SRR24210634 - Ips nitidus

Basic Information

Run: SRR24210634

Assay Type: WGS

Bioproject: PRJNA956988

Biosample: SAMN34209773

Bytes: 2318578047

Center Name: CHINESE ACADEMY OF FORESTRY

Sequencing Information

Instrument: Illumina NovaSeq 6000

Library Layout: SINGLE

Library Selection: RANDOM

Platform: ILLUMINA

Geographic Information

Country: China

Continent: Asia

Location Name: China: Qinghai

Latitude/Longitude: 35.3275 N 101.9361 E

Sample Information

Host: Ips nitidus

Isolation: from Picea crassifolia

Biosample Model: Metagenome or environmental

Collection Date: 2020-07

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
Bacillus cereus Species-level Match Host Order Match	RISB1056	Oryctes rhinoceros Order: Coleoptera	provide symbiotic digestive functions to Oryctes	13.18%	29.1
Bacillus cereus Species-level Match Host Order Match	RISB1778	Lissorhoptrus oryzophilus Order: Coleoptera	might be promising paratransgenesis candidates	13.18%	29.1
Pseudomonas sp. CIP-10 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	6.15%	26.0
Pseudomonas sp. CIP-10 Species-level Match Host Order Match	RISB2224	Leptinotarsa decemlineata Order: Coleoptera	Colorado potato beetle (Leptinotarsa decemlineata) larvae exploit bacteria in their oral secretions to suppress antiherbivore defenses in tomato (Solanum lycopersicum)	6.15%	24.5
Bacillus cereus Species-level Match	RISB2161	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.	13.18%	23.2
Pseudomonas sp. CIP-10 Species-level Match Host Order Match	RISB0815	Hypothenemus hampei Order: Coleoptera	might contribute to caffeine breakdown using the C-15 oxidation pathway	6.15%	22.6
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	1.62%	20.0
Vibrio Host Order Match	RISB1810	Monochamus galloprovincialis Order: Coleoptera	Have the ability for degradation of cellulose, proteins and starch	8.30%	19.6
Enterobacter sp. T2 Species-level Match Host Order Match	RISB2221	Leptinotarsa decemlineata Order: Coleoptera	Colorado potato beetle (Leptinotarsa decemlineata) larvae exploit bacteria in their oral secretions to suppress antiherbivore defenses in tomato (Solanum lycopersicum)	1.12%	19.5
Lactococcus lactis Species-level Match 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.	0.22%	18.8
Stenotrophomonas maltophilia Species-level Match Host Order Match	RISB0139	Tenebrio molitor Order: Coleoptera	correlated with polyvinyl chloride PVC degradation	2.72%	18.7
Enterobacter sp. T2 Species-level Match Host Order Match	RISB0496	Sitophilus oryzae Order: Coleoptera	bacteria can degrade malathion, pirimiphos-methyl, and deltamethrin and utilize these insecticides as the carbon source in vitro.	1.12%	18.7
Escherichia coli Species-level Match Host Order 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	0.95%	18.7
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	1.62%	18.6
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	1.62%	18.4
Streptomyces sp. T12 Species-level Match Host Order Match	RISB0777	Copris tripartitus Order: Coleoptera	contribute brood ball hygiene by inhibiting fungal parasites in the environment	1.56%	18.1
Citrobacter freundii Species-level Match 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)	0.23%	18.1
Citrobacter freundii Species-level Match Host Order 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	0.23%	18.0
Proteus vulgaris Species-level Match 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	0.25%	18.0
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.	0.37%	18.0
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	0.37%	17.7
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	0.10%	17.2
Lactococcus lactis Species-level Match Host Order Match	RISB1430	Rhynchophorus ferrugineus Order: Coleoptera	promote the development and body mass gain of RPW larvae by improving their nutrition metabolism	0.22%	17.1
Enterobacter sp. T2 Species-level Match Host Order Match	RISB1779	Lissorhoptrus oryzophilus Order: Coleoptera	might be promising paratransgenesis candidates	1.12%	17.0
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	0.10%	16.9
Wolbachia Host Order Match	RISB1452	Octodonta nipae Order: Coleoptera	Wolbachia harbored dominantly in a female than the male adult, while, no significant differences were observed between male and female body parts and tissues	3.69%	16.8
Enterococcus faecalis Species-level Match Host Order Match	RISB0374	Tribolium castaneum Order: Coleoptera	modulates host phosphine resistance by interfering with the redox system	0.37%	16.8
Serratia marcescens Species-level Match Host Order Match	RISB1158	Nicrophorus vespilloides Order: Coleoptera	produces an antibacterial cyclic lipopeptide called serrawettin W2	0.10%	16.4
Klebsiella pneumoniae Species-level Match Host Order Match	RISB1153	Tenebrio molitor Order: Coleoptera	degrading plastics	1.02%	16.4
Wolbachia Host Order Match	RISB2107	Sitophilus zeamais Order: Coleoptera	Wolbachia directly favored weevil fertility and exhibited only mild indirect effects, usually enhancing the SZPE effect	3.69%	16.1
Lactococcus lactis Species-level Match Host Order Match	RISB1065	Oryctes rhinoceros Order: Coleoptera	gut microbe	0.22%	15.4
Wolbachia Host Order Match	RISB1282	Ips sp. Order: Coleoptera	inducing cytoplasmic incompatibility, resulting in reproductive distortions and hence	3.69%	15.4
Lysinibacillus fusiformis Species-level Match Host Order Match	RISB1066	Oryctes rhinoceros Order: Coleoptera	gut microbe	0.14%	15.4
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	0.10%	15.1
Sphingobium 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.	0.08%	14.1
Spiroplasma Host Order Match	RISB0343	Harmonia axyridis Order: Coleoptera	female ladybirds co-infected with Hesperomyces harmoniae and Spiroplasma had a significantly lower fecundity and hatchability compared to females with only one or no symbiont	0.33%	13.8
Nostoc Host Order Match	RISB0812	Hypothenemus hampei Order: Coleoptera	might contribute to caffeine breakdown using the C-18 oxidation pathway	1.53%	13.0
Bacteroides Host Order Match	RISB1183	Oryzaephilus surinamensis Order: Coleoptera	supplement precursors for the cuticle synthesis and thereby enhance desiccation resistance of its host	0.80%	12.8
Spiroplasma Host Order Match	RISB1483	Brachinus elongatulus Order: Coleoptera	may manipulate host reproduction (e.g., cause male-killing) or provide resistance to nematodes and/or parasitoid wasps	0.33%	12.7
Rickettsia Host Order Match	RISB1279	Ips sp. Order: Coleoptera	inducing cytoplasmic incompatibility, resulting in reproductive distortions and hence	0.45%	12.2
Corynebacterium Host Order Match	RISB0363	Pagiophloeus tsushimanus Order: Coleoptera	terpenoid-degrading: the highest degradation rates of D-camphor, linalool, and eucalyptol	0.28%	12.1
Rickettsia Host Order Match	RISB0970	Oulema melanopus Order: Coleoptera	may be associated with insect reproduction and maturation of their sexual organs	0.45%	12.1
Rickettsia Host Order Match	RISB1954	Sitona obsoletus Order: Coleoptera	potential defensive properties against he parasitoid Microctonus aethiopoides	0.45%	12.0
Stenotrophomonas maltophilia Species-level Match	RISB1122	Bombyx mori Order: Lepidoptera	facilitate host resistance against organophosphate insecticides, provides essential amino acids that increase host fitness and allow the larvae to better tolerate the toxic effects of the insecticide.	2.72%	11.7
Halomonas Host Order Match	RISB1808	Monochamus galloprovincialis Order: Coleoptera	Have the ability for degradation of cellulose, proteins and starch	0.35%	11.7
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.	1.02%	11.0
Spiroplasma Host Order Match	RISB0250	Tenebrio molitor Order: Coleoptera	associated with PE biodegradation	0.33%	11.0
Streptomyces sp. T12 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	1.56%	10.5
Buchnera aphidicola Species-level Match	RISB0236	Acyrthosiphon pisum Order: Hemiptera	Buchnera the nutritional endosymbiont of A. pisum is located inside of bacteriocytes and requires aspartate from the aphid host, because it cannot make it de novo. Further Buchnera needs aspartate for the biosynthesis of the essential amino acids lysine and threonine, which the aphid and Buchnera require for survival	0.43%	10.4
Stenotrophomonas maltophilia Species-level Match	RISB1227	Delia antiqua Order: Diptera	six bacteria protect larvae from infection with the entomopathogen Beauveria bassiana through symbiotic bacterium-derived organic acids	2.72%	10.4
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	0.95%	10.3
Streptomyces sp. T12 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	1.56%	10.3
Buchnera aphidicola Species-level Match	RISB2485	Macrosiphum euphorbiae Order: Hemiptera	symbiont expression patterns differ between aphid clones with differing levels of virulence, and are influenced by the aphids' host plant. Potentially, symbionts may contribute to differential adaptation of aphids to host plant resistance	0.43%	10.2
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.	0.10%	10.1
Clostridium sp. JS66 Species-level Match	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	0.09%	9.3
Clostridium sp. MB40-C1 Species-level Match	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	0.05%	9.3
Buchnera aphidicola Species-level Match	RISB0685	Acyrthosiphon pisum Order: Hemiptera	It supplies the host with vitamins and essential amino acids, such as arginine and methionine that aphids cannot synthesize or derive insufficiently from their diet, the phloem sap of plants	0.43%	9.2
Mammaliicoccus sciuri Species-level Match	RISB0075	Bombyx mori Order: Lepidoptera	could produce a secreted chitinolytic lysozyme (termed Msp1) to damage fungal cell walls，completely inhibit the spore germination of fungal entomopathogens Metarhizium robertsii and Beauveria bassiana	0.10%	9.1
Blattabacterium cuenoti Species-level Match	RISB0133	Panesthiinae Order: Blattodea	enables hosts to subsist on a nutrient-poor diet; endosymbiont genome erosions are associated with repeated host transitions to an underground life	0.63%	8.6
Citrobacter freundii Species-level Match	RISB1221	Delia antiqua Order: Diptera	six bacteria protect larvae from infection with the entomopathogen Beauveria bassiana through symbiotic bacterium-derived organic acids	0.23%	7.9
Pantoea agglomerans Species-level Match	RISB2579	Schistocerca gregaria Order: Orthoptera	produces an antifungal and antibacterial molecule serving as antimicrobial defense against gut pathogens	0.10%	7.2
Klebsiella pneumoniae Species-level Match	RISB2459	Bombyx mori Order: Lepidoptera	degradation of cellulose, xylan, pectin and starch	1.02%	7.0
Snodgrassella alvi Species-level Match	RISB1423	Bombus spp. Order: Hymenoptera	The bumble bee microbiome slightly increases survivorship when the host is exposed to selenate	0.07%	7.0
Escherichia coli Species-level Match	RISB2120	Galleria mellonella Order: Lepidoptera	mediate trans-generational immune priming	0.95%	6.8
Blattabacterium cuenoti Species-level Match	RISB0518	Cryptocercus punctulatus Order: Blattodea	collaborative arginine biosynthesis	0.63%	6.3
Proteus vulgaris Species-level Match	RISB2460	Bombyx mori Order: Lepidoptera	degradation of cellulose, xylan, pectin and starch	0.25%	6.3
Lactiplantibacillus plantarum Species-level Match	RISB0674	Drosophila melanogaster Order: Diptera	could effectively inhibit fungal spore germinations	0.21%	6.2
Lysinibacillus fusiformis Species-level Match	RISB1417	Psammotermes hypostoma Order: Blattodea	isolates showed significant cellulolytic activity	0.14%	6.1
Acinetobacter calcoaceticus Species-level Match	RISB0017	Scirpophaga incertulas Order: Lepidoptera	degrade Chlorpyrifos and Chlorantraniliprole in vitro	0.05%	6.1
Blattabacterium cuenoti Species-level Match	RISB0093	Blattella germanica Order: Blattodea	obligate endosymbiont	0.63%	6.1
Salmonella enterica Species-level Match	RISB0413	Melanaphis sacchari Order: Hemiptera	None	0.78%	5.8
Sphingobacterium multivorum Species-level Match	RISB0671	Melanaphis bambusae Order: Hemiptera	None	0.57%	5.6
Lactiplantibacillus plantarum Species-level Match	RISB0608	Drosophila melanogaster Order: Diptera	None	0.21%	5.2
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	0.16%	5.2
Candidatus Erwinia haradaeae Species-level Match	RISB1632	Lachninae Order: Hemiptera	None	0.10%	5.1
Snodgrassella alvi Species-level Match	RISB1947	Apis cerana Order: Hymenoptera	None	0.07%	5.1
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.	0.16%	3.5
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	0.11%	3.5
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	0.12%	3.3
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	0.12%	3.2
Bacteroides	RISB0256	Leptocybe invasa Order: Hymenoptera	Differences in Male-Killing Rickettsia Bacteria between Lineages of the Invasive Gall-Causing Pest Leptocybe invasa	0.80%	3.1
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	0.16%	3.1
Bacteroides	RISB0090	Hyphantria cunea Order: Lepidoptera	enhance the compatibility of invasive pests to new hosts and enable more rapid adaptation to new habitats.	0.80%	2.9
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	0.12%	2.9
Yersinia	RISB0492	Cimex hemipterus Order: Hemiptera	the disruption of the abundant Yersinia possibly could be related to the enhanced susceptibility towards the insecticides	0.13%	2.6
Streptococcus	RISB2625	Galleria mellonella Order: Lepidoptera	suppress bacteria ingested with food by producing bacteriocin and by releasing a lysozyme like enzyme	0.30%	2.3
Corynebacterium	RISB0531	Helicoverpa armigera Order: Lepidoptera	Corynebacterium sp. 2-TD, mediates the toxicity of the 2-tridecanone to H. armigera	0.28%	1.9
Streptococcus	RISB2624	Reticulitermes flavipes Order: Blattodea	can be broken down into substances such as carbon dioxide, ammonia and acetic acid	0.30%	1.9
Streptococcus	RISB2604	Homona magnanima Order: Lepidoptera	influence the growth of Bacillus thuringiensis in the larvae	0.30%	1.5
Chryseobacterium	RISB2092	Aedes aegypti Order: Diptera	axenic larvae cannot develop	0.93%	1.5
Chryseobacterium	RISB1874	Aedes aegypti Order: Diptera	gut microbiome	0.93%	1.2
Paraclostridium	RISB0028	Sesamia inferens Order: Lepidoptera	degrade Chlorpyrifos and Chlorantraniliprole in vitro	0.13%	1.2
Pectobacterium	RISB0798	Pseudoregma bambucicola Order: Hemiptera	may help P. bambucicola feed on the stalks of bamboo	0.11%	1.2
Corynebacterium	RISB2360	Bombyx mori Order: Lepidoptera	producing lipase in a gut environment	0.28%	1.0
Chryseobacterium	RISB0015	Aedes aegypti Order: Diptera	None	0.93%	0.9
Flavobacterium	RISB0659	Melanaphis bambusae Order: Hemiptera	None	0.79%	0.8
Metabacillus	RISB0902	Myzus persicae Order: Hemiptera	None	0.76%	0.8
Cupriavidus	RISB0694	Alydus tomentosus Order: Hemiptera	None	0.65%	0.7
Priestia	RISB0839	Helicoverpa armigera Order: Lepidoptera	producing amylase	0.27%	0.6
Peribacillus	RISB1877	Aedes aegypti Order: Diptera	gut microbiome	0.15%	0.4
Sphingobium	RISB1880	Aedes aegypti Order: Diptera	gut microbiome	0.08%	0.4
Halomonas	RISB1374	Bemisia tabaci Order: Hemiptera	None	0.35%	0.4
Helicobacter	RISB0662	Melanaphis bambusae Order: Hemiptera	None	0.17%	0.2
Legionella	RISB1687	Polyplax serrata Order: Phthiraptera	None	0.15%	0.2
Yersinia	RISB0407	Anaphes nitens Order: Hymenoptera	None	0.13%	0.1
Pectobacterium	RISB1772	Muscidae Order: Diptera	None	0.11%	0.1
Candidatus Phytoplasma	RISB1620	Cacopsylla pyricola Order: Hemiptera	None	0.10%	0.1
Paraburkholderia	RISB0125	Physopelta gutta Order: Hemiptera	None	0.08%	0.1
Fructobacillus	RISB0638	Formica Order: Hymenoptera	None	0.05%	0.1