10:12:06 From vera benavente : Not everyone has a pet ;) 10:14:49 From Tingting Yang : I heard stories about babies change their gut microbiota community when they start taking table food. 10:15:09 From Alfred Spormann : True! 10:15:47 From Maaike Sangster : But I guess that's because they have to digest different things, rather than there being microbes on the food? 10:17:51 From Alfred Spormann : Yes. 10:23:14 From Otto X. Cordero : What is the residence time of microbes in the termite gut? 10:25:17 From Shayna Holness : Do humans not produce lactase either? Is that all produced by the gut microbiome? 10:28:45 From Sahana Kuthyar : How does the concentration of metabolites found in blood differ compared to the concentration of metabolites in the gut? 10:34:12 From Avi Flamholz : Wouldn’t it be easier to engineer the diet than the microbes? 10:35:03 From Alfred Spormann : Hold this thought and bring it up later. 10:35:53 From David Ngugi : Is it also possible that the species extinction is related with the evolution of humans (genetics; host factors) rather food (rather stochastic process as it were) 10:36:27 From vera benavente : @avi if the microbes come mainly from family then the problem/issue wouldn’t be solved with diet right?! 10:37:04 From Avi Flamholz : apparently diet has an effect 10:37:13 From Avi Flamholz : this is a repeated observation in the literature 10:37:15 From vera benavente : Yes it doesn’t on the abundance 10:37:46 From Avi Flamholz : so then I guess I repeat my question above - if we engineer the diet then we will engineer the abundance, no? 10:38:03 From vera benavente : That’s why the microbiome changes when you introduce solid food in babies 10:38:26 From vera benavente : Well yes you change the abundance but can’t bring back strains that you don’t have 10:39:08 From vera benavente : But may create a good environment for those strains if you are able to get them back 10:42:19 From Hanieh Shakeri Moghaddam : Do we use the same FMT for curing different diseases? I mean in terms of the microbes composition. 10:42:46 From Wanying Tian : do we know if the immune disorder diseases are associated with just gut microbes or also skin microbes and microbes in other systems? 10:46:53 From Shayna Holness : Do we have a microbiome in the small intestine as well, or only in the large intestine? 10:47:11 From Cristal Zuniga : Where are most of the microbes? or are they evely distributed? 10:48:28 From Jonas Cremer : Always wondering about this: there some good estimation how important death rates are (compared to growth and what we loose daily via bowel movements)? 10:50:35 From Ramis Rafay : So does this mean the colon is almost like a steady state sequential batch reactor? 10:50:37 From Meriem ElKaroui : how is the immigration rate calculated? 10:51:06 From Alfred Spormann : Ramis: I think this is a very good approximation 11:01:37 From Ramis Rafay : Doesn't the formation of butyrate from acetate also produce H2 as a byproduct? 11:01:48 From Sammy Pontrelli : What percentage of electrons go to H2? 11:02:17 From Alfred Spormann : Not necessarily. It depends on the specific fermentation patterns of the microbe and pH2 in vivo 11:02:34 From Ramis Rafay : Thanks Alfred 11:05:42 From Avi Flamholz : Are there no other terminal acceptors eg nitrate, iron, sulfur compounds? 11:05:51 From Avi Flamholz : or just very low levels of these? 11:06:58 From Alfred Spormann : Not in the gut. the gut is pretty much limited for inorganic electron acceptors, unless a pathogen ‘trick’s the host to produce a specific electron acceptor (e.g. tetrathionate. 11:07:13 From Eric De Giuli : If you know someone’s diet (say in steady state), and that they’re healthy, how well can you estimate the composition of their gut biota? 11:09:34 From Avi Flamholz : thanks @alfred! 11:09:39 From Avi Flamholz : I assume that there are also high levels of CO2 and HCO3- that some bugs use in their metabolism 11:11:14 From Jonas Cremer : I once tried to figure out the numbers more quantitative, which hydrogen releases paths are most important and what are the hydrogen levels within the gut. Hard to find the numbers. But we have numbers of gas composition Hydrogen varies but can make up to 50%. 11:11:15 From Ashish B. George : Is the net electron consumption in anabolism zero? Is that why one needs to balance electrons in catabolism? 11:11:33 From Alfred Spormann : YES!! And this is where acetogens and methanogens come in because they use the abundant CO2 as electron acceptor. 11:11:35 From Jonas Cremer : It is really unclear, I would say, which release path is most important. 11:12:05 From Avi Flamholz : @alfred, yes this for sure, but I believe that there are also heterotrophs doing similar tricks 11:12:46 From Avi Flamholz : This lovely paper “eating for two” from michael fishbach discusses this point. https://pubmed.ncbi.nlm.nih.gov/22018234/ 11:13:24 From Alfred Spormann : Fermenting heterotrophs usually do not use CO2 as electron acceptor, unless it’s an acetone in a fermentative mode. 11:13:44 From Ramis Rafay : In the same vein, could propionate also be involved in these chain elongation type reactions (Acetate -> Butyrate) to make longer odd-carbon acids like valerate? 11:14:13 From Avi Flamholz : Not as a primary acceptor, but as part of important catabolic and anabolic pathways. 11:14:33 From Avi Flamholz : @jonas seems like the field would benefit a lot from better collections of quantitative values... 11:16:03 From Alfred Spormann : Chain elongation is another way to generate electron sinks. The question of which path to go for ‘creating’ electron acceptors, depends on the fermentation. Syntrophic CO2 reduction to formate is also CO2 utilization. 11:18:29 From Jonas Cremer : @Avi: yes, 100% agree. 11:19:19 From Avi Flamholz : Bionumbers would be a good home for the values you have already collected. 11:23:23 From Korin Jones : What role does host regulation play in this scenario (if any)? 11:24:50 From Avi Flamholz : @Terry to your point about 12-24 dilution times, the fast-growing gut bacteria wont grow nearly as fast anaerobically on recalcitrant fibers 11:25:00 From Korin Jones : Also, would you suggest that there are situations where historical contingencies would be determining factors in community composition? 11:25:30 From Avi Flamholz : I don’t know what their growth rates are on these substrates, but certainly not 1 hour doublings 11:26:01 From Korin Jones : I should also specify that by host regulation, I'm speaking beyond just dietary intake, but more on host chemical signaling 11:27:48 From Otto X. Cordero : Is there any data on biomass per “species” in the gut? In some environments there can be huge differences (100x), so rare microbes can contribute significantly to biomass turnover. Anything like this in the gut? 11:29:55 From Avi Flamholz : @otto I wonder if sequencing is a reasonable proxy for biomass. ie. how variable is biomass/genome? relatedly: there are some measurements of turnover in other systems, e.g. from mary firestone using 13C uptake into DNA. 11:30:09 From Otto X. Cordero : @Korin: this in cows, but related to your question it shows that different animals develop their microbiome in different ways because of contingency effects https://www.nature.com/articles/s41467-020-15652-8 11:30:25 From Tingting Yang : A dumb question: what's inside the mucus? Or what resources would mucus provide? 11:30:45 From Otto X. Cordero : Avi: sequencing is not a proxy for biomass 11:32:43 From Wanying Tian : Is there any gut organoid built already? 11:32:53 From Korin Jones : @Otto X. Cordero That article looks really interesting, thank you! 11:52:03 From Otto X. Cordero : Very artistic illustration 11:52:32 From Ramis Rafay : Wonder what the waiver form for that one looked like 11:53:06 From Tingting Yang : No H2S in the gas components? (Sorry I can't use mic today...) 12:09:56 From Otto X. Cordero : I think residence time is too shjort 12:11:35 From Otto X. Cordero : Dilution, yes 12:12:13 From Avi Flamholz : This is certainly the qualitative result of many years of cellulosic biofuel research - cellulose and lignin are very hard to degrade biotically 12:13:12 From Ramis Rafay : Perhaps the environment of the gut is not conducive for cellulose degraders 12:13:30 From Ramis Rafay : as opposed to cows, I guess 12:14:02 From Alfred Spormann : Something along these lines…. 12:27:20 From Cristal Zuniga : Where all the students "healthy"? 12:27:34 From Ramis Rafay : Is it possible the available ecological niches cannot accommodate more diversity? 12:34:35 From Hector Hernandez Gonzalez : 1. What about A. muciniphila? As far as I know it is also a butyrate producer and highly abundant in healthy individuals. 2. Did the increase in butyrate in your study correlate with abundance of A. muciniphila? 3. Can a healthy core microbiome be engineered without A. muciniphila or any other organism that seem to be an indicator of healthy metabolic status? 12:36:10 From Otto X. Cordero : What about the energetics? What is the free energy of acetate -> butyrate vs alternative fermentation pathways? 12:41:33 From Veronika Dubinkina : Maybe there is some additional cross-feeding (? 12:41:57 From Veronika Dubinkina : e.g. cofactors, amino acids 12:44:07 From Ramis Rafay : Or preference of certain metabolites by Fp and Er that could be produced by B. faecale and R.bromii, which is what I thought Alfred was alluding to 12:48:04 From Ramis Rafay : Could you then potentially enhance butyrate production by feeding people a methanogen inhibitor? 12:49:02 From Ramis Rafay : like BES (or something non toxic if that doesn't work) 12:51:10 From Tingting Yang : I am wondering if the sampling protocol is very standardized? Since the sample-taking is quite private, how to guarantee the quality of the samples?