Saturday, February 09, 2019

Symbiosis paper of interest: Host-Microbe Coevolution and Complex Marine Invertebrate Holobionts | mBio

This looks potentially interesting.



Host-Microbe Coevolution: Applying Evidence from Model Systems to Complex Marine Invertebrate Holobionts | mBio



O’Brien PA, Webster NS, Miller DJ, Bourne DG. 2019. Host-microbe coevolution: applying evidence from model systems to complex marine invertebrate holobionts. mBio 10:e02241-18. https://doi.org/10.1128/mBio.02241-18.

ABSTRACT
Marine invertebrates often host diverse microbial communities, making it difficult to identify important symbionts and to understand how these communities are structured. This complexity has also made it challenging to assign microbial functions and to unravel the myriad of interactions among the microbiota. Here we propose to address these issues by applying evidence from model systems of host-microbe coevolution to complex marine invertebrate microbiomes. Coevolution is the reciprocal adaptation of one lineage in response to another and can occur through the interaction of a host and its beneficial symbiont. A classic indicator of coevolution is codivergence of host and microbe, and evidence of this is found in both corals and sponges. Metabolic collaboration between host and microbe is often linked to codivergence and appears likely in complex holobionts, where microbial symbionts can interact with host cells through production and degradation of metabolic compounds. Neutral models are also useful to distinguish selected microbes against a background population consisting predominately of random associates. Enhanced understanding of the interactions between marine invertebrates and their microbial communities is urgently required as coral reefs face unprecedented local and global pressures and as active restoration approaches, including manipulation of the microbiome, are proposed to improve the health and tolerance of reef species. On the basis of a detailed review of the literature, we propose three research criteria for examining coevolution in marine invertebrates: (i) identifying stochastic and deterministic components of the microbiome, (ii) assessing codivergence of host and microbe, and (iii) confirming the intimate association based on shared metabolic function.


Found out about it on Slack, Twitter and via Google Scholar automated searches so .. caught my attention.
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Today's microbial diversity reading: A census-based estimate of Earth's bacterial and archaeal diversity

Looking at this today: A census-based estimate of Earth's bacterial and archaeal diversity

Louca S, Mazel F, Doebeli M, Parfrey LW (2019) A census-based estimate of Earth's bacterial and archaeal diversity. PLoS Biol 17(2): e3000106. https://doi.org/10.1371/journal.pbio.3000106

Definitely worth a look:

Abstract
The global diversity of Bacteria and Archaea, the most ancient and most widespread forms of life on Earth, is a subject of intense controversy. This controversy stems largely from the fact that existing estimates are entirely based on theoretical models or extrapolations from small and biased data sets. Here, in an attempt to census the bulk of Earth's bacterial and archaeal ("prokaryotic") clades and to estimate their overall global richness, we analyzed over 1.7 billion 16S ribosomal RNA amplicon sequences in the V4 hypervariable region obtained from 492 studies worldwide, covering a multitude of environments and using multiple alternative primers. From this data set, we recovered 739,880 prokaryotic operational taxonomic units (OTUs, 16S-V4 gene clusters at 97% similarity), a commonly used measure of microbial richness. Using several statistical approaches, we estimate that there exist globally about 0.8–1.6 million prokaryotic OTUs, of which we recovered somewhere between 47%–96%, representing >99.98% of prokaryotic cells. Consistent with this conclusion, our data set independently "recaptured" 91%–93% of 16S sequences from multiple previous global surveys, including PCR-independent metagenomic surveys. The distribution of relative OTU abundances is consistent with a log-normal model commonly observed in larger organisms; the total number of OTUs predicted by this model is also consistent with our global richness estimates. By combining our estimates with the ratio of full-length versus partial-length (V4) sequence diversity in the SILVA sequence database, we further estimate that there exist about 2.2–4.3 million full-length OTUs worldwide. When restricting our analysis to the Americas, while controlling for the number of studies, we obtain similar richness estimates as for the global data set, suggesting that most OTUs are globally distributed. Qualitatively similar results are also obtained for other 16S similarity thresholds (90%, 95%, and 99%). Our estimates constrain the extent of a poorly quantified rare microbial biosphere and refute recent predictions that there exist trillions of prokaryotic OTUs.

Author summary
The global diversity of Bacteria and Archaea ("prokaryotes"), the most ancient and most widespread forms of life on Earth, is subject to high uncertainty. Here, to estimate the global diversity of prokaryotes, we analyzed a large number of 16S ribosomal RNA gene sequences, found in all prokaryotes and commonly used to catalogue prokaryotic diversity. Sequences were obtained from a multitude of environments across thousands of geographic locations worldwide. From this data set, we recovered 739,880 prokaryotic operational taxonomic units (OTUs), i.e., 16S gene clusters sharing 97% similarity, roughly corresponding to prokaryotic species. Using several statistical approaches and through comparison with existing databases and previous independent surveys, we estimate that there exist globally between 0.8 and 1.6 million prokaryotic OTUs. When restricting our analysis to the Americas, while controlling for the number of studies, we obtain similar estimates as for the global data set, suggesting that most OTUs are not restricted to a single continent but are instead globally distributed. Our estimates constrain the extent of a commonly hypothesized but poorly quantified rare prokaryotic biosphere and refute recent predictions that there exists trillions of prokaryotic OTUs. Our findings also indicate that, contrary to common speculation, extinctions may strongly influence global prokaryotic diversity.
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Tuesday, January 29, 2019

Wakelet of UC Davis "Research Quality and Design Symposium"

Made a mini Wakelet:
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Wednesday, January 09, 2019

And today in the Twisted Tree of Life Award - the only way to study evolution is to try and make fake reconstructions of past events

See Tweets ...
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Monday, December 10, 2018

Twisted Tree of Life Award: University of Nebraska Lincoln Press Release on Archaeal Epigenetics

Well this one is really painful.  So painful I am re-starting my "Twisted Tree of Life" Award posts here.

See Tweets about it below:








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Thursday, November 29, 2018

YAMMMM: Yet Another Mostly Male Microbiome Meeting - Gut Microbiota for Health World Summit 2019

Uggh. In the middle of a faculty retreat and saw a Tweet about this meeting and could not help looking at their speaker list. And am not impressed.  Too many male speakers.

Gut Microbiota for Health World Summit 2019
A Meeting to Hear Men (81%) Not Women (19%) Discussing Microbiota*, **
YAMMMM: Yet Another Mostly Male Microbiome Meeting

Gail A. Hecht, MD, MS, Loyola University Medical Center (U.S.)
Jack A. Gilbert, PhD, University of Chicago (U.S.)
Session Moderator: Giovanni Barbara, MD, University of Bologna (Italy)
Suzanne Devkota, PhD, Cedars-Sinai Medical Center (U.S.)
Magnus Simren, MD, PhD, AGAF, University of Gothenburg (Sweden)
Christoph Thaiss, PhD, University of Pennsylvania (U.S.)
Session Moderator: Purna Kashyap, MBBS, Mayo Clinic
Eric Martens, PhD, University of Michigan (U.S.)
Liping Zhao, PhD, Rutgers, The State University of New Jersey (U.S.)
Paul Cotter, PhD, University College Cork (Ireland)
Robert Britton, PhD, Baylor College of Medicine (U.S.)
Joseph Zackular, PhD, University of Pennsylvania (U.S.)
Premysl Bercik, MD, McMaster University (Canada)
Dirk Haller, PhD, Technical University of Munich (Germany)
Eran Elinav, MD, PhD, Weizmann Institute of Science (Israel)
Karine Clément, MD, PhD, Pitié-Salpêtrière Hospital (France)
Alexander Khoruts, MD, University of Minnesota (U.S.)
Diane Hoffmann, JD, MS, University of Maryland (U.S.)
Francisco Guarner, MD, PhD, University Hospital Vall d’Hebron (Spain)
Dylan Dodd, PhD, Stanford University (U.S.)
Stanley L. Hazen, MD, PhD, Cleveland Clinic (U.S.)
Rohit Loomba, MD, University of California, San Diego (U.S.)
Gary D. Wu, MD, University of Pennsylvania (U.S.)
Session Moderator: Hania Szajewska, MD, Medical University of Warsaw (Poland)
Purna Kashyap, MBBS, Mayo Clinic (U.S.)
Geoffrey Preidis, MD, PhD, Baylor College of Medicine (U.S.)
Pinaki Panigrahi, University of Nebraska (U.S.)

 * Gender inferred by Google Searches, looking at personal websites, and some guessing
** Assuming just M:F genders which is clearly a bad assumption
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Saturday, November 03, 2018

Pumpkin Carving as a model for Genome Assembly

So - we have this pumpkin carving contest every year in the UC Davis Genome Center.  And people from my lab have done some excellent pumpkins in the past.

See for example some details on their 2014 pumpkin:






And I have on and off carved pumpkins on sciency themes every once in a while.




So this year, when the Genome Center admins sent around an email saying they had bought pumpkins for people to use, I decided it would be fun to do something this year.  But then 10/30 came and we had still not done anything.

So I came up with a crazy idea.  Cut up pumpkins in different ways as an example of genome sequencing strategies.  And, with the help of a few people in my lab and some of the people in neighboring labs, this is what we did.

So - first - we took three pumpkins.

And we decided to make one of them a representation of long read sequencing and another a representative of short read sequencing.  So - using a saw provided by people in Justin Siegel's lab, I cut one pumpkin into horizontal slices and remove the innards and made that the "long read sequencing" example.  And then I took pumpkin #2 and again cut into horizontal slices but this time I  then cut those slices up into chunks.  And we then stored the pumpkin pieces overnight and Katie Dahlhausen in my lab made some nice signs to add to the display. In addition, the decorated pumpkin #3 with some "Shotgun sequencing" motifs.  And voila, we had our pumpkins ready for the contest for 10/31.

So I headed in to work early, and set up our display.





And I posted about it to Twitter.


But something seemed lacking.  So I went and got another pumpkin


And now it felt complete.

And then, after the symposium I decided - hey - we should try to reassemble these.  I took some pics of this and made them into videos / gifs.
Long piece assembly. 

 Assembling the long piece pumpkin shotgun was easy.



Linking assembly.

 Assembling from the linking pieces was harder.  And in the end we did not quite get it back together.




We did not even try to assemble the small pieces. But the next day I did ponder recovering them and the other pieces and doing a meta pumpkin assembly.


Anyway - this ended up being pretty fun.  Lots of ideas about how to do it better (e.g., we should have barcoded / labelled the pieces so that we could guide the assembly if we failed to do it without guidance).   And thanks to all the discussions with people out there and to the people in my lab who helped put this all together.

Also I made a Wakelet of some of the Twitter discussion

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