Harnessing the landscape of microbial culture media to predict new organism–media pairings
نویسندگان
چکیده
Culturing microorganisms is a critical step in understanding and utilizing microbial life. Here we map the landscape of existing culture media by extracting natural-language media recipes into a Known Media Database (KOMODO), which includes >18,000 strain-media combinations, >3300 media variants and compound concentrations (the entire collection of the Leibniz Institute DSMZ repository). Using KOMODO, we show that although media are usually tuned for individual strains using biologically common salts, trace metals and vitamins/cofactors are the most differentiating components between defined media of strains within a genus. We leverage KOMODO to predict new organism-media pairings using a transitivity property (74% growth in new in vitro experiments) and a phylogeny-based collaborative filtering tool (83% growth in new in vitro experiments and stronger growth on predicted well-scored versus poorly scored media). These resources are integrated into a web-based platform that predicts media given an organism's 16S rDNA sequence, facilitating future cultivation efforts.
منابع مشابه
آلودگی باکتریایی در دستگاه آندوسکوپ بخش فوقانی دستگاه گوارش به باکتریهای رایج بیمارستانی در شهر همدان
Introduction: Fiberoptic techniques have been used for diagnosis and also for treatment of gastrointestinal disorders very largely. Infection is a complication of endoscopy and fiberoptic endoscopy may serve as vehicle for transmission of infection. Methods: Before doing gastroscopy, all parts of the endoscope were disinfected (as normally done in the ward). Then, samples for culture were take...
متن کاملAn investigation on the effects of photoperiod, aging and culture media onvegetative growth and sporulation of rice blast pathogen pyricularia oryzae
Pyricularia oryzae (Tel. Magnaporthegrisea) is currently used as a fungal model for plantmicrobeinteraction studies as well as an indicative model for anticancer drug discovery. Thepresent study introduces the optimal condition in which P. oryzae grows and sporulates beston common culture media. We have considered three fungal culture media, i.e. PDA, PCA andWA, based on which P. oryzae sporula...
متن کاملThe Study on Microbial Polymers: Pullulan and PHB
Microbial cells are producers of natural polymers present in plant cells. Production of pullulan (an extracellular microbial polysaccharide) by Aureobasidium pullularia pullulans (P. pullulans) was studied under fermentation conditions, and kinetic parameters were determined. Pullulan formation obeyed a growth and non-growth associated term. PHB (polyhydroxybutyrates) an intracellular biopo...
متن کاملInvestigating the Relationship between the Use of Modern Social Media and the Tendency of Tabriz Youth to Deviant Behaviors
One of the consequences of the new era threatening the cultural health of societies is the prevalence of deviant behaviors among young people. Young people today are more exposed to the use of new media and modern media culture, and this has significant effects on their behavior. The purpose of this study was to study the relationship between the amount and type of social media use with the ten...
متن کاملEffects of Peptone Supplementation in Different Culture Media on Growth, Metabolic Pathway and Productivity of CHO DG44 Cells a New Insight into Amino Acid Profiles
Background: The optimization of bioprocess conditions towards improved growth profile and productivity yield is considered of great importance in biopharmaceutical manufacturing. Peptones as efficient sources of nutrients have been studied for their effect on media development however, their role on metabolic pathway is not well understood. Methods: In the present study, the effect of different...
متن کامل