Welcome to all things microbiology. If you like the videos here, please like and subscribe to the channel. Thanks. I am currently affiliated with the Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia. I have published an ebook "Practical Bacteriology" to guide readers on the culturing, enumeration and identification of bacteria. For the enumeration, I cover both culture dependent (pour plating, spread plating, most probable number, membrane filtration technique) and culture independent methods. You can buy it from here: www.lulu.com/en/us/shop/choon-weng-lee/practical-bacteriology/ebook/product-6ed57m.html?page=1&pageSize=4
Hi i went through a lot of paper and. I got this software through this but i am unable to find the exemplar file for allelic frequency data because we have a lot of locus and lots of population so how we do that??
EDIT: Ok, I realized that PAST is the actual name of the program you're using. Couldn't tell that at first! And just FYI, the sound is super soft on my computer, despite that not beingn the case for other videos. But I'm still eager to get your opinion on my second question! Do you think that this method (ANOSIM & SIMPER) is justifiable for partly non-abundance, non-species data (some numeric, some ordinal and dummy-coded)? Am looking to compare contribution of forest habitat attributes (some of which are tree-species based, but some not) to differences between where competing predators are foraging. I'm doing it in R but would love to verify it with a different program to ensure my results are similar. But I also kinda just want to make sure it's ok to even do because no one on my committee knows. ><
Simper usually done after Anosim if significant. For Anosim, i isually use ratio or count data. Although Anosim ranks the data, i don’t think ordinal data is suitable as its distance is not comparable
Hi, I am trying to run a ONE-WAY ANOSIM on my data to see if there is a similarity among treatments and once I try to run, an error pops up saying, at least two groups are required. How do I go about this?
Plz can u help me Q1 Determine the value of microorganisms and describe their role in different industries and/or as pathogens 2.Explain different methods of sterilization and disinfection and their mechanism of action 3. explain how microbial diversity may be determined relate the structures and functions of marine microorganisms to their habitats 4 describe the metabolic pathways in major primary producers in the marine environment 5 identify the classes of metabolic types present in various marine habitats relate microbial processes to global processes and to climate change 6 describe the various adaptations that have evolved in marine microorganisms relate these adaptations to the microenvironment design strategies to apply such adaptations in biotechnology
@@LeeChoonWeng can u help me in these questions Plz can u help me Q1 Determine the value of microorganisms and describe their role in different industries and/or as pathogens 2.Explain different methods of sterilization and disinfection and their mechanism of action 3. explain how microbial diversity may be determined relate the structures and functions of marine microorganisms to their habitats 4 describe the metabolic pathways in major primary producers in the marine environment 5 identify the classes of metabolic types present in various marine habitats relate microbial processes to global processes and to climate change 6 describe the various adaptations that have evolved in marine microorganisms relate these adaptations to the microenvironment design strategies to apply such adaptations in biotechnology
thank you dr. i want to ask you about how authenticity is PAST in the research usage for example when publishing a paper is it possible use it as far as I know I haven;t seen a paper mentioning it as a statistic tool unlike R package one. thank you
Hi Sir, can I used data before recompute the "Or pool all groups" ? Seems like my data wont recompute after i tick the "Or pool all groups" box. Your reply is highly appreciated. Tq!
Sorry for the late reply. You may save your file as a dat file. For results of analysis, I usually copy and paste into excel. For graphs, you may export as svg or png files
@@akshayasrini6542 Lim JH, Lee CW (2017). Effects of eutrophication on diatom abundance, biovolume and diversity in tropical coastal waters. Environmental Monitoring and Assessment 189: 432
Log transformed data uses paretric stats e.g. ANOVA and tukey's test. If not transformed, and if data does not fit normal distribution, use kruskal Wallis test. If p<0.05, then Mann Whitney pairwise
The title of the column should follow your require ments. However PAST does not support graphical editing, and does not support spaces in column title. What I usually do is get the clearest column title possible before pasting
If you are familiar with R, go for it. It is worth learning R. However if you are just looking for a quick and easy solution, PAST is good. Sorry but I am not familiar with maximum entropy.
@@LeeChoonWeng I only surveyed the islands (group) A and B once and divided their abundance into 2 rows so each island (group) has 2 rows. PAST was able to analyzed it. I also tried putting the second rows of each island (group) as 0 abundance, PAST was able to analyzed it too but a totally different result that doesn't reflect the abundance table was produced. I believe the 1st method like the one you did in the video is correct.
@@syunsn7230 I remembered you said you measured 5 islands. I will probably calculate the alpha and beta diversities. Then use cluster analysis to check for similarities with Bray Curtis coefficient.
@@LeeChoonWeng Those 5 islands are from a different set of locations. Yes, I've calculated the diversity indices at every site and had run the cluster analysis, but it was Jaccard instead of Bray Curtis. I will run Bray Curtis too. Thank you for your input.
Hi. I'm running a test on the abundance of mammals captured on 5 islands. I input the data into PAST as species (rows) and abundance on each island (columns). My ANOVA P value is less than 0.05, which is 0.02 but at Tukey's pairwise, no pairs are highlighted. The lowest P between the pairs is 0.06. How do I interpret this result?
Sorry but count data would probably not fit the criteria of ANOVA (parametric stats). If you wish to test if the community profile differs among the islands, try ANOSIM (analysis of similarities).
@@LeeChoonWeng Thank you so much for your input, I shall consider ANOSIM. Btw, I ran Normality test on the abundance data on each island and Shapiro Wilk are below 0.05 for all islands. I read that Mann Whitney U test is recommended for non-normally distributed data which is similar to ANOVA. Should I report Mann Whitney U results? Some pairs of island are significantly different according to Mann Whitney U.
@@syunsn7230 since p<0.05 in Shapiro, your data do not follow normal distribution. You may report kruskal Wallis for anova, and Mann whitney pair wise for post hoc.
@@LeeChoonWeng Thank you so much for your input. I've run Kruskal Wallis in PAST and the P is 0.15. No significant difference between sample medians. However, when I checked the Mann Whitney pairwise tab next to it, 2 pairs are highlighted with significant difference with P<0.05. The results are contradicting, how do I report this?
Thanks for the video...please i have a question. For example, i want to compare my core data with another core data with different ages and total number of data... How can i use regular interpolation to make all the ages from both cores to correspond so that i can compare
Good question. The chemicals are added to the soil, and must be mixed properly. If not mixed properly, microbial growth will be in patches. The chemicals added are to see what kind of chemolithotrophy is occurring. So one has CaSO4 and the other has FeSO4. This is the main difference.
That is a very good question. I looked it up, and it is not really explained anywhere. For me, the middle set best represents the average concentration for the group.
@@LeeChoonWeng thnks for the reply. Can i have another question. If for example im looking for the fecal coliforms.that means i have to run the presumptive test first which uses lauryl tryptose broth. Then proceed to EC medium for fecal coliforms. If i get 5-5-5-0-0 result for the presumptive. So i will plant the first 3 tubes to the EC medium and get 5-5-5 as the EC medium result. The question is, should i include the first 0 in the presumptive to get a 5-5-0 result. Because 5-5-5 fecal result doest give justice to the the decrese in number of bacteria in the presumptive. TIA 😊
@@rbb6194 From your first set of results, 5-5-5-0-0, I would have chosen 5-0-0 for the EC medium. The first rule for MPN is to choose the highest dilution with all positive tubes and the subsequent two dilutions.
