10:10:01 From Shayna Holness to Everyone : What's activated sludge? 
10:19:41 From Avi Flamholz to Everyone : Is there any chance that there is a “lamppost” here i.e. some very weird organisms that are not amplified by these primers?
10:19:59 From Avi Flamholz to Everyone : And would not be represented well in 16S studies
10:27:26 From Akshit Goyal to Everyone : Even strains that are 100 base pairs apart (whole genome, 100% identical 16S) have very different abundance dynamics in the same community: https://www.biorxiv.org/content/10.1101/2021.01.04.425224v1
10:29:34 From Avi Flamholz to Everyone : But pH is a logarithmic variable unlike concentration
10:32:31 From Hector Hernandez Gonzalez to Everyone : What is the relationship between a bacterial “species” defined by 16S rRNA with the concept of ecotype?
10:49:40 From Isaac Klapper to Everyone : When you say “can’t be cultured” do you mean that we don’t know what medium to use for a culture, or that some organisms simply can’t be monoculture regardless?
11:01:34 From Wanying Tian to Everyone : can RNAs can be sequenced and analyze by this method?
11:02:24 From Nidhi Gupta to Everyone : What is the use of amplicon sequencing?
11:03:46 From Ramis Rafay to Everyone : Are there ways to then infer identity from assembled contigs? Could I tell that a 'kiwi slice' I see in my sample came from a kiwi, for example?
11:06:30 From Nidhi Gupta to Everyone : Coming back to amplicon sequencing - it means it will identify only identified phyla and function. It is not helpful for unidentified phyla/function where as metagenomic sequencing can give that idea as well.
11:07:11 From Petra Steffen to Everyone : but could there also be organisms that have some part of the genome with high gc content and other parts with low gc content? Why should it be the same gc level for the whole genome?
11:07:35 From Avi Flamholz to Everyone : E.g. from horizontal gene transfer
11:08:42 From Petra Steffen to Everyone : do we know why the gc level generally is simmilar for one species?
11:10:00 From Petra Steffen to Everyone : okay thanks!
11:12:34 From Petra Steffen to Everyone : Can there no inhibiting compound that might possibly change to ratio of reads?
11:13:11 From Petra Steffen to Everyone : sorry, can there be an inhibiting compound ...
11:13:33 From Avi Flamholz to Everyone : You purify the DNA
11:13:45 From Avi Flamholz to Everyone : To separate it from the cells and growth environment
11:13:58 From Avi Flamholz to Everyone : Should be relatively free of contaminants once on the sequencer
11:14:18 From Petra Steffen to Everyone : I do that for PCR as well, but I still sometimes have problems, don't I?
11:14:39 From Petra Steffen to Everyone : Or is it a different approach of purifying?
11:15:30 From Avi Flamholz to Everyone : No, it’s the same. There are biases, but probably mostly due to the extraction efficency
11:15:39 From Avi Flamholz to Everyone : Rather than compounds making it onto the sequencer
11:17:52 From Petra Steffen to Everyone : thanks1
11:18:38 From Avi Flamholz to Everyone : Can always purify a second time if you are worried about such things. There are lots of quality control checks one can do for DNA/RNA seq libraries.
11:22:57 From Ting He to Everyone : Is that possible to use the FISH to directly detect the endophytic fungi from the healthy plant organ (like leaf or stem)? Or normally is that just too less of the organism to detect for the healthy plant material ?
11:23:22 From Avi Flamholz to Everyone : You can do this I believe
11:23:35 From Avi Flamholz to Everyone : Fungal protocols are a bit different from bacterial ones from what I remember
11:25:54 From Ting He to Everyone : Thanks
11:29:57 From Wanying Tian to Everyone : on average how much of the genome we know the function?
11:55:38 From Wanying Tian to Everyone : maybe upload the ppt to google slides and use browser to present?
11:59:40 From Avi Flamholz to Everyone : @wanying - for E. coli I think something like 10% of the proteome is unknown function https://www.proteomaps.net/data_sets/eco_Li_complete/eco_Li_complete_cost_lv2.html
12:00:00 From Avi Flamholz to Everyone : The number is larger as a fraction of the genome. Maybe 30% if I remember correctly
12:04:24 From Veronika Dubinkina to Everyone : For metagenomic studies, if you align the reads to the databases of known genes (e.g. KEGG, COG, etc) the typical fraction that can be matched is on the level of 60-80%, depending on how well-studied is the environment. And many of the genes you’ll match are still some „putative proteins” predicted based on protein domain information. So that might give you some idea of the fraction of the genes that are still out there, but without known function.
12:05:09 From Avi Flamholz to Everyone : Very interesting number Veronika, thank you!
12:10:46 From Ramis Rafay to Everyone : what do those polygon-type structures signify at the endpoints?
12:11:47 From David Ngugi to Everyone : Can ammonia oxidizers also oxidize methane to some extent—if, methane oxidizers can oxidize ammonia partly with their pmoA ..
12:16:24 From Wanying Tian to Everyone : thanks! @avi and Veronika
12:27:07 From Avi Flamholz to Everyone : How does the flux distribution get calculated? Is he maximizing the biomass flux?
12:29:07 From Avi Flamholz to Everyone : I’m also not sure if I follow how you get independent numbers for rate and yield out of these models?
12:39:44 From Ramis Rafay to Everyone : How fast is the conversion of nitrite to N2? Did you see a higher accumulation of nitrite to support the enrichment of this annamox reaction?
13:03:28 From Hector Hernandez Gonzalez to Everyone : Thank you very much!
13:03:30 From Malaika Ebert (she/her/hers) to Everyone : Fantastic talk, Thanks very much!
13:03:40 From Ting He to Everyone : Thanks