scholarly journals Metagenome gene prediction of naturally fermented milk products of India using PICRUSt2 and Piphillin

2020 ◽  
Author(s):  
Jyoti Prakash Tamang ◽  
H. Nakibapher Jones Shangpliang ◽  
Ranjita Rai
Keyword(s):  
Negative Correlation ◽  
Gene Prediction ◽  
Fermented Milk ◽  
Functional Gene ◽  
Arunachal Pradesh ◽  
Indian States ◽  
Potential Health ◽  
Gabaergic Synapse ◽  
Sequence Method ◽  
Microbial Functional Gene

Abstract Background: Naturally fermented milk (NFM) products are popular food delicacies in Indian states of Sikkim and Arunachal Pradesh. Bacterial communities in these NFM products of India were previously analysed by high-throughput sequence method. However, predictive gene functionality of NFM products of India has not been studied. In this study, raw sequences of NFM products of Sikkim and Arunachal Pradesh were accessed from NCBI database server. PICRUSt2 and Piphillin tools were applied to study microbial functional gene prediction in combination with the commonly used error-corrected denoising programs like DADA2 and Deblur.Results: Significant functional hits were observed from the Piphillin analysis which included some interesting pathways including GABAergic synapse, glutamatergic synapse and serotonergic synapse, which are known to be probiotic-related, among others that are absent in PICRUSt2 analysis. This study also showed the negative correlation of lactic acid bacteria (LAB) members (Lactococcus, Lactobacillus, Leuconostoc) with most of the disease-related functions, which were on the other hand, positively correlated with unwanted contaminants like Staphylococcus, Bacillus and Pseudomonas.Conclusion: The study explored the potential of microbial functional gene prediction using PICRUSt2 and Piphillin software, and indicated the significance of the presence of LAB in these NFM products of India. Since most LAB members are known to be potential health-promoting bacteria, their negative correlation to many of the disease-related functions also indicates their role in combatting unwanted potential contaminants.

scholarly journals Predictive functionality of bacteria in naturally fermented milk products of India using PICRUSt2 and Piphillin pipelines

2021 ◽  
Author(s):  
Nakibapher Jones Shangpliang ◽  
Jyoti Prakash Tamang
Keyword(s):  
Gene Prediction ◽  
Fermented Milk ◽  
Arunachal Pradesh ◽  
Indian States ◽  
Kegg Pathways ◽  
Database Server ◽  
Sequence Method ◽  
Functional Features ◽  
Functional Profiles ◽  
Microbial Functional Gene

Naturally fermented milk (NFM) products are popular food delicacies in Indian states of Sikkim and Arunachal Pradesh. Bacterial communities in these NFM products of India were previously analysed by high-throughput sequence method. However, predictive gene functionality of NFM products of India has not been studied. In this study, raw sequences of NFM products of Sikkim and Arunachal Pradesh were accessed from MG-RAST/NCBI database server. PICRUSt2 and Piphillin tools were applied to study microbial functional gene prediction. MUSiCC-normalized KOs and mapped KEGG pathways from both PICRUSt2 and Piphillin resulted in higher percentage of the former in comparison to the latter. Though, functional features were compared from both the pipelines, however, there were significant differences between the predictions. Therefore, a consolidated presentation of both the algorithms presented an overall outlook into the predictive functional profiles associated with the microbiota of the NFM products of India.

scholarly journals Microbial Functional Gene Diversity with a Shift of Subsurface Redox Conditions duringIn SituUranium Reduction

2012 ◽  
Vol 78 (8) ◽  
pp. 2966-2972 ◽  
Author(s):  
Yuting Liang ◽  
Joy D. Van Nostrand ◽  
Lucie A. N′Guessan ◽  
Aaron D. Peacock ◽  
Ye Deng ◽  
...  
Keyword(s):  
Functional Diversity ◽  
Field Experiments ◽  
Gene Diversity ◽  
Functional Gene ◽  
Redox Conditions ◽  
Functional Genes ◽  
Microbial Functional Diversity ◽  
Content Type ◽  
Microbial Functional Gene

ABSTRACTTo better understand the microbial functional diversity changes with subsurface redox conditions duringin situuranium bioremediation, key functional genes were studied with GeoChip, a comprehensive functional gene microarray, in field experiments at a uranium mill tailings remedial action (UMTRA) site (Rifle, CO). The results indicated that functional microbial communities altered with a shift in the dominant metabolic process, as documented by hierarchical cluster and ordination analyses of all detected functional genes. The abundance ofdsrABgenes (dissimilatory sulfite reductase genes) and methane generation-relatedmcrgenes (methyl coenzyme M reductase coding genes) increased when redox conditions shifted from Fe-reducing to sulfate-reducing conditions. The cytochrome genes detected were primarily fromGeobactersp. and decreased with lower subsurface redox conditions. Statistical analysis of environmental parameters and functional genes indicated that acetate, U(VI), and redox potential (Eh) were the most significant geochemical variables linked to microbial functional gene structures, and changes in microbial functional diversity were strongly related to the dominant terminal electron-accepting process following acetate addition. The study indicates that the microbial functional genes clearly reflect thein situredox conditions and the dominant microbial processes, which in turn influence uranium bioreduction. Microbial functional genes thus could be very useful for tracking microbial community structure and dynamics during bioremediation.

Sanitary landfill improved CNPS microbial functional gene abundance compared to non-sanitary landfill

2019 ◽  
Vol 20 (1) ◽  
pp. 99-108 ◽  
Author(s):  
Yuzhen Luo ◽  
Weiwei Zhang ◽  
Yaying Li ◽  
Yongjie Wang ◽  
Huaiying Yao ◽  
...  
Keyword(s):  
Functional Gene ◽  
Sanitary Landfill ◽  
Gene Abundance ◽  
Functional Gene Abundance ◽  
Microbial Functional Gene

EVALUATION OF COVID 19 IMPACT ON THE LEARNING STRATEGIES OF HEALTH SCIENCE STUDENTS: A SURVEY

2021 ◽  
pp. 72-75
Author(s):  
Padmanabhan Rajesh ◽  
Amalendu Vijay ◽  
Shankar Sethuraman ◽  
PV Sai Karthik ◽  
Prakhar Rustagi ◽  
...  
Keyword(s):  
Deep Learning ◽  
Negative Correlation ◽  
Health Science ◽  
Learning Approach ◽  
Science Students ◽  
Strategic Learning ◽  
Indian States ◽  
Health Science Students ◽  
South Indian ◽  
Surface Learning

Background: The lockdown period following the COVID 19 pandemic has affected students in many ways. The present study aims to investigate any changes in learning practice during this pandemic. We conducted this study to investigate any variations in the learning approach by health science students during the Covid 19 pandemic and also to assess possible confounding factors on learning. Methods: A survey was conducted on 630 health science students from South Indian states through 2 pre-validated questionnaires - Approaches and Study Skills Inventory for Students (ASSIST) and Generalised Anxiety Disorder Assessment (GAD 7), to assess learning approach and anxiety levels respectively. Another set of questionnaire consisting 10 questions were prepared that may affect learning approach. These questionnaires were shared via Google forms across various health science institutions of South India. Results: A signicant decrease in strategic and deep learning scores and increase in surface learning scores were observed after Covid 19 pandemic. Anxiety scores were increased after pandemic. A signicant negative correlation was observed between change in deep learning scores vs change in anxiety scores and change in strategic scores vs change anxiety scores. A positive correlation was observed between change in surface learning scores vs anxiety scores. Decrease in strategic and deep learning scores were signicantly correlated with students perceptions on worsening study environment, decreased effectiveness of academic assessments, decreased time devoted for studies, decreased ability to gure out high yielding questions and a decreased ability to frame quality answers. Increase in surface learning negatively correlated with worsening study environment and decreased study time. A negative correlation was observed between suitable study environment and change in anxiety scores. Conclusion: Increased anxiety level was associated with decrease in deep and strategic learning and increase in surface learning approach after Covid 19 pandemic. Appropriate measures are essential to improve students' academic performance

Survival of a native toxigenic isolate of Listeria monocytogenes CFR 1302 during storage of milk-based foods can be a potential cause of health risk

2017 ◽  
Vol 23 (5) ◽  
pp. 426-436 ◽  
Author(s):  
Hampapura S Jayanth ◽  
Mandyam C Varadaraj
Keyword(s):  
Listeria Monocytogenes ◽  
Health Hazard ◽  
Food Products ◽  
Fermented Milk ◽  
Culture Broth ◽  
Initial Population ◽  
Listeriolysin O ◽  
Potential Health ◽  
Initial Inoculum ◽  
Toxigenic Culture

The ability of a native toxigenic culture of Listeria monocytogenes CFR 1302 to survive and elaborate associated toxigenic trait in ice cream and mango pulp-based lactic fermented milk was studied. The culture of L. monocytogenes inoculated at two initial levels of 4.6 and 5.6 log10 CFU/ml almost remained unaltered during storage of the food products. However, in both the milk-based products, a marginal increase in viable population was observed during 2–4 d of storage as against the initial inoculum levels. The toxigenic trait, listeriolysin “O” was detected by PCR based on species-specific hlyA primers in the two products without any step of enrichment. The positive amplification in PCR was evidenced with initial population levels of 6.3, 7.3, and 8.3 log10 CFU/ml of the respective products. In culture broth, PCR detection was positive with the lowest level of 2.3 log10 CFU/ml. The established pathogenic strain of L. monocytogenes Scott A used as a reference culture revealed almost the same behavior to that of native culture in the food products. The findings of present study bring into focus that, irrespective of low storage temperatures, there exists the potential health hazard associated with foods initially contaminated with risk population levels of L. monocytogenes.

scholarly journals Application of the “SCOBY” and Kombucha Tea for the Production of Fermented Milk Drinks

2021 ◽  
Vol 9 (1) ◽  
pp. 123
Author(s):  
Marcin Kruk ◽  
Monika Trząskowska ◽  
Iwona Ścibisz ◽  
Patryk Pokorski
Keyword(s):  
Ph Value ◽  
Descriptive Analysis ◽  
Microbiological Quality ◽  
Fermented Milk ◽  
Hplc Method ◽  
Sensory Profile ◽  
Glucose Content ◽  
Potential Health ◽  
Microbiological Methods ◽  
Kombucha Tea

For the production of fermented milk drinks, cultures of microorganisms other than traditionally applied can be used. Such possibilities are created by the symbiotic culture of bacteria and yeast (SCOBY), which is used to produce kombucha. The aim of the study was to evaluate the possibility of using kombucha and the SCOBY for fermented milk drink products. The drinks were developed with a lactose-free variant and traditional milk. For the analysis of the obtained beverages, microbiological methods (CFU method), chemical methods (pH method and HPLC method) and the quantitative descriptive analysis (QDA) sensory method were used. As a result of the research, a recipe and the fermentation parameters for fermented milk drinks were developed. In the developed lactose milk drinks, the average lactose content was 4.25 g/100 g. In lactose-free milk drinks, the average glucose content was 2.26 g/100 g. Lactic acid in both types of products was at the highest average level of 0.68 g/100 g. The products had a characteristic pH value for fermented milk drinks and a very good microbiological quality, which followed the FAO/WHO guidelines. Drinks also had a typical sensory profile for this products group. However, slight sensory defects were detected. The developed fermented milk drinks have a potential health-promoting value, thanks to the content of active microflora and organic acids, which have a confirmed positive effect on the human body. The drinks produced require further testing to optimize their cost of production, possible health benefits and sensory quality.

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