*Thread Reply:* A SPAAMily is a small group of people we put together to help build community and stronger connections amidst the conference! There will be a few short sessions for you to get to know your SPAAMily :)
*Thread Reply:* Yes! Same zoom link for every day, and weβll pin it to the channel
*Thread Reply:* (1) Abby (2) she/her (3) US, PA (4) ancient human microbiomes/health (5) my first research job was extracting gametes from California purple sea urchins.... via light electrocution
*Thread Reply:* (1) Laura (2) she/her (3) Mexico (4) ancient human pathogens in colonial period (5) I don't know why, but I can't smell or taste very well, so I can eat all kinds of food.
*Thread Reply:* (1) Cameron (2) he/him (3) US, PA (Philadelphia) but originally from Seattle, WA (4) pangenomics of human keystone pathogens (modern for now, but once I start my PhD I will switch to ancient samples!) (5) I am a semi-competitive curler π₯
*Thread Reply:* (1) Jasmin (2) she/her (3) Germany (4) Paleobiotechnology: natural products/resistance genes from aDNA (5) I am a semi-competitive Quidditch player π§Ήπ
*Thread Reply:* Athletes in weird sports, unite!
*Thread Reply:* (1) Maria (2) she/her (3) UK-based, but from Belgium (4) Paleobiology - currently working on a PhD with a mix of pop gen (extinct giant sloths, locally extinct Pacific rat population, and extant endangered Hispaniolan solenodon) and metagenomics to reconstruct the diet of Darwin's ground sloth from coprolites (talking tomorrow!! π©πΏπ§¬) (5) I once got slapped in the leg by a grumpy penguin while volunteering to do animal training at a local aquarium
*Thread Reply:* (1) Alina (2) she/her (3) Germany (4) ancient pathogens, mainly Hepatitis B virus (5) I separate different kinds of food on my plate and love to eat things plain, like plain riceβ¦
*Thread Reply:* (1) Carly (2) she/her (3) US, TX, (4) Coral genetics and symbiosis at long-term timescales - I do a lot of genetics, modeling, and recently, ancient DNA work! (5) I spend my free time rock climbing when it's not too hot in Texas
*Thread Reply:* (1) Nikolay (2) he / him (3) Sweden (4) bioinformatics (5) love cats
*Thread Reply:* (1) Kelly (2) she/her (3) UK-based but from USA (4) Pathogen aDNA and evolution, paleopathology/bioarchaeology, relationship between social structure and disease (5) the first thing I look up when traveling to a new city is if there is a ropes course/adventure parkβ¦.if so I promptly go
*Thread Reply:* (1) Megan (2) she/her (3) Germany (but from the US) (4) Ancient pathogen genomics (5) I grew up on my familyβs small Christmas tree farm
*Thread Reply:* (1) Aida (2) she/her (3) working in Germany (4) all things to do with ancient pathogens, interested in new ways to analyse the data we have on hand (5) I love the artist Joan MirΓ³, and after a visit to his museum when I was 4, I just painted in his style for a few years
*Thread Reply:* (1) Christine (2) she/her (3) PA, USA (4) shifts in oral microbiome due to antimicrobial agents (5) I cannot draw anything else but bones :D
*Thread Reply:* (1) Kadir (2) he/him (3) based in the Netherlands from Turkey (4) ancient DNA from archaeological sediments (currently Roman period) (5) Too much interested in basketball statistics.
*Thread Reply:* (1) Hannah (2) she/they (3) United States (4) mobility in the Iron Age and Roman mediterranean (and how that articulates with health and disease) (5) I once ran the Rome-to-Ostia half marathon, so whenever someone asked me how far the port (Ostia) is from Rome, I know :D
*Thread Reply:* (1) Iseult (2) she/her (3) Ireland (4) ancient genomics & disease ... (mainly humans but also a tiny bit of pathogens!) (5) not sure if this is that fun a fact, but in keeping with sporty theme I love trail running and climbing π
*Thread Reply:* (1) Constanza (2) she/they (3) based on USA, but from Chile (4) population history in South America (5) i own an inflatable dinosaur custom :party_dino:
*Thread Reply:* (1) Olivia (2) she/her (3) Texas, USA (4) Metagenomes of ancient mammals (5) I host a disco radio show once a week π πͺ© πΊ
*Thread Reply:* (1) Arumi (2) she/her (3) Mexico (4) ancient diet (5) I spend a lot of my free time watching funny/cute cat videos :catjam:
*Thread Reply:* (1) Sarah (2) she/her (3) USA, OK (4) evolution of microbial pathogens, commensals, and communities in response to human activity in antiquity (5) I also enjoy climbing and am fairly decent at juggling
*Thread Reply:* (1) Valentina (2) she/her (3) Italian newly based in Israel (4) I am about to start a postdoc project combining geochemical and sedimentological characterisation of archaeological sediments and sedaDNA analyses in the Levant region, mainly. (5) I dont dislike pineapple on pizza
*Thread Reply:* (1) Shreya (2) she/her (3) Chicago, USA (4) ancient pathogens + modern gut microbiomes in diverse populations (5) I miss my dog back home in California and would be very happy to see pictures of your pets over in <#C02D992D5TN|spaam-pets> π
*Thread Reply:* Hi all! (1) Sam (2) she/her (3) Canada (4) Health and disease in the past and their relationship with the oral microbiome (5) I do fibre arts in my spare time and crocheted little microbe stuffies for my lab's winter holiday gift exchange one year.
*Thread Reply:* Hello all! 1) Tre, 2) he/him, 3) U.S.A, 4) Identifying correlation between Neolithic environment and crowd disease in the Trypillia, Ukraine, 5) I enjoy downhill skiing and am working on beating my personal speed record of 50mph this winter
get your Bingo card--don't forget to save the url of your specific card so you can go back to it! https://bingobaker.com/#2274d77c663bc366
*Thread Reply:* One of the papers @Maria Spyrou mentioned at the end of her talk regarding ymt gene- https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1009995
*Thread Reply:* follow-up comment on @Nikolay Oskolkovβs question: in @Meriam Guellil et al. 2022, SI text, we speculate if an infection with Y. pestis might facilitate bacteremia of other already present pathogens, and therefore those might be easier to find in plague victims as coinfections than in other individuals.
*Thread Reply:* Also, in shameless self promotion (or for more info), here's the paper we just published on our coral aDNA work π https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.16642
*Thread Reply:* Hi Nikolay! Yeah, feel free to ask questions here. The low number of coral reads posed a big challenge in making popgen comparisons. The most "classic" way we worked around this was by first calling variants in our high quality modern coral samples, constructing a PCA, then projecting our ancient samples into this space. Of course, this biases the data because you're only looking at ancient samples in the context of modern day variation. However, it also removes the bias of what might be "uniquely ancient" from your samples (otherwise they almost always cluster together in PCA space due to low coverage or damage patterns).
*Thread Reply:* To get more certainty about their locations with the respect to modern samples, we did chromosome-level jackknifing - basically we projected them in PCA space 16 times, each time leaving out data from one chromosome. This tells us whether the patterns we see are being driven by just one region of the genome or represent a genome-wide signal.
*Thread Reply:* Ultimately, coverage and sample size limited us to just species-level comparisons for the coral.
*Thread Reply:* Cool, you did lots of careful analyses, congratulations with a very nice work!
Day 1 comic (need to rush to my bus so i don't get stuck in the UK wastelands overnight! see you all tomorrow)
https://bingobaker.com#ebd81fbaa3bb05a8 SPAAMily bingo!
*Thread Reply:* Lol thatβs okay Bjorn! I was adopted by the Clostridiaceae family π
*Thread Reply:* Sorry, I need to apologise too! I didn't realise that the conference is in the middle of the night for me!
*Thread Reply:* Same for me (Neisseriaceae), sorry I can only join tomorrow for the SPAAMily Group gathering!
*Thread Reply:* Sorry for the delay!
The only thing that the classifier influences is that that drives which key you need to use for your isolation source database
*Thread Reply:* You need to make sure that the species name and/or taxonomic id is the same between both your otu table and the database
*Thread Reply:* If that makes sense?
Bingo! Posting here because I don't have twitter.
rushing to bus! here is day 2 π (had to modify last minute because i didnt expect 5 lightning talks!!)
*Thread Reply:* Also, if you are interested in helping organise awesome conferences there will be a call for the next SPAAM5 committee volunteers in our 'Future of SPAAM session' π π if you are interested and can't make the session/need some time to decide, let us know!
*Thread Reply:* Yeah! Sorry, my bad! I thought it was a template! :)
*Thread Reply:* No worries!!
*Thread Reply:* Should've said at the beginning
*Thread Reply:* Aha sorry, I didn't see it was written spaam2
*Thread Reply:* No worries, sorry should've said that first , didn't mean anything by the change rejections!
*Thread Reply:* Okay, I tried something else, did a mess and now I stop touching it π«£π
*Thread Reply:* You added Zoe Agree's right?
*Thread Reply:* I accepted that
*Thread Reply:* Hi James! We have breakout groups on the zoom
*Thread Reply:* Thank youuuu
*Thread Reply:* I wonβt join either today, too much workβ¦
Bacteroidaceae are highly abundant in poop so we have a distinguished pile of poop. They're Gram negative so we have a dignified double membrane (and the 3rd one is part of a blebbing. Also holes are for the proteins). Then at the top we have a luxurious chain of bacilli b/c they're bacilli (description by @irinavelsko)
*Thread Reply:* @irinavelsko can you do the description?
*Thread Reply:* Bacteroidaceae are highly abundant in poop so we have a distinguished pile of poop. They're Gram negative so we have a dignified double membrane (and the 3rd one is part of a blebbing. Also holes are for the proteins). Then at the top we have a luxurious chain of bacilli b/c they're bacilli
*Thread Reply:* itβs a family of ds DNA viruses (the virus representing the head, the mouth the dsDNA). Monkeypox are part of this family, therefore the monkey (although we are aware that monkeys arent really the primary host!). the red dots are the rash caused by the virus. itβs quite a big virus, so in the left bottom we have another small virus as comparison. left top is a antibody looking out for the virus
Lactobacillaceae: They are gram-positive bacteria so we decided to make this little bacillus purple!! (we are not the best artists ever ahahahahh)
For Filoviridae We went for a sort of topical (both pathogens and Halloween) family crest with a bleeding eye, bat hosts, a monkey, and bloody diarrhea (a little graphic butβ¦weβre going for the gold here!)
Neisseriaceae: an oral pathogen that can also affect brains! can have a flagellum or be coccus form. Not pictured: a representation of famous family member Neisseria gonorrhoeae
SPAAMily Treponemataceae: family of spirochEATS, some of which cause treponemal disease in humans and animals and all of which look like ramen noodles π @ZoΓ© Pochon @Tre Blohm
Kelly Harkins LinkedIn that she shared in the Zoom chat: https://www.linkedin.com/in/kelly-harkins-claretbio/ And the Twitter accounts for the Career panel today: https://twitter.com/spaam_community/status/1580952458452344833
}
Twitter
Day 3! will make a big poster again and send it around in the next few days π
doodle that got kicked out of yesterday's panel because there was one talk that i didn't expect whops
*Thread Reply:* I think the following would really help:
- giving them a sense that there is already a bit of a sedaDNA community here to talk to, and the great advantages of SPAAM
- A bit more eukaryotic chats when discussing databases and classification methods (e.g. I would get a bit "so what about me?" if all that was taught was HOPS and pathogen-oriented methods)
- some of us already here could do a little more chatting to get things going in the seda channel?
*Thread Reply:* 1. Well do!
- We need experts in this though, we don't have that expertise in soaam (afaik) :( can you suggest anyone?
- That would be awesome we already have 2-3 publications from sedaDNa that haven't been added to theDir yet... And I'm sure we are missing lots still. Do you have any other ideas of what would be useful projects for you guys?
*Thread Reply:* But that is useful! Thank you!
*Thread Reply:* regarding number 2: We need more sedaDNA postdocs who feel chatty!
*Thread Reply:* Lovely!! We will be in touch! Think about what you might want to write about π
@channel here is the poster versions of the SPAAM4 meeting! both an A1 and A3 sized version whichever you feel like having/printing π
*Thread Reply:* @Gunnar Neumann we can ask multimedia to print off and put it next to spaam3 poster
*Thread Reply:* We should think about moving them elsewhere where they are more visible
*Thread Reply:* We will tweet it later too π
The coloring book is a success with my daughters
@channel you have until 11 am Mexico City time, 9 AM NYC time, 5 PM UK time, 6 PM Germany time TODAY to VOTE for your favorite full-length talk and lightning talk! And the next week to let us know if you got bingo π https://docs.google.com/forms/d/e/1FAIpQLSciT6aJhF2jEf9lA8G9XhjuX7vSqKxd8kfLwT9P5C26cixqXQ/viewform?usp=sf_link
*Thread Reply:* You mean 9 AM NYC time? π§
*Thread Reply:* Check section s3 ;)
https://www.biorxiv.org/content/10.1101/2022.10.03.510579v1.full
*Thread Reply:* Right, exactly! But in the talk, Nikolay talked about how MALT is great for following-up, so I guess Iβm just interested in whether it is necessary at this stage. If I ran aMeta today would I still need to include the MALT step?
*Thread Reply:* Hi @Shreya, we have a Bowtie 2 in aMeta as well, directly after the KrakenUniq step. I did not emphasize this during the talk, and we do not really stress this in the pre-print (there is the whole section about Bowtie2 for following up KrakenUniq in the supplementary though) because Bowtie2 does not have LCA. So MALT is a bit more intelligent and metagenomic-specific alignment, while Bowtie2 is a general purpose aligner. I personally think that following up KrakenUniq with Bowtie2 is fine if one runs sam2lca https://github.com/maxibor/sam2lca or ngsLCA https://github.com/miwipe/ngsLCA on the top of Bowtie2 alignments. This will be perhaps much faster and less resource demanding than MALT. Not properly checked though π
*Thread Reply:* Got it, thank you very much! Maybe I will do some testing there and let you know what I find π
*Thread Reply:* Wow, thank you so much! π€© Honestly all talks were fantastic!
