• exploring the microbiome

Microbiome Knowledge Base

Click to learn more Screen Shot 2017-10-20 at 15.28.55

We hope you find the library of information in this knowledge base valuable.

We’d welcome your contribution of public material. Please contribute via the form below.

  • Screen Shot 2017-10-03 at 10.34.28  Using Machine Learning to Identify Major Shifts in Human Gut Microbiome Protein Family Abundance in Disease (View)
  • Screen Shot 2017-10-03 at 11.13.44  Optimizing methods and dodging pitfalls in microbiome research (View)
  • Screen Shot 2017-10-03 at 11.17.22  Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics (View)
  • Screen Shot 2017-10-03 at 12.04.11  Revealing large metagenomic regions through long DNA fragment hybridization capture (View)
  • Screen Shot 2017-10-04 at 10.56.44  Rapid MinION metagenomic profiling of the preterm infant gut microbiota to aid in pathogen diagnostics (View)
  • journal.pbio.2005245.g001Which experimental systems should we use human microbiome science? (View)
  • ismej201759f1Capturing the genetic makeup of the active microbiome in situ (View)
  • 1-s2.0-S2352304217300351-gr1_lrgHypothesis testing and statistical analysis of microbiome (View)

  • Screen Shot 2017-09-13 at 13.51.46  Balance Trees Reveal Microbial Niche Differentiation (View)
  • Screen Shot 2017-10-03 at 11.25.00  Machine learning for metagenomics: methods and tools (View)
  • Screen Shot 2017-10-03 at 11.44.21  A powerful microbiome-based association test and a microbial taxa discovery framework for comprehensive association mapping (View)
  • Screen Shot 2017-10-03 at 14.01.52  Improved OTU-picking using long-read 16S rRNA gene amplicon sequencing and generic hierarchical clustering (View)
  • Screen Shot 2017-10-03 at 10.53.16  The metagenomic data life-cycle: standards and best practices (View)
  • 12866_2017_927_Fig1_HTMLOptimisation of the methods for bacterial skin microbiome investigation: primer selection and comparison of the 454 versus MiSeq platform (View)
  • fmicb-08-02360-g001Using Click-Chemistry for visualising in situ changes of translational activity in planktonic marine bacteria (View)
  • nature11209-f1.2A framework for human microbiome research (View)

Health and Disease

  • publication in nature  A randomised clinical study to determine the effect of a toothpaste containing enzymes and proteins on plaque oral microbiome ecology (Unilever) (View)
  • Screen Shot 2017-10-03 at 10.22.57  Environmental factors dominate over host genetics in shaping human gut microbiota composition (View)
  •  nm.4272-F1 Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of delivery (View)
  • Screen Shot 2017-10-03 at 11.30.14 A Bacterial Component to Alzheimer’s-Type Dementia Seen via a Systems Biology Approach that Links Iron Dysregulation and Inflammagen Shedding to Disease (View)
  • Screen Shot 2017-10-03 at 11.40.50  A Dormant Microbial Component in the Development of Preeclampsia (View)
  • Screen Shot 2017-10-03 at 15.29.40  The Hygiene Hypothesis and its implications for home hygiene, lifestyle and public health (View)
  • 543291d-i1  Yeast worsens gut disorder (View)
  • Screen Shot 2017-10-04 at 11.30.56  Role of female intimate hygiene in vulvovaginal health: Global hygiene practices and product usage (View)
  • Screen Shot 2017-10-04 at 15.09.17  Microbial biofilms and the human skin microbiome (View)
  • 1-s2.0-S2095809917301595-gr1_lrgEmerging trends for microbiome analysis: from single-cell function imaging to microbiome big data (View)
  • helicobacterEssential Science: Is our microbiome based on genetics? (View)
  • tileshopGeography, Ethnicity or Subsistence-specific variations in Human Microbiome composition and diversity (View)
  • nature25973-f3Environment dominates over host genetics in shaping human gut microbiota (View)
  • 40168_2018_472_Fig1_HTMLGestational diabetes is associated with change in the gut microbiome composition in third trimester of pregnancy and postpartum (View)
  • 40168_2018_467_Fig1_HTMLMind the gut: Genomic insights to population divergence and gut microbial composition of two marine keystone species (View)
  • 40168_2018_448_Fig1_HTMLDrinking alcohol is associated with variation in the human oral microbiome in a large study of American adults (View)
  • 40168_2018_414_Fig1_HTMLThe antibiotic resistome and microbiota landscape of refugees from Syria, Iraq and Afghanistan in Germany (View)
  • asdfghjStudy provides new insight on how antibiotics affect the gut microbiome (View) 


  • Screen Shot 2017-10-03 at 11.07.48  Microbiome restoration diet improves digestion, cognition and physical and emotional wellbeing (View)
  • cranberries  Cranberries may aid the gut microbiome, food scientists find (View)
  • CaptureThe microbiome-gut-brain axis: from bowel to behaviour (View)
  • ccide-7-107Fig2Cariogram outcome after 90 days of oral treatment with Streptococcus salivarius M18 in children at high risk for dental caries: results of a randomized, controlled study (View)

Food Microbiology

  • Screen Shot 2017-10-03 at 14.09.38  Recent and emerging innovations in Salmonella detection: a food and environmental perspective (View)
  • Screen Shot 2017-10-04 at 11.27.40  Microbial Succession and Flavor Production in the Fermented Dairy Beverage Kefir (View)
  • marmite Genome-Wide Association Studies Identify 15 Genetic Markers Associated with Marmite Taste Preference (View)
  • MBT2-10-91-g001Metagenomics insights into food fermentations (View)
  • capture2Recent past, present and future of the food microbiome (View)

Antibiotics Resistance

  • rstb20140087-g3  The human gut resistome (View)
  • 400px-Klebsiella_pneumoniae  Mechanisms of increased resistance to chlorhexidine and cross-resistance to colistin following exposure of Klebsiella pneumoniae clinical isolates to chlorhexidine (View)
  • Screen Shot 2017-10-04 at 10.46.03  Antibiotic Selection Pressure Determination through Sequence-Based Metagenomics (View)
  • F3.mediumPrevalence of Antibiotic resistance genes among the human gut microbiome (View)

Soil Microbiology

  • Screen Shot 2017-10-04 at 10.49.32  Lignocellulose-Degrading Microbial Communities in Landfill Sites Represent a Repository of Unexplored Biomass-Degrading Diversity (View)
  • nmicrobiol2016242-f1Relic DNA is abundant in soil and obscures estimates of soil microbial diversity (View)


  • Screen Shot 2017-10-04 at 11.05.49  Humans differ in their personal microbial cloud (View)
  • Screen Shot 2017-11-02 at 16.38.10  A communal catalogue reveals Earth’s multiscale microbial diversity (View)
  • F1.mediumEarth microbiome project and global systems biology (View)
  • img-1New insights into microbiome study for environmental health (View)

Health and Disease

  • Screen Shot 2017-10-03 at 14.29.28  ‘How do I know my tampons are safe?’: More women push for detailed labels on feminine care products (View)
  • _97066312_jordanbartliffbaby  Asda Little Angels nappy withdrawn after baby ‘left blistered’ (View)
  • 1493981422117  Cosmetics: The next microbiome frontier (View)
  • contact-lenses-eyes-bacteria-illo  Your Eyes Might Be Full of Bacteria. Here’s Why That’s a Good Thing (View)
  • Screen Shot 2017-10-04 at 11.21.08  Dreaming of a microbial perfume (View)
  • 25616  Innovative Fine Fragrance Concept Launched In London (View)
  • downloadYour Gut, Your Emotions (View)
  • download (1)Gut microbiome markers show promise for Colorectal cancer diagnosis (View)
  • download (2)Microbiome imbalance linked to Chronic Fatigue Syndrome (View)
  • 7In the battle against cancer, microbes could be the answer (View)
  • download (2)Powerful new method for microbiome analysis developed (View)
  • fpsyt-08-00153-g001‘I Am I and My Bacterial Circumstances’: Linking Gut Microbiome, Neurodevelopment, and Depression (View)
  • helicobacterHuman Skin Microbiome Differs From Other Mammals (View)


  • colgate-master768  Why a Chemical Banned From Soap Is Still in Your Toothpaste (View)
  • Screen Shot 2017-10-04 at 10.52.44  Drug-resistant ‘Japanese fungus’ infecting hospitals across the UK (View)
  • 141005134915_1_540x360‘Programmable’ antibiotic harnesses an enzyme to attack drug-resistant microbes (View)

Food Microbiology

  • FDA  FDA Information: Outbreak Investigation (View)
  • Screen Shot 2017-10-03 at 14.42.35  Data Management and the Food Safety Modernization Act (View)
  • 2016-01-02-14.49.13-e1451847926798Water activity related to microbial growth (View)

Soil Microbiology

  • Screen Shot 2017-10-04 at 11.01.55  Mighty Farming Microbes: Companies Harness Bacteria To Give Crops A Boost (View)
  • download (3)Microbiomes could help plants grow, resist disease and make agriculture more sustainable (View)
  • park_16x9In 1996, scientists found a fuel-producing bacterium at the bottom of a Swiss lake. Now, they know how it works (View)


  • wpihhypu5chdmpxrfguo Scientists made music from the human microbiome, and its seriously cool (View) (Audio)
  • pf6040_07_aa35556d-8603-481d-8c4f-6a901ddccc49_f Federal partners release Interagency Strategic Plan for Microbiome Research (View)
  • Screen Shot 2018-06-11 at 10.15.19Using microbes to track down criminals (View)

  • Screen Shot 2017-10-03 at 14.05.53  mockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking (View)
  • Screen Shot 2017-10-03 at 14.21.09  Clear Labs: Revolutionize Your Food Safety Program with Whole Genome Sequencing (View)
  • Screen Shot 2017-10-04 at 11.40.03  Omic Tools: Shotgun metagenomic sequencing data analysis bioinformatics software tools (View)
  • iStock_000025128720_Small  Blog: What taxonomy database should I use? (View)
  • 40168_2018_399_Fig1_HTML ReprDB and panDB: minimalist databases with maximal microbial representation (View)
  • theforsythinThe Forsyth Institute expands key human microbiome database (eHOMD) (View)
  • gkx295fig2MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data (View)
  • 12866_2017_1101_Fig1_HTMLA comparison of sequencing platforms and bioinformatics pipelines for compositional analysis of the gut microbiome (View)
  • nihms819402f1Conducting a Microbiome Study (View)
  • 40168_2018_460_Fig1_HTMLFlexible metagenome analysis using the MGX framework (View)

  • Eagle Genomics Unilever  Webinar: Expert Panel on Industrialising Microbiomics – with Unilever (View)
  • screenrecording  Webinar: Considerations and Challenges in Building an End-To-End Microbiome Workflow (View)
  • Screen Shot 2017-09-13 at 14.20.32  White Paper: Building an End-To-End Microbiome Workflow (Download)
  • Microbiome presentation  Presentation: Considerations and Challenges in Building an End-To-End Microbiome Workflow (Download)
  • ABResistance  Blog: Are household products contributing to antibiotic resistance? (View)
  • Ice cream  Blog: Getting the Scoop on Food Safety (View)
  • supermarket-949912_640  Blog: Managing Food Contamination (View)
  • Screen Shot 2017-10-03 at 14.36.31  Blog: How ice cream maker Blue Bell blew it (View)
  • micro  Blog: Microbiomics/Metagenomics Analysis Part 1: Enabling better product claims faster! (View)
  • Screen Shot 2017-10-20 at 15.17.00  Poster: A Questions-based System for Scientific Data Discovery and Exploration (View)
  • Screen Shot 2017-11-16 at 16.51.31  Video: Microbiome Workflow (Watch)
  • Screen Shot 2017-11-16 at 16.54.54  Video: The Automated Data Scientist (Watch)

Upload Featured Image and Additional Images