SRR24210638 - Ips nitidus

Basic Information

Run: SRR24210638

Assay Type: WGS

Bioproject: PRJNA956988

Biosample: SAMN34209769

Bytes: 2136917082

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

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
Bacillus cereus
RISB1056
Oryctes rhinoceros
Order: Coleoptera
provide symbiotic digestive functions to Oryctes
7.43%
23.4
Bacillus cereus
RISB1778
Lissorhoptrus oryzophilus
Order: Coleoptera
might be promising paratransgenesis candidates
7.43%
23.4
Pseudomonas sp. CIP-10
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
3.42%
23.2
Escherichia coli
RISB0128
Tribolium castaneum
Order: Coleoptera
may produce 4,8-dimethyldecanal (DMD) production that is strongly associated with attraction to females and host pheromone communication
4.12%
21.8
Pseudomonas sp. CIP-10
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)
3.42%
21.8
Klebsiella pneumoniae
RISB1153
Tenebrio molitor
Order: Coleoptera
degrading plastics
5.73%
21.1
Candidatus Sodalis pierantonius
RISB2035
Sitophilus oryzae
Order: Coleoptera
endosymbiont dynamics parallels numerous transcriptional changes in weevil developing adults and affects several biological processes, including metabolism and development
2.55%
21.0
Pseudomonas sp. CIP-10
RISB0815
Hypothenemus hampei
Order: Coleoptera
might contribute to caffeine breakdown using the C-15 oxidation pathway
3.42%
19.8
Candidatus Sodalis pierantonius
RISB0972
Sitophilus oryzae
Order: Coleoptera
produce vitamins and essential amino acids required for insect development and cuticle biosynthesis
2.55%
19.5
Candidatus Sodalis pierantonius
RISB0251
Sitophilus oryzae
Order: Coleoptera
may infulence immunity, metabolism, metal control, apoptosis, and bacterial stress response
2.55%
19.4
Enterobacter sp. T2
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)
0.96%
19.3
Lactococcus lactis
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.
0.31%
18.9
Enterobacter sp. T2
RISB0496
Sitophilus oryzae
Order: Coleoptera
bacteria can degrade malathion, pirimiphos-methyl, and deltamethrin and utilize these insecticides as the carbon source in vitro.
0.96%
18.5
Morganella morganii
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
0.09%
17.9
Proteus vulgaris
RISB0001
Leptinotarsa decemlineata
Order: Coleoptera
produces toxic hydrogen cyanide (HCN) and a mandelonitrile-producing cyanoglucoside, amygdalin, which protect the insect from predation
0.13%
17.8
Enterococcus faecalis
RISB0497
Cryptolestes ferrugineus
Order: Coleoptera
bacteria can degrade malathion, pirimiphos-methyl, and deltamethrin and utilize these insecticides as the carbon source in vitro.
0.24%
17.8
Bacillus sp. T3
RISB1645
Osphranteria coerulescens
Order: Coleoptera
The isolate has cellulolytic activity and can hydrolyze CMC, avicel, cellulose and sawdust with broad temperature and pH stability
0.14%
17.7
Stenotrophomonas maltophilia
RISB0139
Tenebrio molitor
Order: Coleoptera
correlated with polyvinyl chloride PVC degradation
1.65%
17.7
Enterococcus faecalis
RISB2042
Harpalus pensylvanicus
Order: Coleoptera
E. faecalis facilitate seed consumption by H. pensylvanicus, possibly by contributing digestive enzymes to their host
0.24%
17.6
Streptomyces sp. T12
RISB0777
Copris tripartitus
Order: Coleoptera
contribute brood ball hygiene by inhibiting fungal parasites in the environment
0.85%
17.4
Lactococcus lactis
RISB1430
Rhynchophorus ferrugineus
Order: Coleoptera
promote the development and body mass gain of RPW larvae by improving their nutrition metabolism
0.31%
17.2
Serratia marcescens
RISB1295
Nicrophorus vespilloides
Order: Coleoptera
producing antibacterial compound Serrawettin W2, which has antibacterial and nematode-inhibiting effects
0.15%
17.2
Wolbachia
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
3.98%
17.1
Serratia marcescens
RISB0365
Pagiophloeus tsushimanus
Order: Coleoptera
terpenoid-degrading: the highest degradation rates of D-camphor, linalool, and eucalyptol
0.15%
16.9
Enterobacter sp. T2
RISB1779
Lissorhoptrus oryzophilus
Order: Coleoptera
might be promising paratransgenesis candidates
0.96%
16.9
Morganella morganii
RISB1548
Costelytra zealandica
Order: Coleoptera
symbionts residing in the colleterial glands produce phenol 1 as the female sex pheromone
0.09%
16.9
Morganella morganii
RISB1868
Costelytra zealandica
Order: Coleoptera
produces phenol as the sex pheromone of the host from tyrosine in the colleterial gland
0.09%
16.8
Erwinia sp. HDF1-3R
RISB0808
Hypothenemus hampei
Order: Coleoptera
might contribute to caffeine breakdown using the C-12 oxidation pathway
0.35%
16.8
Enterococcus faecalis
RISB0374
Tribolium castaneum
Order: Coleoptera
modulates host phosphine resistance by interfering with the redox system
0.24%
16.7
Vibrio
RISB1810
Monochamus galloprovincialis
Order: Coleoptera
Have the ability for degradation of cellulose, proteins and starch
5.34%
16.7
Serratia marcescens
RISB1158
Nicrophorus vespilloides
Order: Coleoptera
produces an antibacterial cyclic lipopeptide called serrawettin W2
0.15%
16.5
Wolbachia
RISB2107
Sitophilus zeamais
Order: Coleoptera
Wolbachia directly favored weevil fertility and exhibited only mild indirect effects, usually enhancing the SZPE effect
3.98%
16.4
Klebsiella pneumoniae
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.
5.73%
15.7
Wolbachia
RISB1282
Ips sp.
Order: Coleoptera
inducing cytoplasmic incompatibility, resulting in reproductive distortions and hence
3.98%
15.7
Lactococcus lactis
RISB1065
Oryctes rhinoceros
Order: Coleoptera
gut microbe
0.31%
15.5
Lysinibacillus fusiformis
RISB1066
Oryctes rhinoceros
Order: Coleoptera
gut microbe
0.15%
15.4
Staphylococcus epidermidis
RISB1070
Oryctes rhinoceros
Order: Coleoptera
gut microbe
0.15%
15.4
Pantoea agglomerans
RISB1858
Lissorhoptrus oryzophilus
Order: Coleoptera
None
0.24%
15.2
Burkholderia
RISB1172
Lagria villosa
Order: Coleoptera
process a cryptic gene cluster that codes for the biosynthesis of a novel antifungal polyketide with a glutarimide pharmacophore, which led to the discovery of the gladiofungins as previously-overlooked components of the antimicrobial armory of the beetle symbiont
0.12%
15.1
Burkholderia
RISB1729
Lagria hirta
Order: Coleoptera
the symbionts inhibit the growth of antagonistic fungi on the eggs of the insect host, indicating that the Lagria-associated Burkholderia have evolved from plant pathogenic ancestors into insect defensive mutualists
0.12%
14.4
Burkholderia
RISB1836
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.
0.12%
14.1
Sphingobium
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.
0.09%
14.1
Spiroplasma
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
0.34%
13.8
Escherichia coli
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
4.12%
13.4
Spiroplasma
RISB1483
Brachinus elongatulus
Order: Coleoptera
may manipulate host reproduction (e.g., cause male-killing) or provide resistance to nematodes and/or parasitoid wasps
0.34%
12.7
Bacteroides
RISB1183
Oryzaephilus surinamensis
Order: Coleoptera
supplement precursors for the cuticle synthesis and thereby enhance desiccation resistance of its host
0.57%
12.6
Rickettsia
RISB1279
Ips sp.
Order: Coleoptera
inducing cytoplasmic incompatibility, resulting in reproductive distortions and hence
0.47%
12.2
Rickettsia
RISB0970
Oulema melanopus
Order: Coleoptera
may be associated with insect reproduction and maturation of their sexual organs
0.47%
12.1
Corynebacterium
RISB0363
Pagiophloeus tsushimanus
Order: Coleoptera
terpenoid-degrading: the highest degradation rates of D-camphor, linalool, and eucalyptol
0.24%
12.0
Rickettsia
RISB1954
Sitona obsoletus
Order: Coleoptera
potential defensive properties against he parasitoid Microctonus aethiopoides
0.47%
12.0
Nostoc
RISB0812
Hypothenemus hampei
Order: Coleoptera
might contribute to caffeine breakdown using the C-18 oxidation pathway
0.47%
11.9
Klebsiella pneumoniae
RISB2459
Bombyx mori
Order: Lepidoptera
degradation of cellulose, xylan, pectin and starch
5.73%
11.7
Halomonas
RISB1808
Monochamus galloprovincialis
Order: Coleoptera
Have the ability for degradation of cellulose, proteins and starch
0.32%
11.6
Spiroplasma
RISB0250
Tenebrio molitor
Order: Coleoptera
associated with PE biodegradation
0.34%
11.0
Stenotrophomonas maltophilia
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.
1.65%
10.7
Buchnera aphidicola
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
0.51%
10.5
Buchnera aphidicola
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
0.51%
10.3
Pantoea agglomerans
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.
0.24%
10.2
Micromonospora
RISB2034
Harpalus sinicus
Order: Coleoptera
None
0.06%
10.1
Escherichia coli
RISB2120
Galleria mellonella
Order: Lepidoptera
mediate trans-generational immune priming
4.12%
9.9
Streptomyces sp. T12
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
0.85%
9.8
Streptomyces sp. T12
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
0.85%
9.6
Stenotrophomonas maltophilia
RISB1227
Delia antiqua
Order: Diptera
six bacteria protect larvae from infection with the entomopathogen Beauveria bassiana through symbiotic bacterium-derived organic acids
1.65%
9.4
Clostridium sp. C1
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
0.12%
9.3
Buchnera aphidicola
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
0.51%
9.3
Clostridium sp. MB40-C1
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. AWRP
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
0.08%
9.3
Mammaliicoccus sciuri
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
0.21%
9.2
Acinetobacter pittii
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
0.11%
8.9
Agrobacterium tumefaciens
RISB0650
Melanaphis bambusae
Order: Hemiptera
None
3.84%
8.8
Blattabacterium cuenoti
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
0.67%
8.6
Pantoea agglomerans
RISB2579
Schistocerca gregaria
Order: Orthoptera
produces an antifungal and antibacterial molecule serving as antimicrobial defense against gut pathogens
0.24%
7.3
Snodgrassella alvi
RISB1423
Bombus spp.
Order: Hymenoptera
The bumble bee microbiome slightly increases survivorship when the host is exposed to selenate
0.08%
7.0
Chryseobacterium sp. G0186
RISB2092
Aedes aegypti
Order: Diptera
axenic larvae cannot develop
1.30%
6.9
Blattabacterium cuenoti
RISB0518
Cryptocercus punctulatus
Order: Blattodea
collaborative arginine biosynthesis
0.67%
6.4
Salmonella enterica
RISB0413
Melanaphis sacchari
Order: Hemiptera
None
1.23%
6.2
Proteus vulgaris
RISB2460
Bombyx mori
Order: Lepidoptera
degradation of cellulose, xylan, pectin and starch
0.13%
6.1
Lysinibacillus fusiformis
RISB1417
Psammotermes hypostoma
Order: Blattodea
isolates showed significant cellulolytic activity
0.15%
6.1
Blattabacterium cuenoti
RISB0093
Blattella germanica
Order: Blattodea
obligate endosymbiont
0.67%
6.1
Erwinia sp. HDF1-3R
RISB1986
Bombyx mori
Order: Lepidoptera
producing cellulase and amylase
0.35%
6.0
Sphingobacterium multivorum
RISB0671
Melanaphis bambusae
Order: Hemiptera
None
0.54%
5.5
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
0.23%
5.2
Candidatus Erwinia haradaeae
RISB1632
Lachninae
Order: Hemiptera
None
0.11%
5.1
Snodgrassella alvi
RISB1947
Apis cerana
Order: Hymenoptera
None
0.08%
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.
0.23%
3.6
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
0.10%
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
0.10%
3.2
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
0.23%
3.1
Bacteroides
RISB0256
Leptocybe invasa
Order: Hymenoptera
Differences in Male-Killing Rickettsia Bacteria between Lineages of the Invasive Gall-Causing Pest Leptocybe invasa
0.57%
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
0.10%
2.8
Bacteroides
RISB0090
Hyphantria cunea
Order: Lepidoptera
enhance the compatibility of invasive pests to new hosts and enable more rapid adaptation to new habitats.
0.57%
2.7
Yersinia
RISB0492
Cimex hemipterus
Order: Hemiptera
the disruption of the abundant Yersinia possibly could be related to the enhanced susceptibility towards the insecticides
0.14%
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
Streptococcus
RISB2624
Reticulitermes flavipes
Order: Blattodea
can be broken down into substances such as carbon dioxide, ammonia and acetic acid
0.30%
1.9
Corynebacterium
RISB0531
Helicoverpa armigera
Order: Lepidoptera
Corynebacterium sp. 2-TD, mediates the toxicity of the 2-tridecanone to H. armigera
0.24%
1.9
Streptococcus
RISB2604
Homona magnanima
Order: Lepidoptera
influence the growth of Bacillus thuringiensis in the larvae
0.30%
1.5
Paraclostridium
RISB0028
Sesamia inferens
Order: Lepidoptera
degrade Chlorpyrifos and Chlorantraniliprole in vitro
0.20%
1.3
Corynebacterium
RISB2360
Bombyx mori
Order: Lepidoptera
producing lipase in a gut environment
0.24%
1.0
Flavobacterium
RISB0659
Melanaphis bambusae
Order: Hemiptera
None
0.99%
1.0
Metabacillus
RISB0902
Myzus persicae
Order: Hemiptera
None
0.96%
1.0
Cupriavidus
RISB0694
Alydus tomentosus
Order: Hemiptera
None
0.76%
0.8
Priestia
RISB0839
Helicoverpa armigera
Order: Lepidoptera
producing amylase
0.41%
0.8
Peribacillus
RISB1877
Aedes aegypti
Order: Diptera
gut microbiome
0.21%
0.5
Sphingobium
RISB1880
Aedes aegypti
Order: Diptera
gut microbiome
0.09%
0.4
Halomonas
RISB1374
Bemisia tabaci
Order: Hemiptera
None
0.32%
0.3
Helicobacter
RISB0662
Melanaphis bambusae
Order: Hemiptera
None
0.20%
0.2
Legionella
RISB1687
Polyplax serrata
Order: Phthiraptera
None
0.17%
0.2
Yersinia
RISB0407
Anaphes nitens
Order: Hymenoptera
None
0.14%
0.1
Candidatus Phytoplasma
RISB1620
Cacopsylla pyricola
Order: Hemiptera
None
0.08%
0.1
Paraburkholderia
RISB0125
Physopelta gutta
Order: Hemiptera
None
0.07%
0.1
Fructobacillus
RISB0638
Formica
Order: Hymenoptera
None
0.07%
0.1
Vagococcus
RISB0042
Aldrichina grahami
Order: Diptera
None
0.07%
0.1
Micromonospora
RISB2033
Palomena viridissima
Order: Hemiptera
None
0.06%
0.1

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