home Meeting Reports Lake Arrowhead Microbial Genomics Meeting 2012: Microbiology of the Built Environment Session

Lake Arrowhead Microbial Genomics Meeting 2012: Microbiology of the Built Environment Session

Last night was the Microbiology of the Built Environment session at the bi-annual Lake Arrowhead meeting.  This session was organized and sponsored by microBEnet.  I recorded some of the talks and will post those videos here after some editing.

Here’s a summary of the speakers and the topics discussed.

The first speaker was James Meadow from the BioBE Center.   He gave a talk entitled “Architectural Influences on the Built Environment Microbiome”.  This was an overview of some of the projects going on at the BioBE Center including their hospital ventilation study, work on dust/air samples collected around campus, and their work on classroom microbiomes.  For some more information search microBEnet for “BioBE Center” or check out their website.

The second speaker was Jason Stajich from UC Riverside and a member of the MoBEDAC project.  His slides for his talk “Fungi in the Built Environment” can be found here.  Since Jason was the only speaker at this entire conference talking about fungi he gave a good intro into why fungi are cool.  He also talked about the 1000 Fungal genomes project, the FungiDB, fungal taxonomy, and the ITS barcoding scheme.

Next up was Laura Sauder from the University of Waterloo who gave a talk entitled “Exploring Archaeal Ecology and Abundance in Built Freshwater Environments”.  She talked about the discovery that archaea, particularly thaumarchaeota, play an important role in nitrogen cycling in built environments such as aquaria and wastewater treatment plants.  Also worth noting that microBEnet will be collaborating with this group (Josh Neufeld) on an undergrad research project in aquariums over the next year.

Our fourth speaker was Tara Schwartz from UC San Diego who was replacing her PI (Scott Kelley) at the last minute.  Her talk was entitled “Viral and Bacterial Communities in Public Restrooms”.   This work grew out of work produced by another Sloan funded lab on the “Microbial Biogeography of Public Restroom Surfaces”.  Tara talked about studying fewer sites in more detail, particularly in trying to catch the viruses as well as the bacteria and archaea.

The last speaker of this section was Susanna Remold from the University of Louisville.  She talked about “Pseudomonas as a Model for Studies of Microbes in the Home”.  Her group went into homes and sampled a huge number of sites (150/house, 12,000 in total).  Unlike many of the projects we’ve blogged about, they are actually culturing strains from their samples and comparing the phenotypes.  They then hope to move into “genomics informed by culture-based studies”.

Good talks and a very informative session overall.

Here is a “Storification” of the Tweets from the meeting:

Microbiology of the Built Environment Session at #LAMG12

Storified by Jonathan Eisen · Sat, Sep 22 2012 07:54:02

The Tree of Life: Lake Arrowhead Microbial Genomes 2012 …Jul 11, 2012 … Helping the organizers plan the Lake Arrowhead Microbial Genomes meeting … In particular I organized a session on Mi…
Microbial Genomics (Lake Arrowhead, CA) | microBEnet: The …Jul 12, 2012 … Lake Arrowhead Microbial Genomics Meeting 2012: Microbiology of the Built Environment Session | microBEnet: The microb…
microBEnet Blog | microBEnet: The microbiology of the Built …2 days ago … Last night was the Microbiology of the Built Environment session at the bi-annual Lake Arrowhead meeting. This session w…
People Behind the Science: Jason Stajichmicrobenet
James Meadows
Micro of the built environment special session #LAMG12Paul Orwin
First up James meadow from u oregon #LAMG12Paul Orwin
Uploaded my slides for my talk tonight at #LAMG12 on Fungi in the Built Environment http://www.slideshare.net/jasonstajich/stajich-lamg12-indoor-fungiJason Stajich
James Meadow from UO (aka a young John Heidelberg, of TIGR fame) talking about architecural influence on microbiome #LAMG12 @phagecologistBen Tully
5 talks starting up on Microbes in the Built Environment, now called MicrobeBegnet (super yummy, no?) http://Microbe.net #LAMG12Gautam Dantas
@phylogenomics failed to respond tweet while speaking #LAMG12 #disappointingPaul Orwin
Architectural influences in built environment #LAMG12Paul Orwin
Lol even sounds like JHeidelberg #LAMG12 @phantomBugs @phagecologistRohan Sachdeva
Session tonight at #LAMG12 is on "microbiology of the built environment" and is sponsored by my microBEnet project http://microbe.netJonathan Eisen
#lamg12 James Meadow is talking about how architectural choices affect the microbiome of the built environment.Jenna Morgan Lang
And my http://microbe.net project itself is sponsored by the Alfred P. SLoan Foundation #LAMG12Jonathan Eisen
Now up at #LAMG12 James Meadow from the U. Oregon Biology of the Built Environment (BioBE) Center http://biobe.uoregon.eduJonathan Eisen
Energy efficient design. Lots of airflows in, lots of microbes #LAMG12Paul Orwin
Evening #LAMG12 "Microbiology of the Built Environment" session kicking off now with James MeadowHolly Bik
James Meadow discussing Kembel et al. ISME paper http://www.nature.com/ismej/journal/v6/n8/abs/ismej2011211a.html on architecture & built environment microbiome #LAMG12Jonathan Eisen
Meadow: Architecture influences the diversity and structure of the built environment microbiome – see paper http://www.ncbi.nlm.nih.gov/pubmed/22278670 #LAMG12Holly Bik
@hyphaltip, how about this… MicrobeBeignet #LAMG12 http://pic.twitter.com/yd9QOZ0hGautam Dantas
Meadow: "College kids are filthy" #LAMG12 #lamgquotesHolly Bik
College kids are filthy. Tough but fair #LAMG12Paul Orwin
Meadow says "college kids are filthy" to introduce their work on studying microbes in building at U. Oregon #LAMG12Jonathan Eisen
@volatilebug @hyphaltip this needs to be done #LAMG12Paul Orwin
James Meadow (U Oregon): microbiology of built environment; "college kids are filthy" #LAMG12 #lamgquotesGautam Dantas
Meadow: "we used a high throughput dust sampling device – this one is made by shopvac" #LAMG12Jonathan Eisen
Recording the talk by James Meadow, video will be at http://www.microbenet.net #LAMG12David Coil
#lamg12 In case anyone was wondering about the 100% uncertainty figure for wetlands: http://pubs.usgs.gov/sir/2010/5233/pdf/sir2010-5233-Main.pdf See page 38 of pdfSusannah
Biogeography within a university campus hall… here comes things I don’t want to know. #LAMG12 AND biogeography based on surface sampled.Ben Tully
Surface sampling shows lots of variation. Bonus goofy pic of boss #LAMG12Paul Orwin
Meadow shows pic of @JessicaLeeGreen and says"since my bosses are not here I get to show goofy pictures of them #LAMG12Jonathan Eisen
@PMOrwin @volatilebug @hyphaltip So should the microBeignet be a *very tiny* beignet, or a beignet covered in a microbial biofilm? #LAMG12Holly Bik
#lamg12 Walls, chairs, floors and desks in the same room have completely different microbiomes!!Jenna Morgan Lang
Chairs look like butts floors look like skin #LAMG12 #ewwwPaul Orwin
Chairs — "this is nasty" — chairs look like butts. Floors look like skin. In terms of community composition #LAMG12Ben Tully
Meadow: Microbial communities on chairs show more similarity to human fecal communities. Euuuughhh #TMI #LAMG12Holly Bik
Meadow: 16s profile of floors, desks, walls, chairs all ordinate (by principal coordinatesl) separately, "chairs look like butts" #LAMG12Gautam Dantas
@Dr_Bik @volatilebug @hyphaltip the acronym is the key. The rest is gravy #LAMG12Paul Orwin
#lamg12 I wonder if James Meadow illustrated his own slides.Jenna Morgan Lang
#LAMG12, was following your stream; however, now the OCD kicked in and I’m cleaning. Thanks for the motivation and sorry for the #hijack ;)Cyrus Radfar
Meadow: Classroom occupancy predicts microbial community composition – you can cut energy in half & not affect microbial communities #LAMG12Holly Bik
Meadow – you can cut energy use in half for cooling at night and not change the interior room/building microbial community. #LAMG12Rohan Sachdeva
Meadow: daily surveys of microbes in air in buildings; comparing / contrasting relation between microbes / air flow / occupancy #LAMG12Jonathan Eisen
Meadow: Outdoor air communities change every day, and this drives what happens inside the built environment #LAMG12Holly Bik
Hard to pay attention to rest of the talk. Just thinking about chair I’m sitting on #Lamg12Paul Orwin
Meadow: "we’ve stripped away a lot of the complexity and have a simplified model – people are filthy" #LAMG12Jonathan Eisen
@phantomBugs @jennomics #typingishard but #LAMG12 red wine is so very goodHolly Bik
Having 10 people (aka filthy students) enter a room has a similar impact as 50 people. Stirring up the community that is there #LAMG12Ben Tully
"We have a simplified model – people are filthy" #LAMG12 #lamgquotesIddo Friedberg
@phantomBugs #LAMG12 Just enough.Jenna Morgan Lang
Jason Stajich
Fungi in be Jason stajich #LAMG12Paul Orwin
3 twitter identities #socialnetworkingftw #LAMG12Paul Orwin
Eukaryotes are teh awesomez!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Jason Stajich now talking about fungi at #LAMG12Holly Bik
I think it’s pronounced fun-guy. Like "Why should you invite a fungi to a party? Because he’s a fun guy" @hyphaltip #LAMG12Ben Tully
#LAMG12 Jason Stajich (a.k.a. Token) is talking about fungi in the built environment.Jenna Morgan Lang
Now up at #LAMG12 Jason Stajich from UC Riverside discussing fungi in the built environmentJonathan Eisen
@hyphaltip talking about Fungi in the built environment. Slides: http://www.slideshare.net/jasonstajich/stajich-lamg12-indoor-fungi #LAMG12Iddo Friedberg
@phantomBugs @hyphaltip Why did the Fungi leave the party? Because there wasn’t mushroom. #LAMG12Holly Bik
Jason Stajich is @hyphaltip on Twitter; has a good blog http://fungalgenomes.org/blog/ and generally pretty active in social media #LAMG12Jonathan Eisen
Least gross fungal infections. Also neat symbioses and communication #LAMG12Paul Orwin
Jason Stajich @hyphaltip emphasizing the diversity of fungi and their environments as a preamble to his talk #LAMG12Surya Saha
Stajich discussing studies estimating the number of fungal species on the planet – most suggest it is in the many millions #LAMG12Jonathan Eisen
Jason Stajich (UC riverside) @hyphaltip : fungi in built environ. cool structures of natural fungi, scary pics of fungal infections #LAMG12Gautam Dantas
400+ fungi genomes?!!! Who knew? #LAMG12 @hyphaltipBen Tully
#LAMG12 @hyphaltip sez pre-genomics: 1.5M species of fungi estimated, but probably >6MIddo Friedberg
Stajich discussing the 1000 fungal genomes project http://1000.fungalgenomes.org/home/ to get two genomes / family #LAMG12Jonathan Eisen
@arturgreensward woohoo! thanks – I teach microbiology/biotech at ARC in Sacto. The #LAMG12 tweets have been great – lots of good info!Ken Kubo
1000 fungal genomes project. Improve coverage #LAMG12Paul Orwin
Jason Stajich – Taking the Noah’s Ark approach of sequencing two genomes per group. #LAMG12Rohan Sachdeva
Stajich: lots of new fungal genomes coming online, http://1000.fungalgenomes.org/home/ #LAMG12Gautam Dantas
Jason Stajich is discussing mush"rooms" in the built environment. #LAMG12Jenna Morgan Lang
Data mining to annotate and I.d. By function. For the nonbioinformatician #LAMG12 #musictomyearsPaul Orwin
Please cut out the fungus jokes on #LAMG12 tweets. Enough with this shitake.Iddo Friedberg
After Meadows butt-microbes-on-chairs talk, I may not sit down in a mini skirt ever again. #LAMG12Fiona Brinkman
Stajich: naming of fungi is a bit of a mess and creates complexities for working on them #LAMG12Jonathan Eisen
Sexual & asexual morphologies of fungi cause confusion in species identification. #LAMG12Iddo Friedberg
Many fungi have separate names. Difficult to teach mycology #LAMG12 didn’t know they still teach mycologyPaul Orwin
Morel fungi jokes, you say? Why I’d be glad to oblige… #LAMG12Holly Bik
Stajich referencing this press release http://newscenter.berkeley.edu/2012/09/14/fungus-expert-celebrates-10000th-citation-for-1990-publication/ about 10000 citations for a fungal rRNA taxonomy paper #LAMG12Jonathan Eisen
Fungal barcoding agreed upon sequence for species typing #LAMG12Paul Orwin
Stajich – Talking about hightroughput sequencing of fungal ITS rather than 18S (more resolving). Btw – ITS is my favorite region. #LAMG12Rohan Sachdeva
Stajich referencing this PNAS paper on indoor fungal diversity / biogeography http://www.pnas.org/content/early/2010/06/22/1000454107 #LAMG12Jonathan Eisen
#lamg12 Stajich: ITS is the official fungal markerSusannah
.@hyphaltip talking abt fungal nomenclature mess and "official" ITS barcoding region. Both relevant for interpreting environ. data #LAMG12Holly Bik
Earth latitude strong driving force in fungi diversity. Like other euks, really. #LAMG12Iddo Friedberg
More genomic than morpho information available for fungi. Trying to change that using isolation techniques #LAMG12Iddo Friedberg
Stajich – mentions Keith Siefert’s indoor fungi project http://www.microbe.net/im-bol-the-indoor-mycota-barcode-of-life/ #LAMG12Jonathan Eisen
Stajich – Fungal diversity increases with latitude. Opposite of bacteria and mostly everything else. #LAMG12Rohan Sachdeva
Admire challenges @hyphaltip deals with, re fungal genomics and taxonomy. Not easy! #LAMG12Fiona Brinkman
Laura Sauder
Next up Laura sauder on archaea #LAMG12Paul Orwin
Archaea in the built freshwater environment. By Laura Sauder from University of Waterloo. Just like SCM1 from Seattle Aquarium? #LAMG12Ben Tully
Now up at #LAMG12 – Laura Sauder @LauraASauder "Exploring archaeal ecology and abundance in built freshwater environments"Jonathan Eisen
Archaea in freshwater built environment. Looking at nitrogen cycle in particular ammonia oxidation #LAMG12Paul Orwin
Sauder: two main environments being looked at – aquariums and wastewater treatment #LAMG12Jonathan Eisen
Shout out to winogradsky #LAMG12Paul Orwin
Laura Sauder at #LAMG12 discussing work of Winogradsky http://en.wikipedia.org/wiki/Sergei_Winogradsky and how it was ruined by metagenomicsJonathan Eisen
Relevant to Sauder’s talk – Nitrifying archaea in NASA clean rooms: http://bit.ly/PphD6L #LAMG12Rohan Sachdeva
Metagenomics came along and ruined everything #LAMG12Paul Orwin
"I hope you recognize this is Sergei Winograndsky, if you are medical microbiology, you are excused." -Sauder #LAMG12 #lamgquotesBen Tully
Sauder: "and then of course metegenomics had to come around and ruin everything" #LAMG12 #metagenomicsGautam Dantas
Woohoo! A paper about culturing something #LAMG12Paul Orwin
Laura Sauder #LAMG12 – Venter 2004 paper sugg that Archaea capable of ammonia oxidation. Novel b/c process was thought to be only bacterialHolly Bik
New archaea phylum thaumarchaeota #LAMG12Paul Orwin
Just heard at dinner from @jennomics : "I’m just a whore for twitter followers" #LAMG12 #lamgquotesGautam Dantas
Laura Sauder (U waterloo): archeae in built env (in this case env built by humans but not inhab’d by it) #LAMG12Gautam Dantas
Laura Sauder talking about nitrification in bacteria and archaea. Also an upcoming Eisen lab project. #lamg12David Coil
@phylogenomics #LAMG12 you organized has 12 female speakers out of 34 (35.3%). Does it an acceptable number for a science conference?Dawei Lin
Aoa more abundant than aob. What have w been missing #LAMG12Paul Orwin
Sauder discussing Venter et al Sargasso Study single sentence on ammonia oxidation http://phylogenomics.files.wordpress.com/2012/02/74-venter-2004.pdf #LAMG12Jonathan Eisen
Sauder: "my adivsor is kinda an aquarium nerd" #LAMG12 #lamgquotesGautam Dantas
Suader discussing how they collected aquarium samples with help from citizens around Waterloo http://www.microbe.net/2011/08/20/what-microbes-are-lurking-in-your-fish-tank-good-candidate-for-some-citizen-microbiology-i-think/ #LAMG12Jonathan Eisen
@kbradnam @phylogenomics And at *this* particular moment, *three* lab members plus boss are live tweeting from #LAMG12Holly Bik
@volatilebug #LAMG12 #lamgquotes "He is sensitive about that, so please don’t tweet it."Jenna Morgan Lang
Sauder: many orders more ammonia oxidizing archaea in various environs than ammmonia oxidizing bacteria. #LAMG12Gautam Dantas
Sauder discussing how many aquarium nuts pour ammonia oxidizing bacteria into their fish tanks but that might not help #LAMG12Jonathan Eisen
Lessons learned from #LAMG12: By prefacing a sentence with "please don’t tweet this", you will guarantee extensive Twitter coverageHolly Bik
Dgge! Awesome #LAMG12Paul Orwin
#LAMG12DGGE What ! What!Jenna Morgan Lang
PlosONE paper #LAMG12 # openaccessPaul Orwin
Laura Sauder talking about Thaumarchaeota being the dominant Ammonia Oxidizers in freshwater aquar. biofilters http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0023281 #LAMG12Surya Saha
Aoa adapted to low ammonia. Look at wastewater plant. Reactors with flow in series. Nice correlation of low nh4 to high aoa! #LAMG12Paul Orwin
Talk too long? Just carry "ninja slides" on your PPT file. #LAMG12Ben Tully
Ninja slides – awesome talk technique #LAMG12Paul Orwin
@joshdneufeld We just heard Laura Sauder talk at #LAMG12 – awesome project! We Eisen labbers <3 aquarium mircobiomes!Holly Bik
@phantomBugs @jennomics @Dr_Bik Shamelessly alking about strategies for getting more twitter followers. #LAMG12Rohan Sachdeva
Nota bene after drinks thru posters and dinner tweets r more free flowing #LAMG12Paul Orwin
Tara Schwartz
Following up on gross chair microbiome – microbiome of public bathrooms #LAMG12Paul Orwin
Tara Schwartz: Bacteria and viral communities in public restrooms, San Deigo State U. #LAMG12Ben Tully
Next up at #LAMG12 Tara Schwartz from SDSU discussing "viral and bacterial communities in public restrooms"Jonathan Eisen
Differing hygienic routines of people who us public restrooms #LAMG12 #tactPaul Orwin
I <3 agar slants. #LAMG12Ben Tully
This is going to be good. Bacterial diversity in public restrooms. #LAMG12Iddo Friedberg
Tara Schwartz giving a talk that will keep us all out of public restrooms. #lamg12David Coil
Schwartz: viral diversity in indoor environments has been largely ignored #LAMG12Jonathan Eisen
Nice treatment of great plate count anomaly. No mention of "unculturable" #LAMG12Paul Orwin
Corrections This is going to be good. Bacterial AND VIRAL diversity in public restrooms. #LAMG12 #sorryIddo Friedberg
Three sites. Toilet seat. Floor in front of toilet. Hand dispenser. Both male and female. #LAMG12 #ivegotabadfeelingaboutthisBen Tully
Schwartz discussing how they are following up Flores study of bacteria in public restrooms http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0028132 #LAMG12Jonathan Eisen
Tara Schwartz (sdsu): the great indoors – biodiversity of bugs and viruses in public restrooms. #LAMG12Gautam Dantas
Toilet associated, floor associated, and toilet associated. Male & female restrooms, 8 week long. study. . #LAMG12Iddo Friedberg
Microbial biogeography of public restrooms http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0028132. Schwartz building on this #LAMG12Paul Orwin
Each day they reset the surfaces using 10% bleach 8hrs. prior to collection. #LAMG12 #toiletomeIddo Friedberg
@arturgreensward @Dr_Bik real question does the paper help? #LAMG12Paul Orwin
Interesing: floor samples (but not other surfaces) in restrooms had cyanobacteria #LAMG12 #restroomomeIddo Friedberg
Schwartz:Planning on using RpoB sequencing rather than 16S to get finer phylogenetic resolution. Might be hard to get "universality" #LAMG12Rohan Sachdeva
Susie Remold
Final talk Susie remold. Pseudomonas as model for microbes in home #LAMG12Paul Orwin
The #LAMG12 culture demands you provide one title in the program and another in your slides.Iddo Friedberg
"I’m going to read the title that is here" After a night of changes to talk titles. Susanna Remold, University of Louisville. #LAMG12Ben Tully
Last in "microbiology of the built environment" session: Susie Remold "Pseudomonas as model for studies of the microbes in the home" #LAMG12Jonathan Eisen
Susan Remold describes her work as using retro-future techniques. #LAMG12Iddo Friedberg
A culture based approach. " once u have something in culture, u have it in culture" #LAMG12Paul Orwin
Remold: "One benefit of culturing is that once you have things in culture, you have them in culture" #LAMG12Jonathan Eisen
Susanna remold (u of louisville): pseudomonas as a model for studies of microbes in the home #LAMG12Gautam Dantas
Trick 1st gen college students into liking microbial ecology #LAMG12Paul Orwin
Remold showing cartoon of Hutchinson’s model of the realized niche #LAMG12Jonathan Eisen
The #LAMG12 meeting: still tweeting from late-night talks long after the rest of drank a bottle of wine and called it a night. #gogenomesgoJennifer Gardy
Remold has 150 sampling sites in a home! #lamg12David Coil
Find pseudo in homes. Look at lots of sites. Old school culture approach. Found lots of putida some aeru #LAMG12Paul Orwin
Remold discussing in part this paper http://www.ncbi.nlm.nih.gov/pubmed/21503776 on Pseudomonas in human homes #LAMG12Jonathan Eisen
@jennifergardy still going and yet no @kittenmicrobiome talk. #LAMG12Jason Stajich
Lots of aeruginosa in drains. Biofilms ftw! #LAMG12Paul Orwin
@hyphaltip @jennifergardy @kittenmicrobiome Remold had a pic of cat getting mouth swabbed though. #LAMG12 #CatNotHappyPicIddo Friedberg
Test dispersal v adaptation effect w phylogenetic analysis #LAMG12Paul Orwin
Remold, 12,000 samples in a longitudinal study. Must be fun to organize. #lamg12David Coil
@phylogenomics @iddux thanks guys, really been enjoying the #LAMG12 tweets the past couple of days.Paul Glasser
@fionabrinkman: "Admire challenges @hyphaltip deals with" #LAMG12 <– Jason is a fun guy, he conidia it that without chitin.Iddo Friedberg
@iddux @hyphaltip @jennifergardy @gilbertjacka Cat too old – more of a #LOLcatsmicrobiome than a @kittenmicrobiome #LAMG12Holly Bik
Pseudomonas as a model for studying microbes in the home MT @phylogenomics Remold discussing in part this paper http://www.ncbi.nlm.nih.gov/pubmed/21503776 #LAMG12Fiona Brinkman
Someone just told me they are unfollowing me for excessive tweeting (am live tweeting #LAMG12) – should I tweet back a response to them?Jonathan Eisen
Interesting data on biofilm attachment drains v upper respiratory #LAMG12Paul Orwin
Remold’s work highlights the utility of culture-based approaches. Can compare actual phenotypes. #lamg12David Coil
Remold examining variation in how diverse Pseudomonas strains are killed by pyocins #LAMG12Jonathan Eisen
Hard core undergrad thesis on pyocin production. Hope my whiny students see this #LAMG12Paul Orwin
Gets to genomes on second to last slide. Nice! #LAMG12Paul Orwin
@phylogenomics Good job getting everyone to shorten their talks. They were still great!! #LAMG12Jenna Morgan Lang



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