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Functional Basis of Microorganism Classification

Chengsheng Zhu, Tom O. Delmont, Timothy M. Vogel, Yana Bromberg, Christine A. Orengo
2015 PLoS Computational Biology  
Using over thirteen hundred sequenced bacterial genomes, we built a novel function-based microorganism classification scheme, functional-repertoire similarity-based organism network (FuSiON; flattened  ...  Evolutionary relatedness, inferred from phylogenetic markers, facilitates classification but does not guarantee functional identity between members of the same taxon or lack of similarity between different  ...  We also thank all of those who deposit their experimental and sequence data into public databases. Author Contributions Conceived and designed the experiments: CZ YB. Performed the experiments: CZ.  ... 
doi:10.1371/journal.pcbi.1004472 pmid:26317871 pmcid:PMC4552647 fatcat:pfhc7di35bhdbdjbefu7sqyjem

Identifying Robust Microbiota Signatures and Interpretable Rules to Distinguish Cancer Subtypes

Lei Chen, Zhandong Li, Tao Zeng, Yu-Hang Zhang, Dejing Liu, Hao Li, Tao Huang, Yu-Dong Cai
2020 Frontiers in Molecular Biosciences  
We identified several core regulatory microorganisms that contribute to the classification of multiple tumor subtypes and established quantitative predictive models for interpretable prediction by using  ...  On the basis of the systematic microbiome analyses of blood and cancer-associated tissues in cancer patients/controls in public domain, we performed interpretable analyses.  ...  effective prediction rules for the accurate prediction of certain cancer subtypes on the basis of the detailed microorganism abundance.  ... 
doi:10.3389/fmolb.2020.604794 pmid:33330634 pmcid:PMC7672214 fatcat:327umdhbqbctxj2ujnwpobw5e4

Volumetric three-dimensional recognition of biological microorganisms using multivariate statistical method and digital holography

Inkyu Moon, Bahram Javidi
2006 Journal of Biomedical Optics  
The multivariate joint density functions are calculated from the pixel values of each section image at the same random pixel points.  ...  We present a new statistical approach to real-time sensing and recognition of microorganisms using digital holographic microscopy.  ...  We compare classification of microorganisms using a volumetric 3D image with one sec-tion image.  ... 
doi:10.1117/1.2397576 pmid:17212527 fatcat:dyz3ph42arg3lpdgwpsv7dxiam

Page 256 of Journal of Experimental Medicine Vol. 90, Issue 3 [page]

1949 Journal of Experimental Medicine  
can conclude on the basis of excellent serological evidence that the ; phage susceptibility of certain Gram-negative microorganisms can be intimately ^ correlated with their thermostable antigens, but  ...  In addition, knowledge of bacterial viruses, I their classification, morphology, and host relationships has likewise been greatly broadened.  ... 

Classification of root canal microorganisms using electronic-nose and discriminant analysis

Bekir H Aksebzeci, Musa H Asyalı, Yasemin Kahraman, Özgür Er, Esma Kaya, Hatice Özbilge, Sadık Kara
2010 BioMedical Engineering OnLine  
For this reason, identification of microorganisms is not a routinely used procedure in root canal treatment.  ...  Identification of microorganisms may help clinicians decide on treatment alternatives such as using different irrigants, intracanal medicaments and antibiotics.  ...  Acknowledgements This study has been supported by the Fund for Scientific Research Projects of Erciyes University (Project No: FBT-07-14 and SBT-07-38).  ... 
doi:10.1186/1475-925x-9-77 pmid:21092166 pmcid:PMC3224911 fatcat:6mvkzxbqobb5bkvog32zv47cry

Two Classes of Plant Antibiotics: Phytoalexins versus "Phytoanticipins"

Hans D. VanEtten, John W. Mansfield, John A. Bailey, Edward E. Farmer
1994 The Plant Cell  
Another requirement of Müller's original definition was that to be called a phytoalexin, the antimicrobial compound must function as the basis of a disease resistance mechanism.  ...  We hope that our proposed classification of H. D. VanEtten, J. W. Mansfield, J. A. Bailey and E. E.  ... 
doi:10.2307/3869817 pmid:12244269 fatcat:n2ntlbkxhzat7buhygezurioe4

Microecological disorders and its modern correction (review)

S. V. Kalinichenko, O. O. Korotkykh, I. Yu. Tishchenko
2016 Ukraïns'kij bìofarmacevtičnij žurnal  
type, functional food, nutraceuticals.  ...  It was considered a wide range of drugs (products) that affect different parts microecological process: probiotics, preparations based on inactivated microorganisms, prebiotics, sinbiotics, drugs metabolic  ...  The most popular is the classification for the intended purpose for the supply of healthy and sick people, taking into account the functional properties of dairy products, their nutritional and biological  ... 
doi:10.24959/ubphj.16.20 fatcat:ijoon6ljdnemlg3ur5wzswk3mi

Two Classes of Plant Antibiotics: Phytoalexins versus "Phytoanticipins"

H. D. VanEtten
1994 The Plant Cell  
Another requirement of Müller's original definition was that to be called a phytoalexin, the antimicrobial compound must function as the basis of a disease resistance mechanism.  ...  We hope that our proposed classification of H. D. VanEtten, J. W. Mansfield, J. A. Bailey and E. E.  ... 
doi:10.1105/tpc.6.9.1191 pmid:12244269 fatcat:kop5pk7fkra6zeguvjuow2lfzq

Metagenomic Analysis of Suansun, a Traditional Chinese Unsalted Fermented Food

Yaping Hu, Xiaodong Chen, Jie Zhou, Wenxuan Jing, Qirong Guo
2021 Processes  
A total of 8 phyla, 16 classes, 30 orders, 63 families, 92 genera, and 156 species of microorganisms were identified in the suansun samples, with Lactiplantibacillus predominating, accounting for up to  ...  traditional producing areas in southern China, and the microbial community structure, diversity, and functional genes were analyzed.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/pr9091669 fatcat:exqg3rlspnh7veevniiggsc37y

Phenotypic characterization of pseudomonas bacteria isolated from polluted sites of Ostrava, Czech Republic

Hana Vojtková, Romana Janulková, Pavla Švanová
2012 GeoScience Engineering  
The paper offers an overview of the significance of phenotypic characterization for identification of microorganisms and their correct taxonomic classification.  ...  The degradation potential of contaminated soils greatly depends on the diversity and function of the microbial ecosystem in the given locality; in individual communities, it is possible to diagnose identical  ...  However, in practical applications, problems occur with ambiguous identification of microorganisms on the basis of biochemical tests as microorganisms isolated from the natural environment mostly lack  ... 
doi:10.2478/v10205-011-0019-x fatcat:oounvqvg4rhaxbba5s3pphkmue

Dynamic Changes in the Subgingival Microbiome and Their Potential for Diagnosis and Prognosis of Periodontitis

Baochen Shi, Michaela Chang, John Martin, Makedonka Mitreva, Renate Lux, Perry Klokkevold, Erica Sodergren, George M. Weinstock, Susan K. Haake, Huiying Li
2015 mBio  
Our longitudinal study revealed changes in the microbiota in taxonomic composition, cooccurrence of subgingival microorganisms, and functional composition.  ...  that coordinated interactions among the pathogenic microorganisms are essential to disease pathogenesis.  ...  Cooccurrence networks were constructed on the basis of the relative abundance profiles of subgingival microorganisms in the diseased state (a) and in the resolved state (b).  ... 
doi:10.1128/mbio.01926-14 pmid:25691586 pmcid:PMC4337560 fatcat:vj76nkjgqbab3hoxfszaaxqefm

Fast and reliable MALDI-TOF MS–based microorganism identification

Thomas Maier, Stefan Klepel, Uwe Renner, Markus Kostrzewa
2006 Nature Methods  
Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) fingerprinting is a fast and reliable method for the classification and identification of microorganisms, with  ...  The general workflow of microorganism profiling is a straightforward approach (Fig. 1) . Starting from a single colony or other biological material, samples can be analyzed within a few minutes.  ...  Thousands of microorganisms can easily be analyzed with the BioTyper, and then serve as the basis for further analysis.  ... 
doi:10.1038/nmeth870 fatcat:72j2s7uqgzatxcuzzwdxayxtoy

Serum antibody in Actinobacillus actinomycetemcomitans-infected patients with periodontal disease

J L Ebersole, M N Sandoval, M J Steffen, D Cappelli
1991 Infection and Immunity  
of A. actinomycetemcomitans and antibodies to the microorganism in infected patients with various clinical classifications.  ...  classification.  ...  Tanner from the Forsyth Dental Center for supplying the disease classification and primary cultivation plates from some of the patients included in this study.  ... 
doi:10.1128/iai.59.5.1795-1802.1991 fatcat:5yull3gpg5achcxxy4ptq2c2oa

Serum antibody in Actinobacillus actinomycetemcomitans-infected patients with periodontal disease

J L Ebersole, M N Sandoval, M J Steffen, D Cappelli
1991 Infection and Immunity  
of A. actinomycetemcomitans and antibodies to the microorganism in infected patients with various clinical classifications.  ...  classification.  ...  Tanner from the Forsyth Dental Center for supplying the disease classification and primary cultivation plates from some of the patients included in this study.  ... 
pmid:2019443 pmcid:PMC257918 fatcat:g2zlymghqbah3bwpvk4wqzaukq

METAGENOMICS: DNA SEQUENCING OF UNCULTURED MICROORGANISMS

Aarushi Ravi Shankar
2022 Zenodo  
One such method, Metagenomics, refers to the study of microorganisms on the basis of their genomic diversity, acquired directly from environmental samples.  ...  It facilitates the study of physiology and ecology of environmental microorganisms through a vast array of sequencing and functional techniques.  ...  One such method, Metagenomics, refers to the study of microorganisms on the basis of their genomic diversity, acquired directly from environmental samples.  ... 
doi:10.5281/zenodo.7092123 fatcat:msuqpshf4nelhgy65cabdadi3u
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