bombyx mori Order: Lepidoptera	producing lipase in a gut environment	0.11%	0.9
Aeromonas	RISB2086	Aedes aegypti Order: Diptera	axenic larvae cannot develop	0.21%	0.8
Chryseobacterium	RISB2092	Aedes aegypti Order: Diptera	axenic larvae cannot develop	0.13%	0.7
Yersinia	RISB0407	Anaphes nitens Order: Hymenoptera	None	0.61%	0.6
Chryseobacterium	RISB1874	Aedes aegypti Order: Diptera	gut microbiome	0.13%	0.4
Candidatus Zinderia	RISB1640	Clastoptera arizonana Order: Hemiptera	Nitrogen-Fixing	0.07%	0.4
Ralstonia	RISB0243	Spodoptera frugiperda Order: Lepidoptera	None	0.20%	0.2
Chryseobacterium	RISB0015	Aedes aegypti Order: Diptera	None	0.13%	0.1
Brevibacterium	RISB0897	Myzus persicae Order: Hemiptera	None	0.11%	0.1
Glutamicibacter	RISB0438	Helicoverpa armigera Order: Lepidoptera	None	0.10%	0.1
Flavobacterium	RISB0659	Melanaphis bambusae Order: Hemiptera	None	0.10%	0.1