SRR12668546 - Tribolium castaneum

Basic Information

Run: SRR12668546

Assay Type: WGS

Bioproject: PRJNA663749

Biosample: SAMN16178261

Bytes: 101668974

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	0.56%	38.3
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	1.75%	38.2
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	34.11%	37.9
Xanthomonas	RISB0217	Xylocopa appendiculata Order: Hymenoptera	strains biodegraded polyethylene terephthalate PET powder, broke it into its degradation products	34.11%	36.1
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	0.05%	31.5
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.	3.86%	21.4
Bacillus sp. ZHX3 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	3.33%	20.9
Pantoea sp. At-9b Species-level Match Host Order Match	RISB0736	Psylliodes chrysocephala Order: Coleoptera	Laboratory-reared and field-collected P. chrysocephala all contained three core genera Pantoea, Acinetobacter and Pseudomonas, and reintroduction of Pantoea sp. Pc8 in antibiotic-fed beetles restored isothiocyanate degradation ability in vivo (by 16S rRNA gene sequencing and LC-MS)	0.26%	20.3
Bacillus sp. ZHX3 Species-level Match Host Order Match	RISB0805	Hypothenemus hampei Order: Coleoptera	might contribute to caffeine breakdown using the C-8 oxidation pathway	3.33%	19.7
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.	1.75%	19.3
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	1.75%	19.1
Serratia marcescens Species-level Match Host Order Match	RISB1295	Nicrophorus vespilloides Order: Coleoptera	producing antibacterial compound Serrawettin W2, which has antibacterial and nematode-inhibiting effects	0.05%	17.1
Serratia marcescens Species-level Match Host Order Match	RISB0365	Pagiophloeus tsushimanus Order: Coleoptera	terpenoid-degrading: the highest degradation rates of D-camphor, linalool, and eucalyptol	0.05%	16.8
Streptomyces sp. NBC_00310 Species-level Match Host Order Match	RISB0777	Copris tripartitus Order: Coleoptera	contribute brood ball hygiene by inhibiting fungal parasites in the environment	0.11%	16.7
Pantoea sp. At-9b Species-level Match Host Order Match	RISB0814	Hypothenemus hampei Order: Coleoptera	might contribute to caffeine breakdown using the C-14 oxidation pathway	0.26%	16.7
Paenibacillus sp. FSL R5-0701 Species-level Match Host Order Match	RISB0813	Hypothenemus hampei Order: Coleoptera	might contribute to caffeine breakdown using the C-9 oxidation pathway	0.04%	16.4
Serratia marcescens Species-level Match Host Order Match	RISB1158	Nicrophorus vespilloides Order: Coleoptera	produces an antibacterial cyclic lipopeptide called serrawettin W2	0.05%	16.4
Klebsiella pneumoniae Species-level Match Host Order Match	RISB1153	Tenebrio molitor Order: Coleoptera	degrading plastics	0.33%	15.7
Staphylococcus epidermidis Species-level Match Host Order Match	RISB1070	Oryctes rhinoceros Order: Coleoptera	gut microbe	0.12%	15.3
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)	0.05%	14.7
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.	0.33%	14.4
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	0.32%	13.7
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	0.32%	13.6
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.	0.05%	13.5
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	0.32%	13.3
Corynebacterium Host Order Match	RISB0363	Pagiophloeus tsushimanus Order: Coleoptera	terpenoid-degrading: the highest degradation rates of D-camphor, linalool, and eucalyptol	0.06%	11.8
Lysinibacillus Host Order Match	RISB1066	Oryctes rhinoceros Order: Coleoptera	gut microbe	0.14%	10.4
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.	0.33%	10.3
Pantoea sp. At-9b Species-level Match	RISB0118	Nezara viridula Order: Hemiptera	plays an important role in interactions between insects and plants and could therefore be considered a valuable target for the development of sustainable pest control strategies;transmitted bacteria impacted plant chemical defenses and were able to degrade toxic plant metabolites, aiding the shield bug in its nutrition	0.26%	10.3
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.	0.23%	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.	0.04%	10.0
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	0.56%	9.9
Streptomyces sp. NBC_00310 Species-level Match	RISB0943	Polybia plebeja Order: Hymenoptera	this bacterium produces antimicrobial compounds that are active against Hirsutella citriformis, a natural fungal enemy of its host, and the human pathogens Staphylococcus aureus and Candida albicans	0.11%	9.1
Streptomyces sp. NBC_00310 Species-level Match	RISB2334	Sirex noctilio Order: Hymenoptera	degrading woody substrates and that such degradation may assist in nutrient acquisition by S. noctilio, thus contributing to its ability to be established in forested habitats worldwide	0.11%	8.8
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	0.10%	8.7
Paenibacillus sp. FSL R5-0701 Species-level Match	RISB0774	Delia antiqua Order: Diptera	showed significant contact inhibition activity against fungal entomopathogen Fusarium moniliforme, Botryosphaeria dothidea and both Fusarium oxysporum respectively	0.04%	8.3
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	0.10%	7.8
Enterobacter ludwigii Species-level Match	RISB1397	Delia antiqua Order: Diptera	suppressed Beauveria bassiana conidia germination and hyphal growth	0.10%	6.4
Escherichia coli Species-level Match	RISB2120	Galleria mellonella Order: Lepidoptera	mediate trans-generational immune priming	0.56%	6.4
Klebsiella pneumoniae Species-level Match	RISB2459	Bombyx mori Order: Lepidoptera	degradation of cellulose, xylan, pectin and starch	0.33%	6.3
Salmonella enterica Species-level Match	RISB0413	Melanaphis sacchari Order: Hemiptera	None	1.08%	6.1
Brevundimonas sp. Bb-A Species-level Match	RISB1703	Phlebotomus papatasi Order: Diptera	None	0.34%	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	0.13%	5.1
Candidatus Karelsulcia muelleri Species-level Match	RISB1591	Philaenus spumarius Order: Hemiptera	None	0.05%	5.1
Brevundimonas sp. M20 Species-level Match	RISB1703	Phlebotomus papatasi Order: Diptera	None	0.03%	5.0
Clostridium	RISB2301	Pyrrhocoris apterus Order: Hemiptera	could play an important role for the insect by degrading complex dietary components, providing nutrient supplementation, or detoxifying noxious chemicals (e.g. cyclopropenoic fatty acids or gossypol) in the diet	0.15%	4.4
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	0.13%	3.6
Streptococcus	RISB2625	Galleria mellonella Order: Lepidoptera	suppress bacteria ingested with food by producing bacteriocin and by releasing a lysozyme like enzyme	0.78%	2.8
Nocardia	RISB0947	Acromyrmex Order: Hymenoptera	Pseudonocardia in the Acromyrmex leaf-cutter ants as a protective partner against the entomopathogenic fungus Metarhizium	0.05%	2.5
Streptococcus	RISB2624	Reticulitermes flavipes Order: Blattodea	can be broken down into substances such as carbon dioxide, ammonia and acetic acid	0.78%	2.4
Nocardia	RISB1218	Mycocepurus smithii Order: Hymenoptera	produce secondary metabolites with antibiotic activity that protects the fungus garden against pathogens	0.05%	2.1
Streptococcus	RISB2604	Homona magnanima Order: Lepidoptera	influence the growth of Bacillus thuringiensis in the larvae	0.78%	2.0
Corynebacterium	RISB0531	Helicoverpa armigera Order: Lepidoptera	Corynebacterium sp. 2-TD, mediates the toxicity of the 2-tridecanone to H. armigera	0.06%	1.7
Clostridium	RISB0028	Sesamia inferens Order: Lepidoptera	degrade Chlorpyrifos and Chlorantraniliprole in vitro	0.15%	1.2
Lysinibacillus	RISB1416	Psammotermes hypostoma Order: Blattodea	isolates showed significant cellulolytic activity	0.14%	1.1
Corynebacterium	RISB2360	Bombyx mori Order: Lepidoptera	producing lipase in a gut environment	0.06%	0.8
Priestia	RISB0839	Helicoverpa armigera Order: Lepidoptera	producing amylase	0.18%	0.5
Peribacillus	RISB1877	Aedes aegypti Order: Diptera	gut microbiome	0.06%	0.3
Clostridium	RISB1959	Pyrrhocoridae Order: Hemiptera	None	0.15%	0.2
Bifidobacterium	RISB1944	Apis cerana Order: Hymenoptera	None	0.13%	0.1
Ralstonia	RISB0243	Spodoptera frugiperda Order: Lepidoptera	None	0.11%	0.1