SRR12668537 - Tribolium castaneum

Basic Information

Run: SRR12668537

Assay Type: WGS

Bioproject: PRJNA663749

Biosample: SAMN16178171

Bytes: 43189255

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	7.63%	45.4
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	4.37%	40.8
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.	4.37%	22.0
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	4.37%	21.7
Candidatus Erwinia haradaeae Species-level Match	RISB1632	Lachninae Order: Hemiptera	None	14.20%	19.2
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	3.52%	18.5
Candidatus Sodalis pierantonius Species-level Match 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	0.09%	18.5
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	0.52%	18.4
Klebsiella pneumoniae Species-level Match Host Order Match	RISB1153	Tenebrio molitor Order: Coleoptera	degrading plastics	2.96%	18.3
Bacillus subtilis Species-level Match Host Order Match	RISB0494	Sitophilus oryzae Order: Coleoptera	bacteria can degrade malathion, pirimiphos-methyl, and deltamethrin and utilize these insecticides as the carbon source in vitro.	0.27%	17.9
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	13.60%	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	0.52%	17.3
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	0.52%	17.3
Candidatus Sodalis pierantonius Species-level Match Host Order Match	RISB0972	Sitophilus oryzae Order: Coleoptera	produce vitamins and essential amino acids required for insect development and cuticle biosynthesis	0.09%	17.1
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	7.63%	17.0
Candidatus Sodalis pierantonius Species-level Match Host Order Match	RISB0251	Sitophilus oryzae Order: Coleoptera	may infulence immunity, metabolism, metal control, apoptosis, and bacterial stress response	0.09%	16.9
Bacillus cereus Species-level Match Host Order Match	RISB1056	Oryctes rhinoceros Order: Coleoptera	provide symbiotic digestive functions to Oryctes	0.59%	16.6
Bacillus cereus Species-level Match Host Order Match	RISB1778	Lissorhoptrus oryzophilus Order: Coleoptera	might be promising paratransgenesis candidates	0.59%	16.5
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	3.52%	15.9
Xanthomonas	RISB0217	Xylocopa appendiculata Order: Hymenoptera	strains biodegraded polyethylene terephthalate PET powder, broke it into its degradation products	13.60%	15.5
Vibrio Host Order Match	RISB1810	Monochamus galloprovincialis Order: Coleoptera	Have the ability for degradation of cellulose, proteins and starch	3.61%	14.9
Staphylococcus Host Order Match	RISB1070	Oryctes rhinoceros Order: Coleoptera	gut microbe	3.52%	13.7
Salmonella enterica Species-level Match	RISB0413	Melanaphis sacchari Order: Hemiptera	None	8.69%	13.7
Escherichia coli Species-level Match	RISB2120	Galleria mellonella Order: Lepidoptera	mediate trans-generational immune priming	7.63%	13.5
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.	2.96%	13.0
Kosakonia Host Order Match	RISB0810	Hypothenemus hampei Order: Coleoptera	might contribute to caffeine breakdown using the C-16 oxidation pathway	0.18%	11.6
Aeromonas Host Order Match	RISB1145	Tenebrio molitor Order: Coleoptera	degrading plastics	0.19%	10.6
Kosakonia Host Order Match	RISB1155	Tenebrio molitor Order: Coleoptera	degrading plastics	0.18%	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	0.26%	10.3
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	0.26%	9.8
Weissella cibaria Species-level Match	RISB1982	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	0.91%	9.7
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	1.00%	9.6
Klebsiella pneumoniae Species-level Match	RISB2459	Bombyx mori Order: Lepidoptera	degradation of cellulose, xylan, pectin and starch	2.96%	9.0
Streptococcus	RISB2625	Galleria mellonella Order: Lepidoptera	suppress bacteria ingested with food by producing bacteriocin and by releasing a lysozyme like enzyme	6.82%	8.8
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	1.00%	8.7
Weissella cibaria Species-level Match	RISB0641	Formica Order: Hymenoptera	exhibited abilities in catabolizing sugars (sucrose, trehalose, melezitose and raffinose) known to be constituents of hemipteran honeydew	0.91%	8.7
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	0.26%	8.6
Streptococcus	RISB2624	Reticulitermes flavipes Order: Blattodea	can be broken down into substances such as carbon dioxide, ammonia and acetic acid	6.82%	8.5
Streptococcus	RISB2604	Homona magnanima Order: Lepidoptera	influence the growth of Bacillus thuringiensis in the larvae	6.82%	8.0
Enterobacter ludwigii Species-level Match	RISB1397	Delia antiqua Order: Diptera	suppressed Beauveria bassiana conidia germination and hyphal growth	1.00%	7.3
Listeria	RISB2308	Drosophila melanogaster Order: Diptera	L. monocytogenes infection disrupts host energy metabolism by depleting energy stores (triglycerides and glycogen) and reducing metabolic pathway activity (beta-oxidation and glycolysis). The infection affects antioxidant defense by reducing uric acid levels and alters amino acid metabolism. These metabolic changes are accompanied by melanization, potentially linked to decreased tyrosine levels.	0.47%	5.5
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.	0.20%	5.2
Brevundimonas sp. Bb-A Species-level Match	RISB1703	Phlebotomus papatasi Order: Diptera	None	0.19%	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.	0.20%	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	0.20%	4.3
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	0.21%	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	0.30%	2.7
Lactiplantibacillus	RISB1465	Drosophila melanogaster Order: Diptera	L. plantarum increases its growth-promotion ability by adapting to Drosophila diet	0.13%	1.8
Lactiplantibacillus	RISB0674	Drosophila melanogaster Order: Diptera	could effectively inhibit fungal spore germinations	0.13%	1.2
Aeromonas	RISB2456	Bombyx mori Order: Lepidoptera	able to utilize the CMcellulose and xylan	0.19%	1.0
Methylobacterium	RISB2053	Atractomorpha sinensis Order: Orthoptera	associated with cellulolytic enzymes	0.21%	0.9
Aeromonas	RISB2086	Aedes aegypti Order: Diptera	axenic larvae cannot develop	0.19%	0.8
Methylobacterium	RISB2340	Saturniidae Order: Lepidoptera	Nitrogen fixation	0.21%	0.6
Yersinia	RISB0407	Anaphes nitens Order: Hymenoptera	None	0.30%	0.3
Ralstonia	RISB0243	Spodoptera frugiperda Order: Lepidoptera	None	0.16%	0.2
Lactiplantibacillus	RISB0608	Drosophila melanogaster Order: Diptera	None	0.13%	0.1