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Welcome to ReFDash Database exploration. Here you will find an exhaustive ensemble of 16S based functional metagenomics projects, alongwith their abundance datasets (taxonomic and functional profiles), coupled with a detailed dashboard, which represents various analyses and visualizations performed in the project. Clicking on the first cell of each entry will generate a pop-up window having further details about the entry/ project. |
| Title | Study ID | Host Category | Sub Category | Samples | Geography | Entry Date | Dashboard | Journal | OTU Data | Meta Data | V-Region | Accession ID | Classifier | Sequencer | Description | Contributor E-mail | Tags |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Parkinson's Disease | 81fd0a18ec | Human | Gut | 148 | Finland | 11.04.2019 | V1-V3 | PRJEB4927 | RDP | 454 | Analysis pertains to the public data provided by the published study titled "Gut microbiota are related to Parkinson's disease and clinical phenotype". iVikodak was utilized for inferring as well as analyzing microbial functional potential in 148 16S metagenomic fecal samples collected from 72 PD patients and 72 control subjects. Originally, authors were first to investigate gut microbiome in Parkinson's Disease (PD). They observed that the intestinal microbiome is altered in PD and is related to motor phenotype. | sunil.nagpal@tcs.com | brain, nervous, parkinson's, first | ||||
| Human Microbiome Project (HMP) | ee93f92f95 | Human | Oral | 1346 | USA | 11.04.2019 | V1-V3 | https://www.hmpdacc.org/HM16STR/ | Obtained from HMP (QIIME1 reported) | 454 | Analysis pertains to the public data provided by the "Human Microbiome Project". iVikodak was utilized for inferring as well as analyzing microbial functional potential in 225 16S metagenomic samples collected from oral environment sites of the participants of HMP. | sunil.nagpal@tcs.com | hmp, oral, saliva, tonsils, palate, gingiva, tongue, throat, plaque | ||||
| Human Microbiome Project (HMP) | 0b3dd8c433 | Human | Vagina | 225 | USA | 11.04.2019 | V1-V3 | https://www.hmpdacc.org/HM16STR/ | Obtained from HMP (QIIME1 reported) | 454 | Analysis pertains to the public data provided by the "Human Microbiome Project". iVikodak was utilized for inferring as well as analyzing microbial functional potential in 225 16S metagenomic samples collected from vaginal sites of the female participants of HMP. | sunil.nagpal@tcs.com | hmp, reproductive tract, females, introitus, mid vagina | ||||
| Human Microbiome Project (HMP) | 1952ad04a4 | Human | Skin | 585 | USA | 10.04.2019 | V1-V3 | https://www.hmpdacc.org/HM16STR/ | Obtained from HMP (QIIME1 reported) | 454 | Analysis pertains to the public data provided by the "Human Microbiome Project". iVikodak was utilized for inferring as well as analyzing microbial functional potential in 585 16S metagenomic samples collected from skin of the participants of HMP. | sunil.nagpal@tcs.com | skin, human, hmp, fossa, crease | ||||
| Home Microbiome Project | 6b68f0f83a | Human | Bodysites Environment |
1625 | USA | 05.04.2019 | V4 | PRJEB6292 | Mgnify (v: 4.1) | HiSeq | Analysis pertains to the public data provided by the study, "Longitudinal analysis of microbial interaction between humans and the indoor environment". iVikodak was utilized for inferring as well as analyzing microbial functional potential in 1625 16S metagenomic samples collected from seven houses, 18 people, three dogs, and one cat. The people comprised 3 children under 10 years old, and 15 adults over 20 years old. The children comprised 2 males and 1 female in separate houses. The adults comprised 7 females and 8 males. Authors originally identified that "When families moved, their microbiological “aura” followed. If one person left the home even for a few days, their contribution to the microbiome diminished". | sunil.nagpal@tcs.com | indoor, dog, cat, door, knob, children, travel, movement | ||||
| Colorectal Cancer (CRC) | da098e21c7 | Human | Tumor Colon Tissue |
88 | USA | 05.04.2019 | V5-V6 | PRJNA284355 | RDP | MiSeq | Analysis pertains to the public data provided by the study, "Virulence genes are a signature of the microbiome in the colorectal tumor microenvironment". iVikodak was utilized for inferring as well as analyzing microbial functional potential in 88 16S metagenomic samples collected from 44 primary tumor and 44 patient-matched normal colon tissue samples. Authors originally identified bacterial taxa significantly correlated with colorectal cancer, including a novel finding of an elevated abundance of Providencia in the tumor microenvironment. They also described the predicted metabolic pathways and enzymes differentially present in the tumor-associated microbiome, and presented an enrichment of virulence-associated bacterial genes in the tumor microenvironment. | sunil.nagpal@tcs.com | crc, tissue, Providencia, virulence,normal colon tissue, tumor | ||||
| Volcanic Soil Microbiome | 0e2f3921b1 | Environment | Soil | 127 | USA | 05.04.2019 | V4 | PRJEB15174 | Mgnify (v: 4.1) | HiSeq 2000 | Analysis pertains to the public data provided by the study, "Volcanic soils from Hawaii Kohana" on NCBI. Taxonomic profile was sourced from EBI Mgnify. iVikodak was utilized for inferring as well as analyzing microbial functional potential in 127 16S metagenomic samples collected from Hawaian Kohala Volcanic Soils (one sample pertaining to cow dung was omitted for uniformity of environment). Authors originally intended to study a network of sites along an extreme rainfall gradient that ranges from 200 mm to 3500 mm/year over a short distance of 12 km due to orographic moisture interception by Kohala Mountain in Hawaii. | sunil.nagpal@tcs.com | soil, environment, volcano,Hawaii,Mountain | ||||
| Arabidopsis Root Microbiome | 39d115330a | Plant and Environment | Soil and Plant | 1277 | USA | 04.04.2019 | V7–V8 | PRJEB2989 | Mgnify (v: 2.0) | 454 | Analysis pertains to the public data provided by the study, "Defining the core Arabidopsis thaliana root microbiome". iVikodak was utilized for inferring as well as analyzing microbial functional potential in 1277 16S metagenomic samples collected from Soil, Rhizosphere, Tissue, Endophyte of Arabidopsis Root Environment. Authors originally intended to test the hypotheses that the root rhizosphere and endophytic compartment microbiota of plants grown under controlled conditions in natural soils are sufficiently dependent on the host to remain consistent across different soil types and developmental stages, and sufficiently dependent on host genotype to vary between inbred Arabidopsis accessions. | sunil.nagpal@tcs.com | plant, arabidopsis, root, endophyte,rhizosphere, yissue , soil | ||||
| Temperate Bog Lakes | 6318fe0e9e | Environment | Fresh-water | 1505 | USA | 04.04.2019 | V4 | PRJEB15148 | Mgnify (v: 4.1) | HiSeq 2000 | Analysis pertains to the public data provided by the study, "Bacterial Community Spatial and Temporal Variation in a North Temperate Bog Lake". iVikodak was utilized for inferring as well as analyzing microbial functional potential in 1505 16S metagenomic samples collected freshwater environment of Temperate Bog Lakes. Authors originally intended to investigate microbial communities due to easily identified spatial boundaries and well characterized seasonal ecosystem dynamics in Mary Lake of northern Wisconsin. | sunil.nagpal@tcs.com | bog, lake, ecosystem, freshwater | ||||
| TwinsUK Cohort Microbiome | f8f993ad6c | Human | Gut | 3288 | United Kingdom (UK) | 04.04.2019 | V4 | PRJEB13747 | Mgnify (v: 3.0) | Miseq | Analysis pertains to the public data provided by the publication titled, "Genetic Determinants of the Gut Microbiome in UK Twins". iVikodak was utilized for inferring as well as analyzing microbial functional potential in 3288 (triplicated) 16S metagenomic samples collected from 1,126 twins in UK. Authors originally suggested that their results 'highlighted gene-microbe interactions from recent evolutionary adaptation to diet, its sensing, and metabolism in the gut. In the case of the Bifidobacterium-LCT link, host genetics most likely shape the microbiome through diet preference, which itself is heritable'. | sunil.nagpal@tcs.com | twins, Bifidobacterium,diet preference, inheritance | ||||
| Wildlife Rodent Microbiome | 88998c82c2 | Rodent | Spleen | 1016 | West Africa | 04.04.2019 | V4 | https://doi.org/10.5061/dryad.m3p7d/3 | SILVA | MiSeq | Analysis pertains to the public data provided by the publication titled, "16S rRNA Amplicon Sequencing for Epidemiological Surveys of Bacteria in Wildlife". iVikodak was utilized for inferring as well as analyzing microbial functional potential in 1016 16S metagenomic samples collected from spleen of rodents (Mus musculus domesticus, Rattus rattus, Mastomys natalensis, and Mastomys erythroleucus). Authors originally detected several zoonotic bacterial species, including some at high prevalence, despite their never before having been reported for West Africa. | sunil.nagpal@tcs.com | murine, mouse,rodents, wildlife,spleen, zoonotic | ||||
| Cow Rumen bacteriome | bbf563edda | Cow | Rumen | 334 | China | 28.03.2019 | V3-V4 | PRJNA474702 | SILVA | HiSeq 2500 | Analysis pertains to the public data provided by the publication titled, "A collection of rumen bacteriome data from 334 mid-lactation dairy cows". iVikodak was utilized for inferring as well as analyzing microbial functional potential in 334 16S metagenomic samples collected from rumen of cows. Authors originally intended to understand the rumen bacteriome in dairy cows. | sunil.nagpal@tcs.com | cow, animal, rumen,dairy | ||||
| Cheese Microbiome | 2e13bd36c9 | Food | Parmesan Cheese | 165 | Italy | 28.03.2019 | V3 | PRJNA482503, PRJNA503103 | SILVA | MiSeq | Analysis pertains to the public data provided by the publication titled, "Colonization of the human gut by bovine bacteria present in Parmesan cheese". iVikodak was utilized for inferring as well as analyzing microbial functional potential in 165 16S metagenomic samples collected from five cheese making sites which are highly specialized in the manufacture of Parmesan cheese and located in distinct geographical areas in the provinces of Parma and Reggio Emilia in Italy, named here as P1, P2, P3, RE1, and RE2. . Authors originally intended to study "the abilities of certain microorganisms to be transferred across the food production chain, persistence in the final product and, potential, colonization of the human gut". | sunil.nagpal@tcs.com | cheese, microbiome transfer,colonization | ||||
| Pre-term Birth | 3fafe4b000 | Human | Urine | 100 | USA | 20.03.2019 | V4 | PRJNA325160 | RDP | MiSeq | Analysis pertains to the public data provided by the study titled, "Urinary microbiota and preterm birth" downloaded from NCBI SRP076356. Publication was titled, "Urinary Microbiota Associated with Preterm Birth: Results from the Conditions Affecting Neurocognitive Development and Learning in Early Childhood (CANDLE) Study". iVikodak was utilized for inferring as well as analyzing microbial functional potential in 100 (Urine) 16S metagenomic samples. Authors originally suggested a limited role for the urinary microbiota in PTB when measured during the second trimester by 16S rRNA gene sequencing. | sunil.nagpal@tcs.com | ptb, urine | ||||
| Type 1 Diabetes | 618c4245bc | Human | Stool | 111 | USA | 19.03.2019 | V4 | Unavailable | sina, silva_reference | MiSeq | Analysis pertains to the public data provided by the study titled, "Alterations in Intestinal Microbiota Correlate With Susceptibility to Type 1 Diabetes". iVikodak was utilized for inferring as well as analyzing microbial functional potential in 111 16S metagenomic samples (stool) collected from four subject cohorts with or without evidence of islet autoimmunity residing in the Denver metro area. | sunil.nagpal@tcs.com | diabetes, type 1 | ||||
| Arthritis Microbiome | 1f6a1c824c | Human | Stool | 114 | USA | 19.03.2019 | V1-V2 | PRJNA203810 | RDP | 454 | Analysis pertains to the public data provided by the study titled, "Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis". iVikodak was utilized for inferring as well as analyzing microbial functional potential in 114 16S metagenomic samples (stool) collected from rheumatoid arthritis patients and controls. | sunil.nagpal@tcs.com | Arthritis, rheumatoid arthritis | ||||
| Obesity Gut Microbiome | 050bdf0b61 | Human | Stool | 321 | USA | 19.03.2019 | V1-V3 | PRJNA46319 | bayesian_gg, rdp_on_gg_db | 454 | Analysis pertains to the public data provided by the study titled, "Analysis of the Gut Microbiota in the Old Order Amish and Its Relation to the Metabolic Syndrome". iVikodak was utilized for inferring as well as analyzing microbial functional potential in 321 16S metagenomic samples (stool) collected from Amish adults of Lancaster County. The Amish sect originated in Berne, Switzerland in 1693 as an ultraconservative wing of the Mennonite movement. Authors originally intended to "explore the possible dysbiosis of gut microbiota in obesity and its metabolic complications". | sunil.nagpal@tcs.com | obsesity, Amish adults | ||||
| Obesity Gut Microbiome | 73864fbfb5 | Human | Stool | 63 | USA | 19.03.2019 | V3-V1 | PRJNA273824 | Silva | 454 | Analysis pertains to the public data provided by the study titled, "16S gut community of the Cameron County Hispanic Cohort". iVikodak was utilized for inferring as well as analyzing microbial functional potential in 63 16S metagenomic samples (stool) collected from the Cameron County Hispanic Cohort (CCHC). Authors originally observed a "persistent ‘disease’-related gut microbial community in CCHC subjects may enhance existing genetic or lifestyle predispositions to the prevalent diseases of the CCHC, leading to increased attack rates of obesity, T2D, non-alcoholic fatty liver disease, and others". | sunil.nagpal@tcs.com | obesity,lifestyle predispositions | ||||
| Obesity Gut Microbiome | 45cb0b3f7b | Human | Stool | 281 | USA | 19.03.2019 | V2 | PRJNA32089 | blast_gg | 454 | Analysis pertains to the public data provided by the study titled, "A core gut microbiome in obese and lean twins". iVikodak was utilized for inferring as well as analyzing microbial functional potential in 281 16S metagenomic samples (fecal) collected from adult female monozygotic and dizygotic twin pairs concordant for leanness or obesity, and their mothers. Authors originally postulated that "a diversity of organismal assemblages can nonetheless yield a core microbiome at a functional level, and that deviations from this core are associated with different physiological states (obese compared with lean)". | sunil.nagpal@tcs.com | twins, obesity | ||||
| Obesity Gut Microbiome | 95198329cc | Human | Stool | 1017 | USA | 19.03.2019 | V4 | PRJEB6702, PRJEB6705 | closed_ref_gg | MiSeq | Analysis pertains to the public data provided by the study titled, "Human Genetics Shape the Gut Microbiome". iVikodak was utilized for inferring as well as analyzing microbial functional potential in 1017 16S metagenomic samples (fecal) collected from 171 MZ and 245 DZ twin pairs. Authors originally postulated that "host genetics influence the composition of the human gut microbiome and can do so in ways that impact host metabolism". | sunil.nagpal@tcs.com | obesity, obese, twins, heritable taxa | ||||
| Nonalcoholic Steatohepatitis (NASH) |
ce27ad3634 | Human | Stool | 63 | USA | 19.03.2019 | V4 | MGP1195 | qiime_closed_ref | 454 | Analysis pertains to the public data provided by the study titled, "Characterization of gut microbiomes in nonalcoholic steatohepatitis (NASH) patients: A connection between endogenous alcohol and NASH". iVikodak was utilized for inferring as well as analyzing microbial functional potential in 63 16S metagenomic samples (fecal) collected from three groups of children and adolescents in this study (NASH patients, obese patients, and healthy controls). Authors originally postulated that "The distinct composition of the gut microbiome among NASH, obese, and healthy controls could offer a target for intervention or a marker for disease". | sunil.nagpal@tcs.com | NASH,children, adolescents, obesity | ||||
| Nonalcoholic Steatohepatitis (NASH) |
90aa6c8d96 | Human | Stool | 54 | China | 19.03.2019 | V1-V2 | SRP011160 | RDP | 454 | Analysis pertains to the public data provided by the study titled, "Molecular Characterization of the Fecal Microbiota in Patients with Nonalcoholic Steatohepatitis – A Longitudinal Study". iVikodak was utilized for inferring as well as analyzing microbial functional potential in 54 16S metagenomic samples (fecal) collected from histology-proven NASH patients and healthy controls. Authors originally reported that "NASH patients have fecal dysbiosis, and changes in microbiota correlate with improvement in hepatic steatosis." | sunil.nagpal@tcs.com | NAFLD, nash, hepatic steatosis | ||||
| Minimal hepatic encephalopathy (MHE) |
69ec259f44 | Human | Stool | 77 | China | 18.03.2019 | V1-V2 | PRJNA174838 | qiime_blast | 454 | Analysis pertains to the public data provided by the study titled, "Large-scale survey of gut microbiota associated with MHE Via 16S rRNA-based pyrosequencing". iVikodak was utilized for inferring as well as analyzing microbial functional potential in 77 16S metagenomic samples (stool) collected from 26 MHE-matched normal relatives and 25 cirrhotic patients without MHE as controls. Authors originally intended to elucidate that the minimal hepatic encephalopathy (MHE)-associated gut microbiome may help in predicting and lowering the high risk for MHE in patients with cirrhosis. | sunil.nagpal@tcs.com | MHE, cirrhosis | ||||
| Complete logMPIE | 3562abc4d0 | Human | Stool | 1004 | India | 18/03/2019 | V3 and V4 | PRJEB25642 | QIIME | Ion S5 System | Analysis pertains to the public data provided by the study titled, "LogMPIE, pan-India profiling of the human gut microbiome using 16S rRNA sequencing". iVikodak was utilized for inferring as well as analyzing microbial functional potential in 1004 16S metagenomic samples (stool) collected throughout India under this study. Authors originally observed 993 unique microorganisms across the Indian microbiome diaspora. The data in this database entry was brought to genus level assignments through aggregation/ cumulative numbers. The Metadata was uniformly converted to categorical classes. | sunil.nagpal@tcs.com | indian, healthy, gut | ||||
| IBD Huttenhower | bc56e75f28 | Human | Stool and Tissue | 228 | USA | 18/03/2019 | V3-V5 | PRJNA82111, PRJNA175224 | RDP | 454 | Analysis pertains to the public data provided by the study titled, "Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment". iVikodak was utilized for inferring as well as analyzing microbial functional potential in 228 16S metagenomic samples (stool and biopsy) collected from Ocean State Crohn's and Colitis Area Registry (OSCCAR) and the Prospective Registry in IBD Study at MGH (PRISM) database. Authors originally observed that "there were major shifts in oxidative stress pathways, as well as decreased carbohydrate metabolism and amino acid biosynthesis in favor of nutrient transport and uptake. The microbiome of ileal Crohn's disease was notable for increases in virulence and secretion pathways". | sunil.nagpal@tcs.com | ibd, Colitis, crohn's | ||||
| IBD Phenotypes | 1a936a4837 | Human | Stool | 128 | Sweden | 18/03/2019 | V5-V6 | Not Submitted | blast_rdp | 454 | Analysis pertains to the public data provided by the study titled, "A Pyrosequencing Study in Twins Shows That Gastrointestinal Microbial Profiles Vary With Inflammatory Bowel Disease Phenotypes". iVikodak was utilized for inferring as well as analyzing microbial functional potential in 128 16S metagenomic samples (stool as well as tissue) pertaining to aset of 40 twin pairs (29 monozygotic, 11 dizygotic). Authors observed that "The profiles of the microbial community differed with disease phenotypes; relative amounts of bacterial populations correlated with IBD phenotypes". | sunil.nagpal@tcs.com | IBD, phenotypes, twins | ||||
| IBD Children | dc95d886a8 | Human | Stool | 91 | USA | 18/03/2019 | V3-V5 | Not Submitted | RDP | 454 | Analysis pertains to the public data provided by the study titled, "Non-Invasive Mapping of the Gastrointestinal Microbiota Identifies Children with Inflammatory Bowel Disease". iVikodak was utilized for inferring as well as analyzing microbial functional potential in 91 16S metagenomic fecal samples pertaining to the study. Authors developed classification/ risk categorization towards IBD based on microbial diversity. | sunil.nagpal@tcs.com | IBD, children | ||||
| Sexual Preference and HIV Infection |
a59aa59b34 | Human | Stool | 350 | Sweden and Spain |
14/03/2019 | V3-V4 | PRJNA307231 | RDP | 454 | Analysis pertains to the public data provided by the study titled, "Gut Microbiota Linked to Sexual Preference and HIV Infection". iVikodak was utilized for inferring as well as analyzing microbial functional potential in 356 16S metagenomic fecal samples pertaining to the study. Authors intended to improve HIV-1-associated immune dysfunction through microbiome based intervention(s). | sunil.nagpal@tcs.com | HIV, sexual preferences, HIV-1, microbiome intervention, gut microbiome | ||||
| Chronic HIV Infection | edeb583dad | Human | Stool | 36 | USA | 14/03/2019 | V3-V5 | PRJNA233597 | rdp_on_gg_db | 454 | Analysis pertains to the public data provided by the study titled, "Intestinal Microbiota, Microbial Translocation, and Systemic Inflammation in Chronic HIV Infection". iVikodak was utilized for inferring as well as analyzing microbial functional potential in 36 16S metagenomic fecal samples pertaining to the study. Authors had originally observed that the fecal microbial community composition was significantly different between cases and controls. The functional profiles might provide insights into how those differences manifest at functional level. | sunil.nagpal@tcs.com | chronic hiv, HIV, Microbial Translocation | ||||
| Acute Enteric Infections | 0dd4a4fb38 | Human | Stool | 304 | USA | 11/03/2019 | V3-V5 | m9.figshare.1447256 | closed_ref_gg, qiime | 454 | Analysis pertains to the public data provided by the study titled, "Intestinal microbial communities associated with acute enteric infections and disease recovery". iVikodak was utilized for inferring as well as analyzing microbial functional potential in 304 16S metagenomic faecal samples pertaining to the study. The original work was supported by the NIH Enterics Research Investigational Network Cooperative Research Center at Michigan State University (U19AI090872) and in part by the USDA NIFA (2011-67005-30004) and Michigan State University, as declared by authors of the research. | sunil.nagpal@tcs.com | EDD, enteric infections, recovery, NIH | ||||
| Colorectal Cancer (CRC) | c6183c3525 | Human | Stool | 101 | China | 11/03/2019 | V3 | SRP005150 | RDP | 454 | Analysis pertains to the public data provided by the study titled, "Structural segregation of gut microbiota between colorectal cancer patients and healthy volunteers". iVikodak was utilized for inferring as well as analyzing microbial functional potential in 101 16S metagenomic faecal samples pertaining to the study. Participants in this study were aged 42–77 years, and were from Shanghai Cancer Hospital, Shanghai Medical College, Fudan University (Shanghai, China). | sunil.nagpal@tcs.com | CRC, cancer, colon cancer, colorectal cancer | ||||
| Colorectal Cancer (CRC) | 529241e289 | Human | Stool | 156 | France | 11/03/2019 | V4 | PRJEB6070 | RDP | MiSeq | Analysis pertains to the public data provided by the study titled, "Potential of fecal microbiota for early‐stage detection of colorectal cancer". iVikodak was utilized for inferring as well as analyzing microbial functional potential in 156 16S metagenomic faecal samples pertaining to the study. | sunil.nagpal@tcs.com | CRC, colon cancer, early detection | ||||
| Colorectal Cancer (CRC) | 91199e2dda | Human | Stool | 90 | Canada and USA |
11/03/2019 | V4 | mothur.org/MicrobiomeBiomarkerCRC/ | RDP | MiSeq | Analysis pertains to the public data provided by the study titled, "The Human Gut Microbiome as a Screening Tool for Colorectal Cancer". iVikodak was utilized for inferring as well as analyzing microbial functional potential in 90 16S metagenomic faecal samples pertaining to the study. | sunil.nagpal@tcs.com | CRC, screening, diagnosis | ||||
| Colorectal Cancer (CRC) | 82483e2035 | Human | Stool | 490 | Canada and USA |
08/03/2019 | V4 | PRJNA290926 | RDP | MiSeq | Analysis pertains to the public data provided by the study titled, "Microbiota-based model improves the sensitivity of fecal immunochemical test for detecting colonic lesions". iVikodak was utilized for inferring as well as analyzing microbial functional potential in 490 16S metagenomic faecal samples pertaining to the study. Authors aimed at finding microbial biomarkers through random forest classification model that could detect colonic lesions using the relative abundance of gut microbiota and the concentration of hemoglobin in stool. | sunil.nagpal@tcs.com | CRC, diagnostic model, colonic lesions, detection, biomarker, random forest | ||||
| Colorectal Cancer (CRC) | 58aae5f7bc | Human | Stool | 43 | China | 08/03/2019 | V1-V3 | SRP009633 | Silva_mothur | 454 | Analysis pertains to the public data provided by the study titled, "Human Intestinal Lumen and Mucosa-Associated Microbiota in Patients with Colorectal Cancer". iVikodak was utilized for inferring as well as analyzing microbial functional potential in 43 16S metagenomic stool samples pertaining to the study. | sunil.nagpal@tcs.com | CRC, lumen, mucosa, colon | ||||
| FMT CDI | 6cfdb27c3b | Human | Stool | 100 | USA | 08/03/2019 | V4 | PRJNA240307 | RDP | MiSeq | Analysis pertains to the public data provided by the study titled, "Fecal Microbiota Transplant for Relapsing Clostridium difficile Infection Using a Frozen Inoculum From Unrelated Donors: A Randomized, Open-Label, Controlled Pilot Study". iVikodak was utilized for inferring as well as analyzing microbial functional potential in 100 16S metagenomic faecal samples pertaining to the study. Authors aimed at investigating the outcomes of fecal microbiota transplant (FMT) for relapsing CDI using a frozen suspension from unrelated donors, comparing colonoscopic and nasogastric tube (NGT) administration | sunil.nagpal@tcs.com | C.diff, FMT,Clostridium difficile Infection, relapsing CDI | ||||
| Nosocomial CDI | 28fb04fea2 | Human | Stool | 50 | Canada | 08/03/2019 | V3-V5 | Not SUubmitted | RDP | 454 | iVikodak was utilized for inferring as well as analyzing microbial functional potential in 16S metagenomic faecal samples collected before the onset of the first CDI episode (if multiple occurred) for 25 cases, and 25 matched controls. The study was conducted by McGill University and the data was publicly provided. | sunil.nagpal@tcs.com | CDI, Nosocomial | ||||
| Autism Spectrum Disorder | a5cff5928a | Human | Stool | 103 | USA | 07/03/2019 | V1-V2 | PRJNA282013 | RDP | MiSeq | iVikodak was utilized for inferring as well as analyzing microbial functional potential in 103 publicly available 16S metagenomic faecal samples of children belonging to simplex families (which had only a single ASD proband and neurotypical (NT) siblings). | sunil.nagpal@tcs.com | ASD, children, simplex families | ||||
| CDI, non-CDI Diarrhea | ae8bf7652c | Human | Stool | 336 | USA | 07/03/2019 | V3-V5 | mothur.org/CDI_MicrobiomeModeling | RDP | 454 | iVikodak was utilized for inferring as well as analyzing microbial functional potential in 336 publicly available 16S metagenomic diarrheal stool and normal faecal samples. Diarrheal stool samples were obtained from inpatients at the University of Michigan Hospital, including subjects both with CDI and without CDI; while normal faecal samples were obtained from healthy controls. | sunil.nagpal@tcs.com | CDI, non-CDI, Diarrhea | ||||
| Autism Spectrum Disorder | bce002d919 | Human | Stool | 39 | USA | 07/03/2019 | V2-V3 | PRJNA168470 | RDP | 454 LS | iVikodak was utilized for inferring as well as analyzing microbial functional potential in 39 publicly available 16S metagenomic faecal samples of ASD affected children and comparative controls studied originally by Autism Research Institute (San Diego, CA) | sunil.nagpal@tcs.com | ASD, autism, children | ||||
| HIV-1 Infection | 5f4d7c1b50 | Human | Stool | 55 | USA | 07/03/2019 | V4 | PRJEB4335 | RDP | MiSeq | iVikodak was utilized for inferring as well as analyzing functional potential in 55 publicly available 16S metagenomic faecal samples of individuals with chronic HIV infection. | sunil.nagpal@tcs.com | HIV, HIV-1, chronic HIV | ||||
| Periodontitis | 50a7bef1a5 | Human | Oral | 91 | USA | 18/04/2018 | V1-V2 | SRP009299 | RDP | 454 Life Sciences Genome Sequencer FLX (Roche Diagnostics, IN, USA) | iVikodak was utilized for inferring as well as analyzing microbial funtional potential in 91 publicly available 16S metagenomic datasets corresponding to sub-gingival microbiome samples from 30 Periodontally healthy control subjects (HC), and sub-gingival samples from 30 shallow (PS) and 29 deep (PD) periodontal pockets of subjects with Periodontitis. | sunil.nagpal@tcs.com | Periodontitis, plaque | ||||
| Comparison of Soil and Nematode |
5cb3a79c2a | Complex | Soil Nematode |
54 | USA and Belgium |
18/04/2018 | Nematode Soil |
Soil: V4; Nematode: V6-V8 | ERP009665 | RDP | Roche 454 | Presented as a case study of iVikodak's inferring and analyzing microbial functional potential for complex metagenomic environment systems | sunil.nagpal@tcs.com | soil, nematode | |||
| Skin Microbiome Psoriasis | c01bc8c4e9 | Human | Skin | 236 | USA | 15/09/2018 | V1-V3 | phs000251 | RDP | 454-FLX (454 Life Sciences, Branford, CT, USA) | Inference of microbial functional potential for Skin Microbiome of Psoriasis affected individuals, as compared against controls. | sunil.nagpal@tcs.com | psoriasis, skin | ||||
| Type 1 Diabetes | f3e0a275fe | Human | Stool | 29 | Mexico | 26/09/2018 | V4 | Not Submitted | RDP | 454 | Originally, this study compared the structure of the fecal microbiota in 29 mestizo children aged 7-18 years, including 8 T1D at onset, 13 T1D after 2 years treatment, and 8 healthy controls. Here we have used iVikodak for inferring as well as analyzing the functional potential of the said microbiota in various classes of samples (as provided in the meta data). | sunil.nagpal@tcs.com | Type 1 Diabetes, T1D, mestizo children, onset |