Wrap up of recent posts of relevance on microBEnet

I have been doing a lot of blogging at microBEnet and don't always do a good job of cross posting or even posting here to let people know of the cross talk / related posts.

So I am trying to do that briefly now.  Here are some posts from the last few months on microBEnet that may be of interest, These are posts from March through today.

• Great article by Maryn McKenna on the hunt for new antibiotics w/ crowdsourcing help
• Worth a look: Are Pets the New Probiotic? in the NY Times
• Alleged mishandling of Flint Legionnaire’s outbreak leads to manslaughter charges for MI health chief
• Report: Guests leave Las Vegas’ Rio hotel with Legionnaires’ disease
• A hairy pacman approach to “microbial dark matter” in drinking water
• Pre-microbiology – Ancient Imaginations of the Microbial World
• New paper of interest on antibiotic resistance genes in 4 CA cities but dangerous PR from UCLA
• Compiling a list of Microbiology of the Built Environment related presentations at ASMicrobe17
• Love the #AgarArt contest from ASM …
• Dirty money: interesting data but unclear what implications are
• Who are the microbes in your neighborhood? In your neighborhood? In your neighborhood?
• A fascinating side story to brain-defect microbiome study – major role of the built environment
• Kristen DeAngelis slides for “Microbial Diversity” Course
• Why use Bracken instead of Kraken?
• This is calling out for a large microbiome study: Salt from icy roads is contaminating North America’s lakes
• Your help is wanted in this #CitizenMicrobiology project: “BashTheBug – Help us fight antibiotic resistance!”
• Dr. Director & Duflo: Dogs Dropping Doody Do Digestive DNA Data Duty 
• Day 2 of #NeLLi17: From New Lineages of Life To New Functions
• Interesting discussion of data vs. metadata started at #NeLLi17 & continuing
• Day 1 of #NeLLi17 – From New Lineages of Life To New Functions 
• Journal of Bacteriology minireview collection on host-microbe interactions
• Paper of interest comparing taxonomies of SILVA, RDP, Greengenes, NCBI and OTT 
• Are ‘germ-zapping’ robots useful in fighting hospital acquired infections?
• Wanted – help compiling a list of academic #microbiome centers
• Quick post – this looks potentially very useful – ATLAS – comprehensive infrastructure for assembly, annotation, & genomic binning of metagenomic data 
• Reasonably cautious but optimistic editorial on “The human microbiome: an emerging tool in forensics” 
• The microbiomes of built environments when the builder is not human
• 
  

How to keep up with microbial ecology and the built environment: microBEnet is your place

Just posting a wrap up of posts on microBEnet (where I blog frequently as do many other folks that work on something related to microbial ecology, the built environment, or the intersection of the two).  microBEnet is really becoming a central place to find out what is going on in the world of microbial ecology and the built environment.  And I love that we are getting more and more posts from outsiders about their work, their meetings, their ideas and more.  Anyway - here is a wrap up of the posts for the last month.  If you are interesting in joining microBEnet and writing posts about relevant topics, let me know.

Jenna Lang (staff scientist in my lab) -- meeting reports from a Planetary Protection meeting

• Planetary Protection Workshop (Forward Contamination)
• Workshop on Planetary Protection Knowledge Gaps for Human Extraterrestrial Missions (Intro)

My posts:

• Is the MinION thumb drive sequencer taking off? Seems so …
• Interesting analysis of data sharing in paleogenetics #OpenScience
• Great “Hidden Life” (of homes and people) Learning Activity from the NY Times #microbiology
• Important read from Aaron Darling: Not so fast, FastTree
• Fascinating and distressing look at cruise ship turnaround
• Resistance (The Film) coming to UC Davis April 9
• Great #openaccess collection of papers on RNA
• Today in germophobia and antimicrobiomism: grandparents who hate microbes
• I love that @eLIFE is publishing draft papers now (brewery microbiome)
• Evolution of DNA Sequencing 2015 Version
• Methylisothiazolinone in household items – a growing (or well, killing) problem #germophobia
• Cool: James Clemens High School-Hudson Alpha Classroom Microbiome Project
• Well, I guess this means microbiome engineering has arrived (sort of)
• Today in “where’s the pathogen?” Can you find Burkholderia on 500 acres with 50 samples?
• Yes Virginia, there is a paper on microbial transfer during beer pong
• Healthy Buildings 2015 meeting promo / preview

Alexander Sczyrba on the Critical Assessment of Metagenome Interpretation (CAMI)

• CAMI Challenge is Now Open for Participation

Who are the contaminants in your sequencing project? (crosspost from #microBEnet)

This was originally posted on microBEnet: Who are the contaminants in your sequencing project?

Well, been having many discussions recently about PCR amplification happening from "negative" controls where no sample DNA was added. Such amplification is alas pretty common - due to contamination occurring in some other material added to the PCR reaction.  Obviously it would be best to eliminate all DNA contamination of all reagents and all PCRs.  But if that does not happen, it is possible to try to detect contamination after it has happened.  Below I post some papers related to post-sequencing detection of contamination:

• Common Contaminants in Next-Generation Sequencing That Hinder Discovery of Low-Abundance Microbes.
• Abundant Human DNA Contamination Identified in Non-Primate Genome Databases
• Fast identification and removal of sequence contamination from genomic and metagenomic datasets
• Mycoplasma contamination in the 1000 Genomes Project
• ContEst: estimating cross-contamination of human samples ...
• DeconSeq @ SourceForge.net
• AlienTrimmer: A tool to quickly and accurately trim off ...
• Kraken
• Blobology: exploring raw genome data for contaminants, symbionts, and parasites using taxon-annotated GC-coverage plots

Any other suggestions or comments would be welcome. UPDATE 10:30 AM 7/25 - Was reminded on Twitter of a new, critically relevant publication on this issue: Reagent contamination can critically impact sequence-based microbiome analyses

@pathogenomenick @gregcaporaso crap - can't believe I left that off — Jonathan Eisen (@phylogenomics) July 25, 2014

Why I don't like to pre-submit slides for talks - lessons from #AAASMoBE meeting

So - I gave a talk at a meeting on Thursday.  The meeting was called "Microbiomes of the Built Environment" and it was sponsored by the Alfred P. Sloan Foundation and run by AAAS.

The meeting organizers, as is often the case, wanted me to submit my slides a few days in advance, in theory to make sure they were loaded into their system and that all worked OK.  Well, as usual, I did not do this.  I like to make my talks fresh - just before the meeting so that I can incorporate new ideas into them and so that they do not have that canned feeling that a lot of talks do.

My talk was to be 15 minutes long and was to focus on my Sloan Foundation funded project "microBEnet: the microbiology of the built environment network" (see http://microbe.net for information about the project). I figured, I would work on the talk on the plane - five plus hours to edit a talk I had given relatively recently on the topic of this project.  And all would be good.  Plus, United had told me there would be WiFi on the plane so if I needed any new material I should be able to get it from the web right?  Well, the flight took off on time - 8 AM on Wednesday morning.  And I opened my laptop once allowed and paid the $15+ dollars for the WiFi and got to work.  Then, about 10 minutes later, the WiFi died and despite heroic efforts by the flight attendants, it never came back. And I plugged away at my slides doing some edits of the following presentation.

Talk about microBEnet (http://microbe.net) from Jonathan Eisen

Crosspost: I never meta data I didn't like - especially re: standards for the built environment #IndoorMicro

New paper out from the microbiology of the built environment community: MIxS-BE: a MIxS extension defining a minimum information standard for sequence data from the built environment. The joint first authors are Elizabeth Glass and Yekaterina Dribinsky. And the senior author is Lynn Schriml.

The paper is simple but I think very important – it describes the development of what is a “suggested list of parameters to record and report for each sequenced sample and to compare data across studies”. Or, in other words, it is a recommended list of metadata to collect and record about samples from the built environment that are being sequenced. If you are interested in microbial diversity and/or the indoor/built environment, this is worth a look.

Oh, and, full disclosure, I am an author too.

Thanks to Software Carpentry (@swcarpentry) for coming to #UCDavis

Quick post here.  Jenna Lang in my lab has a post at microBEnet about the recent workshop that the Software Carpentry folks ran at UC Davis: Software Carpentry comes to UC Davis! | microBEnet: The microbiology of the Built Environment network.  It was a major success.  For those who don't know Software Carpentry's mission is is to build basic computing skills among researchers.  From their web site:

Software Carpentry helps researchers be more productive by teaching them basic computing skills. We run boot camps at dozens of sites around the world, and also provide open access material online for self-paced instruction. The benefits are more reliable results and higher productivity: a day a week is common, and a ten-fold improvement isn't rare.

A great idea and done really well.  Others out there should consider hosting or attending one of their Boot Camps and checking out their materials on their web site.  See for example their videos and their reading list and their lessons.  They really do great things ...

Crosspost: Woohoo – two more genome announcement papers from our undergraduate project on built environment reference genomes

Crossposting this from the microBEnet blog.

Two new papers out from the microBEnet Undergraduate Research: Built Environment Reference Genomes  project:

• Coil DA, Doctor JI, Lang JM, Darling AE, Eisen JA. 2013. Draft Genome Sequence of Kocuria sp. Strain UCD-OTCP (Phylum Actinobacteria). Genome Announc. 1(3):e00172-13. doi:10.1128/genomeA.00172-13.
• Diep AL, Lang JM, Darling AE, Eisen JA, Coil DA. 2013. Draft genome sequence of Dietzia sp. strain UCD-THP (phylum Actinobacteria). Genome Announc. 1(3):e00197-13. doi:10.1128/genomeA.00197-13.

These go with two previously published ones:

• Lo JR, Lang JM, Darling AE, Eisen JA, Coil DA. 2013. Draft genome sequence of an actinobacterium, Brachybacterium muris strain UCD-AY4. Genome Announc. 1(2):e00086-13. doi:10.1128/genomeA.00086-13
• Bendiks ZA, Lang JM, Darling AE, Eisen JA, Coil DA. 2013. Draft genome sequence of Microbacterium sp. strain UCD-TDU (phylum Actinobacteria). Genome Announc. 1(2):e00120-13. doi:10.1128/genomeA.00120-13.

And two more coming. So proud of the undergrads in my lab who did this work and David Coil for coordinating it with help from Jenna Lang and Aaron Darling.  Undergrads at UC Davis sequencing genomes of organisms they isolated. So cool.

Just out from TED - Jessica Green on buildings and microbes

Go microbes:

 

Crosspost: New papers from our undergraduate “microbiology of the built environment” genome sequencing project

Crossposting from microBEnet.

We have two new papers out from our lab as part of our microBEnet supported undergraduate genome sequencing project:

•  Lo JR, Lang JM, Darling AE, Eisen JA, Coil DA. 2013. Draft Genome Sequence of an Actinobacterium, Brachybacterium muris Strain UCD-AY4. Genome Announc. 1(2):e00086-13. doi:10.1128/genomeA.00086-13. 
• Bendiks ZA, Lang JM, Darling AE, Eisen JA, Coil DA. 2013. Draft Genome Sequence of Microbacterium sp. Strain UCD-TDU (Phylum Actinobacteria) Genome Announc. 1(2):e00120-13. doi:10.1128/genomeA.00120-13. 

Congratulations to all involved especially Jonathan Lo and Zack Bendiks, the undergrads who are first authors, and to David Coil who coordinated all the work.

More information about the project can be found on blog posts from my lab blog (http://phylogenomics.wordpress.com/category/undergraduate-genome-project/) and on a page here on microBEnet (http://www.microbe.net/undergraduate-research-built-environment-genomes/) and the YouTube video below:

  .

In summary, the point of the project was to (1) start generating some reference genomes for microbes from the built environment and (2) to engage undergraduates at UC Davis in genome sequencing and microbiology of the built environment projects.

The papers are published in a new open access journal from the American Society for Microbiology called "Genome Announcements".

Thanks also to the Alfred P. Sloan Foundation which funds microBEnet and to the UC Davis Genome Center DNA Technologies Core facility which ran the sequencing.  More papers are coming.  Stay tuned.

Undergraduate Research: Built Environment Genomes #microBEnet #Sloan

Just a quick post here.  We are continuing working on our Undergraduate Research projects in the "microbiology of the built environment" in my lab as part of our microBEnet project.  For more on the project we did last year on genome sequencing see this web site:Undergraduate Research: Built Environment Genomes | microBEnet: The microbiology of the Built Environment network.

And here is a video with some details on the project:



Also check out our new undergraduate project on sampling microbes in aquariums.

Storify for Lake Arrowhead Microbial Genomes #LAMG12 Meeting

Meeting went well.  Here is a storification of it:

Posts from #microBEnet that may be of interest

Quick post here - posting links to recent blog posts on the microBEnet blog that may be of interest here.  The microBEnet blog is part of the microBEnet project that I run on microbiology of the built environment.

• A year old but still worth pondering – is hospital garb a vector for microbes?
• Session on microbiology of the built environment at ESA 2012 (Portland, August 5-10)
• Genomic Standards Consortium Workshop, April 22-24 2013 (Bethesda MD)
• NewScientist feature on Noah Fierer “Intrepid explorer of the microbe jungle in your home”
• Job: Postdoctoral Position in Environmental Metagenomics of Municipal Water Distribution Systems w/ Norman Pace
• An outdoor microbiologist indoors: Thoughts and ramblings from ASM2012
• Bacteria a potential threat to nuclear waste repositories
• CBC radio has a podcast by @radiobhardwaj on the “Hotel Rooms and Bacteria” that was all the rage at #ASM2012 last week
• New Sloan-funded program in the built environment: Microbial diversity in 1,000 homes across the United States
• ASM Live video on bacteria in hotel rooms

Quick summary of session at #ASM2012 on “The Great Indoors” #microBEnet

 The session at the ASM 2012 meeting on “The Great Indoors” seems to have gone well. I will be writing up a more detailed report but here is a quick summary done via “Storify”.

Some notes from GSC13 session on microbiology of the built environment #microBEnet

At the GSC13 meeting a few months ago there was a session on microbiology of the built environment which was sponsored by my microBEnet project.

Posting some details from the meeting here.

Meeting notes and reports

• Meeting report for the whole meeting in SIGS.
• GSC13: From Genomes to Interactions to Communities to Models
• Guest Post: Metadata for the Built Environment – MIxS-BE package

Talk videos:

Paula Olsiewski

 

Coming up at the #ASM2012 mtg. "The Great Indoors: Recent Advances in the Ecology of Built Environments"

The American Society for Microbiology meeting is starting tomorrow and there are multiple things related to microbiology of the built environment there.  These include a session that was organized by Brendan Bohannan which I am chairing.

The details of the session are below:

Session Title: The Great Indoors: Recent Advances in the Ecology of Built Environments

Session Date/Time: Sunday Jun 17, 2012 3:00 PM - 5:30 PM

Session Room: Esplanade Ballroom 300

Description: Although humans in industrialized countries spend nearly 90% of their time in enclosed buildings, we know very little about the biology of the indoor environment. However, this is starting to change. Over the past few years, the field of indoor ecology has grown dramatically. Ecologists are beginning to apply ecological theory and concepts to understanding buildings as ecosystems. A new understanding of the biodiversity of built environments is emerging, as well as a new appreciation of the importance of interactions between humans and non-human life indoors. The proposed symposium will showcase this emerging understanding. We will feature presentations that demonstrate the utility of ecological theory for understanding built environments, that describe the dynamics of biodiversity indoors and that illustrate the interactions of humans with indoor ecology. Our focus will be on the ecology of the dominant forms of non-human life indoors - microorganisms - and their interactions with humans.

ABC radio news story on Indoor Ecology

Quick post here and it is not about OccupyUCDavis

Check out the story from ABC news (Australia, that is): Indoor ecology - RN Future Tense - 24 November 2011. Their summary:

We're used to hearing about threats to our outdoor environment. But we rarely think about some of the challenges that we face in our indoor environment.

A growing number of researchers are interested in the idea of 'indoor ecology' - treating the indoors like the outdoors and studying the spaces that surround many of us every day.

It has a lot of good stuff about the Sloan Foundation program.

An ecosystem in my house? Yes indeed. And with microbes too. #BostonGlobe #microBEnet

Well I am very excited about this article in the Boston Globe today: Ecosystem, sweet ecosystem - The Boston Globe. By Courtney Humphries the article discusses the Sloan Foundation program in the "Indoor Environment" that is focusing on microbial ecology of the built environment. I am, well, really into this area of work and have a grant from the Sloan Foundation in their program to crete something called "microBEnet" which stands for "microbiology of the Built Environment network." And in case you were wondering, yes, the BE is supposed to be capitalized and the m in microbe is not. My work in microBEnet is focused on Science 2.0 activities to help boost interaction and communication and outreach relating to studies of microbiology of the built environment. Check out the microBEnet site for more detail on that project (more on this in a bit).

Anyway, a little while ago I was interviewed by Courtney Humphries about studies of microbes in the built environment and the conversation seemed to go pretty well. And I kind of forgot about it due to some family things going on in my life. And then yesterday I saw the article. It is quite nice. It starts off with a nice drawing of a house making it look like an ecosystem

and the headline/lead in is really quite perfect "Ecosystem, sweet ecosystem." is the headline with the subtitle "What if we studies the indoors as an environment all it's own".  She goes on to quite Hal Levin (my collaborator on microBEnet), Jessica Green (the head of the BioBE center in Oregon focusing on biology of the built environment), me, Paula Olsiewski (the Program Officer at Sloan in charge of the Indoor Environment program) and Bill Nazaroff from Berkeley, who is also funded by the Sloan Foundation to work in this area.

The article is definitely worth a read.  Only issue really is that I have a feeling people may be distracted by some sort of storm hitting the East Coast right now.  Well, after the storm hits, microbiology of the indoor environment will likely be even more important to pay attention to.

If you want to brush up on studies of microbiology of the built environment check out some of the resources we have made and/or collated at microBEnet including:

• microBEnet Blog with diverse posts such as
• What microbes are lurking in your fish tank? Good candidate for some citizen microbiology I think
• OMG – Nooooooooooooo. There are GERMS in fast food restaurant play areas
• “NIST Finds That Ethanol-Loving Bacteria Accelerate Cracking of Pipeline Steels”
• Microbes in tobacco products: health and policy implications
• Is your dishwasher trying to kill you? Maybe, but no evidence of that from this work
• Travel & meeting notes from #IndoorAir2011 – cross post from Tree of Life blog
• Simple Guides (sort of introductory material for background purposes)
• Full List of Sloan IE Grants
• Mendeley Group for microBEnet (collection of publications related to microbiology of the built environment)

Stay tuned for more, from microBEnet, from Sloan funded researchers, and from others studying microbiology of the built environment.  We spend on the order of 90% of our lives in built environments like buildings, cars, trains, etc.  It's about time we started studying such environments as ecosystems ...

Some recent posts (of mine) from http:microbe.net on microbes of the built environment that may be of interest

Just thought I would post a little list here of some recent blog posts I have made at a relatively new blog for my microBEnet project.  I may cross post occasionally but for now just going to post a list:

• OMG – Nooooooooooooo. There are GERMS in fast food restaurant play areas
• Microbes in buildings getting some love; story featuring @jessicaleegreen
• Unsavory sources of bacteria in urban air (via BioBE center)
• smartplanet article on microbes in buildings featuring @jessicaleegreen
• More on bacteria in city air: “Your faeces, my furry friend, are blowin’ in the wind”
• More on citizen microbiology project from @Penn_State & @NASA on thermophiles in water heaters via @scicheer @Sci4Cits

Would love it if people checked out the blog: http://www.microbe.net/microbenet-blog/ and the web site http://www.microbe.net/ and let me know what you think.   

Travel and meeting notes from #IndoorAir2011 in Austin Texas #microBEnet

Here are some quick notes from my trip to Austin Texas for the Indoor Air 2011 meeting.

About the meeting:
I got involved in helping organize a session at this conference as part of my microBEnet project.  More on the planning and the meeting later but here are some quick notes just to get them out there.  I wrote a bit about the run up to the meeting in the following posts:

• Indoor Air 2011 coming up in Austin, TX – still time to sign up ...
• Reminder – Indoor Air 2011 coming up June 5-10 Austin TX ...
• Indoor Air 2011; Austin, Tx; June 5-10 #microBEnet | Microbiology ...
• The Tree of Life: Off to #IndoorAir 2011 in Austin, TX - to ...

The meeting.
Below are some notes about the trip with twitter posts, pictures, and a few comments.  I will post later with some more "scientific lessons learned" and such.  But wanted to get this out there before I forgot details.

Headed out June 6.
Was going to head out June 7 but decided to head out late on June 6 so I could get to the meeting a bit earlier.  I am posting my tweets below as a guide to the trip.  Tweets are highlighted in yellow.

• Sacramento to Las Vegas to Austin to #IndoorAir2011#fb

Had a two plus hour layover in Las Vegas airport.  What a horrible place with all the noise, the slot machines, and such.  So I finally found a place that was reasonably quiet for dinner.  Plus it had the hockey game on so I was happy.

Quick update (pics, twitter feed) on #IndoorAir2011 in Austin, TX #microBEnet

Here are some pics from my trip to the Indoor Air 2011 meeting. I am going to post more detail about the meeting later.



If you want some information about what happened at the meeting, best place right now is probably twitter




Also see the microBEnet blog which has some recent posts on this.