SRR12668548 - Tribolium castaneum

Basic Information

Run: SRR12668548

Assay Type: WGS

Bioproject: PRJNA663749

Biosample: SAMN16178169

Bytes: 59852625

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
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	4.64%	41.1
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	1.79%	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	29.37%	33.1
Xanthomonas	RISB0217	Xylocopa appendiculata Order: Hymenoptera	strains biodegraded polyethylene terephthalate PET powder, broke it into its degradation products	29.37%	31.3
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.	4.64%	22.2
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	4.64%	22.0
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.	0.70%	18.3
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
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	0.10%	17.7
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 sp. T3 Species-level Match Host Order Match	RISB0805	Hypothenemus hampei Order: Coleoptera	might contribute to caffeine breakdown using the C-8 oxidation pathway	0.10%	16.5
Klebsiella pneumoniae Species-level Match Host Order Match	RISB1153	Tenebrio molitor Order: Coleoptera	degrading plastics	0.60%	16.0
Staphylococcus epidermidis Species-level Match Host Order Match	RISB1070	Oryctes rhinoceros Order: Coleoptera	gut microbe	0.05%	15.3
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	0.13%	13.6
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	0.13%	13.4
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	0.13%	13.1
Vibrio Host Order Match	RISB1810	Monochamus galloprovincialis Order: Coleoptera	Have the ability for degradation of cellulose, proteins and starch	1.48%	12.8
Streptomyces Host Order Match	RISB1074	Xyleborinus saxesenii Order: Coleoptera	Cycloheximide is produced, which inhibits the growth of parasitic fungi Nectria spp. and protects mutualistic fungi Raffaelea spp.	0.09%	12.7
Streptomyces Host Order Match	RISB0920	Odontotaenius disjunctus Order: Coleoptera	resulting in a rich repertoire of antimicrobials, inhibit a fungal entomopathogen, Metarhizium anisopliae	0.09%	12.2
Streptomyces Host Order Match	RISB0777	Copris tripartitus Order: Coleoptera	contribute brood ball hygiene by inhibiting fungal parasites in the environment	0.09%	11.7
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	1.79%	11.1
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.	0.60%	10.6
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.	0.22%	10.2
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.	0.14%	10.1
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	0.06%	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	0.06%	9.6
Candidatus Erwinia haradaeae Species-level Match	RISB1632	Lachninae Order: Hemiptera	None	4.33%	9.3
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	0.17%	8.8
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	0.06%	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	0.17%	7.9
Salmonella enterica Species-level Match	RISB0413	Melanaphis sacchari Order: Hemiptera	None	2.71%	7.7
Escherichia coli Species-level Match	RISB2120	Galleria mellonella Order: Lepidoptera	mediate trans-generational immune priming	1.79%	7.6
Klebsiella pneumoniae Species-level Match	RISB2459	Bombyx mori Order: Lepidoptera	degradation of cellulose, xylan, pectin and starch	0.60%	6.6
Enterobacter ludwigii Species-level Match	RISB1397	Delia antiqua Order: Diptera	suppressed Beauveria bassiana conidia germination and hyphal growth	0.17%	6.5
Lactiplantibacillus plantarum Species-level Match	RISB0674	Drosophila melanogaster Order: Diptera	could effectively inhibit fungal spore germinations	0.39%	6.4
Lactiplantibacillus plantarum Species-level Match	RISB0608	Drosophila melanogaster Order: Diptera	None	0.39%	5.4
Brevundimonas sp. Bb-A Species-level Match	RISB1703	Phlebotomus papatasi Order: Diptera	None	0.28%	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.	0.07%	5.1
Candidatus Karelsulcia muelleri Species-level Match	RISB1591	Philaenus spumarius Order: Hemiptera	None	0.06%	5.1
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.	0.07%	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	0.07%	4.2
Streptococcus	RISB2625	Galleria mellonella Order: Lepidoptera	suppress bacteria ingested with food by producing bacteriocin and by releasing a lysozyme like enzyme	2.05%	4.1
Streptococcus	RISB2624	Reticulitermes flavipes Order: Blattodea	can be broken down into substances such as carbon dioxide, ammonia and acetic acid	2.05%	3.7
Streptococcus	RISB2604	Homona magnanima Order: Lepidoptera	influence the growth of Bacillus thuringiensis in the larvae	2.05%	3.3
Priestia	RISB0839	Helicoverpa armigera Order: Lepidoptera	producing amylase	0.08%	0.4
Ralstonia	RISB0243	Spodoptera frugiperda Order: Lepidoptera	None	0.13%	0.1