Treponema are not "ancient" but absence from some human’s guts is very interesting

So I saw some Tweets today that caught my attention, discussion news stories about “ancient” bacteria being missing from some human’s gut microbiomes:

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These refer to a sadly inappropriate headline in Science

What is wrong with this?  Well, there are no “ancient” bacteria around today.  They are all modern.  I am not even sure what they were trying to say.  Just a really bad evolution argument I guess.  I pondered giving Science a Twisted Tree of Life Award which I give out for exactly this kind of thing –  but decided first to dig into the science here and gloss over the bad evolution headline.

And it turns out – what the news story is about is in fact interesting – a new paper out in Nature Communications:  Subsistence strategies in traditional societies distinguish gut microbiomes.

The paper is freely available and has some really interesting material in it.  They key to me – at least related to this “ancient” bacteria claim is the following part of their abstract:

As observed in previous studies, we find that Treponema are characteristic of traditional gut microbiomes. Moreover, through genome reconstruction (2.2–2.5 MB, coverage depth × 26–513) and functional potential characterization, we discover these Treponema are diverse, fall outside of pathogenic clades and are similar to Treponema succinifaciens, a known carbohydrate metabolizer in swine. Gut Treponema are found in non-human primates and all traditional peoples studied to date, suggesting they are symbionts lost in urban-industrialized societies.

And then some further detail in the paper:

Although Spirochaetes have been previously reported from the gut microbiome of non-human primates and ancient human populations, they have only been observed in high abundance among extant human populations with non-Western lifestyles, such as a traditional community in Burkina Faso and a hunter-gatherer community in Tanzania. As such, they may represent a part of the human ancestral gut microbiome that has been lost through the adoption of industrial agriculture and/or other lifestyle changes. 

So they don’t go into the full detail here but what I think they are saying is that they infer that human ancestors had Spirochaetes (based on the finding of it in non human primates and some human populations).  And thus they further infer that human populations (e.g., the people they studied in Oklahoma) that do not have these Spirochaetes have “lost” them.

I note – I think this terminology of “loss” they are using is not quite right here in a way.  Saying that these Spirochaetes have been lost implies to me that they are heritable.  But they do not in fact show that.  It could be that these are related to diet or environment in some way – something shared by some human populations and non human primates, for example.  And thus the absence from some “Westernized” populations could be more of an environmental thing than a “loss” in the past.


In a similar way, we could say that Westernized humans have “lost” the ability to be skinny (since obesity is high in many such populations).  Non human primates have such abilities and so do some non Westernized populations.  But “losing skinnyness” does not seem quite right since we do not know exactly why obesity is higher in Westernized populations.  I think it would be better in such cases to say something like “do not show an ancestral trait” (the ancestral trait here being skinnyness) and to not use “lost” until we know more about what is going on.  Similarly, I think saying some human populations have “lost” these Spirochaetes is not quite right.

Nevertheless, the absence (or at least, low levels) of these Spirochaetes from some human populations is certainly interesting.  And given that the presence of such Spirochaetes does appear to be an ancestral trait, the absence is even more interesting.  And thus this paper here, which details some of the genomic features of these “missing” Spirochaetes is definitely worth paying attention to.

In addition, I note – the findings in this paper serve as an additional justification for projects to generate genomic data from across the phylogenetic diversity of microbes.  Consider for example their Figure 6 and 7 which show that the most closely related Treponema species and the ones with the most similar genomes to these human Spirochaetes are those from Treponema succinifaciens and Treponema brennabornese.

Both of those genomes were generated by the Genomic Encyclopedia of Bacteria and Archaea project which I coordinated with the DOE-JGI and DSMZ.  See the paper on one of them: Complete genome sequence of Treponema succinifaciens type strain (6091T) and the posted data on the other.

We argued that we needed to sequence reference genomes from across the tree of life because this would help inform studies of uncultured microbes from diverse ecosystems.  Little did I know that one of the key ecosystems we would help inform would be the human gut.

Certainly more needs to be done in regard to these Spirochaetes.  Why are they at low levels or missing from some Westernized populations?  What do they do in other populations?  Would they be helpful if they were reintroduced to populations that do not have them?  So many questions actually.  But despite the misleading news article headline, this paper seems to me on first glace at least to in fact be quite interesting.

I made a Sorify of some comments

DOE-JGI Call for LOIs for Large-Scale Genomics Proposals due April 10, 2014

The DOE Joint Genome Institute (DOE JGI) Community Science Program (CSP) is now accepting Letters of Intent for large-scale sequence-based genomic science projects that address questions of relevance to DOE missions in sustainable biofuel production, global carbon cycling, and biogeochemistry. Priority for this call will be given to projects that address the following areas of special emphasis and exploit the diversity of DOE JGI capabilities. The CSP data is immediately made publicly available, without exception.

A summary of the 2015 CSP Call is below. The full Call can be found here:

I. Functional Genomics and Microbiomes of DOE JGI Flagship Plants: Emphasis will be on proposals related to DOE JGI’s “flagship” plant genomes, including poplar, sorghum, Brachypodium, Chlamydomonas, soybean, foxtail millet, Physcomitrella, switchgrass, and miscanthus. These species are of special interest as biofuel feedstocks or as comparators that provide insight into feedstock evolution and phenotype. Projects may fall into the following categories:

a) Gene Atlas and ENCODE-like projects;

b) Large-scale resequencing projects;

c) Plant microbiomes.

II. Probing functional diversity of microbes: To complement its Genomic Encyclopedia of Bacteria &Archaea (GEBA) and 1000 FungalGenomes initiatives, the DOE JGI has begun to explore microbial functional diversity. Proposals are encouraged that extend this effort using high-throughput sequencing, and the DOE JGI’s DNA synthesis capabilities and are expected to use one or a combination of the DOE JGI’s (meta-) genome, (meta-) transcriptome, single-cell and isolate sequencing and resequencing pipelines. ENCODE-like projects for functional genomics that could serve as model organisms for DOE-relevant problems are encouraged and could include new DOE JGI capabilities for genome-wide transcriptomics, including non-coding and small RNAs, and epigenomics, including methylation detection and ChIP-seq.

III. Microbial emission and capture of greenhouse gases in terrestrial systems: Proposals are encouraged that will provide insight into global carbon (including methane) and nitrogen cycles, and/or suggest novel strategies for carbon capture, nitrogen processing, or methane reduction through gene/genome engineering.

IV. Discovery and expression of natural product pathways relevant to energy-related and environmental processes: The DOE JGI has developed a platform that enables the discovery of novel natural products based on technology combining computational genomics, pathway refactoring, host engineering, and high-throughput analytics.

Deadlines

Letters of intent (LOI) will only be accepted electronically and should be submitted at http://proposals.jgi-psf.org/.

· LOI due: April 10, 2014

· Full proposals invited: April 24, 2014

· Full proposals due: June 5, 2014

· Projects begin: October 2014

Questions? Contact:

Axel Visel (avisel), DOE JGI Strategic Planning-Science Lead.



New paper from Eisen lab: Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes KMG-I project

A new paper of possible interest discussing one of the new phases of the GEBA Genomic Encyclopedia of Bacteria and Archaea project. Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes KMG-I project | Kyrpides | Standards in Genomic Sciences.

 

New paper from some in the Eisen lab: phylogeny driven sequencing of cyanobacteria

(Cross post from my lab blog)

Quick post here.  This paper came out a few months ago but it was not freely available so I did not write about it (it is in PNAS but was not published with the PNAS Open Option — not my choice – lead author did not choose that option and I was not really in the loop when that choice was made).

Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing. [Proc Natl Acad Sci U S A. 2013] – PubMed – NCBI.
Anyway – it is now in Pubmed Central and at least freely available so I felt OK posting about it now.  It is in a way a follow up to the “A phylogeny driven genomic encyclopedia of bacteria and archaea” paper (AKA GEBA) from 2009 with this paper a zooming in on the cyanobacteria.

New paper from some in the Eisen lab: phylogeny driven sequencing of cyanobacteria

Quick post here.  This paper came out a few months ago but it was not freely available so I did not write about it (it is in PNAS but was not published with the PNAS Open Option — not my choice – lead author did not choose that option and I was not really in the loop when that choice was made).

Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing. [Proc Natl Acad Sci U S A. 2013] – PubMed – NCBI.

Anyway – it is now in Pubmed Central and at least freely available so I felt OK posting about it now.  It is in a way a follow up to the “A phylogeny driven genomic encyclopedia of bacteria and archaea” paper (AKA GEBA) from 2009 with this paper a zooming in on the cyanobacteria.

 

The need for a phylogeny driven genomic encyclopedia of eukaryotes

Monday I gave a talk for the SMBE Eukaryotic Omics satellite meeting that has been going on at UC Davis.  When Holly Bik, a post doc in my lab asked me to talk at the meeting, I said, basically “Well, OK, but I don’t really do much work on eukaryotes.”  And then I came up with an idea – I could make my talk about how it might be good to have a better phylogenetic sampling of eukaryotic genome sequences.  I have been a bit obsessed for many many years about phylogenetic sampling of genomes and, well, though I have avoided eukaryotes mostly in most of my genome sequencing work, I figured, I should still get on my soap box about how phylogenetic sampling is a good thing.  So, well, I did.  And I think we (i.e., the scientific community) really needs a better sampling of eukaryotic genomes.

I have posted my talk to Slideshare and I recorded audio of my talk in synch with the slides and posted that to Youtube.  These are below.

I hereby am calling for those people interested in participating in such a phylogeny driven genomic encyclopedia of eukaryotes to make yourselves known.  We NEED to do this.

Related posts

Psyched: have rescued old MobileMe and other websites after Apple annoyingly cancelled them by posting to Dropbox

A few years ago I used to post many things for the Web through Apple’s Mobile Me service.  Annoyingly, Apple ended up treating this like they treat connectors and plugs for their phones and Macs.  They just decided to move their online system to iCloud and deleted all the old websites through Mobile Me.  Which left me in a lurch.  And then I forgot about it.  But I have been rediscovering how annoying this is since I had a lot of information out there on old papers and projects and now it is gone from the interwebs.  So I have ben trying to re-share all of this stuff.

One way has ben to post data from old papers to Figshare.  See for example:

But I also had all sorts of website related material that is annoyingly gone.  And yesterday I discovered at least a simple solution to this.  I can put all my old websites in my Dropbox public folder and share the link to those files with others and they work pretty well.

See for example my re-releasing of some of my April 1 and other joke websites:

 Also – I have reposted some of the my old websites

I have always been into sharing scientific information on the web since, well, the web came out.  And I am going to dig around for other old websites to post them via Dropbox.  If anyone knows an easy way to upload / convert an old website into WordPress, I suppose I could load in all the old pages into my current wordpress site, but this was a much easier temporary solution.  Still annoyed with Apple but glad Dropbox allows a simple solution.

Converting repeated emails into FAQs: Today’s = How to Get Figures/Details from 2009 GEBA paper

OK I am now officially completely driven insane by email.  As part of my attempt to reduce email communication with people I am going to start posting some of the emails I get often into FAQs.

Today’s email relates to the 2009 paper on a “Phylogeny driven genomic encyclopedia of bacteria and archaea” for which I was the senior and corresponding author.  The email is asking for higher resolution figures that were published in the paper.  This person and many others have asked for a higher res. version of our “genome tree” which was Figure 1.  Here is the version from the paper

But alas, as a JPG when you zoom in you can’t see the text very well.  And about 30 or so people, maybe more, have asked for a higher res. version.  Well, the simplest way to get this figure with legible fonts when zoomed in is to get the PDF of the paper and zoom in on it.  But that may not be for everyone – so here is a link to the PDF of the figure that I posted on postures (Blogger does not allow PDF uploads).  I also posted PDFs of the other figures.

Many people also ask for the treefile (which is basically a coded version of the phylogenetic tree for viewing and analysis).  I am directly posting the treefile below and have also submitted it to “Treebase” (which we should have done before).  Enjoy … and in the future I will be pointing people to this page when they ask for the figure/treefile. Not sure this will have saved me anytime but am sick of writing a lot of this in emails back to people …

#NEXUS
BEGIN trees;
TREE ‘Tree1’ = (((((‘GEBA_Thermanaerovibrio_acidaminovorans’:0.190689,’GEBA_Dethiosulfovibrio_peptidovorans’:0.263143):0.276658,((((((((((((((((((((((((((((((((((((((((‘Escherichia_coli_O157_H7_str_Sakai’:0.0,’Escherichia_coli_str_K12_substr_MG1655′:0.0):1.51E-4,’Escherichia_coli_str_K12_substr_DH10B’:0.0):2.0E-5,(‘Escherichia_coli_ATCC_8739′:1.7E-4,’Escherichia_coli_HS’:1.71E-4):1.7E-4):0.0,(‘Escherichia_coli_536′:0.001196,’Escherichia_coli_APEC_O1’:0.0):0.0):0.0,((‘Shigella_flexneri_2a_str_301′:0.001883,’Shigella_flexneri_2a_str_2457T’:0.0):1.71E-4,’Shigella_flexneri_5_str_8401′:3.44E-4):5.12E-4):0.0,(‘Shigella_boydii_CDC_3083_94′:5.13E-4,’Shigella_boydii_Sb227′:8.57E-4):3.42E-4):0.0,’Escherichia_coli_SMS_3_5′:0.0):0.0,’Escherichia_coli_O157_H7_EDL933′:0.0):0.0,’Escherichia_coli_CFT073′:0.0):0.0,’Escherichia_coli_UTI89′:0.0):0.0,’Escherichia_coli_E24377A’:0.0):0.0,’Shigella_dysenteriae_Sd197′:0.001025):1.69E-4,’Shigella_sonnei_Ss046′:0.001028):0.012167,(((((((‘Salmonella_enterica_subsp_enterica_serovar_Typhi_str_Ty2′:0.0,’Salmonella_enterica_subsp_enterica_serovar_Typhi_str_CT18′:1.7E-4):3.4E-4,’Salmonella_typhimurium_LT2′:0.0):0.0,’Salmonella_enterica_subsp_enterica_serovar_Paratyphi_A_str_ATCC_9150′:8.5E-4):2.0E-6,’Salmonella_enterica_subsp_enterica_serovar_Paratyphi_B_str_SPB7′:1.8E-4):1.69E-4,’Salmonella_enterica_subsp_enterica_serovar_Choleraesuis_str_SC_B67′:3.48E-4):0.001774,’Salmonella_enterica_subsp_arizonae_serovar_62_z4_z23_’:0.001673):0.008533,’Citrobacter_koseri_ATCC_BAA_895′:0.007106):0.003103):0.00437,’Klebsiella_pneumoniae_subsp_pneumoniae_MGH_78578′:0.012094):0.004392,’Enterobacter_sakazakii_ATCC_BAA_894′:0.019781):0.007021,’Enterobacter_sp_638′:0.019532):0.027075,(‘Erwinia_tasmaniensis’:0.033979,’Serratia_proteamaculans_568′:0.033607):0.013319):0.008604,’Erwinia_carotovora_subsp_atroseptica_SCRI1043′:0.03122):0.012206,((((((‘Yersinia_pestis_KIM’:0.0,’Yersinia_pseudotuberculosis_IP_31758′:0.0):0.0,’Yersinia_pestis_CO92′:0.0):0.0,’Yersinia_pseudotuberculosis_IP_32953′:0.0):0.0,((((‘Yersinia_pseudotuberculosis_PB1_’:0.0,’Yersinia_pestis_Pestoides_F’:0.0):0.0,(‘Yersinia_pseudotuberculosis_YPIII’:0.0,’Yersinia_pestis_Nepal516′:0.0):0.0):0.0,’Yersinia_pestis_Antiqua’:1.72E-4):0.0,’Yersinia_pestis_biovar_Microtus_str_91001′:0.0):0.0):0.0,’Yersinia_pestis_Angola’:3.44E-4):0.00575,’Yersinia_enterocolitica_subsp_enterocolitica_8081′:0.009468):0.030284):0.008222,((((‘Candidatus_Blochmannia_pennsylvanicus_str_BPEN’:0.111832,’Candidatus_Blochmannia_floridanus’:0.199319):0.14508,(((‘Buchnera_aphidicola_str_APS_Acyrthosiphon_pisum_’:0.081646,’Buchnera_aphidicola_str_Sg_Schizaphis_graminum_’:0.078489):0.090786,’Buchnera_aphidicola_str_Bp_Baizongia_pistaciae_’:0.232468):0.043831,(‘Wigglesworthia_glossinidia_endosymbiont_of_Glossina_brevipalpis’:0.30099,’Buchnera_aphidicola_str_Cc_Cinara_cedri_’:0.303142):0.063766):0.064196):0.054991,’Baumannia_cicadellinicola_str_Hc_Homalodisca_coagulata_’:0.166451):0.081445,’Sodalis_glossinidius_str_morsitans_’:0.026696):0.024889):0.01239,’Photorhabdus_luminescens_subsp_laumondii_TTO1′:0.048195):0.050763,((((‘Haemophilus_somnus_129PT’:9.73E-4,’Haemophilus_somnus_2336′:7.28E-4):0.038446,’Pasteurella_multocida_subsp_multocida_str_Pm70′:0.033371):0.011204,((‘Mannheimia_succiniciproducens_MBEL55E’:0.02899,’Actinobacillus_succinogenes_130Z’:0.035825):0.013874,(((‘Haemophilus_influenzae_Rd_KW20′:0.002043,’Haemophilus_influenzae_PittGG’:0.00105):5.49E-4,’Haemophilus_influenzae_86_028NP’:5.15E-4):2.24E-4,’Haemophilus_influenzae_PittEE’:0.001026):0.040304):0.008478):0.011217,(((‘Actinobacillus_pleuropneumoniae_L20′:0.00137,’Actinobacillus_pleuropneumoniae_serovar_7_str_AP76′:3.39E-4):1.74E-4,’Actinobacillus_pleuropneumoniae_serovar_3_str_JL03′:0.003062):0.011765,’Haemophilus_ducreyi_35000HP’:0.024577):0.038512):0.080775):0.047571,(((((‘Vibrio_cholerae_O1_biovar_eltor_str_N16961′:3.64E-4,’Vibrio_cholerae_O395’:8.38E-4):0.041305,(‘Vibrio_vulnificus_CMCP6′:5.27E-4,’Vibrio_vulnificus_YJ016’:1.72E-4):0.020829):0.011445,(‘Vibrio_parahaemolyticus_RIMD_2210633′:0.00625,’Vibrio_harveyi_ATCC_BAA_1116′:0.010839):0.011481):0.027253,’Vibrio_fischeri_ES114′:0.05376):0.027779,’Photobacterium_profundum_SS9’:0.072105):0.054993):0.023142,(‘Aeromonas_hydrophila_subsp_hydrophila_ATCC_7966′:0.006284,’Aeromonas_salmonicida_subsp_salmonicida_A449’:0.0108):0.109795):0.020707,((((((‘Shewanella_halifaxensis_HAW_EB4′:0.008905,’Shewanella_pealeana_ATCC_700345’:0.003805):0.025082,(‘Shewanella_sediminis_HAW_EB3′:0.019306,’Shewanella_woodyi_ATCC_51908′:0.012326):0.017175):0.016987,’Shewanella_loihica_PV_4’:0.021173):0.024752,((((((‘Shewanella_sp_ANA_3′:0.002092,’Shewanella_sp_MR_4′:9.8E-4):7.54E-4,’Shewanella_sp_MR_7′:3.48E-4):0.003036,’Shewanella_oneidensis_MR_1’:0.002265):0.010027,(‘Shewanella_sp_W3_18_1′:3.26E-4,’Shewanella_putrefaciens_CN_32’:1.85E-4):0.001996):0.006463,((‘Shewanella_baltica_OS155′:0.001236,’Shewanella_baltica_OS195′:0.0):5.23E-4,’Shewanella_baltica_OS185’:6.84E-4):0.009966):0.015626,(‘Shewanella_denitr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′:0.074921,’Zymomonas_mobilis_subsp_mobilis_ZM4’:0.113715):0.03071):0.187787):0.027917,((‘Rhodospirillum_rubrum_ATCC_11170′:0.169238,’Magnetospirillum_magneticum_AMB_1’:0.125062):0.055149,(((‘Gluconobacter_oxydans_621H’:0.101123,’Gluconacetobacter_diazotrophicus_PAl_5′:0.059111):0.060663,’Granulibacter_bethesdensis_CGDNIH1′:0.085514):0.032014,’Acidiphilium_cryptum_JF_5′:0.120348):0.145099):0.055072):0.09899,(((((‘Rickettsia_bellii_RML369_C’:6.4E-4,’Rickettsia_bellii_OSU_85_389′:6.24E-4):0.053585,(((‘Rickettsia_typhi_str_Wilmington’:0.015422,’Rickettsia_prowazekii_str_Madrid_E’:0.012042):0.039247,((‘Rickettsia_felis_URRWXCal2′:0.00684,’Rickettsia_akari_str_Hartford’:0.024586):0.00502,(((‘Rickettsia_rickettsii_str_Iowa’:0.0,’Rickettsia_rickettsii_str_Sheila_Smith_’:0.0):0.00663,’Rickettsia_conorii_str_Malish_7′:0.002765):0.00386,’Rickettsia_massiliae_MTU5′:0.00794):0.008218):0.002179):0.00446,’Rickettsia_canadensis_str_McKiel’:0.030982):0.03239):0.199956,(‘Orientia_tsutsugamushi_Boryong’:0.012903,’Orientia_tsutsugamushi_str_Ikeda’:0.003049):0.386268):0.180586,((((‘Anaplasma_phagocytophilum_HZ’:0.123173,’Anaplasma_marginale_str_St_Maries’:0.120008):0.159306,((‘Ehrlichia_ruminantium_str_Gardel’:0.002292,’Ehrlichia_ruminantium_str_Welgevonden’:0.002453):0.053871,(‘Ehrlichia_canis_str_Jake’:0.027749,’Ehrlichia_chaffeensis_str_Arkansas’:0.027236):0.031378):0.134774):0.151991,((‘Wolbachia_pipientis’:0.072061,’Wolbachia_endosymbiont_of_Drosophila_melanogaster’:0.04265):0.018425,’Wolbachia_endosymbiont_strain_TRS_of_Brugia_malayi’:0.077353):0.269684):0.141145,’Neorickettsia_sennetsu_str_Miyayama’:0.697366):0.171539):0.064736,’Candidatus_Pelagibacter_ubique_HTCC1062′:0.549831):0.056614):0.089191,’Magnetococcus_sp_MC_1′:0.339568):0.063213):0.093791,((‘Acidobacteria_bacterium_Ellin345′:0.221486,’Solibacter_usitatus_Ellin6076’:0.235193):0.269435,((((((‘Geobacter_sulfurreducens_PCA’:0.05188,’Geobacter_metallireducens_GS_15′:0.04331):0.045927,’Geobacter_uraniireducens_Rf4′:0.08407):0.035503,(‘Pelobacter_propionicus_DSM_2379′:0.107415,’Geobacter_lovleyi_SZ’:0.104313):0.062144):0.11137,’Pelobacter_carbinolicus_DSM_2380′:0.218315):0.102231,(((((((‘Desulfovibrio_vulgaris_subsp_vulgaris_DP4′:2.75E-4,’Desulfovibrio_vulgaris_subsp_vulgaris_str_Hildenborough’:2.47E-4):0.096556,’Desulfovibrio_desulfuricans_subsp_desulfuricans_str_G20′:0.130391):0.041935,’Lawsonia_intracellularis_PHE_MN1_00′:0.194671):0.108731,(‘GEBA_Desulfohalobium_retbaense’:0.206905,’GEBA_Desulfomicrobium_baculatum’:0.21572):0.039647):0.204436,’Desulfotalea_psychrophila_LSv54′:0.368324):0.05185,(‘Desulfococcus_oleovorans_Hxd3′:0.325853,’Syntrophobacter_fumaroxidans_MPOB’:0.267991):0.045811):0.045242,’Syntrophus_aciditrophicus_SB’:0.335728):0.039815):0.036306,(((‘Sorangium_cellulosum_So_ce_56_’:0.340758,’GEBA_Haliangium_ochraceum’:0.326975):0.069132,((‘Anaeromyxobacter_sp_Fw109_5′:0.05281,’Anaeromyxobacter_dehalogenans_2CP_C’:0.046187):0.14976,’Myxococcus_xanthus_DK_1622′:0.199974):0.121235):0.065096,’Bdellovibrio_bacteriovorus_HD100′:0.487944):0.045793):0.04331):0.033782):0.033693,’GEBA_Denitrovibrio_acetiphilus’:0.52279):0.036282,(((((((‘Sulfurimonas_denitrificans_DSM_1251′:0.23347,’Arcobacter_butzleri_RM4018′:0.208618):0.040632,’Sulfurovum_sp_NBC37_1’:0.230443):0.030751,(((((‘Campylobacter_jejuni_subsp_jejuni_NCTC_11168′:0.001263,’Campylobacter_jejuni_RM1221’:9.27E-4):6.61E-4,((‘Campylobacter_jejuni_subsp_doylei_269_97′:0.006051,’Campylobacter_jejuni_subsp_jejuni_81116′:3.16E-4):0.001123,’Campylobacter_jejuni_subsp_jejuni_81_176’:9.26E-4):3.5E-4):0.119606,((‘Campylobacter_curvus_525_92′:0.03145,’Campylobacter_concisus_13826′:0.037212):0.061724,’Campylobacter_fetus_subsp_fetus_82_40′:0.097271):0.023098):0.020182,’Campylobacter_hominis_ATCC_BAA_381′:0.16927):0.075991,’GEBA_Sulfurospirillum_deleyianum’:0.136694):0.07072):0.026032,((((((‘Helicobacter_pylori_HPAG1′:0.003032,’Helicobacter_pylori_26695′:0.004293):9.24E-4,’Helicobacter_pylori_Shi470′:0.004956):0.002035,’Helicobacter_pylori_J99′:0.00625):0.008252,’Helicobacter_acinonychis_str_Sheeba’:0.010673):0.199339,’Helicobacter_hepaticus_ATCC_51449′:0.121696):0.062387,’Wolinella_succinogenes_DSM_1740′:0.107844):0.108511):0.052813,’Nitratiruptor_sp_SB155_2′:0.132215):0.401479,(‘Aquifex_aeolicus_VF5′:0.291771,’Sulfurihydrogenibium_sp_YO3AOP1′:0.270137):0.202377):0.049843,’Elusimicrobium_minutum_Pei191’:0.667875):0.034753):0.023181,(((((((‘GEBA_Dyadobacter_fermentans’:0.115999,’GEBA_Spirosoma_linguale’:0.124662):0.074785,’Cytophaga_hutchinsonii_ATCC_33406′:0.182703):0.054101,’Candidatus_Amoebophilus_asiaticus_5a2′:0.332349):0.041954,((‘GEBA_Pedobacter_heparinus’:0.181859,’GEBA_Chitinophaga_pinensis’:0.30193):0.037197,(((((‘Flavobacterium_psychrophilum_JIP02_86′:0.059237,’Flavobacterium_johnsoniae_UW101′:0.052582):0.072716,’Gramella_forsetii_KT0803′:0.133872):0.034419,’GEBA_Capnocytophaga_ochracea’:0.123672):0.087924,’Candidatus_Sulcia_muelleri_GWSS’:0.665368):0.057908,((((‘Bacteroides_fragilis_YCH46′:0.0,’Bacteroides_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33L’:5.32E-4):0.001131,(‘Bacillus_cereus_ATCC_14579′:0.002251,’Bacillus_weihenstephanensis_KBAB4′:0.013987):0.004118):0.001515,’Bacillus_cereus_ATCC_10987′:2.57E-4):0.020967,’Bacillus_cereus_subsp_cytotoxis_NVH_391_98’:0.013733):0.085584,(((‘Bacillus_subtilis_subsp_subtilis_str_168′:0.015012,’Bacillus_amyloliquefaciens_FZB42′:0.015183):0.020109,’Bacillus_pumilus_SAFR_032′:0.040049):0.011797,’Bacillus_licheniformis_ATCC_14580’:0.023456):0.065389):0.021459,(‘Geobacillus_thermodenitrificans_NG80_2′:0.011367,’Geobacillus_kaustophilus_HTA426’:0.01873):0.094956):0.020796,((((((((‘Staphylococcus_aureus_subsp_aureus_Mu3′:0.0,’Staphylococcus_aureus_subsp_aureus_Mu50′:1.67E-4):1.67E-4,’Staphylococcus_aureus_subsp_aureus_N315’:1.67E-4):0.0,(‘Staphylococcus_aureus_subsp_aureus_JH9′:0.001001,’Staphylococcus_aureus_subsp_aureus_JH1’:0.0):3.34E-4):5.16E-4,(((‘Staphylococcus_aureus_subsp_aureus_MRSA252′:6.67E-4,’Staphylococcus_aureus_RF122’:3.35E-4):0.0,(((‘Staphylococcus_aureus_subsp_aureus_NCTC_8325′:6.77E-4,’Staphylococcus_aureus_subsp_aureus_USA300_TCH1516′:0.0):0.0,’Staphylococcus_aureus_subsp_aureus_USA300’:0.0):0.0,(‘Staphylococcus_aureus_subsp_aureus_COL’:6.68E-4,’Staphylococcus_aureus_subsp_aureus_str_Newman’:3.33E-4):3.34E-4):1.67E-4):0.0,(‘Staphylococcus_aureus_subsp_aureus_MSSA476′:0.0,’Staphylococcus_aureus_subsp_aureus_MW2’:0.0):3.34E-4):1.51E-4):0.032187,((‘Staphylococcus_epidermidis_ATCC_12228′:3.35E-4,’Staphylococcus_epidermidis_RP62A’:1.66E-4):0.023543,’Staphylococcus_haemolyticus_JCSC1435′:0.025193):0.012868):0.014679,’Staphylococcus_saprophyticus_subsp_saprophyticus_ATCC_15305′:0.045225):0.208482,((((((((((‘Streptococcus_pyogenes_SSI_1′:1.69E-4,’Streptococcus_pyogenes_MGAS315’:3.35E-4):3.86E-4,(((((‘Streptococcus_pyogenes_M1_GAS’:3.34E-4,’Streptococcus_pyogenes_MGAS5005′:1.67E-4):3.34E-4,(((‘Streptococcus_pyogenes_MGAS8232′:6.78E-4,’Streptococcus_pyogenes_MGAS10750′:8.62E-4):1.67E-4,’Streptococcus_pyogenes_str_Manfredo’:5.01E-4):3.34E-4,’Streptococcus_pyogenes_MGAS10394′:5.01E-4):0.0):1.67E-4,(‘Streptococcus_pyogenes_MGAS9429′:5.01E-4,’Streptococcus_pyogenes_MGAS2096′:0.0):5.01E-4):0.0,’Streptococcus_pyogenes_MGAS10270′:5.09E-4):3.34E-4,’Streptococcus_pyogenes_MGAS6180’:5.01E-4):2.83E-4):0.032705,((‘Streptococcus_agalactiae_2603V_R’:5.02E-4,’Streptococcus_agalactiae_A909′:0.0):5.02E-4,’Streptococcus_agalactiae_NEM316′:0.0):0.032531):0.009744,((‘Streptococcus_thermophilus_LMG_18311′:4.96E-4,’Streptococcus_thermophilus_CNRZ1066′:6.75E-4):0.001002,’Streptococcus_thermophilus_LMD_9′:8.46E-4):0.042346):0.010989,’Streptococcus_mutans_UA159’:0.053241):0.014154,((‘Streptococcus_suis_98HAH33′:1.41E-4,’Streptococcus_suis_05ZYH33’:0.003069):0.045053,((((‘Streptococcus_pneumoniae_D39′:0.0,’Streptococcus_pneumoniae_R6’:0.0):0.001089,(‘Streptococcus_pneumoniae_TIGR4′:7.57E-4,’Streptococcus_pneumoniae_CGSP14′:0.001274):5.04E-4):1.79E-4,’Streptococcus_pneumoniae_Hungary19A_6’:5.78E-4):0.025464,(‘Streptococcus_gordonii_str_Challis_substr_CH1′:0.013866,’Streptococcus_sanguinis_SK36’:0.013168):0.014048):0.01685):0.015608):0.079689,((‘Lactococcus_lactis_subsp_cremoris_SK11′:0.001565,’Lactococcus_lactis_subsp_cremoris_MG1363′:8.56E-4):0.005333,’Lactococcus_lactis_subsp_lactis_Il1403′:0.005458):0.157584):0.124114,’Enterococcus_faecalis_V583’:0.096988):0.030082,(((((‘Lactobacillus_acidophilus_NCFM’:0.017053,’Lactobacillus_helveticus_DPC_4571′:0.025039):0.047802,(‘Lactobacillus_gasseri_ATCC_33323′:0.008251,’Lactobacillus_johnsonii_NCC_533’:0.00468):0.081515):0.035749,(‘Lactobacillus_delbrueckii_subsp_bulgaricus_ATCC_BAA_365′:0.001075,’Lactobacillus_delbrueckii_subsp_bulgaricus_ATCC_11842’:9.47E-4):0.095385):0.189762,((‘Lactobacillus_casei_BL23′:1.67E-4,’Lactobacillus_casei_ATCC_334′:1.71E-4):0.13496,’Lactobacillus_sakei_subsp_sakei_23K’:0.116042):0.029638):0.037981,(((((‘Lactobacillus_brevis_ATCC_367′:0.113171,’Lactobacillus_plantarum_WCFS1′:0.09989):0.023598,’Pediococcus_pentosaceus_ATCC_25745’:0.140539):0.018317,(‘Lactobacillus_fermentum_IFO_3956′:0.075472,’Lactobacillus_reuteri_F275’:0.062813):0.114981):0.022679,((‘Leuconostoc_mesenteroides_subsp_mesenteroides_ATCC_8293′:0.031056,’Leuconostoc_citreum_KM20′:0.035589):0.124121,’Oenococcus_oeni_PSU_1′:0.234536):0.131959):0.021585,’Lactobacillus_salivarius_UCC118’:0.124879):0.034651):0.077386):0.111668,(((‘Listeria_monocytogenes_EGD_e’:0.00208,’Listeria_monocytogenes_str_4b_F2365′:7.75E-4):0.001511,’Listeria_welshimeri_serovar_6b_str_SLCC5334′:0.003974):0.001047,’Listeria_innocua_Clip11262′:0.001031):0.107265):0.033808):0.044404,’Lysinibacillus_sphaericus_C3_41′:0.152339):0.036331):0.021337,’Oceanobacillus_iheyensis_HTE831′:0.18896):0.019902,(‘Bacillus_clausii_KSM_K16′:0.093196,’Bacillus_halodurans_C_125′:0.066964):0.053506):0.027554,’Exiguobacterium_sibiricum_255_15′:0.211271):0.115095,’GEBA_Alicyclobacillus_acidocaldarius’:0.223192):0.06559,(((((‘Clostridium_acetobutylicum_ATCC_824′:0.123954,’Clostridium_novyi_NT’:0.114099):0.023517,((((‘Clostridium_perfringens_ATCC_13124′:5.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Tropheryma_whipplei_str_Twist’:6.79E-4):0.478476):0.120846,’GEBA_Acidimicrobium_ferrooxidans’:0.43829):0.090081,(((‘GEBA_Cryptobacterium_curtum’:0.142154,’GEBA_Eggerthella_lenta’:0.088587):0.047811,’GEBA_Slackia_heliotrinireducens’:0.117231):0.104268,’GEBA_Atopobium_parvulum’:0.269623):0.198082):0.036936,(‘GEBA_Conexibacter_woesei’:0.383152,’Rubrobacter_xylanophilus_DSM_9941′:0.357989):0.109409):0.087352,(((((((((‘Synechococcus_sp_WH_7803′:0.023543,’Synechococcus_sp_CC9311’:0.044194):0.014221,((‘Synechococcus_sp_CC9605′:0.022222,’Synechococcus_sp_WH_8102′:0.025798):0.006423,’Synechococcus_sp_CC9902’:0.032326):0.022152):0.016325,(((‘Prochlorococcus_marinus_subsp_marinus_str_CCMP1375′:0.058394,’Prochlorococcus_marinus_str_MIT_9211’:0.053438):0.019947,((‘Prochlorococcus_marinus_str_NATL2A’:0.00276,’Prochlorococcus_marinus_str_NATL1A’:0.002109):0.070906,((‘Prochlorococcus_marinus_str_MIT_9515′:0.013908,’Prochlorococcus_marinus_subsp_pastoris_str_CCMP1986’:0.016702):0.023743,(((‘Prochlorococcus_marinus_str_AS9601′:0.005031,’Prochlorococcus_marinus_str_MIT_9301′:0.005416):0.003975,’Prochlorococcus_marinus_str_MIT_9215′:0.011185):0.004908,’Prochlorococcus_marinus_str_MIT_9312’:0.010415):0.020455):0.117983):0.022565):0.040798,(‘Prochlorococcus_marinus_str_MIT_9313′:0.00429,’Prochlorococcus_marinus_str_MIT_9303′:0.003453):0.043557):0.012995):0.046129,’Synechococcus_sp_RCC307’:0.067465):0.195828,(‘Synechococcus_elongatus_PCC_7942′:3.21E-4,’Synechococcus_elongatus_PCC_6301’:0.00142):0.098101):0.061386,(((((‘Nostoc_sp_PCC_7120′:0.004827,’Anabaena_variabilis_ATCC_29413′:0.003501):0.036361,’Nostoc_punctiforme_PCC_73102′:0.042386):0.086848,’Trichodesmium_erythraeum_IMS101’:0.151445):0.024405,(((‘Cyanothece_sp_ATCC_51142′:0.088208,’Microcystis_aeruginosa_NIES_843′:0.108904):0.018975,’Synechocystis_sp_PCC_6803′:0.111161):0.027275,’Synechococcus_sp_PCC_7002’:0.127272):0.053965):0.023778,(‘Acaryochloris_marina_MBIC11017′:0.127345,’Thermosynechococcus_elongatus_BP_1’:0.138774):0.035212):0.017944):0.063385,(‘Synechococcus_sp_JA_3_3Ab’:0.023735,’Synechococcus_sp_JA_2_3B_a_2_13_’:0.025648):0.172906):0.056598,’Gloeobacter_violaceus_PCC_7421′:0.211642):0.301851,(((((‘Roseiflexus_castenholzii_DSM_13941′:0.02822,’Roseiflexus_sp_RS_1′:0.017828):0.118476,’Chloroflexus_aurantiacus_J_10_fl’:0.154341):0.066504,’Herpetosiphon_aurantiacus_ATCC_23779′:0.219302):0.124086,(‘GEBA_Sphaerobacter_thermophilus’:0.242004,’GEBA_Thermobaculum_terrenum’:0.272557):0.055029):0.055648,((‘Dehalococcoides_sp_CBDB1′:5.54E-4,’Dehalococcoides_sp_BAV1′:8.51E-4):0.017643,’Dehalococcoides_ethenogenes_195’:0.014048):0.50406):0.083393):0.032459):0.039409):0.035188):0.022061):0.039665):0.054226,(((‘Thermosipho_melanesiensis_BI429′:0.127803,’Fervidobacterium_nodosum_Rt17_B1’:0.188887):0.074834,(((‘Thermotoga_maritima_MSB8′:0.007577,’Thermotoga_sp_RQ2′:5.3E-4):0.005057,’Thermotoga_petrophila_RKU_1′:0.006656):0.159923,’Thermotoga_lettingae_TMO’:0.230211):0.037393):0.080613,’Petrotoga_mobilis_SJ95′:0.362128):0.246177):0.287154,((‘Thermus_thermophilus_HB8′:0.001498,’Thermus_thermophilus_HB27’:0.001224):0.144321,(‘GEBA_Meiothermus_ruber’:0.114423,’GEBA_Meiothermus_silvanus’:0.077947):0.086289):0.12529):0.1212895,(‘Deinococcus_geothermalis_DSM_11300′:0.043888,’Deinococcus_radiodurans_R1’:0.07314):0.1212895);
END;

What’s Hot in Biology 2011? Why, the Genomic Encyclopedia paper I am senior author on #Yay?

And now back to some science. Got an email a few days ago from Nikos Kyrpides pointing to this: What’s Hot in Biology – 2011. Very cool – the paper on the “Genomic Encyclopedia of Bacteria and Archaea” project that I coordinated (and for which I am the senior author) has been identified as the hot biology paper of November/December 2011 by “Science Watch”. Plus they have a reasonably detailed story about it “BRANCHING OUT WITH PHYLOGENETICALLY DRIVEN GENOME SEQUENCING” by Jeremy Cherfas. I note – the project was done at the DOE-Joint genome Institute and involved an enormous number of people there (I have an Adjunct Appointment there). It was done in collaboration with the DSMZ – a microbial culture collection in Germany.
The paper A phylogeny driven genomic encyclopedia of bacteria and archaea apparently has been getting a lot of citations, which I guess is how it got picked as being “hot”.

Some videos of talks or interviews about the project

Talk at DOE JGI User Meeting 2009 http://www.scivee.tv/flash/embedCast.swf

Talk at GME Meeting 2008 http://www.scivee.tv/flash/embedCast.swf

JGI Video about the project http://www.scivee.tv/flash/embedCast.swf

A "work" trip to Catalina Island: USC, Wrigley, C-DEBI, dark energy biosphere, Virgin Oceanic, Deep Five, & more

Panorama of Catalina Island

Well, the last few days have been completely eye opening for me. I have been on a little trip to the USC Wrigley Marine Science Center near the town of Two Harbors on Santa Catalina Island. Alas, this has not been a vacation. This has been work trip. I was invited a bit ago to come to a workshop here by Bill Nelson, a friend and colleague of mine I used to work with at The Institute for Genomic Research (TIGR). Bill is part of a project called the Center for Dark Energy Biosphere Investigations (C-DEBI). The workshop he invited me to was to discuss evolutionary studies as part of this project.

I note this is a general post about the trip – I will post more about the individual science topics including C-DEBI and Virgin Oceanic later.

As is usual, I did not fully commit to going to the workshop immediately and I dragged out committing for a very long time (driving Bill I am crazy I am sure).  But eventually I accepted and then kept flip-flopping on exactly when I would go, but eventually settled on dates too.

What is C-DEBI:

When Bill first invited me to this workshop, I had no clue what this C-DEBI project was.  And Bill must have assumed I knew because he did not provide any detail about what C-DEBI was.  So of course, that is what that Google thing is for.  And what I found was quite intriguing:

A simple description comes from their web site:

Welcome to the Center for Dark Energy Biosphere Investigations (C-DEBI), a National Science Foundation (NSF)-funded Science and Technology Center on the deep biosphere. Our mission is to explore life beneath the seafloor and make transformative discoveries that advance science, benefit society, and inspire people of all ages and origins. We are a multi-institutional distributed center establishing the intellectual, educational, technological, cyber-infrastructural and collaborative framework needed for transformative experimental and exploratory research on the subseafloor biosphere.


This certainly intrigued me.  And the fact that the workshop was going to be at the George and MaryLou Boone Center for Science and Environmental Leadership (which is part of the USC Marine Station on Catalina Island) also appealed – I had visited the Marine Station on Catalina Island in the summer of 2009 for a week and it was very very very nice.

But the real final thing that convinced me to go was that the Director of the C-DEBI project is Katrina Edwards.  Not only does she do fascinating science, but, well, I kind of owed her (and Bill reminded me of this).  She gave my kids (and me) a spectacular tour of the Atlantis and the submersibles Jason and ALVIN when Atlantis was docked in San Francisco

Katrina Edwards telling us about the Atlantis

My family thinks the tour is awesome

Add caption

Katrina Edwards showing us ALVIN

So I kind of had to say yes. Rough I know – being forced to go to a meeting on Catalina Island because my kids had gotten a great submersible tour.

Heading to Catalina Island

So I finally got my act together and headed down to LAX from Sacramento.

I arrived in LAX and got a cab to the Catalina Island Ferry terminal. I picked up my ticket and alas, the deli there was closed and there was nowhere to get lunch. I wandered around a bit and took some pictures.

As a bit of a side story, a PhD student in my lab Russell Neches was visiting his mom in the LA area and he and his mom dropped by for a few minutes. Then Katrina and her daughter were dropped off by her husband Eric Webb (who does some interesting marine microbiology research himself).

After saying goodbyes, we boarded the ferry and headed out.  Katrina and I were both pleased (and surprised) to hear the announcement that we were going to Two Harbors first, rather than Avalon, so we would get there much earlier.

We headed out into San Pedro harbor, slowly, and I and everyone else took pics as we went by some of the sights.

It is always amazing to me to see the giant container ships and the massive size of San Pedro Harbor.

The pirate ship was a bit weird, but I guess it must be some sort of tour thing.

Then we got out into the more “open” water.  The seas were pretty small – but the ferry goes quite fast so it was bouncing up and down a little bit. Unlike on my last trip, when we say a few blue whales from the ferry, we did not see much animal life in the water.

We got the Catalina Island pretty quickly.  And it was looking gorgeous – much greener than the last time I was there. And we passed by the Marine Station – and headed to the dock (see the panoramic pictures I made using Adobe Photoshop’s stitching function):

Some of the C-DEBI personnel picked us up in town and we headed up/down the dirt road in the USC Van to the marine station.  We got there and I found out I was in the same townhouse/apartment I had stayed in in 2009.  Nice.  After dumping my stuff there was a reception in the Boone Center.  I got to meet the rest of the people there for the meeting – it was a small collection of folks.  We had some wine and cheese and other goodies, enjoyed the view of the lab and the water and then headed over to the dining hall for dinner.

After dinner we went back to the Boone Center and spent the night telling stories and getting to know each other and the Woolly Bear caterpillars wandering around everywhere.

Katrina Edwards and wooly bear

Katrina Edwards

I went to sleep and got up semi-early the next AM.  I made myself some coffee and headed to breakfast.  Then down to the lab for a full day of meetings and discussion. But first I took a look around and took a few pictures:

This was when I finally got a better introduction to the whole point of the meeting.  The point of the meeting was that Bill Nelson was tasked with organizing a “theme” for the C-DEBI project on evolution.  In essence, our meeting was to discuss what interesting evolution-related questions could be asked/answered as part of the C-DEBI project.

The people there were Bill Nelson, Katrina Edwards, me, John Heidelberg, Jennifer Biddle, Jason Sylvan, Bill Brazelton, Ben Tully, and Craig Moyer.

Basically, just as the meeting started we all headed down to the dock to welcome the arrival of some other folks from the mainland.  The new arrivals were Ann Close and two members of the Virgin Oceanic ProjectChris Welsh and Loretta Whitesides.   This project was announced very recently and is a project to explore the five deepest sites in each major ocean in a one person submersible.  The pilot of the submersible will be Chris Welsh.  The project is being supported in part by Sir Richard Branson and thus the “Virgin” connection.   The sub is being designed by Graham Hawkes a well known ROV designer.  More on this in a bit. I note I had written about this in my blog a few days ago –— not knowing I would soon be meeting some of the people involved.

We then headed back to the meeting room (the library) and got going.  We did mini introductions.  At the suggestion of Chris Welsh, everyone in addition to saying who they were also said who their hero was.  Among the people listed were relatives of participants, Charles Lindberg, Yoda, Charles Darwin, superheroes, and oceanographers.   We then got a more detailed introduction to the C-DEBI project and also got a very brief introduction to the Virgin Oceanic Deep-Five project (more on this below).

We then had a mini coffee break and I somehow handed over digital SLR my camera to Katrina’s daughter.  She then took it and generated quite a collection of good pictures of the people at the meeting.

Jonathan Eisen
Bill Nelson
Katrina Edwards
Loretta Whitesides
Jennifer Biddle
Jason Sylvan
Craig Moyer
Billy Brazelton

Chris Welsh
Ben Tully
John Heidelberg

We then had some additional discussions about evolution and the C-DEBI project.  I learned, for example, about a group of bacteria I alas had not heard of before – the Zeta proteobacteria (see Moyer’s PLoS One paper on them here).  This is a group that is particularly abundant in some C-DEBI related sites.  In particular they seem to do well in iron-oxidizing microbial mat communities.  Moyer presented some interesting data on biogeography of this group of bacteria.  I also learned some new things from the others at the meeting. And then we broke for lunch up the hill in the dining hall.

After lunch we hear much more detail on the Virgin Oceanic project.  It is completely fascinating, though a bit scary.  The plan is for Chris Welsh to pilot the submersible down into the deepest sites on each of the five main oceans.  Right now the submersible is still being finished.  We also learned about the sailboat that will be the mother ship for the submersible.  The boat seems quite fast and has some nice features but it will also be a bit tight on space.  I note Welsh mentioned they are still looking for crew for the boat so if you are interested …

Their plan is to do some testing in a few months in various places and to then do the deep dives.  What was most interesting to me about the project is that the people involved really seem to be committed to doing interesting science.  Loretta Whitesides has a science background and seemed to have an excellent grasp of many of the scientific issues being discussed.  Welsh also seems to have a deep interest in the science.  The group also has some good people lined up that they are working with and are still looking for other ideas and collaborators to participate in the science.  It reminded me of some of the stories I have heard about the great explorer’s doing science along the course of their voyages.

I briefly discussed a few things including the Genomic Encyclopedia of Bacteria and Archaea project I coordinate and our recent study of phylogenetically very novel sequences that we found in metagenomic data.  And then the Virgin crew had to take off:

Then back for some more meeting and discussion.  During the course of the day I learned about an enormous number of cruises and surveys and plans for drilling in various sites and how the C-DEBI folks study microbes beneath the sea floor.  I also learned that they have a lot of education and outreach activities and are looking for more.  I also learned that if you want to keep up to date on C-DEBI related activities and if you want to participate in some of their projects, they are very open.  A good way to keep up to date is to join their mailing list.  One can also learn a great deal by browsing their web site and some of the publications listed there.  Anyway – I am going to do a whole post just on C-DEBI later — focusing here on the big picture parts of my trip.

After the discussions we went back to Boone House for another reception and then dinner.  After dinner we hung out in the Boone House again.  And then went to sleep (though there were rumors of some weird sightings in and around the housing complex that night.

The next morning I got up a bit late and missed breakfast but I grabbed some cereal from the dining hall, made some coffee and headed down the hill again. We had some discussions in the AM about the future plans for evolutionary studies associated with the C-DEBI project and then headed back up the hill for lunch. There was a little bit of time before lunch so I wandered around the hills and took a few pictures.

Then we had our last group lunch and many of the folks headed down to the USC boat to get back to the mainland.

I spend the next few hours doing a bit of work and also went to the beach to collect some shells for my kids.  You see, I did not have to get on the USC boat because I had snagged a ride on a helicopter back to the mainland.

The helicopter eventually arrived and Katrina gave me a ride down to the water in her golf cart (she had recently injured her leg and had a hard time walking around).

And we got in the chopper and were off.  Katrina’s daughter and John and Karla Heidelberg’s son enjoyed the ride quite a bit.  It was my first helicopter ride too – and it was quite fun.  The best part the pilot saw and then flew over a massive pod of dolphins.

And then we headed on into San Pedro (which freaked me out a bit as they had said we were going to Long Beach and I had to catch a plane).

John Heidelberg however had figured this out and met us there.  The chopper took off, Katrina and her daughter went to wait for her husband, and John gave me a ride to the airport and I got there in time for my flight home.

All pics from this trip are in the slideshow here.