Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

10.3791/63115 ◽  
2021 ◽  
Author(s):  
Natasha Pavlovikj ◽  
Joao Carlos Gomes-Neto ◽  
Andrew K. Benson
Keyword(s):  
Bacterial Populations ◽  
Accessory Genome

scholarly journals PANINI: Pangenome Neighbor Identification for Bacterial Populations

2017 ◽  
Author(s):  
Khalil Abudahab ◽  
Joaquín M. Prada ◽  
Zhirong Yang ◽  
Stephen D. Bentley ◽  
Nicholas J. Croucher ◽  
...  
Keyword(s):  
Machine Learning ◽  
Core Genome ◽  
Population Genomics ◽  
Genomic Analysis ◽  
Diverse Populations ◽  
Data Set ◽  
Bacterial Populations ◽  
Accessory Genome ◽  
The Core ◽  
Link Type

ABSTRACTThe standard workhorse for genomic analysis of the evolution of bacterial populations is phylogenetic modelling of mutations in the core genome. However, in the current era of population genomics, a notable amount of information about evolutionary and transmission processes in diverse populations can be lost unless the accessory genome is also taken into consideration. Here we introduce PANINI, a computationally scalable method for identifying the neighbours for each isolate in a data set using unsupervised machine learning with stochastic neighbour embedding. PANINI is browser-based and integrates with the Microreact platform for rapid online visualisation and exploration of both core and accessory genome evolutionary signals together with relevant epidemiological, geographic, temporal and other metadata. Several case studies with single-and multi-clone pneumococcal populations are presented to demonstrate ability to identify biologically important signals from gene content data. PANINI is available at http://panini.wgsa.net/ and code at http://gitlab.com/cgps/panini

COUNTING TOTAL BACTERIA IN LAND ORGANIC WASTE HOUSEHOLD AND LAND INORGANIC WITH TOTAL PLATE COUNT METHOD (TPC)

2017 ◽  
Vol 4 (2) ◽  
pp. 87-91
Author(s):  
Ekamaida Ekamaida
Keyword(s):  
Soil Fertility ◽  
Bacterial Population ◽  
Organic Soil ◽  
Biological Properties ◽  
Plate Count ◽  
Bacterial Populations ◽  
Fertility Data ◽  
Plate Count Method ◽  
The Mean ◽  
Total Bacteria

The soil fertility aspect is characterized by the good biological properties of the soil. One important element of the soil biological properties is the bacterial population present in it. This research was conducted in the laboratory of Microbiology University of Malikussaleh in the May until June 2016. This study aims to determine the number of bacterial populations in soil organic and inorganic so that can be used as an indicator to know the level of soil fertility. Data analysis was done by T-Test that is by comparing the mean of observation parameter to each soil sample. The sampling method used is a composite method, which combines 9 of soil samples taken from 9 sample points on the same plot diagonally both on organic soil and inorganic soil. The results showed the highest bacterial population was found in total organic soil cfu 180500000 and total inorganic soil cfu 62.500.000

Microbiological substantiation of application of phytopreparations in treatment of inflammatory periodontal diseases

2019 ◽  
Vol 24 (3) ◽  
pp. 196-202 ◽  
Author(s):  
S. A. Abdurakhmanova ◽  
G. S. Runova ◽  
M. S. Podporin ◽  
E. V. Tsareva ◽  
E. V. Ippolitov ◽  
...  
Keyword(s):  
Tooth Loss ◽  
Periodontal Diseases ◽  
Adult Population ◽  
Experimental Studies ◽  
Herbal Medicines ◽  
Growth Dynamics ◽  
Integrated Approach ◽  
Bacterial Populations ◽  
Streptococcus Constellatus ◽  
Urgent Task

Relevance: Inflammatory-destructive periodontal diseases are the most complicated and became the main cause of tooth loss in adult population. Herbal medicines have a variety of pharmacological properties, so the development and introduction of new forms for the treatment of inflammatory periodontal diseases is an urgent task today.Purpose – experimental evaluation of effectiveness of the use of herbal medicines “Tonzinal” and “CM-1” in relation to the priority periodontal pathogenes.Materials and methods: in experimental studies, the basis for the experiment was the system for the cultivation of microorganisms in real time – the Revers-Spinner RTS-1 bioreactor. With the priority strains of periodontitis pathogens, the study of the growth dynamics of the culture was carried out in several parallels.Results: herbal medicines “CM-1” and “Tonsinal” has a multilateral therapeutic effect, exerting a diverse influence on the key stages of development of such bacterial populations as Aggregatibacter actinomycetemcomitans, Streptococcus constellatus, Candida albicans.Conclusion: tan integrated approach in the treatment of patients with inflammatory periodontal diseases is promising and will contribute to a more prolonged remission and increase the effectiveness of treatment. 

The comparison of the diversity of activated sludge plants

1998 ◽  
Vol 37 (4-5) ◽  
pp. 71-78 ◽  
Author(s):  
Thomas P. Curtis ◽  
Noel G. Craine
Keyword(s):  
Cluster Analysis ◽  
Activated Sludge ◽  
Treatment Process ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Optimal Sampling ◽  
Bacterial Populations ◽  
Large Numbers ◽  
Probable Presence ◽  
Gradient Gel Electrophoresis ◽  
Sampling Regime

The explicit engineering of bacterial populations requires that we know which organisms perform which tasks. The comparison of the bacterial diversity of activated sludge plants may give important information about the functions of different bacteria. This difficult task may be made easier by the use of technologies based on 16S rRNA based techniques. In this study we have used denaturing gradient gel electrophoresis (DGGE) to determine the optimal sampling regime for comparative studies and used cluster analysis to show how plants may be quantitatively compared. We sought evidence of spatial, diurnal and intrasample variation in a number of sites. No evidence for variation was found in the plants studied and we concluded that a single sample of an activated sludge plant was sufficient for a plant to plant comparison. The cluster analysis was able to distinguish between plants, though further work is required to find the most appropriate basis for such comparisons. We found organisms from raw sewage in the mixed liquor samples, these organisms may have no functional significance in the treatment process and thus complicate plant to plant comparisons as will the probable presence of heteroduplex rDNA products. Nevertheless we believe that these drawbacks do not outweigh the advantages of being able to take and compare relatively large numbers of samples.

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