SRR12668496 - Tribolium castaneum

Basic Information

Run: SRR12668496

Assay Type: WGS

Bioproject: PRJNA663749

Biosample: SAMN16178353

Bytes: 71257744

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: 2018-02-05

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	2.59%	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	1.15%	37.6
Acinetobacter sp. NCu2D-2 Species-level Match Host Order Match Host Species Match	RISB0993	Tribolium castaneum Order: Coleoptera	may play a role in the larval gut for biodegradation of Polystyrene PS	0.14%	36.5
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	26.86%	30.6
Xanthomonas	RISB0217	Xylocopa appendiculata Order: Hymenoptera	strains biodegraded polyethylene terephthalate PET powder, broke it into its degradation products	26.86%	28.8
Pseudomonas sp. MPDS Species-level Match 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	1.08%	20.9
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	3.94%	20.7
Pseudomonas sp. FSL L8-0168 Species-level Match 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	0.39%	20.2
Acinetobacter sp. NCu2D-2 Species-level Match 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)	0.14%	19.8
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.	1.15%	18.7
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	1.15%	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	0.04%	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	0.16%	18.0
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.	0.38%	18.0
Corynebacterium Host Order Match	RISB0363	Pagiophloeus tsushimanus Order: Coleoptera	terpenoid-degrading: the highest degradation rates of D-camphor, linalool, and eucalyptol	5.76%	17.5
Novosphingobium Host Order Match	RISB1837	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.	3.27%	17.3
Acinetobacter sp. NCu2D-2 Species-level Match Host Order Match	RISB0706	Curculio chinensis Order: Coleoptera	facilitate the degradation of tea saponin; genome contains 47 genes relating to triterpenoids degradation	0.14%	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	0.04%	17.0
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	0.16%	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	0.16%	16.9
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	0.04%	16.9
Bacillus cereus Species-level Match Host Order Match	RISB1056	Oryctes rhinoceros Order: Coleoptera	provide symbiotic digestive functions to Oryctes	0.26%	16.2
Bacillus cereus Species-level Match Host Order Match	RISB1778	Lissorhoptrus oryzophilus Order: Coleoptera	might be promising paratransgenesis candidates	0.26%	16.2
Klebsiella pneumoniae Species-level Match Host Order Match	RISB1153	Tenebrio molitor Order: Coleoptera	degrading plastics	0.81%	16.2
Staphylococcus epidermidis Species-level Match Host Order Match	RISB1070	Oryctes rhinoceros Order: Coleoptera	gut microbe	0.12%	15.3
Pantoea agglomerans Species-level Match Host Order Match	RISB1858	Lissorhoptrus oryzophilus Order: Coleoptera	None	0.04%	15.0
Candidatus Erwinia haradaeae Species-level Match	RISB1632	Lachninae Order: Hemiptera	None	9.35%	14.4
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.	0.05%	13.6
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	0.05%	13.5
Vibrio Host Order Match	RISB1810	Monochamus galloprovincialis Order: Coleoptera	Have the ability for degradation of cellulose, proteins and starch	1.28%	12.6
Lactococcus Host Order Match	RISB1430	Rhynchophorus ferrugineus Order: Coleoptera	promote the development and body mass gain of RPW larvae by improving their nutrition metabolism	0.05%	12.0
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	2.59%	11.9
Rhizobium Host Order Match	RISB0135	Coccinella septempunctata Order: Coleoptera	be commonly found in plant roots and they all have nitrogen fixation abilities	0.22%	11.8
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.	0.81%	10.8
Aeromonas Host Order Match	RISB1145	Tenebrio molitor Order: Coleoptera	degrading plastics	0.06%	10.4
Lysinibacillus Host Order Match	RISB1066	Oryctes rhinoceros Order: Coleoptera	gut microbe	0.05%	10.3
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	0.08%	10.1
Pantoea agglomerans Species-level Match	RISB2197	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.	0.04%	10.0
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	0.08%	9.6
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	0.28%	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	0.08%	8.5
Escherichia coli Species-level Match	RISB2120	Galleria mellonella Order: Lepidoptera	mediate trans-generational immune priming	2.59%	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	0.28%	8.0
Salmonella enterica Species-level Match	RISB0413	Melanaphis sacchari Order: Hemiptera	None	2.66%	7.7
Corynebacterium	RISB0531	Helicoverpa armigera Order: Lepidoptera	Corynebacterium sp. 2-TD, mediates the toxicity of the 2-tridecanone to H. armigera	5.76%	7.4
Pantoea agglomerans Species-level Match	RISB2579	Schistocerca gregaria Order: Orthoptera	produces an antifungal and antibacterial molecule serving as antimicrobial defense against gut pathogens	0.04%	7.1
Klebsiella pneumoniae Species-level Match	RISB2459	Bombyx mori Order: Lepidoptera	degradation of cellulose, xylan, pectin and starch	0.81%	6.8
Enterobacter ludwigii Species-level Match	RISB1397	Delia antiqua Order: Diptera	suppressed Beauveria bassiana conidia germination and hyphal growth	0.28%	6.6
Corynebacterium	RISB2360	Bombyx mori Order: Lepidoptera	producing lipase in a gut environment	5.76%	6.5
Brevundimonas sp. Bb-A Species-level Match	RISB1703	Phlebotomus papatasi Order: Diptera	None	0.30%	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	0.29%	5.3
Brevundimonas sp. M20 Species-level Match	RISB1703	Phlebotomus papatasi Order: Diptera	None	0.28%	5.3
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.	0.27%	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.	0.05%	5.1
Candidatus Karelsulcia muelleri Species-level Match	RISB1591	Philaenus spumarius Order: Hemiptera	None	0.04%	5.0
Deinococcus	RISB1649	Camponotus japonicus Order: Hymenoptera	Four new aminoglycolipids, deinococcucins A–D, were discovered from a Deinococcus sp. strain isolated from the gut of queen carpenter ants, Camponotus japonicus, showed functional ability of inducing the quinone reductase production in host cells	0.07%	5.0
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.	0.05%	4.8
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	0.05%	4.2
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.	0.29%	3.7
Streptococcus	RISB2625	Galleria mellonella Order: Lepidoptera	suppress bacteria ingested with food by producing bacteriocin and by releasing a lysozyme like enzyme	1.53%	3.6
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	0.29%	3.2
Streptococcus	RISB2624	Reticulitermes flavipes Order: Blattodea	can be broken down into substances such as carbon dioxide, ammonia and acetic acid	1.53%	3.2
Yersinia	RISB0492	Cimex hemipterus Order: Hemiptera	the disruption of the abundant Yersinia possibly could be related to the enhanced susceptibility towards the insecticides	0.47%	2.9
Streptococcus	RISB2604	Homona magnanima Order: Lepidoptera	influence the growth of Bacillus thuringiensis in the larvae	1.53%	2.7
Bartonella	RISB1673	Apis mellifera Order: Hymenoptera	a gut symbiont of insects and that the adaptation to blood-feeding insects facilitated colonization of the mammalian bloodstream	0.05%	2.6
Blautia	RISB0091	Hyphantria cunea Order: Lepidoptera	enhance the compatibility of invasive pests to new hosts and enable more rapid adaptation to new habitats.	0.11%	2.2
Sphingomonas	RISB0420	Aphis gossypii Order: Hemiptera	Sphingomonas could mediate A. gossypii resistance to imidacloprid by hydroxylation and nitroreduction	0.17%	2.2
Sphingomonas	RISB1307	Aphis gossypii Order: Hemiptera	have been previously described in associations with phloem-feeding insects, in low abundances	0.17%	2.0
Sphingomonas	RISB0134	Spodoptera frugiperda Order: Lepidoptera	provide a protective effect to against chlorantraniliprole stress to S. frugiperda	0.17%	1.8
Lactiplantibacillus	RISB1465	Drosophila melanogaster Order: Diptera	L. plantarum increases its growth-promotion ability by adapting to Drosophila diet	0.05%	1.7
Brevibacterium	RISB0464	Acrida cinerea Order: Orthoptera	correlated with the hemicellulose digestibility	0.31%	1.3
Lactiplantibacillus	RISB0674	Drosophila melanogaster Order: Diptera	could effectively inhibit fungal spore germinations	0.05%	1.1
Brevibacterium	RISB2359	Bombyx mori Order: Lepidoptera	producing lipase in a gut environment	0.31%	1.1
Lysinibacillus	RISB1416	Psammotermes hypostoma Order: Blattodea	isolates showed significant cellulolytic activity	0.05%	1.0
Aeromonas	RISB2456	Bombyx mori Order: Lepidoptera	able to utilize the CMcellulose and xylan	0.06%	0.9
Chryseobacterium	RISB2092	Aedes aegypti Order: Diptera	axenic larvae cannot develop	0.25%	0.8
Aeromonas	RISB2086	Aedes aegypti Order: Diptera	axenic larvae cannot develop	0.06%	0.6
Chryseobacterium	RISB1874	Aedes aegypti Order: Diptera	gut microbiome	0.25%	0.5
Yersinia	RISB0407	Anaphes nitens Order: Hymenoptera	None	0.47%	0.5
Brevibacterium	RISB0897	Myzus persicae Order: Hemiptera	None	0.31%	0.3
Ralstonia	RISB0243	Spodoptera frugiperda Order: Lepidoptera	None	0.27%	0.3
Chryseobacterium	RISB0015	Aedes aegypti Order: Diptera	None	0.25%	0.3
Sediminibacterium	RISB0244	Spodoptera frugiperda Order: Lepidoptera	None	0.07%	0.1
Lactiplantibacillus	RISB0608	Drosophila melanogaster Order: Diptera	None	0.05%	0.1
Flavobacterium	RISB0659	Melanaphis bambusae Order: Hemiptera	None	0.04%	0.0