Spark-Tech Diagnostyka

Taxonomy Report SPARKbiom

Report example - Sample analysis using 3rd generation NGS DNA sequencing

Microbiological Report of Sample Analysis
Using DNA Sequencing by NGS III Generation Method

Type of Analysis:	SPK_H-KAL-ENG
Test Number:	89hDyynfS
Test Name:	SPARKbiom
Full name and national ID number (PESEL):	$O$ENTITY$O$
Material type and sample number:	Stool / $O$ORDER_NUMBER$O$
Order name and code:	Spark-Tech / 26_05_22_EB_B27_B0610
Date and time of kit receipt:	$O$ORDER_KITRECIEVED$O$
Referring physician:	Requested by the patient

Section 1: Summary of the Analysis

Dysbiosis Index

The gut microbiome dysbiosis index is an indicator that assesses the state of bacterial balance in the intestines based on the analysis of various microbiological and biochemical parameters. The scale of this index ranges from 0 to 12, where a value of 12 indicates an optimal state of the microbiome, characterized by a healthy and balanced bacterial flora. Lower index values signal gradual disturbances in the composition of the microbiome, which can lead to dysbiosis and related health problems.

276 organisms were identified at the Species level.
This includes 8 eukaryotic organisms.

List of Pathogens and Conditionally Pathogenic Organisms

Typ	Nazwa	NCBI ID	Poziom	Organizmy
Gram-positive bacteria (possible pathogenicity)	Streptococcus	1301	Medium	S. sp. Marseille-Q3604, S. sp., S. parasanguinis, S. vestibularis, S. koreensis, S. sp. VBH1, S. genomosp. C6, S. sp. oral clone FN042
Gram-positive bacteria (possible pathogenicity)	Clostridium	1485	Low	C. saudiense, C. fessum, C. sp., C. sp. ES1, C. sp. Marseille-Q5894, C. sp. Marseille-P2415, C. sp. ACB-29, C. mucosae
Gram-negative bacteria (possible pathogenicity)	Yersinia	629	Medium	Y. enterocolitica, Y. sp. (in: enterobacteria), Y. canariae, Y. hibernica, Y. frederiksenii
Gram-negative bacteria (possible pathogenicity)	Citrobacter	544	Low	C. koseri, C. sp. WZH-F19, C. gillenii
Gram-negative bacteria (possible pathogenicity)	Escherichia	561	Medium	E. sp. UIWRF0625, E. sp., E. albertii, E. marmotae, E. sp. XJ148-1212-2NFX1, E. sp. UIWRF0478, E. sp. MLS, E. sp. CR1, E. sp. UIWRF0206, E. sp. 102C.3, E. sp. UIWRF0784, E. sp. UIWRF0246, E. sp. UIWRF1149, E. sp. M1N2G03, E. sp. UIWRF0882, E. sp. GDR06, E. sp. UIWRF0681, E. sp. 2011SOCPBJ1, E. sp. UIWRF0892
Gram-negative bacteria (possible pathogenicity)	Klebsiella	570	Low	K. sp. mixed culture J2-8, K. pneumoniae
Gram-negative bacteria (possible pathogenicity)	Haemophilus	724	Low	H. parainfluenzae, H. sp. HGH0209
Absolute bacterial pathogens	Shigella	620	Medium	S. flexneri, S. boydii, S. sonnei, S. sp., S. sp. 86.4, S. dysenteriae, S. sp. p-11, S. sp. DBC-1, S. sp. 4104
Absolute bacterial pathogens	Salmonella	590	Medium	S. sp., S. enterica, S. sp. WZH-F17
Fungi from the phylum Ascomycota (possible pathogenicity)	Candida	5475	Medium	C. albicans

Bionome Indices and Indicators

Shannon Index: Measure of Biological Diversity

The Shannon index is used to assess biological diversity in a microbiome sample. Values of the index ranging from 2.5 to 4.5 (at the species level) and from 1.5 to 3.5 (at the genus level) are considered indicative of good diversity. Lower values may signal diversity issues that could potentially impact health, while higher values, although generally beneficial, might also indicate problems in certain clinical situations. Interpretation of the results should be tailored to the individual clinical context of the patient.

Dysbiosis Index - Bacillota (Firmicutes) [NCBI ID: 1239]/Bacteroidota (Bacteroidetes) [NCBI ID: 976]:

Dysbiosis Index - Actinomycetota (Actinobacteria) [NCBI ID: 201174]/Pseudomonadota (Proteobacteria) [NCBI ID: 1224]

Dysbiosis Index - Prevotella [NCBI ID: 838]/Bacteroides [NCBI ID: 816]

Summary

LABORATORY:
SPARK-TECH DIAGNOSTYKA
Ul. Lelewela 14/1-2
31-108
Kraków/POLAND
Tel. 572260126/12-3110032

LABORATORY MANAGER:
Dr. med., M.Sc. Biol.
Mateusz Adamski
Specialist in Neurology

Recommendations:

Proper interpretation of the result and additional recommendations are only possible in conjunction with a thorough clinical assessment of the patient and a careful analysis of the medical history. A medical consultation may be necessary. If you are interested in the aforementioned services, please contact our team to complete the MEDICAL HISTORY questionnaire and receive further interpretation of the results and recommendations regarding diet, supplementation, lifestyle, probiotic therapy, and/or specialist medical consultations. Additional information is available on the website sparkbiom.com .

Result approved by:
M.Sc. Katarzyna Pietruś Laboratory Diagnostician No. 17797

Section 2: Characteristics of the Microbiome: Comprehensive Organism Analysis

Identified 90 organisms at the Genus level	Identified 276 organisms at the Species level
Distribution of organisms by Genus	Distribution of organisms by Species

Microbiome Analysis

Section 1 presents a comprehensive view of the microbiome, encompassing all groups of microorganisms such as bacteria, fungi, protozoa, and other microbes. The identified organisms are presented at two classification levels: genus and species, allowing for an in-depth analysis of their diversity.

Graphical Analysis: Pie Charts
Pie charts show the percentage representation of different genera or species of microorganisms in the analyzed microbiome. This facilitates the identification of dominant microbes and the assessment of their diversity. The "others" category includes organisms that individually constitute less than 1% of the sample.
Difference between Genus and Species:
Genus and species are terms referring to different levels of biological classification, with genus being a higher category than species. Genus-level analysis provides a general overview of microbiome diversity, while species-level analysis offers more detailed information. It is worth noting that the number of organisms identified at the species level is usually greater than at the genus level.

Description of the Most Common Organisms at the Species Level

#	Nazwa	NCBI ID	Opis
1	Escherichia coli	562	Escherichia coli, also known as E. coli, is a bacterium commonly found in the intestines of humans and animals. Most strains are harmless and aid in digestion and the synthesis of vitamins K and B. However, some strains can cause serious infections and illnesses.
2	Blautia wexlerae	418240	Blautia wexlerae is a fermentative bacterium residing in the human digestive system, contributing to gut health by producing fatty acids. It participates in metabolic transformations and is associated with positive health effects, with studies suggesting a role in weight regulation and inflammation prevention.
3	Faecalibacterium prausnitzii	853	Faecalibacterium prausnitzii is an important commensal bacterium residing in the human gut. It plays a key role in maintaining gut health by producing short-chain fatty acids. It is considered a marker of good gastrointestinal health.
4	[Eubacterium] rectale	39491	[Eubacterium] rectale is one of the main butyrate-producing bacteria in the human colon. It plays a crucial role in maintaining the intestinal barrier's health and regulating the inflammatory process. It is part of the healthy gut flora, influencing immune system function.
5	Phocaeicola vulgatus	821	Phocaeicola vulgatus is a bacterium that belongs to the human gut microbiota, previously classified as Bacteroides vulgatus. Known for its ability to break down complex carbohydrates, it plays a vital role in maintaining microbial balance in the gut.
6	Faecalibacterium sp.	1971605	Faecalibacterium sp. refers to unprecisely identified strains of the genus Faecalibacterium. These bacteria are positively regarded for their health-promoting effects in the gut microbiome. They exhibit anti-inflammatory properties and support gut health.
7	Ruminococcus bromii	40518	Ruminococcus bromii is a key bacterial species in the human gut, specializing in the breakdown of resistant starch. Its activity contributes to the production of short-chain fatty acids, important for gut health. It is considered a significant player in maintaining metabolic health.
8	Blautia sp.	1955243	Blautia sp. refers to a group of bacteria that are important components of a healthy human gut microbiota. These bacteria help produce lactic acid and other beneficial compounds. They are responsible for maintaining microbial balance and may protect against diseases.
9	Faecalibacterium duncaniae	411483	Faecalibacterium duncaniae is a newly discovered strain of the Faecalibacterium genus, known for its beneficial impact on gut health. It has anti-inflammatory properties and helps maintain a healthy gut microbiota. Its presence is seen as an indicator of good gastrointestinal health.
10	Faecalibacterium sp. Marseille-Q4164	2817020	Faecalibacterium sp. Marseille-Q4164 is a recently discovered bacterial strain from the Faecalibacterium genus. It is characterized by its health-promoting potential, particularly its anti-inflammatory properties. Its impact on gut diseases and therapeutic possibilities are being studied.
11	Roseburia faecis	301302	Roseburia faecis is an important bacterial species found in the human intestines, belonging to the Lachnospiraceae family. It plays a crucial role in producing butyric acid, one of the main energy sources for intestinal epithelial cells. Its potential impact on gut health, including protection against certain diseases and inflammation, is being studied.
12	Hafnia alvei	569	Hafnia alvei is a gram-negative bacterium from the family Enterobacteriaceae, often isolated from various environments, including food products and the human gastrointestinal tract. Considered an opportunistic pathogen, it can contribute to infections in immunocompromised individuals. Research on H. alvei focuses on its probiotic properties and potential applications in the food industry and medicine.
13	Roseburia inulinivorans	360807	Roseburia inulinivorans is a fiber-fermenting bacterium that processes inulin into butyric acid, beneficial for gut health. It is a significant component of healthy gut flora, supporting the intestinal barrier function and modulating immune response. Its presence is associated with better gastrointestinal health.
14	Obesumbacterium proteus	82983	Obesumbacterium proteus is a bacterium known for its ability to ferment sugars, making it important in the brewing industry. It is known for inducing certain off-flavors in beer and is intensely studied to prevent its negative impacts on fermentation processes. This species was described based on genetic and biochemical studies, revealing its metabolic and adaptive diversity.
15	Anthropogastromicrobium aceti	2981768	Anthropogastromicrobium aceti is a recently discovered bacterium that contributes to vinegar fermentation. It may be present in various fermentative environments, including the human digestive tract. Research on its health impact is in the early stages.
16	Saccharomyces cerevisiae	4932	Saccharomyces cerevisiae, also known as baker's yeast, is widely used in baking, brewing, and winemaking for fermentation. These single-celled fungi are among the most well-studied microorganisms in the world. Due to their fermentative properties, S. cerevisiae is crucial in food and beverage production.

Section 3: Composition of the Gut Microbiome - Types and Families

Phylum (Type)

Name	NCBI ID	Level	Reference Range (%)		Value
Bacillota	1239	Normal	49.7	60.68	57.48
Bacteroidota	976	Low	27.56	37.72	8.39
Actinomycetota	201174	Low	2.01	10.27	1.02
Pseudomonadota	1224	High	0.93	3.43	31.54

Family

Name	NCBI ID	Level	Reference Range (%)		Value
Bacteroidaceae	815	Low	20.17	32.59	6.82
Lachnospiraceae	186803	High	15.78	28.49	31.08
Oscillospiraceae	216572	Normal	16.61	27.23	23.75
Bifidobacteriaceae	31953	Normal	0.42	5.62	0.56
Rikenellaceae	171550	Low	0.49	3.55	0.2
Coriobacteriaceae	84107	Low	0.29	3.4	0.06
Enterobacteriaceae	543	High	0.24	2.3	27.21
Tannerellaceae	2005525	Normal	0.45	2.17	0.96
Lactobacillaceae	33958	Normal	0.04	1.74	0.31
Clostridiaceae	31979	Low	0.53	1.62	0.43
Veillonellaceae	31977	Normal	0.05	1.24	0.17
Barnesiellaceae	2005519	Normal	0.14	1.21	0.47

Class

Name	NCBI ID	Level	Reference Range (%)		Value
Clostridia	186801	Normal	45.48	59.1	55.97
Bacteroidia	200643	Low	27.56	37.72	8.39
Actinomycetes	1760	Low	0.9	5.67	0.86
Coriobacteriia	84998	Low	0.66	4.12	0.16
Gammaproteobacteria	1236	High	0.24	2.35	31.49
Bacilli	91061	Normal	0.21	2.19	1.25
Negativicutes	909932	Low	0.52	1.46	0.17

Order

Name	NCBI ID	Level	Reference Range (%)		Value
Bacteroidales	171549	Low	27.56	37.72	8.39
Eubacteriales	186802	High	24.49	34.92	55.97
Lachnospirales	3085636	Low	16.05	28.79	0
Bifidobacteriales	85004	Normal	0.42	5.62	0.56
Coriobacteriales	84999	Low	0.31	3.54	0.06
Enterobacterales	91347	High	0.26	2.3	31.28
Lactobacillales	186826	Normal	0.18	2.18	1.25
Veillonellales	1843489	Normal	0.05	1.24	0.17

Genus

Name	NCBI ID	Level	Reference Range (%)		Value
Bacteroides	816	Low	8.15	17.2	1.49
Phocaeicola	909656	Low	7.35	16.31	5.94
Faecalibacterium	216851	High	5.29	15.14	19.78
Blautia	572511	High	4.66	13.27	15.2
Ruminococcus	1263	Normal	2.1	6.91	5.47
Bifidobacterium	1678	Normal	0.42	5.62	0.62
Collinsella	102106	Low	0.36	3.38	0.07
Alistipes	239759	Low	0.47	3.25	0.22
Gemmiger	204475	Low	0.4	2.76	0.22
Roseburia	841	High	0.41	2.42	5.17
Vescimonas	2892396	Low	0.06	2.39	0
Parabacteroides	375288	Normal	0.45	2.17	1.04
Anaerostipes	207244	Low	0.74	1.93	0.41
Escherichia	561	High	0.16	1.78	26.23
Agathobacter	1766253	Low	0.06	1.78	0
Lachnospira	28050	Normal	0.31	1.64	0.61
Clostridium	1485	Low	0.51	1.53	0.46
Dialister	39948	Normal	0.12	1.27	0.16
Dorea	189330	Low	0.4	1.09	0
Barnesiella	397864	Normal	0.16	1.05	0.51

Section 4: Identification and Quantitative Analysis of Pathogenic and Potentially Pathogenic Organisms

Gram-positive bacteria (possible pathogenicity)

Name	NCBI ID	Level	Found Organisms
Staphylococcus	1279	None
Corynebacterium	1716	None
Bacillus cereus group	86661	None
Streptococcus	1301	Medium	S. sp. Marseille-Q3604, S. sp., S. parasanguinis, S. vestibularis, S. koreensis, S. sp. VBH1, S. genomosp. C6, S. sp. oral clone FN042
Clostridium	1485	Low	C. saudiense, C. fessum, C. sp., C. sp. ES1, C. sp. Marseille-Q5894, C. sp. Marseille-P2415, C. sp. ACB-29, C. mucosae

Gram-negative bacteria (possible pathogenicity)

Name	NCBI ID	Level	Found Organisms
Helicobacter	209	None
Borrelia	138	None
Yersinia	629	Medium	Y. enterocolitica, Y. sp. (in: enterobacteria), Y. canariae, Y. hibernica, Y. frederiksenii
Legionella	445	None
Rickettsia	780	None
Vibrio	662	None
Anaplasma	768	None
Listeria	1637	None
Pseudomonas	286	None
Acinetobacter	469	None
Neisseria	482	None
Bordetella	517	None
Citrobacter	544	Low	C. koseri, C. sp. WZH-F19, C. gillenii
Escherichia	561	Medium	E. sp. UIWRF0625, E. sp., E. albertii, E. marmotae, E. sp. XJ148-1212-2NFX1, E. sp. UIWRF0478, E. sp. MLS, E. sp. CR1, E. sp. UIWRF0206, E. sp. 102C.3, E. sp. UIWRF0784, E. sp. UIWRF0246, E. sp. UIWRF1149, E. sp. M1N2G03, E. sp. UIWRF0882, E. sp. GDR06, E. sp. UIWRF0681, E. sp. 2011SOCPBJ1, E. sp. UIWRF0892
Klebsiella	570	Low	K. sp. mixed culture J2-8, K. pneumoniae
Morganella	581	None
Proteus	583	None
Providencia	586	None
Serratia	613	None
Aeromonas	642	None
Plesiomonas	702	None
Haemophilus	724	Low	H. parainfluenzae, H. sp. HGH0209
Porphyromonas	836	None

Absolute bacterial pathogens

Name	NCBI ID	Level	Found Organisms
Brucella	234	None
Yersinia pestis	632	None
Burkholderia mallei	13373	None
Clostridium perfringens	1502	None
Legionella pneumophila	446	None
Coxiella burnetii	777	None
Bacillus anthracis	1392	None
Chlamydia trachomatis	813	None
Shigella	620	Medium	S. flexneri, S. boydii, S. sonnei, S. sp., S. sp. 86.4, S. dysenteriae, S. sp. p-11, S. sp. DBC-1, S. sp. 4104
Mycobacterium tuberculosis	1773	None
Campylobacter	194	None
Bordetella pertussis	520	None
Leptospira	171	None
Neisseria gonorrhoeae	485	None
Salmonella	590	Medium	S. sp., S. enterica, S. sp. WZH-F17
Francisella tularensis	263	None

Absolute eukaryotic pathogens

Name	NCBI ID	Level
Echinococcus granulosus	6210	None
Echinococcus multilocularis	6211	None
Taenia solium	6204	None
Giardia intestinalis	5741	None
Cryptosporidium	5806	None
Plasmodium	5820	None

Fungi from the phylum Ascomycota (possible pathogenicity)

Name	NCBI ID	Level	Found Organisms
Aspergillus	5052	None
Talaromyces	5094	None
Penicillium	5073	None
Paecilomyces	33202	None
Fusarium	5506	None
Trichophyton	5550	None
Microsporum	34392	None
Nannizzia	1915381	None
Epidermophyton	34390	None
Histoplasma	5036	None
Blastomyces	229219	None
Coccidioides	5500	None
Paracoccidioides	38946	None
Sporothrix	29907	None
Pneumocystis	4753	None
Candida	5475	Medium	C. albicans
Nakaseomyces	374468	None
Pichia	4919	None
Clavispora	36910	None
Macrorhabdus	349298	None
Geotrichum	43987	None
Debaryomyces	4958	None

Fungi from the phylum Basidiomycota (possible pathogenicity)

Name	NCBI ID	Level
Schizophyllum commune	5334	None
Malassezia	55193	None
Rhodotorula	5533	None
Cryptococcus	5206	None
Trichosporon	5552	None

Fungi from the phylum Mucoromycota (possible pathogenicity)

Name	NCBI ID	Level
Rhizopus	4842	None
Lichtheimia	688353	None
Mucor	4830	None

Single-celled pathogens (Protists) - Algae and related organisms

Name	NCBI ID	Level
Pentatrichomonas	5727	None
Trichomonas	5721	None
Dientamoeba	43351	None
Histomonas	135587	None
Babesia	5864	None
Theileria	5873	None

Single-celled pathogens (Protists) - Various protist pathogens

Name	NCBI ID	Level
Leishmania	5658	None
Chilomastix	450634	None
Giardia	5740	None
Endolimax	110787	None
Entamoeba	5758	None
Blastocystis	12967	None
Balantioides	2038102	None

Special bacterial pathogens (possible pathogenicity)

Name	NCBI ID	Level
Francisella	262	None
Bartonella	773	None
Mycobacterium	1763	None
Coxiella	776	None
Treponema	157	None
Mycoplasmoides	2995234	None
Ureaplasma	2129	None
Chlamydia	810	None

Section 5: Species List

Bacteria

Name	Count	Percentage	Match %	Taxonomy
Escherichia coli	4968	23.1	99.43	Superkingdom: Bacteria Phylum: Pseudomonadota Class: Gammaproteobacteria Order: Enterobacterales Family: Enterobacteriaceae Genus: Escherichia Species: Escherichia coli
Blautia wexlerae	2129	9.9	98.51	Superkingdom: Bacteria Phylum: Bacillota Class: Clostridia Order: Eubacteriales Family: Lachnospiraceae Genus: Blautia Species: Blautia wexlerae
Faecalibacterium prausnitzii	1780	8.3	98.7	Superkingdom: Bacteria Phylum: Bacillota Class: Clostridia Order: Eubacteriales Family: Oscillospiraceae Genus: Faecalibacterium Species: Faecalibacterium prausnitzii
[Eubacterium] rectale	1525	7.1	98.4	Superkingdom: Bacteria Phylum: Bacillota Class: Clostridia Order: Eubacteriales Family: Lachnospiraceae Species: [Eubacterium] rectale
Phocaeicola vulgatus	1177	5.5	99.19	Superkingdom: Bacteria Phylum: Bacteroidota Class: Bacteroidia Order: Bacteroidales Family: Bacteroidaceae Genus: Phocaeicola Species: Phocaeicola vulgatus
Faecalibacterium sp.	1157	5.4	98.81	Superkingdom: Bacteria Phylum: Bacillota Class: Clostridia Order: Eubacteriales Family: Oscillospiraceae Genus: Faecalibacterium Species: Faecalibacterium sp.
Ruminococcus bromii	1044	4.8	98.88	Superkingdom: Bacteria Phylum: Bacillota Class: Clostridia Order: Eubacteriales Family: Oscillospiraceae Genus: Ruminococcus Species: Ruminococcus bromii
Blautia sp.	566	2.6	97.75	Superkingdom: Bacteria Phylum: Bacillota Class: Clostridia Order: Eubacteriales Family: Lachnospiraceae Genus: Blautia Species: Blautia sp.
Faecalibacterium duncaniae	487	2.3	98.97	Superkingdom: Bacteria Phylum: Bacillota Class: Clostridia Order: Eubacteriales Family: Oscillospiraceae Genus: Faecalibacterium Species: Faecalibacterium duncaniae
Faecalibacterium sp. Marseille-Q4164	459	2.1	99.1	Superkingdom: Bacteria Phylum: Bacillota Class: Clostridia Order: Eubacteriales Family: Oscillospiraceae Genus: Faecalibacterium Species: Faecalibacterium sp. Marseille-Q4164
Roseburia faecis	455	2.1	98.33	Superkingdom: Bacteria Phylum: Bacillota Class: Clostridia Order: Eubacteriales Family: Lachnospiraceae Genus: Roseburia Species: Roseburia faecis
Hafnia alvei	423	2.0	98.75	Superkingdom: Bacteria Phylum: Pseudomonadota Class: Gammaproteobacteria Order: Enterobacterales Family: Hafniaceae Genus: Hafnia Species: Hafnia alvei
Roseburia inulinivorans	331	1.5	98.08	Superkingdom: Bacteria Phylum: Bacillota Class: Clostridia Order: Eubacteriales Family: Lachnospiraceae Genus: Roseburia Species: Roseburia inulinivorans
Obesumbacterium proteus	268	1.2	99.2	Superkingdom: Bacteria Phylum: Pseudomonadota Class: Gammaproteobacteria Order: Enterobacterales Family: Hafniaceae Genus: Obesumbacterium Species: Obesumbacterium proteus
Anthropogastromicrobium aceti	256	1.2	98.08	Superkingdom: Bacteria Phylum: Bacillota Class: Clostridia Order: Eubacteriales Family: Lachnospiraceae Genus: Anthropogastromicrobium Species: Anthropogastromicrobium aceti
Fusicatenibacter saccharivorans	213	1.0	98.44	Superkingdom: Bacteria Phylum: Bacillota Class: Clostridia Order: Eubacteriales Family: Lachnospiraceae Genus: Fusicatenibacter Species: Fusicatenibacter saccharivorans
Salmonella sp.	196	0.9	97.85	Superkingdom: Bacteria Phylum: Pseudomonadota Class: Gammaproteobacteria Order: Enterobacterales Family: Enterobacteriaceae Genus: Salmonella Species: Salmonella sp.
Roseburia intestinalis	192	0.9	98.28	Superkingdom: Bacteria Phylum: Bacillota Class: Clostridia Order: Eubacteriales Family: Lachnospiraceae Genus: Roseburia Species: Roseburia intestinalis
Blautia obeum	147	0.7	98.05	Superkingdom: Bacteria Phylum: Bacillota Class: Clostridia Order: Eubacteriales Family: Lachnospiraceae Genus: Blautia Species: Blautia obeum
Hafnia sp.	142	0.7	99.11	Superkingdom: Bacteria Phylum: Pseudomonadota Class: Gammaproteobacteria Order: Enterobacterales Family: Hafniaceae Genus: Hafnia Species: Hafnia sp.
Salmonella enterica	137	0.6	98.69	Superkingdom: Bacteria Phylum: Pseudomonadota Class: Gammaproteobacteria Order: Enterobacterales Family: Enterobacteriaceae Genus: Salmonella Species: Salmonella enterica Subspecies: Salmonella enterica subsp. enterica
Lachnospiraceae bacterium	137	0.6	97.81	Superkingdom: Bacteria Phylum: Bacillota Class: Clostridia Order: Eubacteriales Family: Lachnospiraceae Species: Lachnospiraceae bacterium
Blautia faecis	122	0.6	98.11	Superkingdom: Bacteria Phylum: Bacillota Class: Clostridia Order: Eubacteriales Family: Lachnospiraceae Genus: Blautia Species: Blautia faecis
Lachnospiraceae bacterium MC_36	113	0.5	97.99	Superkingdom: Bacteria Phylum: Bacillota Class: Clostridia Order: Eubacteriales Family: Lachnospiraceae Species: Lachnospiraceae bacterium MC_36
Parabacteroides sp.	106	0.5	98.91	Superkingdom: Bacteria Phylum: Bacteroidota Class: Bacteroidia Order: Bacteroidales Family: Tannerellaceae Genus: Parabacteroides Species: Parabacteroides sp.
Barnesiella sp.	102	0.5	98.56	Superkingdom: Bacteria Phylum: Bacteroidota Class: Bacteroidia Order: Bacteroidales Family: Barnesiellaceae Genus: Barnesiella Species: Barnesiella sp.
Lachnospira eligens	99	0.5	98.09	Superkingdom: Bacteria Phylum: Bacillota Class: Clostridia Order: Eubacteriales Family: Lachnospiraceae Genus: Lachnospira Species: Lachnospira eligens
Escherichia fergusonii	93	0.4	99.0	Superkingdom: Bacteria Phylum: Pseudomonadota Class: Gammaproteobacteria Order: Enterobacterales Family: Enterobacteriaceae Genus: Escherichia Species: Escherichia fergusonii
Streptococcus sp. Marseille-Q3604	91	0.4	99.23	Superkingdom: Bacteria Phylum: Bacillota Class: Bacilli Order: Lactobacillales Family: Streptococcaceae Genus: Streptococcus Species: Streptococcus sp. Marseille-Q3604
Bacteroides caccae	89	0.4	98.43	Superkingdom: Bacteria Phylum: Bacteroidota Class: Bacteroidia Order: Bacteroidales Family: Bacteroidaceae Genus: Bacteroides Species: Bacteroides caccae
Parabacteroides distasonis	82	0.4	98.68	Superkingdom: Bacteria Phylum: Bacteroidota Class: Bacteroidia Order: Bacteroidales Family: Tannerellaceae Genus: Parabacteroides Species: Parabacteroides distasonis
Eubacteriales bacterium	81	0.4	97.94	Superkingdom: Bacteria Phylum: Bacillota Class: Clostridia Order: Eubacteriales Species: Eubacteriales bacterium
Anaerostipes hadrus	80	0.4	98.17	Superkingdom: Bacteria Phylum: Bacillota Class: Clostridia Order: Eubacteriales Family: Lachnospiraceae Genus: Anaerostipes Species: Anaerostipes hadrus
Klebsiella sp. mixed culture J2-8	76	0.4	98.01	Superkingdom: Bacteria Phylum: Pseudomonadota Class: Gammaproteobacteria Order: Enterobacterales Family: Enterobacteriaceae Genus: Klebsiella Species: Klebsiella sp. mixed culture J2-8
Agathobaculum butyriciproducens	70	0.3	98.62	Superkingdom: Bacteria Phylum: Bacillota Class: Clostridia Order: Eubacteriales Family: Oscillospiraceae Genus: Agathobaculum Species: Agathobaculum butyriciproducens
Gallintestinimicrobium propionicum	68	0.3	98.08	Superkingdom: Bacteria Phylum: Bacillota Class: Clostridia Order: Eubacteriales Family: Lachnospiraceae Genus: Gallintestinimicrobium Species: Gallintestinimicrobium propionicum
Lactobacillus rogosae	67	0.3	98.17	Superkingdom: Bacteria Phylum: Bacillota Class: Bacilli Order: Lactobacillales Family: Lactobacillaceae Genus: Lactobacillus Species: Lactobacillus rogosae
Clostridiales bacterium L2-14	67	0.3	98.86	Superkingdom: Bacteria Phylum: Bacillota Class: Clostridia Order: Eubacteriales Species: Clostridiales bacterium L2-14
Shigella flexneri	66	0.3	98.38	Superkingdom: Bacteria Phylum: Pseudomonadota Class: Gammaproteobacteria Order: Enterobacterales Family: Enterobacteriaceae Genus: Shigella Species: Shigella flexneri
Shigella boydii	63	0.3	97.56	Superkingdom: Bacteria Phylum: Pseudomonadota Class: Gammaproteobacteria Order: Enterobacterales Family: Enterobacteriaceae Genus: Shigella Species: Shigella boydii
Yersinia enterocolitica	63	0.3	99.08	Superkingdom: Bacteria Phylum: Pseudomonadota Class: Gammaproteobacteria Order: Enterobacterales Family: Yersiniaceae Genus: Yersinia Species: Yersinia enterocolitica
Bacteroides uniformis	61	0.3	98.66	Superkingdom: Bacteria Phylum: Bacteroidota Class: Bacteroidia Order: Bacteroidales Family: Bacteroidaceae Genus: Bacteroides Species: Bacteroides uniformis
Anaerobutyricum hallii	60	0.3	98.48	Superkingdom: Bacteria Phylum: Bacillota Class: Clostridia Order: Eubacteriales Family: Lachnospiraceae Genus: Anaerobutyricum Species: Anaerobutyricum hallii
Shigella sonnei	60	0.3	99.73	Superkingdom: Bacteria Phylum: Pseudomonadota Class: Gammaproteobacteria Order: Enterobacterales Family: Enterobacteriaceae Genus: Shigella Species: Shigella sonnei
Streptomyces sp. Q1	57	0.3	96.61	Superkingdom: Bacteria Phylum: Actinomycetota Class: Actinomycetes Order: Kitasatosporales Family: Streptomycetaceae Genus: Streptomyces Species: Streptomyces sp. Q1
Bacteroides xylanisolvens	55	0.3	98.71	Superkingdom: Bacteria Phylum: Bacteroidota Class: Bacteroidia Order: Bacteroidales Family: Bacteroidaceae Genus: Bacteroides Species: Bacteroides xylanisolvens
Oscillospiraceae bacterium	44	0.2	97.21	Superkingdom: Bacteria Phylum: Bacillota Class: Clostridia Order: Eubacteriales Family: Oscillospiraceae Species: Oscillospiraceae bacterium
Haemophilus parainfluenzae	44	0.2	98.49	Superkingdom: Bacteria Phylum: Pseudomonadota Class: Gammaproteobacteria Order: Pasteurellales Family: Pasteurellaceae Genus: Haemophilus Species: Haemophilus parainfluenzae
Gemmiger formicilis	44	0.2	98.6	Superkingdom: Bacteria Phylum: Bacillota Class: Clostridia Order: Eubacteriales Genus: Gemmiger Species: Gemmiger formicilis
Roseburia sp. 1120	42	0.2	97.76	Superkingdom: Bacteria Phylum: Bacillota Class: Clostridia Order: Eubacteriales Family: Lachnospiraceae Genus: Roseburia Species: Roseburia sp. 1120
Bacteroides fragilis	40	0.2	98.99	Superkingdom: Bacteria Phylum: Bacteroidota Class: Bacteroidia Order: Bacteroidales Family: Bacteroidaceae Genus: Bacteroides Species: Bacteroides fragilis
Clostridium saudiense	35	0.2	98.94	Superkingdom: Bacteria Phylum: Bacillota Class: Clostridia Order: Eubacteriales Family: Clostridiaceae Genus: Clostridium Species: Clostridium saudiense
Faecalibacterium sp. Marseille-P9312	34	0.2	98.86	Superkingdom: Bacteria Phylum: Bacillota Class: Clostridia Order: Eubacteriales Family: Oscillospiraceae Genus: Faecalibacterium Species: Faecalibacterium sp. Marseille-P9312
Clostridium fessum	34	0.2	98.35	Superkingdom: Bacteria Phylum: Bacillota Class: Clostridia Order: Eubacteriales Family: Clostridiaceae Genus: Clostridium Species: Clostridium fessum
Streptococcus sp.	33	0.2	98.83	Superkingdom: Bacteria Phylum: Bacillota Class: Bacilli Order: Lactobacillales Family: Streptococcaceae Genus: Streptococcus Species: Streptococcus sp.
Yersinia sp. (in: enterobacteria)	32	0.1	98.7	Superkingdom: Bacteria Phylum: Pseudomonadota Class: Gammaproteobacteria Order: Enterobacterales Family: Yersiniaceae Genus: Yersinia Species: Yersinia sp. (in: enterobacteria)
Streptococcus parasanguinis	32	0.1	98.78	Superkingdom: Bacteria Phylum: Bacillota Class: Bacilli Order: Lactobacillales Family: Streptococcaceae Genus: Streptococcus Species: Streptococcus parasanguinis
Escherichia sp. UIWRF0625	28	0.1	99.58	Superkingdom: Bacteria Phylum: Pseudomonadota Class: Gammaproteobacteria Order: Enterobacterales Family: Enterobacteriaceae Genus: Escherichia Species: Escherichia sp. UIWRF0625
Romboutsia timonensis	27	0.1	98.59	Superkingdom: Bacteria Phylum: Bacillota Class: Clostridia Order: Eubacteriales Family: Peptostreptococcaceae Genus: Romboutsia Species: Romboutsia timonensis
Bifidobacterium faecale	27	0.1	98.83	Superkingdom: Bacteria Phylum: Actinomycetota Class: Actinomycetes Order: Bifidobacteriales Family: Bifidobacteriaceae Genus: Bifidobacterium Species: Bifidobacterium faecale
Bifidobacterium sp.	25	0.1	98.46	Superkingdom: Bacteria Phylum: Actinomycetota Class: Actinomycetes Order: Bifidobacteriales Family: Bifidobacteriaceae Genus: Bifidobacterium Species: Bifidobacterium sp.
Dialister invisus	25	0.1	98.28	Superkingdom: Bacteria Phylum: Bacillota Class: Negativicutes Order: Veillonellales Family: Veillonellaceae Genus: Dialister Species: Dialister invisus
Bifidobacterium pseudocatenulatum	25	0.1	98.68	Superkingdom: Bacteria Phylum: Actinomycetota Class: Actinomycetes Order: Bifidobacteriales Family: Bifidobacteriaceae Genus: Bifidobacterium Species: Bifidobacterium pseudocatenulatum
Blautia sp. Marseille-P2398	24	0.1	96.47	Superkingdom: Bacteria Phylum: Bacillota Class: Clostridia Order: Eubacteriales Family: Lachnospiraceae Genus: Blautia Species: Blautia sp. Marseille-P2398
Alistipes sp. RMA 9912	22	0.1	99.27	Superkingdom: Bacteria Phylum: Bacteroidota Class: Bacteroidia Order: Bacteroidales Family: Rikenellaceae Genus: Alistipes Species: Alistipes sp. RMA 9912
Eubacteriaceae bacterium DJF_CR57k1	22	0.1	96.46	Superkingdom: Bacteria Phylum: Bacillota Class: Clostridia Order: Eubacteriales Family: Eubacteriaceae Species: Eubacteriaceae bacterium DJF_CR57k1
Lachnospira pectinoschiza	21	0.1	97.44	Superkingdom: Bacteria Phylum: Bacillota Class: Clostridia Order: Eubacteriales Family: Lachnospiraceae Genus: Lachnospira Species: Lachnospira pectinoschiza
Sellimonas sp.	20	0.1	98.16	Superkingdom: Bacteria Phylum: Bacillota Class: Clostridia Order: Eubacteriales Family: Lachnospiraceae Genus: Sellimonas Species: Sellimonas sp.
Bifidobacterium longum	20	0.1	99.12	Superkingdom: Bacteria Phylum: Actinomycetota Class: Actinomycetes Order: Bifidobacteriales Family: Bifidobacteriaceae Genus: Bifidobacterium Species: Bifidobacterium longum Subspecies: Bifidobacterium longum subsp. longum
Escherichia sp.	20	0.1	97.81	Superkingdom: Bacteria Phylum: Pseudomonadota Class: Gammaproteobacteria Order: Enterobacterales Family: Enterobacteriaceae Genus: Escherichia Species: Escherichia sp.
Ruminococcus sp. K-1	19	0.1	96.58	Superkingdom: Bacteria Phylum: Bacillota Class: Clostridia Order: Eubacteriales Family: Oscillospiraceae Genus: Ruminococcus Species: Ruminococcus sp. K-1
bacterium enrichment culture clone NBAR007	19	0.1	96.18	Superkingdom: Bacteria Species: bacterium enrichment culture clone NBAR007
Escherichia albertii	18	0.1	97.83	Superkingdom: Bacteria Phylum: Pseudomonadota Class: Gammaproteobacteria Order: Enterobacterales Family: Enterobacteriaceae Genus: Escherichia Species: Escherichia albertii
Bacteroides clarus	18	0.1	98.53	Superkingdom: Bacteria Phylum: Bacteroidota Class: Bacteroidia Order: Bacteroidales Family: Bacteroidaceae Genus: Bacteroides Species: Bacteroides clarus
Escherichia marmotae	18	0.1	98.66	Superkingdom: Bacteria Phylum: Pseudomonadota Class: Gammaproteobacteria Order: Enterobacterales Family: Enterobacteriaceae Genus: Escherichia Species: Escherichia marmotae
Parabacteroides sp. dnLKV8	18	0.1	98.52	Superkingdom: Bacteria Phylum: Bacteroidota Class: Bacteroidia Order: Bacteroidales Family: Tannerellaceae Genus: Parabacteroides Species: Parabacteroides sp. dnLKV8
Bifidobacterium bifidum	17	0.1	98.61	Superkingdom: Bacteria Phylum: Actinomycetota Class: Actinomycetes Order: Bifidobacteriales Family: Bifidobacteriaceae Genus: Bifidobacterium Species: Bifidobacterium bifidum
Shigella sp.	16	0.1	98.1	Superkingdom: Bacteria Phylum: Pseudomonadota Class: Gammaproteobacteria Order: Enterobacterales Family: Enterobacteriaceae Genus: Shigella Species: Shigella sp.
Lachnospiraceae bacterium DJF_VP18k1	15	0.1	96.27	Superkingdom: Bacteria Phylum: Bacillota Class: Clostridia Order: Eubacteriales Family: Lachnospiraceae Species: Lachnospiraceae bacterium DJF_VP18k1
Coprococcus comes	15	0.1	97.56	Superkingdom: Bacteria Phylum: Bacillota Class: Clostridia Order: Eubacteriales Family: Lachnospiraceae Genus: Coprococcus Species: Coprococcus comes Strain: Coprococcus comes ATCC 27758
Bacteroides bouchesdurhonensis	14	0.1	96.38	Superkingdom: Bacteria Phylum: Bacteroidota Class: Bacteroidia Order: Bacteroidales Family: Bacteroidaceae Genus: Bacteroides Species: Bacteroides bouchesdurhonensis
Collinsella aerofaciens	14	0.1	99.1	Superkingdom: Bacteria Phylum: Actinomycetota Class: Coriobacteriia Order: Coriobacteriales Family: Coriobacteriaceae Genus: Collinsella Species: Collinsella aerofaciens
Mediterraneibacter faecis	12	0.1	96.77	Superkingdom: Bacteria Phylum: Bacillota Class: Clostridia Order: Eubacteriales Family: Lachnospiraceae Genus: Mediterraneibacter Species: Mediterraneibacter faecis
Alistipes putredinis	12	0.1	98.92	Superkingdom: Bacteria Phylum: Bacteroidota Class: Bacteroidia Order: Bacteroidales Family: Rikenellaceae Genus: Alistipes Species: Alistipes putredinis
Shigella sp. 86.4	12	0.1	98.37	Superkingdom: Bacteria Phylum: Pseudomonadota Class: Gammaproteobacteria Order: Enterobacterales Family: Enterobacteriaceae Genus: Shigella Species: Shigella sp. 86.4
Shigella dysenteriae	11	0.1	98.91	Superkingdom: Bacteria Phylum: Pseudomonadota Class: Gammaproteobacteria Order: Enterobacterales Family: Enterobacteriaceae Genus: Shigella Species: Shigella dysenteriae
Escherichia sp. XJ148-1212-2NFX1	11	0.1	99.53	Superkingdom: Bacteria Phylum: Pseudomonadota Class: Gammaproteobacteria Order: Enterobacterales Family: Enterobacteriaceae Genus: Escherichia Species: Escherichia sp. XJ148-1212-2NFX1
Enterococcus faecalis	10	0.0	98.26	Superkingdom: Bacteria Phylum: Bacillota Class: Bacilli Order: Lactobacillales Family: Enterococcaceae Genus: Enterococcus Species: Enterococcus faecalis
[Clostridium] nexile	10	0.0	96.55	Superkingdom: Bacteria Phylum: Bacillota Class: Clostridia Order: Eubacteriales Family: Lachnospiraceae Genus: Tyzzerella Species: [Clostridium] nexile
Ruminococcus sp. CE2	10	0.0	95.87	Superkingdom: Bacteria Phylum: Bacillota Class: Clostridia Order: Eubacteriales Family: Oscillospiraceae Genus: Ruminococcus Species: Ruminococcus sp. CE2
butyrate-producing bacterium M50/1	9	0.0	97.15	Superkingdom: Bacteria Phylum: Bacillota Class: Clostridia Order: Eubacteriales Species: butyrate-producing bacterium M50/1
Streptococcus oralis	9	0.0	99.23	Superkingdom: Bacteria Phylum: Bacillota Class: Bacilli Order: Lactobacillales Family: Streptococcaceae Genus: Streptococcus Species: Streptococcus oralis
Escherichia sp. UIWRF0478	9	0.0	99.2	Superkingdom: Bacteria Phylum: Pseudomonadota Class: Gammaproteobacteria Order: Enterobacterales Family: Enterobacteriaceae Genus: Escherichia Species: Escherichia sp. UIWRF0478
Adlercreutzia equolifaciens	9	0.0	98.39	Superkingdom: Bacteria Phylum: Actinomycetota Class: Coriobacteriia Order: Eggerthellales Family: Eggerthellaceae Genus: Adlercreutzia Species: Adlercreutzia equolifaciens
Evtepia gabavorous	9	0.0	97.82	Superkingdom: Bacteria Phylum: Bacillota Class: Clostridia Order: Eubacteriales Genus: Evtepia Species: Evtepia gabavorous
Enterobacter sp. Nj-68	8	0.0	97.95	Superkingdom: Bacteria Phylum: Pseudomonadota Class: Gammaproteobacteria Order: Enterobacterales Family: Enterobacteriaceae Genus: Enterobacter Species: Enterobacter sp. Nj-68
Clostridiales bacterium 80/3	8	0.0	98.61	Superkingdom: Bacteria Phylum: Bacillota Class: Clostridia Order: Eubacteriales Species: Clostridiales bacterium 80/3
Blautia provencensis	8	0.0	96.59	Superkingdom: Bacteria Phylum: Bacillota Class: Clostridia Order: Eubacteriales Family: Lachnospiraceae Genus: Blautia Species: Blautia provencensis
Sutterella wadsworthensis	8	0.0	99.24	Superkingdom: Bacteria Phylum: Pseudomonadota Class: Betaproteobacteria Order: Burkholderiales Family: Sutterellaceae Genus: Sutterella Species: Sutterella wadsworthensis
Clostridium sp.	8	0.0	96.54	Superkingdom: Bacteria Phylum: Bacillota Class: Clostridia Order: Eubacteriales Family: Clostridiaceae Genus: Clostridium Species: Clostridium sp.
Other	355	1.6

Eukaryotic Organisms

Name	Count	Percentage	Match %	Taxonomy
Saccharomyces cerevisiae	224	64.2	99.49	Superkingdom: Eukaryota Kingdom: Fungi Subkingdom: Dikarya Phylum: Ascomycota Subphylum: Saccharomycotina Class: Saccharomycetes Order: Saccharomycetales Family: Saccharomycetaceae Genus: Saccharomyces Species: Saccharomyces cerevisiae
Candida albicans	106	30.4	99.41	Superkingdom: Eukaryota Kingdom: Fungi Subkingdom: Dikarya Phylum: Ascomycota Subphylum: Saccharomycotina Class: Saccharomycetes Order: Saccharomycetales Family: Debaryomycetaceae Genus: Candida Species: Candida albicans Strain: Candida albicans SC5314
Other	19	5.4

Section 6: SPARK - biomSCAN. Research Method

Oxford Nanopore Platform: This method utilizes a combination of PCR amplification technology and long-read sequencing.
Proprietary Primers: Custom molecular probes (primers) that recognize over 50,000 species.
High Sequencing Quality: The average Q-score (sequencing quality score) is 17.5, indicating a sequencing error rate of less than 0.02%.
Test Sensitivity and Specificity: The test is characterized by high sensitivity and specificity, ensuring accurate and reliable results even at low levels of microorganism presence.
BLAST-Based Bioinformatics Algorithms: The test relies on bioinformatics algorithms utilizing the most accurate BLAST (Basic Local Alignment Search Tool) analysis model.
Reference Sequence Databases: The test uses reference sequences from renowned databases: NCBI (National Center for Biotechnology Information), SILVA (comprehensive database of quality checked and aligned ribosomal RNA sequence data), and PR2 (Protist Ribosomal Reference database).
Result Precision: The minimum sequence match with reference sequences is 95%, meaning that for every 1000 nucleotides, at least 950 are identical to the reference.
The test result does not exclude the presence of pathogens that are below the detection level of this research method or that are not detectable using this method.

SPARK TECH Sp. z o.o.

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