SRR6033674 - Xylocopa

Basic Information

Run: SRR6033674

Assay Type: WGS

Bioproject: PRJNA407112

Biosample: SAMN07634929

Bytes: 57346329

Center Name: COLUMBIA

Sequencing Information

Instrument: Illumina MiSeq

Library Layout: SINGLE

Library Selection: RANDOM PCR

Platform: ILLUMINA

Geographic Information

Country: Kenya

Continent: Africa

Location Name: Kenya: Mbita

Latitude/Longitude: 0.4734 S 34.1823 E

Sample Information

Host: Xylocopa

Isolation: Whole body homogenate

Biosample Model: Metagenome or environmental

Collection Date: 2015-08-01

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
Pseudomonas sp. CIP-10 Species-level Match Host Order Match	RISB1564	Liometopum apiculatum Order: Hymenoptera	None	19.59%	34.6
Pseudomonas sp. CIP-10 Species-level 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	19.59%	29.4
Pseudomonas sp. CIP-10 Species-level 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)	19.59%	27.9
Stenotrophomonas maltophilia Species-level Match Host Order Match	RISB2004	Trichogramma chilonis Order: Hymenoptera	could significantly increase both female count	11.51%	27.4
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.	11.51%	20.5
Enterobacter sp. T2 Species-level Match	RISB0893	Bactrocera dorsalis Order: Diptera	be beneficial, with some quality control indices, such as adult size, pupal weight, survival rate under stress and nutritionally rich conditions, and mating competitiveness, being significantly increased, while slight nonsignificant increases in emergence rate and flight ability were observed	9.46%	19.5
Streptomyces sp. T12 Species-level Match Host Order 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	0.29%	19.3
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	11.51%	19.2
Streptomyces sp. T12 Species-level Match Host Order 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	0.29%	19.0
Enterobacter sp. T2 Species-level Match	RISB1338	Ceratitis capitata Order: Diptera	Enterobacter sp. AA26 dry biomass can fully replace the brewer’s yeast as a protein source in medfly larval diet without any effect on the productivity and the biological quality of reared medfly of VIENNA 8 GSS	9.46%	18.7
Enterobacter sp. T2 Species-level 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)	9.46%	17.8
Streptomyces sp. T12 Species-level Match Host Order Match	RISB1134	mud dauber wasp Order: Hymenoptera	secondary metabolites derived from a Streptomyces sp. displayed significant inhibitory activity against hexokinase II	0.29%	17.6
Snodgrassella alvi Species-level Match Host Order Match	RISB1423	Bombus spp. Order: Hymenoptera	The bumble bee microbiome slightly increases survivorship when the host is exposed to selenate	0.03%	16.9
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.	6.11%	16.1
Gilliamella Host Order Match	RISB0102	Apis mellifera Order: Hymenoptera	Gilliamella apicola carries the gene for the desaturase FADS2, which is able to metabolize polyunsaturated fatty acids from pollen and synthesize endocannabinoid, a lipogenic neuroactive substance, thereby modulating reward learning and memory in honeybees.	0.12%	15.1
Bacillus cereus Species-level Match	RISB2489	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	6.11%	15.1
Snodgrassella alvi Species-level Match Host Order Match	RISB1947	Apis cerana Order: Hymenoptera	None	0.03%	15.0
Corynebacterium Host Order Match	RISB1285	Aphidius colemani Order: Hymenoptera	Repelling parasitism	4.19%	14.6
Xanthomonas Host Order Match	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	0.01%	13.8
Burkholderia Host Order Match	RISB2149	Osmia bicornis Order: Hymenoptera	may be essential to support Osmia larvae in their nutrient uptake	1.79%	13.1
Bacillus cereus Species-level Match	RISB2237	Anticarsia gemmatalis Order: Lepidoptera	mitigation of the negative effects of proteinase inhibitors produced by the host plant	6.11%	12.8
Lactobacillus Host Order Match	RISB0639	Formica Order: Hymenoptera	exhibited abilities in catabolizing sugars (sucrose, trehalose, melezitose and raffinose) known to be constituents of hemipteran honeydew	0.05%	12.8
Lactobacillus Host Order Match	RISB0529	Apis cerana Order: Hymenoptera	LAB produce organic acids, known as anti-microbial metabolites, inhibiting the growth of spoilage and pathogenic microorganisms	0.05%	12.6
Burkholderia Host Order Match	RISB2101	Formica exsecta Order: Hymenoptera	produce antibiotics	1.79%	12.2
Burkholderia Host Order Match	RISB2580	Tetraponera binghami Order: Hymenoptera	Nitrogen fixation	1.79%	12.1
Lactobacillus Host Order Match	RISB0475	Apis mellifera Order: Hymenoptera	A. kunkeei alleviated acetamiprid-induced symbiotic microbiota dysregulation and mortality in honeybees	0.05%	12.1
Xanthomonas Host Order Match	RISB0217	Xylocopa appendiculata Order: Hymenoptera	strains biodegraded polyethylene terephthalate PET powder, broke it into its degradation products	0.01%	12.0
Acinetobacter Host Order Match	RISB2000	Trichogramma chilonis Order: Hymenoptera	could significantly increase both female count	0.75%	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.	0.93%	10.9
Gilliamella Host Order Match	RISB1945	Apis cerana Order: Hymenoptera	None	0.12%	10.1
Yersinia Host Order Match	RISB0407	Anaphes nitens Order: Hymenoptera	None	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	0.63%	10.0
Escherichia coli Species-level 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	0.63%	8.4
Carnobacterium maltaromaticum Species-level Match	RISB1693	Plutella xylostella Order: Lepidoptera	play an important role in the breakdown of plant cell walls, detoxification of plant phenolics, and synthesis of amino acids.	0.10%	7.6
Klebsiella pneumoniae Species-level Match	RISB2459	Bombyx mori Order: Lepidoptera	degradation of cellulose, xylan, pectin and starch	0.93%	6.9
Carnobacterium maltaromaticum Species-level Match	RISB1692	Plutella xylostella Order: Lepidoptera	participate in the synthesis of host lacking amino acids histidine and threonine	0.10%	6.7
Klebsiella pneumoniae Species-level Match	RISB1994	Diatraea saccharalis Order: Lepidoptera	possess cellulose degrading activity	0.93%	6.7
Salmonella enterica Species-level Match	RISB0413	Melanaphis sacchari Order: Hemiptera	None	1.65%	6.7
Escherichia coli Species-level Match	RISB2120	Galleria mellonella Order: Lepidoptera	mediate trans-generational immune priming	0.63%	6.5
Corynebacterium	RISB0363	Pagiophloeus tsushimanus Order: Coleoptera	terpenoid-degrading: the highest degradation rates of D-camphor, linalool, and eucalyptol	4.19%	6.0
Carnobacterium maltaromaticum Species-level Match	RISB1691	Plutella xylostella Order: Lepidoptera	activity of cellulose and hemicellulose	0.10%	5.9
Corynebacterium	RISB0531	Helicoverpa armigera Order: Lepidoptera	Corynebacterium sp. 2-TD, mediates the toxicity of the 2-tridecanone to H. armigera	4.19%	5.9
Acinetobacter	RISB0140	Nilaparvata lugens Order: Hemiptera	Acinetobacter can effectively degrade cellulose and harmful substances such as polystyrene and phenol.It can help the short-winged BPH to improve its detoxification ability in harsh environments and adapt to environmental changes at any time.	0.75%	5.6
Staphylococcus hominis Species-level Match	RISB1881	Aedes aegypti Order: Diptera	gut microbiome	0.28%	5.6
Staphylococcus hominis Species-level Match	RISB1071	Oryctes rhinoceros Order: Coleoptera	gut microbe	0.28%	5.5
Acinetobacter	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)	0.75%	5.4
Staphylococcus epidermidis Species-level Match	RISB1070	Oryctes rhinoceros Order: Coleoptera	gut microbe	0.13%	5.4
Enterococcus	RISB0728	Cnaphalocrocis medinalis Order: Lepidoptera	The core dominant Enterococcus species possessed complete pathways of 14 carbohydrates metabolism, 11 amino acids biosynthesis, and two vitamins synthesize, implied to contribute an essential role to the nutrition intake and development of C. medinalis	0.08%	5.1
Pantoea	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	0.04%	5.0
Paenibacillus	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.	0.04%	5.0
Lactococcus	RISB0131	Ceratitis capitata Order: Diptera	The intestinal microbiota structure was significantly influenced by the probiotic treatment while still maintaining a stable core dominant community of Enterobacteriacea. The colony with these microbiome had the most improved potential functions in terms of gut microbes as well as the carbohydrates active enzymes most improved potential functions.	0.03%	5.0
Listeria	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.	0.02%	5.0
Streptococcus	RISB2625	Galleria mellonella Order: Lepidoptera	suppress bacteria ingested with food by producing bacteriocin and by releasing a lysozyme like enzyme	2.87%	4.9
Enterococcus	RISB0476	Spodoptera litura Order: Lepidoptera	The ingestion of bacteria negatively affected the development and nutritional physiology of insect. The bacteria after successful establishment started degrading the gut wall and invaded the haemocoel thereby causing the death of the host.	0.08%	4.9
Pantoea	RISB1715	Dolycoris baccarum Order: Hemiptera	The sterilization-produced aposymbiotic nymphs showed high mortality and no insects reached adulthood. In addition, the Pantoea symbiont was uncultivable outside the insect host, indicating an obligate and intimate host-symbiont association	0.04%	4.8
Rahnella	RISB1623	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	0.02%	4.8
Streptococcus	RISB2624	Reticulitermes flavipes Order: Blattodea	can be broken down into substances such as carbon dioxide, ammonia and acetic acid	2.87%	4.5
Lactococcus	RISB2305	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	0.03%	4.3
Pantoea	RISB1671	Spodoptera frugiperda Order: Lepidoptera	modulate plant defense, downregulated the activity of the plant defensive proteins polyphenol oxidase and trypsin proteinase inhibitors (trypsin PI) but upregulated peroxidase (POX) activity in tomatoresponses	0.04%	4.2
Halomonas	RISB1808	Monochamus galloprovincialis Order: Coleoptera	Have the ability for degradation of cellulose, proteins and starch	2.81%	4.1
Streptococcus	RISB2604	Homona magnanima Order: Lepidoptera	influence the growth of Bacillus thuringiensis in the larvae	2.87%	4.1
Enterococcus	RISB2493	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	0.08%	4.1
Lactococcus	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.	0.03%	3.6
Paenibacillus	RISB0774	Delia antiqua Order: Diptera	showed significant contact inhibition activity against fungal entomopathogen Fusarium moniliforme, Botryosphaeria dothidea and both Fusarium oxysporum respectively	0.04%	3.3
Halomonas	RISB1374	Bemisia tabaci Order: Hemiptera	None	2.81%	2.8
Yersinia	RISB0492	Cimex hemipterus Order: Hemiptera	the disruption of the abundant Yersinia possibly could be related to the enhanced susceptibility towards the insecticides	0.04%	2.5
Rahnella	RISB1800	Dendroctonus valens Order: Coleoptera	could alleviate or compromise the antagonistic effects of fungi O. minus and L. procerum on RTB larval growth	0.02%	2.2
Rahnella	RISB0741	Dendroctonus ponderosae Order: Coleoptera	R. aquatilis decreased (−)-α-pinene (38%) and (+)-α-pinene (46%) by 40% and 45% (by GC-MS), respectively	0.02%	2.1
Micrococcus	RISB2276	Ostrinia nubilalis Order: Lepidoptera	extreme cellulolytic enzymes, at extreme (pH 12) conditions, exhibited cellulolytic properties	0.19%	2.1
Rhizobium	RISB0135	Coccinella septempunctata Order: Coleoptera	be commonly found in plant roots and they all have nitrogen fixation abilities	0.32%	1.9
Leuconostoc	RISB0812	Hypothenemus hampei Order: Coleoptera	might contribute to caffeine breakdown using the C-18 oxidation pathway	0.14%	1.6
Vibrio	RISB1810	Monochamus galloprovincialis Order: Coleoptera	Have the ability for degradation of cellulose, proteins and starch	0.13%	1.5
Paenibacillus	RISB0813	Hypothenemus hampei Order: Coleoptera	might contribute to caffeine breakdown using the C-9 oxidation pathway	0.04%	1.4
Actinomyces	RISB1234	Hermetia illucens Order: Diptera	provides the tools for degrading of a broad range of substrates	0.13%	1.4
Neisseria	RISB0512	Plutella xylostella Order: Lepidoptera	None	1.05%	1.1
Aeromonas	RISB2456	Bombyx mori Order: Lepidoptera	able to utilize the CMcellulose and xylan	0.02%	0.8
Nocardioides	RISB1914	Hyles euphorbiae Order: Lepidoptera	able to degrade alkaloids and/or latex	0.04%	0.8
Gordonia	RISB1912	Hyles euphorbiae Order: Lepidoptera	able to degrade alkaloids and/or latex	0.02%	0.8
Mycobacterium	RISB1156	Nicrophorus concolor Order: Coleoptera	produces Antimicrobial compounds	0.07%	0.7
Aeromonas	RISB2086	Aedes aegypti Order: Diptera	axenic larvae cannot develop	0.02%	0.6
Gilliamella	RISB0620	Spodoptera frugiperda Order: Lepidoptera	degrade amygdalin	0.12%	0.5
Aeromonas	RISB1145	Tenebrio molitor Order: Coleoptera	degrading plastics	0.02%	0.4
Brevundimonas	RISB1703	Phlebotomus papatasi Order: Diptera	None	0.12%	0.1
Cupriavidus	RISB0694	Alydus tomentosus Order: Hemiptera	None	0.06%	0.1