SRR12668453 - Tribolium castaneum

Basic Information

Run: SRR12668453

Assay Type: WGS

Bioproject: PRJNA663749

Biosample: SAMN16178167

Bytes: 46411560

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	22.74%	60.5
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	7.40%	43.8
Citrobacter Host Order Match Host Species 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	0.08%	32.8
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	22.74%	32.1
Escherichia coli Species-level Match	RISB2120	Galleria mellonella Order: Lepidoptera	mediate trans-generational immune priming	22.74%	28.6
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.	7.40%	25.0
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	7.40%	24.7
Klebsiella pneumoniae Species-level Match Host Order Match	RISB1153	Tenebrio molitor Order: Coleoptera	degrading plastics	5.21%	20.6
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	0.18%	20.0
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	0.18%	18.0
Salmonella enterica Species-level Match	RISB0413	Melanaphis sacchari Order: Hemiptera	None	12.88%	17.9
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	0.18%	17.4
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	0.18%	17.0
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	0.18%	16.9
Bacillus cereus Species-level Match Host Order Match	RISB1056	Oryctes rhinoceros Order: Coleoptera	provide symbiotic digestive functions to Oryctes	0.46%	16.4
Bacillus cereus Species-level Match Host Order Match	RISB1778	Lissorhoptrus oryzophilus Order: Coleoptera	might be promising paratransgenesis candidates	0.46%	16.4
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	0.79%	15.8
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.	5.21%	15.2
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	0.80%	14.2
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	0.80%	14.0
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	0.80%	13.8
Citrobacter Host Order Match	RISB1357	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.	0.08%	13.5
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	0.79%	13.2
Citrobacter Host Order 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)	0.08%	13.0
Vibrio Host Order Match	RISB1810	Monochamus galloprovincialis Order: Coleoptera	Have the ability for degradation of cellulose, proteins and starch	1.33%	12.7
Kosakonia Host Order Match	RISB0810	Hypothenemus hampei Order: Coleoptera	might contribute to caffeine breakdown using the C-16 oxidation pathway	0.44%	11.9
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	7.49%	11.3
Klebsiella pneumoniae Species-level Match	RISB2459	Bombyx mori Order: Lepidoptera	degradation of cellulose, xylan, pectin and starch	5.21%	11.2
Aeromonas Host Order Match	RISB1145	Tenebrio molitor Order: Coleoptera	degrading plastics	0.81%	11.2
Staphylococcus Host Order Match	RISB1070	Oryctes rhinoceros Order: Coleoptera	gut microbe	0.79%	11.0
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	2.33%	10.9
Kosakonia Host Order Match	RISB1155	Tenebrio molitor Order: Coleoptera	degrading plastics	0.44%	10.8
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.	0.63%	10.6
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	0.45%	10.5
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	2.33%	10.0
Xanthomonas	RISB0217	Xylocopa appendiculata Order: Hymenoptera	strains biodegraded polyethylene terephthalate PET powder, broke it into its degradation products	7.49%	9.4
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	0.27%	9.1
Enterobacter ludwigii Species-level Match	RISB1397	Delia antiqua Order: Diptera	suppressed Beauveria bassiana conidia germination and hyphal growth	2.33%	8.7
Candidatus Ishikawella capsulata Species-level Match	RISB2368	Megacopta punctatissima Order: Hemiptera	Microbe compensates for nutritional deficiency of host diet by supplying essential amino acids	0.08%	7.0
Streptococcus	RISB2625	Galleria mellonella Order: Lepidoptera	suppress bacteria ingested with food by producing bacteriocin and by releasing a lysozyme like enzyme	4.11%	6.1
Candidatus Erwinia haradaeae Species-level Match	RISB1632	Lachninae Order: Hemiptera	None	0.85%	5.9
Candidatus Ishikawella capsulata Species-level Match	RISB2543	Megacopta punctatissima Order: Hemiptera	Enhance pest status of the insect host	0.08%	5.8
Streptococcus	RISB2624	Reticulitermes flavipes Order: Blattodea	can be broken down into substances such as carbon dioxide, ammonia and acetic acid	4.11%	5.8
Candidatus Steffania adelgidicola Species-level Match	RISB2278	Adelges nordmannianae/piceae Order: Hemiptera	None	0.32%	5.3
Streptococcus	RISB2604	Homona magnanima Order: Lepidoptera	influence the growth of Bacillus thuringiensis in the larvae	4.11%	5.3
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	0.29%	5.3
Brevundimonas sp. Bb-A Species-level Match	RISB1703	Phlebotomus papatasi Order: Diptera	None	0.19%	5.2
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	0.29%	3.7
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	0.25%	3.6
Yersinia	RISB0492	Cimex hemipterus Order: Hemiptera	the disruption of the abundant Yersinia possibly could be related to the enhanced susceptibility towards the insecticides	0.97%	3.4
Candidatus Blochmanniella	RISB2542	Camponotus Order: Hymenoptera	Blochmannia provide essential amino acids to its host,Camponotus floridanus, and that it may also play a role in nitrogen recycling via its functional urease	0.09%	3.2
Candidatus Blochmanniella	RISB1827	Camponotus floridanus Order: Hymenoptera	a modulation of immune gene expression which may facilitate tolerance towards the endosymbionts and thus may contribute to their transovarial transmission	0.09%	3.2
Candidatus Blochmanniella	RISB2448	Camponotus floridanus Order: Hymenoptera	nutritional contribution of the bacteria to host metabolism by production of essential amino acids and urease-mediated nitrogen recycling	0.09%	2.8
Aeromonas	RISB2456	Bombyx mori Order: Lepidoptera	able to utilize the CMcellulose and xylan	0.81%	1.6
Aeromonas	RISB2086	Aedes aegypti Order: Diptera	axenic larvae cannot develop	0.81%	1.4
Dickeya	RISB1086	Rhodnius prolixus Order: Hemiptera	supply enzymatic biosynthesis of B-complex vitamins	0.10%	1.1
Methylobacterium	RISB2053	Atractomorpha sinensis Order: Orthoptera	associated with cellulolytic enzymes	0.25%	1.0
Yersinia	RISB0407	Anaphes nitens Order: Hymenoptera	None	0.97%	1.0
Methylobacterium	RISB2340	Saturniidae Order: Lepidoptera	Nitrogen fixation	0.25%	0.6
Bifidobacterium	RISB1944	Apis cerana Order: Hymenoptera	None	0.29%	0.3
Ralstonia	RISB0243	Spodoptera frugiperda Order: Lepidoptera	None	0.29%	0.3