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"The Earth Microbiome Project (EMP) is the most ambitious attempt to provide a systematic characterization of the microbial world that dominates this planet. The ecosystem services provided by microbes in every environment (including the human body) are fundamental to the survival of life on this planet and the continued economic and physical health of the human race. The pilot study of the EMP started in March 2011 and is now reaching its zenith."

This session has four interesting talks on handling the data deluge, a field guide, why we should care, and mathematical modeling. Cool. Can't wait for the speaker notes and the like.

"Bottlenose is a new social media dashboard for influencers of all stripes. But it's not just for posting and reading; it helps you filter and manage your networks with semantics and machine learning. It's all Web-based, written in HTML 5 and Javascript. It does the data crunching on the browser side (for the non-pro users), so you get native performance behind these major operations reading and parsing your stream."

It's about time someone built this. I've been harping about something like this since 2005. And when I was given a was of cash to do it, I f-ed it up by not channeling my inner-Jobs and insisting we stay true to vision.

I'm sure this is better than whatever I would have built in 2007, given how the Web and mobile world have changed since then. Looking forward to trying this out.

Alas, I've also evolved since 2007 and think this should be a P2P system. Take back the Cloud!

"The Original EcoSphere® is the world’s first totally enclosed ecosystem - a complete, self-contained and self-sustaining miniature world encased in glass. Be wary of inferior and lower quality imitations. Easy to care for, an EcoSphere is an incredible learning tool that can provide powerful insights about life on our own planet... and provide a glimpse of technology that's shaping the future of space exploration."

So cool. Will have to get one some day. [via @curisma]

An Analysis of the Existing Regulatory Framework and Recommendations for Alternative Frameworks

A team of researchers at the University of Maryland Baltimore is studying federal regulation of probiotics under a grant from NIH's Human Microbiome Project (HMP). A portion of HMP funds were set aside to study the Ethical, Legal, and Social Implications (often referred to as the ELSI issues) of the Project's scientific goals. The probiotics project is an interdisciplinary collaboration between faculty members from the University of Maryland Schools of Law, Pharmacy and Medicine.

Lots of good info.

"Many yoghurts are loaded with live bacteria, and labelled with claims that consuming these microorganisms can be good for your health. But a study published today shows that such yoghurts have only subtle effects on the bacteria already in the gut and do not replace them."

Yes, but the paper goes to point out that both in humans and mice, there was an upregulation of polysaccharide metabolism genes in the existing gut microbes. Hm, there are some serious implications there.

"A mouthwash that kills S. mutans and leaves the rest of the bacteria to take over S. mutans‘s real estate could spell the end of cavities. In a small clinical study last year, one team found that one application of the mouthwash knocked down S. mutans levels, and that harmless bacteria grew back in its place. If the mouthwash pans out, it could join the ranks of an emerging new type of treatment: better living through hacking the microbiome."

This is really cool. And this article get extra points for the endnotes on probiotics and fecal transplants.

I totally believe we are entering an age where we are going to manipulate our microbiome for health and medicine.

[via @edyong209]

"Now, a new study by Eric Martens, David Bolam, and colleagues has looked into how a pair of the most common species of gut bacteria metabolize polysaccharides, showing that each bacterium is highly specialized. Using a high-throughput system for feeding the bacteria dozens of kinds of carbohydrates, one at a time, and tracking the bacteria's gene expression, they were able to see how these microbes have tailored themselves to fill specific niches in the gut."

This is a really good study. For me, a better understanding of the gut metabolic ecology will allow for the development of better probiotics. One interesting finding in this study is that some bug don't grow well on simple sugar because their sensors are built for complex sugars. Made me think of folks in developed world and what effect eating more simple sugars (high-fructose corn syrup) has on gut flora and any consequential obesity.

"Artificial two-dimensional biological habitats were prepared from porous polymer layers and inoculated with the fungus Penicillium roqueforti to provide a living material. Such composites of classical industrial ingredients and living microorganisms can provide a novel form of functional or smart materials with capability for evolutionary adaptation. We demonstrated a design of such living materials and showed both active (eating) and waiting (dormant, hibernation) states with additional recovery for reinitiation of a new active state by observing the metabolic activity over two full nutrition cycles of the living material (active, hibernation, reactivation). This novel class of living materials can be expected to provide nonclassical solutions in consumer goods such as packaging, indoor surfaces, and in biotechnology."

Hm. Some really practical uses of microbes - impregnating fabrics to provide bioactive activity.

"This study has identified the first bacterial genes required for induction of settlement and metamorphosis of a marine invertebrate animal."

This is an interesting genetic study as to what in the bacteria cause the induction of settlement and metamorphosis. Hooray for Nature for making this paper open so that I could read it. Though the paper focused on the genetic aspects and didn't speculate (unless I missed it) how this connection arose evolutionarily. My speculation is that the bacteria is an environmental marker, telling the worm where to settle and grow.

Cool, huh?

"The story of a group of University of Massachusetts students who set out to initiate the construction of the school’s first permaculture garden a year ago is a remarkable one, but it’s only the beginning of a worldwide movement."

This is really interesting. Small-scale farming was killed by industrial farming to feed huge masses. But could it be that small-scale farming, like it used to be, to feed a local group, say a family or a cafeteria, is making a comeback? That would be cool.

Question: does technology and science help make us better "micro-farmers"?

"Supplements containing a combination of Lactobacillus salivarius and fructo-oligosaccharide for eight weeks were associated with significant reductions in measures of the severity of eczema, compared with a control group receiving only prebiotics, according to findings published in the British Journal of Dermatology."

In addition to the usual yogurt bugs, I am starting to see salivarius popping up more frequently. It's from the mouth, by the way.

"Global Industry Analysts (GIA) predicts the global probiotics market will be worth $28.8bn by 2015, even though the market is still considered to be in infancy. "

I like this.

A Global Strategic Business Report

This report analyzes the worldwide markets for Probiotics in US$ Million. The report provides separate comprehensive analytics for the US, Canada, Japan, Europe, Asia-Pacific, Middle East, and Latin America. Annual estimates and forecasts are provided for each region for the period 2007 through 2015. Also, a seven-year historic analysis is provided for these markets. The report profiles 119 companies including many key and niche players such as BioGaia Biologics AB, Chr. Hansen A/S, Danisco A/S, Groupe Danone, Institut Rosell, Lifeway Foods, Inc., Natren, Inc., Nestlé Nutrition, Probi AB, Seven Seas Ireland Ltd., Stonyfield Farm, Valio Ltd., and Yakult Honsha Co., Ltd. Market data and analytics are derived from primary and secondary research. Company profiles are mostly extracted from URL research and reported select online sources.

"Health claims for probiotics are evaluated by the Panel on Dietetic Products, Nutrition and Allergies of the European Food Safety Authority. Despite a substantial amount of basic and clinical research on the beneficial effects of probiotics, all of the evaluated claim applications thus far have received a negative opinion. With the restrictions on the use of clinical endpoints, validated biomarkers for gut health and immune health in relation to reduction in disease risk are needed. Clear-cut criteria for design as well as evaluation of future studies are needed. An open dialogue between basic and clinical scientists, regulatory authorities, food and nutrition industry, and consumers could bridge the gap between science and marketing of probiotics."

Not sure what to make of this other than the comment that 'clear-cut criteria' will be needed to actually turn claims into science.

An in-vesell composter from San Francisco.

The North American distributors of the Oklin in-vessel composters.

"Horizontal gene transfer — the exchange of genetic material between different species or lineages — is an important factor in bacterial evolution. A study of human microbiome data comprising more than 2,000 full bacterial genomes shows that this environment is a hotbed of horizontal gene transfer: pairs of bacteria isolated from the human body are 25-fold more likely to share transferred DNA than pairs from other environments. Thus microbial ecology — rather than phylogeny or geography — is the most important driver of the patterns of horizontal gene exchange. Further analysis revealed 42 unique antibiotic-resistance genes that had been transferred between human and agricultural isolates, and 43 transfers across national borders."

This paper sets me spinning due to it being about microbes, microbes on humans, human microbial ecology, and horizontal gene transfer. The other thing that is intriguing about this paper is the mention of unique antibiotic-resistance genes.

"A team led by Jay Keasling, a bioengineer at the Joint BioEnergy Institute in Emeryville, California, worked to extend the strategy to make more commonly used fuels. They used Escherichia coli, a bacterium into which it's relatively easy to insert new genes. They started by creating two strains of E. coli, inserting genes for breaking down cellulose in one and genes for breaking down hemicellulose in the other. They then split each of these two strains into three groups and to each group added genes for one of three different metabolic pathways that allow the microbes to make chemical precursors for either gasoline, diesel, or jet fuel."

Nice step towards making this happen.

"Widely described as the point of no return, the event horizon of SgrA* would be the largest in our skies, but still just 30 microarcseconds across — the apparent size of a tennis ball on the Moon when viewed from Earth. To capture its image would be a stunning technical achievement in itself, but it would also open the door to further studies of how black holes spin and gather material, as well as probing some fundamental aspects of space-time and general relativity. And the first picture taken of our local supermassive black hole — the most enigmatic and charismatic of all the wonders of the Universe — would surely be one of the defining images of the time. It might even knock everyday trouble and strife from the front pages, and perhaps even, for a while, from people's minds."

Cool.