The gut microbiome resides in your large intestine and is host to more than 1000 species of bacteria that perform certain important functions from shaping the immune system to influencing metabolism of nutrients to fortifying the intestinal mucosal barrier.
It is important to know the abundances of the bacteria that symbiotically live in the human gastrointestinal tract because imbalances in the gut microbiome may lead to gastrointestinal symptoms, skin conditions, autoimmune disorders, immune system imbalances, and multiple inflammatory disorders.
The Vibrant Gut ZoomerTM report provides you with actionable recommendations that include potential risks for:
- Intestinal permeability (SCFA producing bacteria and tight junction integrity)
- Intestinal disorders (IBD related bacteria)
- Heart health (inflammation influencing and TMAO-related bacteria)
- Autoimmune disorders (celiac, Crohn’s, rheumatoid arthritis, etc)
- Metabolic disorders (Obesity, diabetes, etc)
- Nutrition (Vitamin production, oxalate metabolism)
- Intestinal parasites including Cryptosporidium, Entamoeba and Giardia
- Fungal yeast overgrowth from Candida albicans
The test performs the most comprehensive analysis available of your intestinal microbiome ecosystem from a simple one-time stool collection. This test examines the complex and intricate relative abundance of each species or genus measured, in relation to the rest of the ecosystem, to provide a unique perspective on the gut microbiome and its connection to disease and inflammation.
The Vibrant Gut ZoomerTM also provides patients with an actionable report that includes dietary recommendations and other natural supplementation like prebiotics, probiotics, and polyphenols.
The Vibrant Gut ZoomerTM is the most comprehensive gut microbiome test available on the market to clinicians, including over 100+ species and genus-level measurements, as well as phylum assessments and diversity index. Vibrant’s proprietary microchip technology allows for simultaneous detection of DNA from over 100 species and genera of microorganisms from a one-time collection of stool sample.
- Faecalibacterium prausnitzii
- Escherichia coli
- Eubacterium and many more commensal, as well as pathobiont, bacteria…
Pathogenic bacteria include
- Clostridium difficile toxin A
- Clostridium difficile toxin B
- Campylobacter spp ( jejuni, coli and upsaliensis)
- Plesiomonas shigelloides
- Yersinia enterocolitica
- Vibrio parahaemolyticus
- Vibrio cholerae
- Vibrio vulnificus
- Enteroaggregative E.Coli(EAEC)
- Enteropathogenic E.Coli(EPEC)
- Enterotoxigenic E.Coli(ETEC)lt/st
- Shiga-like toxin producing E.Coli(STEC)stx1/stx2
- E.Coli O157
- Shigella/Enteroinvasive E.Coli ( EIEC)
- Helicobacter pylori
- Klebsiella pneumoniae
- Edwardsiella tarda
Pathogenic bacteria include
- Adenovirus F40/41
- Rotavirus A
- Norovirus GI
- Norovirus GII
- Sapovirus (I,II,IV and V)
- Candida albicans
Imbalances in your gut microbiome may lead to the following symptoms or conditions:
- Gastrointestinal symptoms/IBS
- Autoimmune disease
- Nutritional (or vitamin) deficiencies
- Malabsorption of nutrients
- Weight loss or weight gain
- Inflammatory bowel disorders such as ulcerative colitis and Crohn’s disease
- Skin conditions such as eczema or dermatitis
- Immune system dysfunction
- Autism Spectrum disorders/ADD
- Food sensitivities
- Inflammation or joint pain
- Low energy levels or fatigue
Should I stop probiotic supplements before taking a Vibrant Gut ZoomerTM sample?
The Vibrant Gut ZoomerTM measures microorganism 16sRNA from a person’s stool sample. The results reflect the relative abundance of these microorganisms (bacteria, candida yeast, parasites, and viruses) compared to a reference range at the time of the sample. Thus, if a person is using a probiotic supplement the days/weeks leading up to the sample collection, their sample will reflect the ecosystem as influenced by the probiotics.
Our practitioners usually like to use the Gut ZoomerTM in one of two ways. They will either have the patient remove or discontinue the probiotic for ~2 weeks before sample collection. The sample will then represent a person’s “baseline” microbiome ecosystem and a practitioner can individually recommend probiotic supplementation from baseline. The second strategy would be to run a Gut ZoomerTM about ~one month into probiotic supplement to determine if that particular product is affective for that individual.
Can you tell me about the Gut ZoomerTM 16s RNA technology?
The Gut ZoomerTM is a DNA test. PCR is used to amplify and extend products of genomic DNA in the stool sample and then Vibrant’s microarray technology is used to measure bacteria 16s RNA.
Does this report show all of the bacteria that are growing in my gut?
Over 1,000 microbial species have been identified in the human gastrointestinal tract, and research is still evolving in this area. Of all the bacterial species identified, only about 100 bacterial species have been associated with potential health outcomes based on existing scientific studies published in peer-reviewed journals. The Vibrant Gut ZoomerTM measures those species identified as having the greatest impact on health and disease.
Are there other types of bacteria that may be causing symptoms that are not on this report?
The Gut ZoomerTM looks at three different types of dysbiosis:
- dysbiosis caused by a lack of good flora
- an overgrowth of bacteria that could be considered opportunistic
- a lack of diversity in the types of flora found on the sample.
In the process of putting together a clinical history that takes into account your symptoms, the Gut ZoomerTM test provides multiple correlations/risk factors for certain disease states or metabolic abnormalities. Because this type of testing is still an emerging science, it could be that your symptoms are not explained by the bacteria found on the report, however, since the test provides disease and metabolic associations for ~105 bacteria, this is rare.
Does the check mark on the Gut Pathogen test indicate that the pathogen is present?
The check mark indicates that the pathogen has been detected in the sample at a level that is considered pathogenic. See Vibrant’s validation report that states limit of detection (LOD) for each pathogenic organism.
Does the Gut ZoomerTM test for Candida?
Candida is included on the expanded Gut Zoomer Completepanel.
Does the Gut ZoomerTM test for SIBO?
No. A stool test is never determinate for SIBO, as stool testing evaluates large bowel microorganism ecosystem and SIBO is a manifestation in the small bowel (SIBO = Small Intestinal Bacterial Overgrowth). However, there is a correlation with an overabundance of certain bacteria that are associated with SIBO. If SIBO is suspected, the provider should complete an extensive intake and review of symptoms and consider running Vibrant’s IBSSureTM which includes anti-CdTB and anti-vinculin antibodies that have a strong positive correlation with positive SIBO diagnosis.
Gut Microbiome and leaky gut
Enterobacteriaceae Kim K. A., Gu W., Lee I. A., Joh E. H., Kim D. H. (2012). High fat diet-induced gut microbiota exacerbates inflammation and obesity in mice via the TLR4 signaling pathway.
The Study investigated the effect of endotoxin-induced inflammation at both systemic and intestinal levels in response to a high-fat diet (HFD). The below following observations were seen in the HFD mice reduction in the expression of tight junction-associated proteins claudin-1 and occludin in the colon, induced the growth of Enterobacteriaceae and the production of endotoxin and induced macrophage infiltration and inflammation in the adipose tissue, as well as an increase in the circulating proinflammatory cytokines.
Bacteroides, Bifidobacterium, Propionibacterium, Eubacterium, Lactobacillus, Clostridium, Roseburia, Prevotella Macfarlane G. T., Macfarlane S. (2012). Bacteria, colonic fermentation, and gastrointestinal health.
This review summarizes the role of short-chain fatty acid (SCFA) in energy metabolism in large intestine, starting from the fermentation by the gut microbiota to the uptake by the colon and ending with the effects on gastrointestinal health. Bacteroides are one of the major species involved in the production of the SCFA acid, Acetate which plays an important physiological role in immune system, anti-carcinogenesis, increase colonic blood flow and adipogenesis.
Everard A., Belzer C., Geurts L., Ouwerkerk J. P., Druart C., Bindels L. B., et al. . (2013).Cross-talk between Akkermansiamuciniphila and intestinal epithelium controls diet-induced obesity.
This study aims demonstrate the link between the obesity and type 2 diabetes with the altered gut microbiota. Result indicates a significant contribution from species Akkermansiamuciniphila which seen in decreased amount in genetically and diet-induced obese and type 2 diabetic mice .Furthermore the study demonstrated that prebiotic (oligo fructose) treatment restored A. muciniphila abundance and improved gut barrier and metabolic parameters in obese mice.
Lactobacillus reuteri, Lactobacillus rhamnosus Rosenfeldt V., Benfeldt E., Valerius N. H., Paerregaard A., Michaelsen K. F. (2004).
A total of 41 children with moderate and severe atopic dermatitis completed a 6 week randomized, double-blind,placebo-controlled, crossover study. Subjects were given Lactobacillus supplements containing (L. rhamnosus and L. reuteri). Result showed a significant decrease in gastrointestinal symptoms over the period of the study with the probiotic treatment.
Gut Microbiome and Intestinal Health Dorea, Ruminococcus Rajili-Stojanovi M1, Biagi E, Heilig HG, Kajander K, Kekkonen RA, Tims S, de Vos WM Global and deep molecular analysis of microbiota signatures in fecal samples from patients with irritable bowel syndrome.
The microbiota composition was assessed by global and deep molecular analysis of fecal samples from 62 patients with IBS patients and 46 healthy individuals (controls). Result indicated that the intestinal microbiota of IBS patients have a 2 fold increase in number of Dorea, Ruminococcus, and Clostridium.
Lachnospira, Phascolarctobacterium Xochitl C Morgan, Timothy L Tickle, Harry Sokol, Dirk Gevers, Kathryn L Devaney, Doyle V Ward, Joshua A Reyes, Samir A Shah, Neal LeLeiko, Scott B Snapper, Athos Bousvaros, Joshua Korzenik, Bruce E Sands, Ramnik J Xavier and Curtis Huttenhower.
Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment”. We analyzed the microbiota of intestinal biopsies and stool samples from 231 IBD and healthy subjects by 16S gene pyrosequencing and followed up a subset using shotgun metagenomics.Result indicated Inflammatory bowel diseases (IBD) Crohn’s disease (CD), proportions of the Clostridia are altered: the Roseburia and Faecalibacterium genera of the Lachnospiraceae and Ruminococcaceae families are decreased, whereas Ruminococcusgnavus increased.
Desulfovibriopiger Loubinoux J, Bronowicki JP, Pereira IA, Mougenel JL, Faou AE Sulfate-reducing bacteria in human feces and their association with inflammatory bowel disease.
Sulfate-reducing bacteria were isolated from 10 healthy individuals (24%), 15 patients presenting with inflammatory bowel diseases (68%), and 33 patients with other symptoms (37%). The prevalence of D. piger was significantly higher in inflammatory bowel disease patients (55%) as compared to healthy individuals (12%) or patients with other symptoms (25%) (P < 0.05).
CoprococcusEuctatus Kassinen, A., Krogius-Kurikka, L., Makivuokko, H., Rinttil, T.Paulin, L., Corander, J., Malinen, E.,Apajalahti, J. &Palva, A. The fecal microbiota of irritable bowel syndrome patients differs significantlyfrom that of healthy subjects.
Microbial genomes from fecal samples of 24 patients with IBS and 23 controls were collected and analyzed. Coprococcuseutactus species were significantly decreased in all IBS subtypes (IBS-C, IBS-D) compared with the healthy controls samples.
Lactobacillus, Veillonella, Ruminococcusproductus, Bifidobacterium, catenulatum, Malinen E, Rinttila T, Kajander K et al. Analysis of the fecal microbiota of irritable bowel syndrome patients and healthy controls with real-time PCR.
Fecal Samples of 27 IBS patients were compared with 22 control subjects to extensively analyze the intestinal microbes in IBS. Extensive individual variation was observed in GI microbiota among both IBS and control group, furthermore Result indicated a lower amount of lactobacillus in the samples of diarrhea predominant IBS patients.
Gut Microbiome and Cardiovascular Health Collinsella, Eubacterium Karlsson FH, Fåk F, Nookaew I, Tremaroli V, Fagerberg B, Petranovic D, Bäckhed F, and Nielsen J Symptomatic atherosclerosis is associated with an altered gut metagenome.
The patient samples were from the Goteborg atheroma study group biobank, which includes sample from patients who had undergone surgery to excise an atherosclerotic plaque. All sample were sequenced in the Illumina HISeq2000 instrument,the finding shows an increased amount of Collinsella in cardio vascular patients having relative abundance score >0.015 compared to the control group having lesser than 0.005.
Prevotella, Sporobacter, Peptostreptococcaceae, Peptostreptococcaceaeincertaesedis, Clostridiaceae, Fusibacter, Lachnospira, Clostridium, ClostridialesIncertae Sedis XII R A Koeth et al.Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis.
The study links the contribution of intestinal microbiota towards the L-carnitine, a nutrient in red meat with the increased risk of cardiovascular disease. Based on the result they hypothesized that the dietary l-carnitine in humans, like choline and phosphatidylcholine, might be metabolized to produce TMA and TMAO in a gut microbiota–dependent fashion and be associated with atherosclerosis risk. The major gut microbiota contributed to increase levels of TMAO levels in CVD patients were Prevotella, Sporobacter, Peptostreptococcaceae and Peptostreptococcaceaeincertaesedis, Clostridiaceae, Fusibacter, Lachnospira, Clostridium and ClostridialesIncertaeSedis XII.
Anaerococcus hydrogenalis, Clostridium asparagiforme, Clostridium hathewayi T. Liu et al.Intestinal Microbiota Metabolism and Atherosclerosis.
Study details the link between cardiovascular disease and TMAO. It has been observed that several TMA-containing compounds may be catabolized by specific intestinal microbiota, resulting in TMA release which then converted into TMAO in liver.The major intestinal microbiota contributed to increase levels of TMAO levels were Anaerococcushydrogenalis,Clostridium asparagiforme, Clostridium hathewayi.
Gut Bacteria and Autoimmune Health Helicobacter Lebwohl B, Blaser MJ, Ludvigsson JF, Green PH, Rundle A, Sonnenberg A, Genta RM “Decreased risk of celiac disease in patients with Helicobacter pylori colonization.
In a study consisting of 136,179 patients, atotal of 2,689 (2.0) % had celiac disease and Helicobacter pylori prevalence was significantly lower in patients with CD (4.4%) than in those without CD (8.8%) with the odd ratio of 0.48.
Aggregatibacter, Porphyromonas Luigi Nibali, Brian Henderson, Syed Tariq Sadiq, and Nikos Donos Genetic Dysbiosis: the role of microbial insults in chronic inflammatory diseases.
A recent survey in an US adult population of 3,742 individuals revealed a prevalence of 47% for periodontitis. Periodontopathogenic bacteria include gram-negative bacteria such as Aggregatibacteractinomycetemcomitans, Porphyromonasgingivalis and Tannerella forsythia.
These bacteria are thought be able to enter the bloodstream through infected periodontal, have been found in
atheromatous plaques, amniotic fluid of pregnant women and are thought to initiate rheumatoid arthritis in
Dialister Joossens M1, Huys G, Cnockaert M, De Preter V, Verbeke K, Rutgeerts P, Vandamme P, Vermeire S Dysbiosis of the fecal microbiota in patients with Crohn’s disease and their unaffected relatives.
Focusing on families with at least three members affected with CD, fecal samples of 68 patients with Crohn’s
disease (CD), 84 of their unaffected relatives and 55 matched controls were subjected to community fingerprinting of the predominant microbiota using denaturing gradient gel electrophoresis (DGGE). Results suggests that there is a decrease in Dialisterinvisus (p=0.04) in positive CD patients compared to the control group.
Prevotella GangweiOu , MD, PhD , Maria Hedberg , PhD , Per H ö rstedt , PhD , Vladimir Baranov , MD, PhD , G ö teForsberg , MD, PhD , MirvaDrobni , PhD , Olof Sandstr ö m , MD, PhD , Sun Nyunt Wai , MD, PhD ,IngegerdJohansson , OD, PhD , Marie-Louise Hammarstr ö m , PhD , OlleHernell , MD, PhD and Sten Hammarstr ö m , PhD “Proximal Small Intestinal Microbiota and Identification of Rod-Shaped Bacteria Associated With Childhood Celiac Disease.
45 children with CD and 18 clinical controls were studied. s. The proximal small intestine microbiota in biopsies from CD patients collected during 2004 – 2007 differed only marginally from that of controls, and only one biopsy (4 % ) had rod-shaped bacteria by SEM (SEM + ). In nine frozen SEM +CD biopsies from the previous study, microbiotas were significantly enriched in Clostridium,Prevotella, and Actinomyces compared with SEM biopsies. Bacteria of all three genera were isolated from children born during the Swedish CD epidemic. New Clostridium and Prevotella species and Actinomyces graevenitzii were tentatively identified.
Gut Microbiome and Metabolic Health Lactobacillus Reuteri,Lactobacillus paracasei,Bifidobacterium Animalis,Methanobrevibacter smithii M Million, E Angelakis, M Maraninchi, M Henry, R Giorgi4, R Valer, B Vialettes and D Raoult, “Correlation between body mass index and gut concentrations of Lactobacillus reuteri, Bifidobacterium animalis, Methanobrevibactersmithii and Escherichia coli.
263 individuals, including 134 obese, 38 overweight, 76 lean and 15 anorexic were subjects to test for the correlation between bacterial concentration and body mass index (BMI). M. smithii was found in 63% of individuals. The fecal concentration of Methanobrevibactersmithii OR= 0.43 were negatively associated with the BMI.
Julia K. Goodrich, Jillian L. Waters, Angela C. Poole, Jessica L. Sutter, OmryKoren, Ran Blekhman,Michelle Beaumont, William Van Treuren, Rob Knight, Jordana T. Bell, Timothy D. Spector, Andrew G.Clark, and Ruth E. Ley
Human genetics shape the gut microbiome”. In a study consisted of microbiotas across > 1,000 fecal samples obtained from the Twins UK population, including 416 twin-pairs. Results indicates an increase in Oscillospira in lean subjects compared to high BMI candidates.
Junjie Qin, Yingrui Li, and Zhiming Cai et.al “A metagenome-wide association study of gut microbiota in type 2 diabetes
A two-stage case-control metagenome-wide association study (MGWAS) was developed based on deep next generation shotgun sequencing of DNA extracted from the stool samples from a total of 345 Chinese T2D patients and non-diabetic controls. Using the taxonomic characterization from these MLGs, it was found that almost all of the MLGs enriched in the control samples were from various butyrate producing bacteria,including Roseburia intestinalis and Roseburiainulinivorans.
Qin J, Li Y, Cai Z, Li S, Zhu J, Zhang F, Liang S, Zhang W, Guan Y, Shen D, Peng Y, Zhang D, Jie Z, Wu W,Qin Y, Xue W, Li J, Han L, Lu D, Wu P, Dai Y, Sun X, Li Z, Tang A, Zhong S, Li X, Chen W, Xu R, Wang M,Feng Q, Gong M, Yu J, Zhang Y, Zhang M, Hansen T, Sanchez G, Raes J, Falony G, Okuda S, Almeida M,LeChatelier E, Renault P, Pons N, Batto JM, Zhang Z, Chen H, Yang R, Zheng W, Li S, Yang H, Wang J,Ehrlich SD, Nielsen R, Pedersen O, Kristiansen K, Wang J “A metagenome-wide association study of gut microbiota in type 2 diabetes.
The gut microbial content in patients (345 Chinese individuals) with type 2 diabetes were analyzed through deep shotgun sequencing method. MGWAS analysis showed that patients with type 2 diabetes were characterized by a moderate degree of gut microbial Dysbiosis amongst which Eggerthella species had an OR of 1.57.
Gut Microbiome and Nutrition Bifidobacterium bifidum, Bifidobacterium longum, Bifidobacterium breve,Bifidobacterium adolescentis LeBlanc et al.Bacteria as vitamin suppliers to their host: a gut microbiota perspective.
In humans it has been shown that members of the gut microbiota are able to synthesize vitamin K as well as most of the watersoluble B vitamins, such as biotin, cobalamin, folates, nicotinic acid, panthotenic acid, pyridoxine, riboflavin and thiamine. The study shows that some species of Bifidobacterium such as Bifidobacterium bifidum, B.Longum, B.Breve, B.adolescentis are claimed to be the key components to exhibit the vitamin production.
Bifidobacterium animalis subspecies lactis
Turroni et al. Oxalate-Degrading Activity in Bifidobacterium animalis subsp. lactis: Impact of Acidic Conditions on the Transcriptional Levels of the Oxalyl Coenzyme A (CoA) Decarboxylase and Formyl-CoA Transferase Genes.
Intestinal oxalate degrading bacteria plays an important role in maintaining oxalate homeostasis and reducing the risk of kidney stones. In this study, the oxalate degradation activities of 14 species of Bifidobacterium strains were examined, among which results indicates B. animalis carries the oxc gene, which encodes oxalyl-coenzyme A (CoA) decarboxylase, a key enzyme in oxalate catabolism which then making it a strong candidate for the prophylaxis and management of oxalate-related kidney disease.
Methanobrevibacter smithii Mark Pi mentel MD, Robert P Gunsalus, Satish SC Rao MD and Husen Zhang Methanogens in Human Health and Disease.
The review examines the impact of methanogens in human health and disease.Methanobrevibactersmithii accounts for 94% of the methanogen population. Methanogens oxidize hydrogen to produce methane and ensure more complete fermentation of carbohydrate substrates, leading to higher production and adsorption of short-chain fatty acids, which may lead to obesity. Recent evidence has linked methane production to the pathogenesis of constipation and irritable bowel syndrome (IBS), as well as obesity.