SRR12668522 - Tribolium castaneum

Basic Information

Run: SRR12668522

Assay Type: WGS

Bioproject: PRJNA663749

Biosample: SAMN16178305

Bytes: 80731364

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	22.34%	60.1
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	10.95%	47.4
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	22.34%	31.7
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.	10.95%	28.5
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	10.95%	28.3
Escherichia coli Species-level Match	RISB2120	Galleria mellonella Order: Lepidoptera	mediate trans-generational immune priming	22.34%	28.2
Serratia sp. CMO1 Species-level Match Host Order Match	RISB0308	Rhopalotria slossonae Order: Coleoptera	suggesting the occurrence of an unprecedented desferrioxamine-like biosynthetic pathway,including desferrioxamine B, which may help tolerating diets rich in azoxyglycosides, BMAA, and other cycad toxins, including a possible role for bacterial siderophores	0.07%	20.1
Serratia liquefaciens Species-level Match Host Order Match	RISB1624	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	0.06%	19.9
Klebsiella pneumoniae Species-level Match Host Order Match	RISB1153	Tenebrio molitor Order: Coleoptera	degrading plastics	3.97%	19.3
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	0.07%	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	0.18%	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.	0.17%	17.8
Serratia liquefaciens Species-level Match Host Order Match	RISB1801	Dendroctonus valens Order: Coleoptera	could alleviate or compromise the antagonistic effects of fungi O. minus and L. procerum on RTB larval growth	0.06%	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	0.07%	17.1
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
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	0.07%	16.9
Klebsiella sp. P1954 Species-level Match Host Order Match	RISB0809	Hypothenemus hampei Order: Coleoptera	might contribute to caffeine breakdown using the C-17 oxidation pathway	0.38%	16.8
Enterobacter asburiae Species-level Match Host Order Match	RISB1150	Plodia interpunctella Order: Coleoptera	damaged polyethylene (PE) films	0.08%	15.7
Salmonella enterica Species-level Match	RISB0413	Melanaphis sacchari Order: Hemiptera	None	10.51%	15.5
Staphylococcus epidermidis Species-level Match Host Order Match	RISB1070	Oryctes rhinoceros Order: Coleoptera	gut microbe	0.06%	15.3
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	11.86%	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	0.26%	15.1
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	11.26%	15.0
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	0.26%	14.9
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.	0.58%	14.6
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)	0.26%	14.1
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.	3.97%	14.0
Raoultella Host Order Match	RISB2226	Leptinotarsa decemlineata Order: Coleoptera	Colorado potato beetle (Leptinotarsa decemlineata) larvae exploit bacteria in their oral secretions to suppress antiherbivore defenses in tomato (Solanum lycopersicum)	0.05%	13.4
Xanthomonas	RISB0217	Xylocopa appendiculata Order: Hymenoptera	strains biodegraded polyethylene terephthalate PET powder, broke it into its degradation products	11.26%	13.2
Methylobacterium	RISB2053	Atractomorpha sinensis Order: Orthoptera	associated with cellulolytic enzymes	11.86%	12.6
Corynebacterium Host Order Match	RISB0363	Pagiophloeus tsushimanus Order: Coleoptera	terpenoid-degrading: the highest degradation rates of D-camphor, linalool, and eucalyptol	0.54%	12.3
Methylobacterium	RISB2340	Saturniidae Order: Lepidoptera	Nitrogen fixation	11.86%	12.2
Vibrio Host Order Match	RISB1810	Monochamus galloprovincialis Order: Coleoptera	Have the ability for degradation of cellulose, proteins and starch	0.67%	12.0
Kosakonia Host Order Match	RISB0810	Hypothenemus hampei Order: Coleoptera	might contribute to caffeine breakdown using the C-16 oxidation pathway	0.08%	11.5
Raoultella Host Order Match	RISB1007	Monochamus alternatus Order: Coleoptera	may help M. alternatus degrade cellulose and pinene	0.05%	11.1
Aeromonas Host Order Match	RISB1145	Tenebrio molitor Order: Coleoptera	degrading plastics	0.61%	11.0
Kosakonia Host Order Match	RISB1155	Tenebrio molitor Order: Coleoptera	degrading plastics	0.08%	10.4
Comamonas Host Order Match	RISB1061	Oryctes rhinoceros Order: Coleoptera	gut microbe	0.22%	10.4
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	1.80%	10.4
Bacillus subtilis Species-level Match	RISB0481	Bombyx mori Order: Lepidoptera	B. subtilis can generate a variety of primary and secondary metabolites, such as B vitamins and antimicrobial compounds, to provide micronutrients and enhance the pathogen resistance of their insect host; The antimicrobial compounds secreted by B. subtilis were the primary driving force for the reconstruction of intestinal microbiota	0.17%	10.2
Candidatus Pantoea carbekii Species-level Match	RISB1046	Halyomorpha halys Order: Hemiptera	provides its host with essential nutrients, vitamins, cofactors and protection of the most vulnerable stages of early development (1st nymphal stages). Pantoea carbekii is highly stress tolerant, especially once secreted to cover the eggs, by its unique biofilm-formation properties, securing host offspring survival	0.06%	10.1
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	1.80%	9.5
Bacillus subtilis Species-level Match	RISB2488	Anticarsia gemmatalis Order: Lepidoptera	allow the adaptation of this insect to plants rich in protease inhibitors, minimizing the potentially harmful consequences of protease inhibitors from some of this insect host plants, such as soybean	0.17%	9.2
Acinetobacter pittii Species-level Match	RISB1977	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	0.16%	9.0
Citrobacter amalonaticus Species-level Match	RISB0192	Hermetia illucens Order: Diptera	can directly promote the expression of two gene families related to intestinal protein metabolism: Hitryp serine protease trypsin family and Himtp metallopeptidase family	0.06%	8.5
Candidatus Ishikawella capsulata Species-level Match	RISB2368	Megacopta punctatissima Order: Hemiptera	Microbe compensates for nutritional deficiency of host diet by supplying essential amino acids	0.06%	6.9
Brevundimonas sp. Bb-A Species-level Match	RISB1703	Phlebotomus papatasi Order: Diptera	None	1.22%	6.2
Candidatus Pantoea carbekii Species-level Match	RISB2115	Halyomorpha halys Order: Hemiptera	the primary bacterial symbiont of H. halys	0.06%	5.9
Candidatus Ishikawella capsulata Species-level Match	RISB2543	Megacopta punctatissima Order: Hemiptera	Enhance pest status of the insect host	0.06%	5.8
Candidatus Steffania adelgidicola Species-level Match	RISB2278	Adelges nordmannianae/piceae Order: Hemiptera	None	0.09%	5.1
Candidatus Karelsulcia muelleri Species-level Match	RISB1591	Philaenus spumarius Order: Hemiptera	None	0.06%	5.1
Brevundimonas sp. M20 Species-level Match	RISB1703	Phlebotomus papatasi Order: Diptera	None	0.05%	5.1
Candidatus Annandia adelgestsuga Species-level Match	RISB2207	Adelges tsugae Order: Hemiptera	None	0.05%	5.1
Pectobacterium	RISB1889	Pseudococcus longispinus Order: Hemiptera	a nested symbiotic arrangement, where one bacterium lives inside another bacterium,occurred in building the mosaic metabolic pathways seen in mitochondria and plastids	0.06%	3.4
Candidatus Blochmanniella	RISB2542	Camponotus Order: Hymenoptera	Blochmannia provide essential amino acids to its host,Camponotus floridanus, and that it may also play a role in nitrogen recycling via its functional urease	0.06%	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	0.77%	3.2
Candidatus Blochmanniella	RISB1827	Camponotus floridanus Order: Hymenoptera	a modulation of immune gene expression which may facilitate tolerance towards the endosymbionts and thus may contribute to their transovarial transmission	0.06%	3.1
Streptococcus	RISB2625	Galleria mellonella Order: Lepidoptera	suppress bacteria ingested with food by producing bacteriocin and by releasing a lysozyme like enzyme	0.97%	3.0
Candidatus Blochmanniella	RISB2448	Camponotus floridanus Order: Hymenoptera	nutritional contribution of the bacteria to host metabolism by production of essential amino acids and urease-mediated nitrogen recycling	0.06%	2.8
Comamonas	RISB2021	Bactrocera dorsalis Order: Diptera	This group in the immature stages may be helping the insects to cope with oxidative stress by supplementing available oxygen.	0.22%	2.7
Shewanella	RISB1924	Anopheles gambiae Order: Diptera	may be related with mediating adaptation to different ecological niches or in shaping specific adult behaviors including mating	0.11%	2.7
Streptococcus	RISB2624	Reticulitermes flavipes Order: Blattodea	can be broken down into substances such as carbon dioxide, ammonia and acetic acid	0.97%	2.6
Corynebacterium	RISB0531	Helicoverpa armigera Order: Lepidoptera	Corynebacterium sp. 2-TD, mediates the toxicity of the 2-tridecanone to H. armigera	0.54%	2.2
Streptococcus	RISB2604	Homona magnanima Order: Lepidoptera	influence the growth of Bacillus thuringiensis in the larvae	0.97%	2.2
Glutamicibacter	RISB0606	Phthorimaea operculella Order: Lepidoptera	could degrade the major toxic α-solanine and α-chaconine in potatoes	0.12%	1.5
Aeromonas	RISB2456	Bombyx mori Order: Lepidoptera	able to utilize the CMcellulose and xylan	0.61%	1.4
Raoultella	RISB1672	Spodoptera frugiperda Order: Lepidoptera	downregulated POX but upregulated trypsin PI in this plant species	0.05%	1.4
Corynebacterium	RISB2360	Bombyx mori Order: Lepidoptera	producing lipase in a gut environment	0.54%	1.3
Aeromonas	RISB2086	Aedes aegypti Order: Diptera	axenic larvae cannot develop	0.61%	1.2
Pectobacterium	RISB0798	Pseudoregma bambucicola Order: Hemiptera	may help P. bambucicola feed on the stalks of bamboo	0.06%	1.1
Yersinia	RISB0407	Anaphes nitens Order: Hymenoptera	None	0.77%	0.8
Comamonas	RISB1875	Aedes aegypti Order: Diptera	gut microbiome	0.22%	0.5
Ralstonia	RISB0243	Spodoptera frugiperda Order: Lepidoptera	None	0.48%	0.5
Glutamicibacter	RISB0438	Helicoverpa armigera Order: Lepidoptera	None	0.12%	0.1
Pectobacterium	RISB1772	Muscidae Order: Diptera	None	0.06%	0.1