SRR12668521 - Tribolium castaneum

Basic Information

Run: SRR12668521

Assay Type: WGS

Bioproject: PRJNA663749

Biosample: SAMN16178307

Bytes: 66323621

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: 2018-08-24

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	10.51%	48.2
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	4.43%	40.9
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	0.14%	32.9
Acinetobacter Host Order Match Host Species Match	RISB0993	Tribolium castaneum Order: Coleoptera	may play a role in the larval gut for biodegradation of Polystyrene PS	0.55%	32.0
Vibrio Host Order Match	RISB1810	Monochamus galloprovincialis Order: Coleoptera	Have the ability for degradation of cellulose, proteins and starch	11.44%	22.8
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	7.28%	22.3
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.	4.43%	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	4.43%	21.8
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	10.51%	19.8
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	7.28%	19.6
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.	1.28%	18.9
Klebsiella pneumoniae Species-level Match Host Order Match	RISB1153	Tenebrio molitor Order: Coleoptera	degrading plastics	3.26%	18.6
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	0.06%	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	0.46%	18.3
Bacillus sp. T3 Species-level Match 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	0.24%	17.8
Staphylococcus Host Order Match	RISB1070	Oryctes rhinoceros Order: Coleoptera	gut microbe	7.28%	17.5
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	0.46%	17.2
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	0.46%	17.2
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	0.06%	17.0
Bacillus cereus Species-level Match Host Order Match	RISB1056	Oryctes rhinoceros Order: Coleoptera	provide symbiotic digestive functions to Oryctes	0.99%	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	0.06%	16.9
Escherichia coli Species-level Match	RISB2120	Galleria mellonella Order: Lepidoptera	mediate trans-generational immune priming	10.51%	16.3
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)	0.55%	15.2
Pseudomonas 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	0.41%	15.2
Pseudomonas Host Order Match	RISB1510	Hypothenemus hampei Order: Coleoptera	Antibiotic-treated larvae showed lower caffeine-degrading activity and increased mortality. These deficients were recovered by inoculation of the caffeine-degrading symbiont. A caffeine-degrading gene was detected from the symbiont	0.41%	15.0
Pseudomonas Host Order Match	RISB0740	Hypothenemus hampei Order: Coleoptera	P. fulva processed gene coding one subunit of caffeine demethylase, and reinstatement of P. fulva in germ-free H. hampei degraded all caffeine consumed (by 16S rRNA gene sequencing and GC-MS)	0.41%	14.2
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.	0.55%	14.0
Salmonella enterica Species-level Match	RISB0413	Melanaphis sacchari Order: Hemiptera	None	8.74%	13.7
Lactococcus Host Order Match	RISB0967	Oulema melanopus Order: Coleoptera	contribute to the decomposition of complex carbohydrates, fatty acids, or polysaccharides in the insect gut. It might also contribute to the improvement of nutrient availability.	0.10%	13.7
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.	0.14%	13.5
Lactococcus Host Order Match	RISB0116	Novius pumilus Order: Coleoptera	were predicted to have genes related to hydrocarbon, fatty acids, and chitin degradation, which may assist their hosts in digesting the wax shell covering the scale insects	0.10%	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.	3.26%	13.3
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)	0.14%	13.0
Proteus Host Order Match	RISB0001	Leptinotarsa decemlineata Order: Coleoptera	produces toxic hydrogen cyanide (HCN) and a mandelonitrile-producing cyanoglucoside, amygdalin, which protect the insect from predation	0.18%	12.9
Corynebacterium Host Order Match	RISB0363	Pagiophloeus tsushimanus Order: Coleoptera	terpenoid-degrading: the highest degradation rates of D-camphor, linalool, and eucalyptol	0.97%	12.8
Lactococcus Host Order Match	RISB1430	Rhynchophorus ferrugineus Order: Coleoptera	promote the development and body mass gain of RPW larvae by improving their nutrition metabolism	0.10%	12.0
Aeromonas Host Order Match	RISB1145	Tenebrio molitor Order: Coleoptera	degrading plastics	0.26%	10.6
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	6.67%	10.4
Listeria monocytogenes Species-level Match	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.	0.40%	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	0.18%	10.2
Paenibacillus polymyxa Species-level Match	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%	10.2
Candidatus Hamiltonella defensa Species-level Match	RISB1049	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.	0.08%	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	0.18%	9.7
Candidatus Hamiltonella defensa Species-level Match	RISB1296	Sitobion miscanthi Order: Hemiptera	Increase the reproductive capacity of wheat aphids, increase the number of offspring and reduce the age of first breeding, suppressed the salicylic acid (SA)- and jasmonic acid (JA)-related defense pathways and SA/JA accumulation	0.08%	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	0.88%	9.5
Klebsiella pneumoniae Species-level Match	RISB2459	Bombyx mori Order: Lepidoptera	degradation of cellulose, xylan, pectin and starch	3.26%	9.3
Candidatus Hamiltonella defensa Species-level Match	RISB0630	Acyrthosiphon pisum Order: Hemiptera	In response to ladybirds, symbiont-infected pea aphids exhibited proportionately fewer evasive defences (dropping and walking away) than non-infected (cured) pea aphids, but more frequent aggressive kicking	0.08%	9.2
Candidatus Erwinia haradaeae Species-level Match	RISB1632	Lachninae Order: Hemiptera	None	3.65%	8.7
Xanthomonas	RISB0217	Xylocopa appendiculata Order: Hymenoptera	strains biodegraded polyethylene terephthalate PET powder, broke it into its degradation products	6.67%	8.6
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	0.88%	8.6
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	0.18%	8.6
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	4.53%	7.9
Enterobacter ludwigii Species-level Match	RISB1397	Delia antiqua Order: Diptera	suppressed Beauveria bassiana conidia germination and hyphal growth	0.88%	7.2
Lactiplantibacillus plantarum Species-level Match	RISB0674	Drosophila melanogaster Order: Diptera	could effectively inhibit fungal spore germinations	0.40%	6.4
Brevundimonas sp. Bb-A Species-level Match	RISB1703	Phlebotomus papatasi Order: Diptera	None	0.76%	5.8
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	0.54%	5.5
Lactiplantibacillus plantarum Species-level Match	RISB0608	Drosophila melanogaster Order: Diptera	None	0.40%	5.4
Methylobacterium	RISB2053	Atractomorpha sinensis Order: Orthoptera	associated with cellulolytic enzymes	4.53%	5.3
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
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
Methylobacterium	RISB2340	Saturniidae Order: Lepidoptera	Nitrogen fixation	4.53%	4.9
Streptococcus	RISB2625	Galleria mellonella Order: Lepidoptera	suppress bacteria ingested with food by producing bacteriocin and by releasing a lysozyme like enzyme	2.45%	4.5
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
Streptococcus	RISB2624	Reticulitermes flavipes Order: Blattodea	can be broken down into substances such as carbon dioxide, ammonia and acetic acid	2.45%	4.1
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.	0.54%	3.9
Streptococcus	RISB2604	Homona magnanima Order: Lepidoptera	influence the growth of Bacillus thuringiensis in the larvae	2.45%	3.7
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	0.54%	3.4
Yersinia	RISB0492	Cimex hemipterus Order: Hemiptera	the disruption of the abundant Yersinia possibly could be related to the enhanced susceptibility towards the insecticides	0.34%	2.8
Corynebacterium	RISB0531	Helicoverpa armigera Order: Lepidoptera	Corynebacterium sp. 2-TD, mediates the toxicity of the 2-tridecanone to H. armigera	0.97%	2.6
Proteus	RISB2315	Aedes aegypti Order: Diptera	upregulates AMP gene expression, resulting in suppression of DENV infection in the mosquito gut epithelium	0.18%	2.3
Corynebacterium	RISB2360	Bombyx mori Order: Lepidoptera	producing lipase in a gut environment	0.97%	1.7
Proteus	RISB2460	Bombyx mori Order: Lepidoptera	degradation of cellulose, xylan, pectin and starch	0.18%	1.2
Aeromonas	RISB2456	Bombyx mori Order: Lepidoptera	able to utilize the CMcellulose and xylan	0.26%	1.1
Aeromonas	RISB2086	Aedes aegypti Order: Diptera	axenic larvae cannot develop	0.26%	0.8
Priestia	RISB0839	Helicoverpa armigera Order: Lepidoptera	producing amylase	0.17%	0.5
Yersinia	RISB0407	Anaphes nitens Order: Hymenoptera	None	0.34%	0.3
Ralstonia	RISB0243	Spodoptera frugiperda Order: Lepidoptera	None	0.29%	0.3
Candidatus Profftia	RISB1664	Adelgidae Order: Hemiptera	None	0.11%	0.1