Planetary Protection Workshop (Forward Contamination)

This is the second of three posts about the planetary protection workshop I attended at NASA Ames from March 24-26, 2015. The first is here (and here.)

Forward contamination, in the context of planetary protection, refers to the transport of microbes from Earth to Mars. The title of the workshop, and many talk titles refer to “human extraterrestrial missions,” but really, we’re talking about sending astronauts to Mars to walk on the surface of Mars, drill holes in Mars, scoop up dirt from Mars, and then returning the astronauts to Earth. There was almost no talk about human habitation on Mars. First things first, I suppose.

So, John Rummel kicked things off with a brief history of planetary protection. The gist of it is that, because we at some point deemed the moon devoid of life and uninhabitable, we didn’t think much about planetary protection until we started exploring Mars. In 1991, the stance on planetary protection was basically, “Viking didn’t find life on Mars, therefore no big deal, let’s go explore.” In 2000, gullies were found on Mars, suggesting the presence of water, leading to the Pingree Park Workshop in 2005, which addressed the question: Can we explore Mars without contaminating it?

(I did not know this, but I learned from Gerald (Jerry) Sanders that there is water on Mars in the atmosphere, in hydrated soil, in permafrost, in icy soils, in recurring slope linnea (hypothesized briny water), and in aquifers that are suspected to be >1km below the surface. So, there are defined “Special Regions” on Mars that are more likely than others to be able to support Earth life, and those are to be avoided or treated super-special so as to avoid forward contamination.)

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Is the MinION thumb drive sequencer taking off? Seems so …

Well, I have been digging around a lot into Nanopore sequencing recently.

This started as preparation for a lecture I gave at the Bodega Applied Phylogenetics course a few weeks ago on “The Evolution of DNA sequencing.”

In preparation for my talk I posted my slides from last years talk and asked people on Twitter whether they had any suggestions.   I got back some really useful comments and incorporated them into the talk and did my best to give credit on the slides themselves. I note – I was particularly intrigued by the comments about Oxford Nanopore sequencing:

And in looking at the links people sent I became more intrigued.  There were actual papers using the Nanopore thumb drive minION sequencer.  I really thought the system was not ready for primer time.  But clearly I was wrong.  So I incorporated some of this information into my talk (and added the caveat that I was impressed with the minION papers even though I was biased a bit against the Oxford Nanopore company due to their really lame ratio of M:F speakers at their recent meetings.  Even with my bias, the technology still looked OK.  For the final talk see Evolution of DNA Sequencing 2015 Version.

Anyway – this talk has made me now much more intrigued about Oxford Nanopores.  And here is another thing to look at: A firsthand perspective of trialling mobile DNA sequencing – GigaBlog. A nice blog post by Sam Minot from Signature Science, LLC and Andy Kilianski from the Edgewood Chemical Biological Center.  The post is about a new paper of theirs in Gigascience: Bacterial and viral identification and differentiation by amplicon sequencing on the MinION nanopore sequencer.

While clearly the MinION has a way to go in terms of quality and development, I can now state that I want one.  Or many.  Or like lots of many of them.

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Interesting analysis of data sharing in paleogenetics #OpenScience

There is a new paper out that may be of interest to many: “When Data Sharing Gets Close to 100%: What Human Paleogenetics Can Teach the Open Science Movement”.  It discusses an analysis of paleogenetics and the open science / open data practices in the field.  This seems like it could be of relevance to the microBEnet crowd and to new fields in general.  The earlier we get people thinking about open science activities and their potential benefits, the better (I think).

Full Citation: Anagnostou P, Capocasa M, Milia N, Sanna E, Battaggia C, et al. (2015) When Data Sharing Gets Close to 100%: What Human Paleogenetics Can Teach the Open Science Movement. PLoS ONE 10(3): e0121409. doi:10.1371/journal.pone.0121409

Abstract:

This study analyzes data sharing regarding mitochondrial, Y chromosomal and autosomal polymorphisms in a total of 162 papers on ancient human DNA published between 1988 and 2013. The estimated sharing rate was not far from totality (97.6% ± 2.1%) and substantially higher than observed in other fields of genetic research (evolutionary, medical and forensic genetics). Both a questionnaire-based survey and the examination of Journals’ editorial policies suggest that this high sharing rate cannot be simply explained by the need to comply with stakeholders requests. Most data were made available through body text, but the use of primary databases increased in coincidence with the introduction of complete mitochondrial and next-generation sequencing methods. Our study highlights three important aspects. First, our results imply that researchers’ awareness of the importance of openness and transparency for scientific progress may complement stakeholders’ policies in achieving very high sharing rates. Second, widespread data sharing does not necessarily coincide with a prevalent use of practices which maximize data findability, accessibility, useability and preservation. A detailed look at the different ways in which data are released can be very useful to detect failures to adopt the best sharing modalities and understand how to correct them. Third and finally, the case of human paleogenetics tells us that a widespread awareness of the importance of Open Science may be important to build reliable scientific practices even in the presence of complex experimental challenges.

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CAMI Challenge is Now Open for Participation

cami-logo_smDear metagenome method developers,

The first challenge of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI) begins right now! Over the last three months, we received valuable feedback from the community playing with our toy data sets. We incorporated many of your suggestions, thanks again!

Today, we proudly release the official data sets for the CAMI challenge.

The first part of the competition – metagenome assembly, profiling and (taxonomic) binning of raw read data – starts today. You have six weeks to complete this task and to submit your results until Friday, May 8, 2015. The second part of the challenge – (taxonomic) binning and profiling using assembled data – follows immediately and closes Friday, June 19, 2015. For the second challenge gold standard assemblies will be provided on May 9, 2015.

Head over to https://data.cami-challenge.org to get started! We are looking forward to receiving your reproducible results! CAMI will represent all submitted results in anonymous form and indicate their performance using a range of metrics in comparisons to other tools. So you will be able to use the site to facilitate your benchmarking efforts, already you can do so when submitting results for the provided toy data sets.

We also build upon and are part of the bioboxes community effort -https://github.com/bioboxes/rfc – and ask all CAMI participants to submit their methods standardized inside Docker containers. We are aware of the technical overhead and thus offer our help to prepare your bioboxes. Once integrated, this will allow you to continuously update your method and monitor its performance also for novel challenging data sets, that we will provide in the future.

We wish to include all participants as co-authors on the joint CAMI publication, given that their results are reproducible. Additionally, we will distribute three participation awards of 1000 EUR each among participants across all categories performing better than a baseline method. Two more reasons to join the CAMI challenge!

Lastly, we cordially invite you to the CAMI evaluation meeting in Berlin, May 27–29, 2015. Mark the date and drop us a message if you would like to attend and work with us on the final evaluation metrics and become part of the CAMI team.

Please check the FAQ, mail support@cami-challenge.org or tweet @CAMI_challenge with any feedback, questions or problems. We’re here to help!

Please note the following important changes:

– Changed binning and profiling formats.
– A new camiClient for format validation and fast parallel up- and download.

We are looking forward to your submissions!

The CAMI Team
http://cami-challenge.org
Twitter: @CAMI_challenge

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Great “Hidden Life” (of homes and people) Learning Activity from the NY Times #microbiology

Hidden Life Forms: Investigating Microbial Diversity on Our Bodies and in Our Homes - NYTimes.com
Image from NY Times article

Wow – this is really really cool: Hidden Life Forms: Investigating Microbial Diversity on Our Bodies and in Our Homes.  The article is by Jennifer Cutraro and it goes through a series of course / learning activities regarding microbial diversity – of homes and of people.  It has things like:

  • a warm up activity
  • a pre-activity quiz
  • suggested questions regarding “The Bugs in Our Homes” – a NY Times article from 2014 by Nancy Brill
  • suggested questions regarding Carl Zimmer’s very recent “The Great Indoors: The Next Frontier,” article.
  • a hands on microbial themed activity relating to the Belly Button Biodiversity project from Rob Dunn and colleagues
  • discussion questions about the human microbiome
  • suggestions for getting involved in a citizen microbiology project
  • and more

This is just completely awesome.  Thanks NY Times and Jennifer Cutraro

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

reposted from jennomics.com

http://www.nasa.gov/ames/events/ppw2015workshop/#.VRMLLJPF8mU

I’m at a NASA Ames workshop this week. The goal is to have a discussion about planetary protection with respect to human spaceflight, in particular to Mars, mostly during a “sample and return” mission and a little bit about human habitation on Mars.

I’m tweeting with #planetaryprotection. There’s also live streaming here: https://ac.arc.nasa.gov/planetaryprotection/

The broad goal of planetary protection is to make sure that we don’t contaminate the universe with our Earth stuff and vice versa, forward and reverse contamination, respectively. The first half of the first day was an exhaustive review of previous workshops on the subject. The reports are available here. James Johnson conducted an extensive literature review, which will soon be published in Advances in Space Research Special Issue: New Challenges for Planetary Protection, so keep an eye out for that. The Outer Space Treaty of 1967 was also brought up by many times. Apparently (according to Cassie Conley) if you can decipher the language, Article IX indicates that the “highest priority for planetary protection is to protect the Earth.” Of course, planetary protection was a concern during the Apollo missions to the moon, but the protections (especially with respect to reverse contamination) were pretty flimsy. They splashdown in the ocean, change into a new suit, hop into a helicopter, get paraded past hundreds of people, and then enter quarantine for 21 days.

120718020623-apollo-capsule-peace-signs-color-horizontal-large-gallery

At some point, it was decided that there was no life on the moon, so reverse contamination dropped off the radar. As far as forward contamination is concerned, well, there not just flags and golf balls, but also many, many bags of trash and human waste sitting on the surface of the moon right now.

The second half of the first day consisted of talks on the subject of Microbial and Human Health Monitoring. I’ll post about those later.

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Important read from Aaron Darling: Not so fast, FastTree

Aaron Darling, faculty member of University of Technology Sydney (who used to work with me here at UC Davis) has a very important and interesting read on his blog: Not so fast, FastTree. In it he discusses some informatics archaeology he did (digging around in some code) regading the program FastTree which many researchers have been using for the last few years.  If you use FastTree or do any large scale phylogenetics, especially of microbes, this is worth a look.

 

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Fascinating and distressing look at cruise ship turnaround

Really interesting and distressing story in the New York Times a few days about: A Luxury Liner Docks and the Countdowns On by Jad Mouawad.  So many parts of this story have microbe-themed angles.  Some interesting tidbits (quoted from the story)

  • A treatment system handles all the wastewater generated by the passengers and crew. That system, which processes 1,200 tons of wastewater a day, uses bacteria to break down waste, then mechanical and chemical systems to remove solids, and finally ultraviolet light to disinfect. The water at the end is clean enough to drink but is discarded in the sea. Any remaining solids are held in special tanks to dry and be incinerated.
  • Bottles, cans and compost are crushed and frozen in cold-temperature rooms to prevent the spread of bacteria
  • 189 housekeepers can get more than 2,700 rooms ready by noon.
  • A norovirus outbreak is one of would-be cruisers’ biggest fears. Royal Caribbean said the virus was usually brought on board by passengers who were already sick. For that reason, there are hand-sanitizing stations throughout the ship …
  • The Centers for Disease Control and Prevention counted at least eight instances of norovirus contaminations infecting more than 3 percent of passengers for ships arriving in United States ports last year.

The whole thing seems both fascinating (in terms of the complexity and engineering of the whole operation) and distressing (so little time is spent on cleaning – no wonder Norovirus is a problem).  It seems like Cruise Ships are just ripe (so to speak) for more details microbial ecology studies.

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Resistance (The Film) coming to UC Davis April 9

We will be hosting a screening of “Resistance the film” at UC Davis.

  • April 9, 2015
  • 6: 00 PM (reception from 6:00-6:30)
  • Genome and Biomedical Sciences Facility Auditorium
  • Davis, CA

The filmmaker Michael Graziano will be there.

Reviews have been very positive.  See for example

See the first two minutes of the film below (note – the voice may be familiar to people who know, well, me).

Resistance (first two minutes) from small-r on Vimeo.

Antibiotic resistance is a growing problem and we need to do many things to combat it.  This film is an important contribution to the fight.  I hope to see people at the showing (if you are nearby) and if not – you should find a way to see this film.

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Best of MicrobiomeDigest: Fisherman’s Friends

In this week’s Best of MicrobiomeDigest, we’ll look at the effect of a “sea voyage” on the human oral and belly button microbiome.

For those of you who are not familiar with Fisherman’s Friend (I am not sure if these are as popular in the rest of the world as they are in parts of Europe), it’s a British cough suppressant lozenge that is so strong that it will make your eyes water. They are famous for their TV commercials showing tough fishermen tearing up when they kissed their women goodbye or were homesick on their trip. To hide their emotions, the sailors would then pretend to be coughing and take an FF, while saying: “Strong stuff, that Fisherman’s Friend”. Here are links to one of their Dutch commercials (in English, sort of), and here is a US commercial. But I digress.

A paper that came out in Scientific Reports last week took a look at oral microbes in sailors, before and after their trips to sea. The times spent at sea varied from 105-150 days. The paper consistently calls those trips a “voyage”, making it sound much more glamorous than it probably was. The conditions of these expeditions are described in the paper as “a maritime climate with high temperatures and humidity” where “sailors suffer from dizziness, nausea and a series of physiological and psychological symptoms resulting in declined physical function”. Not your average cruise ship trip!

Swabs were taken from the oral mucosa (cheek swab) and belly button, and stored immediately in a freezer on board.  Specimens were analyzed using 16S rRNA gene amplification and sequencing, as well as whole genome analysis (WGA).

Screen Shot 2015-03-23 at 02.36PM, Mar 23

For both the mouth as well as the belly button samples, the number of bacterial species as well as the bacterial diversity was significantly decreased after a long trip at sea. At the phylum level, Firmicutes increased and Proteobacteria decreased significantly in both sample types after the stay at sea.

In the WGA metagenomic data of the oral samples, Streptococcus was the most abundant genus both before and after the journey, increasing from 79.7% to 96.7%. Several metabolic pathways, including foliate biosynthesis and amino acid synthesis pathways, were decreased after the expeditions. The sailors themselves were monitored as well. After their trip, they showed decreased serum haemoglobin and folic acid levels.

After I looked at this paper in more detail, I am not sure if it really deserves a “Best of MicrobiomeDigest” award. At first glance, it looked very cool because it studied a group of people all undergoing the same, large and prolonged perturbation. It is a microbiome researcher’s dream come true! But there are several unclarities and omissions that I had not expected to see in a Scientific Reports paper, and I wished that peer review would have taken some of these out. For example, is Table 1 showing the 16S rRNA or the WGA data? Is the data shown in Figure 1C the same as shown in 1A/B? and if so, why don’t some numbers not correspond between the 2 figures? In Figure S4, which panel is showing the oral samples?

Most importantly, I would have liked to see if the microbial communities of sailors on the same ship became more similar to each other after the trip. I imagine that staying on a ship for three months and sharing the same food, environmental conditions, and facilities would make the microbiomes of these sailors very similar to each other. This would have been a great opportunity to study that.

Maybe this would make a great summer student project: Download this data and see if the phylogenetic distance between these communities decreased after the trip. I will be happy to be a co-author!

In a somewhat related study, Seifried et al. in Wiley’s Microbiology Open describe the 16S rRNA gene-based bacterial composition in marine bioaerosol samples, during a cruise from the European North Sea to the Baltic Sea. This paper contains detailed descriptions of the location and sampling procedures, but I wish the microbial findings would have been presented in a more visually attractive way. There is also a duplication in the primer description in the Methods.

Screen Shot 2015-03-23 at 02.54PM, Mar 23

The microbial composition of the air-at-sea was characterized by an abundance of Proteobacteria (49% of all reads), followed by Bacteroidetes (23%) and Actinobacteria (16%). Genus Sphingomonas was the most abundant (17% of all sequencing reads). Surprisingly, the SAR11 clade (most abundant in seawater and containing cand. sp. Pelagibacter ubique), was only found at relatively low amounts in most samples

Combining these 2 studies reveals something puzzling: although Proteobacteria are very abundant in marine aerosols, and Firmicutes relatively rare, the sailors experienced a decrease in Proteobacteria and increase in Firmicutes after their sea-exposures. Of course, there are several caveats to be aware of when making that comparison (e.g., these studies were done in very different parts of the world), but it is interesting to hypothesize that exposure to marine aerosols is probably not the main driving factor in the shift in the microbial communities of sailors after a trip at sea.

Metagenomic sequencing reveals altered metabolic pathways in the oral microbiota of sailors during a long sea voyage – Weiwei Zheng – Scientific Reports

Spatial distribution of marine airborne bacterial communities – Jasmin S. Seifried – Microbiology Open

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