• exploring the microbiome

Microbiome Knowledge Base

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

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  • 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)

  • 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)

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)


  • 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)

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)

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)

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)


  • 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)

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)


  • 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)

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)

Soil Microbiology

  • Screen Shot 2017-10-04 at 11.01.55  Mighty Farming Microbes: Companies Harness Bacteria To Give Crops A Boost (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)

  • 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)

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