Season’s Greetings – Time Lapse Kit for $89

Happy Holidays from uBiome – hope you’re staying warm!

‘Tis the season of giving, and also aspirations for the new year.

Give the gift of a gut microbiome kit to three different people for the price of one with our 3-for-1 holiday deal!

More of a Scrooge type? Keep all 3 kits for yourself and see how your new year’s resolution diet affects your microbiome.

Starting right now, Gut Time Lapse kits are only $89. That’s three gut kits for the price of one.

Offer valid until Friday at midnight, or while supplies last.

Use discount code TIMELAPSE89 when you checkout at ubiome.com.

We wish you the most joyous of holiday seasons!

Love,
Your friends at uBiome

How To Make Sauerkraut, The Perfect Christmas Gift For Your Gut

Oh Little Town of Bacterium

Just ten days to Christmas Eve, a night on which Polish families celebrate “Wigilia” (vigil) with a meatless supper of 12 courses, one for each month of the year.

cabbage-541645_640

It’s a meal that often features sauerkraut, a delicious and healthy fermented foodstuff that’s actually dead-easy to brew up at home.

The good news?

If you make a batch now it ought to be ready for your own Christmas celebrations, a perfect present for your about-to-be overwhelmed microbiome.

The even better news?

There’s a recipe below.

But first, a soupçon of sauerkraut history and biology (yup, it’s loaded with yummy bacteria).

Sauerkraut is German for sour cabbage, so it’s not surprising that many think of it as a German invention.

In fact laborers building the Great Wall of China 2,000 years ago commonly ate shredded cabbage fermented in rice wine, and the Roman writer Cato the Elder wrote of preserving cabbage with salt in his book de Agri Cultura in around 160 BC.

It was the use of salt rather than wine which caught on, which is how the sauerkraut which accompanied Captain James Cook’s crews on their voyages in the 18th century was made.

Their fermented cabbage made for great maritime rations as it needed no refrigeration and helped prevent scurvy.

Sauerkraut popped up in the history books again in World War I when American manufacturers worried that the slightest whiff of an affiliation to Germany would be catastrophic for sales, so for the duration of the war they slyly renamed it Liberty Cabbage.

Sauerkraut is formed in a three-part lactic acid fermentation, each stage involving bacteria.

First the anaerobic (oxygen-hating) bacteria Klebsiella and Enterobacter begin creating an acidic environment which favors subsequent fermentation.

Then, when conditions have become more acidic, Leuconostoc take over.

Finally, Lactobacillus get to work fermenting any remaining sugar.

Now although this may sound complicated, all you have to do in fact is sit around while nature does its work.

And the delicious results are great for your gut. Sauerkraut is loaded with vitamins C, B, and K.

It’s low in calories, high in magnesium and calcium, and a great source of dietary fiber.

What’s more, the homemade kind, if uncooked, contains live Lactobacillus – probiotics which tend to improve digestion and promote the growth of healthy gut flora.

Sounds good, doesn’t it?

Here’s a quick summary sauerkraut recipe, courtesy of The Kitchn (please see below for a link to their comprehensive instructions).

Ingredients

One medium-sized cabbage (about 3 pounds)
1.5 tablespoons salt

Equipment

One large glass jar – e.g. a two-quart (about 2 litre) Mason jar
One small jar that fits in the mouth of the larger one – e.g. a jelly (jam) jar
Clean marbles, stones or other weights to go in the small jar

Instructions

1. Discard the cabbage’s outer leaves, then slice it into very thin shreds.

2. Place the cabbage in a mixing bowl and sprinkle it with the salt, working salt and cabbage together with your (clean, please) hands for between 5 and 10 minutes.

3. Pack the cabbage into the jar as tightly as possible, making sure the cabbage is submerged under the brine your handiwork with the salt will have produced.

4. Weigh down the cabbage and its brine using the smaller jar full of marbles/stones.

5. Cover the jar with a cloth, secured with twine or a rubber band.

6. Over the next 24 hours, press down the cabbage with the smaller jar from time time.

7. Ferment the cabbage for 3 to 10 days at cool room temperature (65°F to 75°F) avoiding direct sunlight. You may see bubbles in the cabbage, or foam or white scum on the top. This is fine. They’re simply signs that fermentation is taking place. Scoop off the scum if you like.

8. Start tasting after three days. When it seems good to you, remove the weight, screw on the top, and refrigerate. You can store sauerkraut for several months.

That’s it. You’ve made your own sauerkraut.

Many of us will subject our tummies to an almighty onslaught over the holidays.

The least you can do?

Give your gut the gift of a scrumptious serving of brassica–based bacteria.

Have a great week!


Further reading

From The Kitchn: How To Make Homemade Sauerkraut in a Mason Jar

German Food Guide & Directory

Homemade sauerkraut recipe

Homemade Sauerkraut Recipe

How to make sauerkraut

Polish Christmas Recipes

Sauerkraut

The History of Sauerkraut

Wigilia

Sharing Our Microbiome

Your microbiome can be shaped by the environment you live in, the food you eat, your genes, and even your age. We know this. But can the people and, perhaps, pets you live with also influence the microorganisms that colonize your body?

Some studies suggest they can, and what’s more you may also change the microbial makeup of the places you frequent, leaving traces of your microbiome behind you.

In order to find out how the microbiomes of people and the places they live in differ from one another, researchers studied the microbial composition of six homes and the people and animals who lived in them. They found more similarities between people, their pets, and their homes than they did between people from different homes (Song et al., 2013).

The research also showed that different residences can have significantly different bacterial profiles. According to the study, although bacteria within homes can vary considerably from room to room, the most substantial similarities occur between the kitchen, front door knob, and bedroom floor. Likewise, the hands and feet of any home’s occupants have the greatest tendency to share the same bacteria.

The same study showed that when a family moves home, their new residence soon has a bacterial composition similar to their old one’s. Along similar lines, the research found that hotel rooms soon acquire their occupants’ bacteria, with a room’s surfaces showing traces of its guest’s microorganisms within 24 hours.

Another study explored the ways in which having children and pets in a household affects its microbiome (Lax et al., 2014). The research showed that the presence of either can lead to a home’s occupants sharing more unique bacteria from their individual guts and skin.

The authors proposed that this could be because of an increase in the number of shared sources of unique microbes. For example, one member of the household might transfer their bacteria to the dog’s bowl as they filled it, then this would be picked up by another person as they performed the same duty later.

sharing microbiome

The study also showed that dog owners from different families can share microbes which are not shared between people without dogs. The finding reinforces the idea that who we live with, in both human or animal terms, can shape the bacteria which colonize our bodies.

Some researchers suggest that the tendency for individuals to share their microbiomes in such ways may be caused by each of us having a microbial “aura” – a cloud of bacteria which hangs in the air around our bodies wherever we go (Meadow et al., 2015).

Indeed this has led some scientists to propose that it should be possible to identify an individual person from their microbiome alone, then to go on to develop an algorithm capable of matching someone to a specific gut microbiome using metagenomic markers (Franzosa et al, 2014). In fact they were able to identify individuals with an accuracy rate of 80%. However these researchers were unable to identify certain individuals over time, which they proposed was caused by people changing their habits in ways which affected their microbiome.

Written by Catalina and Daniel of the uBiome data science team

References:

1. Cohabiting family members share microbiota with one another and with their dogs.
Se Jin Song, Christian Lauber, Elizabeth K Costello, Catherine A Lozupone, Gregory Humphrey, Donna Berg-Lyons, J Gregory Caporaso, Dan Knights, Jose C Clemente, Sara Nakielny, Jeffrey I Gordon, Noah Fierer, Rob Knight.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3628085/pdf/elife00458.pdf

2. Longitudinal analysis of microbial interaction between humans and the indoor environment.
Simon Lax, Daniel P. Smith, Jarrad Hampton-Marcell, Sarah M. Owens, Kim M. Handley, Nicole M. Scott, Sean M. Gibbons, Peter Larsen, Benjamin D. Shogan, Sophie Weiss, Jessica L. Metcalf, Luke K. Ursell, Yoshiki Vázquez-Baeza, Will Van Treuren, Nur A. Hasan, Molly K. Gibson, Rita Colwell, Gautam Dantas, Rob Knight, Jack A. Gilbert.
http://www.sciencemag.org/content/345/6200/1048

3. Identifying personal microbiomes using metagenomic codes.
Eric A. Franzosa, Katherine Huang, James F. Meadow, Dirk Gevers, Katherine P. Lemon, Brendan J. M. Bohannan, and Curtis Huttenhower.
http://www.pnas.org/content/112/22/E2930.abstract

4. Humans differ in their personal microbial cloud.
James F. Meadow, Adam E. Altrichter, Ashley C. Bateman, Jason Stenson, GZ Brown, Jessica L. Green, Brendan J.M. Bohannan.
https://peerj.com/articles/1258/

Experimenting with a Gut Cleanse – By Richard Sprague

Guest post by Richard Sprague

Your gut microbiome changes constantly in response to everything from diet to exercise, so when looking at multiple uBiome test results side-by-side it can be complicated to figure out what caused a particular change. What if you could radically alter your microbiome with a cleanse and just track that, along with precisely what you eat afterwards? What could you learn?

I recently tried exactly that, using a colon cleanse – the kind you do before a colonoscopy screening. By flushing most of the bacteria from my system and carefully watching them grow back with side-by-side uBiome tests, I learned a few things that might interest you as well:

My gut microbiome recovers pretty quickly. Unlike antibiotics, which are known to cause long-term (and possibly permanent) changes, losing bacteria this way seems only to affect the total numbers, but they sprout right back just like a haircut. In two weeks I was as good as new.

This is an overall view of how my gut biome changed:

cleanse1

Amounts and ratios changed, but not the specific organisms. Of course I lost a bunch of bacteria – that was the point – but surprisingly I didn’t seem to gain anything really new, even after an aggressive attempt at re-seeding. I didn’t gain or lose a single phyla. Other than amounts and ratios, I had to dig down to the Class level of the biological hierarchy to find anything that was permanently lost, and even at the very fine-grained Genus level, only two taxa that had been regularly present beforehand were now extinct. (Holdemania and Methanomassiliicoccus).

There is more change when you look at this functional view, but even then watch how quickly it bounces back:

cleanse2

A couple of weird ones, at small amounts, made a brief appearance. I was especially intrigued by five new taxa that showed up just once, the day after the cleanse, and then disappeared. Maybe I found some that ordinarily get lost in the noise of the microbiome and only show up when the rest of the forest has been cleared. These are some hardy guys and I’m glad I know their names and can watch for them again: Abiotrophia, Bacillus, Catonella, Christensenella, Parvimonas.

It’s pretty hard to make a significant change. These days a little googling will find plenty of web sites, books, diets, and supplements that claim to “fix” or “change” your microbiome. I’m a healthy, reasonably fit adult, so maybe I didn’t try as hard as somebody might with a specific health problem, but I thought simply popping probiotics and eating a variety of new and fermented foods would have a big effect. Nope. There are exceptions – my past experience with sleep hacking demonstrated conclusively to me that I can temporarily change my bifidobacterium levels for example – but those examples are harder to find than I had hoped.

Here’s another important ratio that microbiologists have found useful to see how the gut biome changes:
cleanse3

See much change? Me neither. There’s a short spike during the cleanse, but then it just pops back to normal.

Follow me on Twitter, or check my personal web site for more details of my experiment, and please let me know if you did or are thinking of something similar!

order

Why Bacteria Could Soon Be Playing a Leading Role in Crime Busting

Solving crimes with bacterial evidence

It was 121 years ago today. December 7, 1894.

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Sir Arthur Conan Doyle, the Scottish physician best known for writing fictional stories about the detective Sherlock Holmes, was spending his final day in New York before heading home to London after a U.S. trip.

If only he’d known then what we know now, because in Sherlock Holmes, Conan Doyle created a forensics expert ahead of his time.

Long before such procedures became commonplace in criminal investigation, Holmes used fingerprints, hair analysis, and blood tests to solve crimes.

Had he been alive today, though, he’d almost certainly have installed a DNA sequencer upstairs at 221B Baker Street.

Not just for its potential in comparing human DNA samples collected from suspects with biological material left at crime scenes, but also because there’s now great potential in using the sequencing of human bacteria for “CSI” purposes.

You see, much like a fingerprint, your microbiome could uniquely identify you.

For example, researchers at Harvard University found that stool samples were particularly reliable.

Apparently your poop has a signature all of its own.

In fact, when the study examined gut bacteria re-taken from participants a year after they’d first “donated”, researchers were able to identify individuals with 86% accuracy.

Everywhere you go, you leave microscopic traces of your bacteria, and you also gather microscopic traces of others.

Dr Josiah Zayner, currently a research fellow at NASA, suggests that banks and convenience stores could purposefully plant rare (but presumably harmless) species of bacteria on their floors which would then get picked up on the soles of criminals’ shoes, allowing investigators to prove that they, or at least their Nikes, had visited at some stage.

What about skin bacteria?

Well, it turns out that a great place to find this is on people’s cellphones, and in a world where more people own mobile phones than have access to working toilets, this could come in handy.

Could your bacteria be used to link your phone to you?

Pretty certainly, according to a University of Chicago researcher who has been able to differentiate between two people with 97% accuracy using only swabs taken from their phones.

Your body’s microbiome contains trillions of bacterial cells and weighs between three and six pounds.

But what happens to the microbiome after death?

The forensics world is extremely interested in this question, and only last year began referring to the “death microbiome” as the thanatomicrobiome (thanatos being the Greek word for death).

It refers to the process in which legions of your own gut bacteria take over your internal organs once you’re deceased.

In a healthy individual the brain, liver, spleen, and heart are free of microorganisms – your immune system keeps them in check.

But after death these bacteria spread, and it turns out that this migration can be used as a pretty accurate measure of the post-mortem interval: a duration which enables investigators to estimate time of death.

A team from Alabama State University (ASU) is working with the Freeman Ranch Body Farm in Texas to understand this better.

The Body Farm houses 150 donated cadavers which are used to study bodily decay. An additional 200 living people have pre-registered as donors.

The ASU team are particularly interested in grave soil, which they say teems with an immense amount of bacterial life after the death of a human.

Applying just the kind of next-generation metagenomic sequencing that we use here at uBiome, they’re developing tests that will enable PMI (post-morten interval) to be estimated with unprecedented accuracy.

All in all, it seems human bacteria is playing an ever-increasing part in the world of crime detection.

But that may not have surprised Sherlock Holmes.

As he might have said to his long-suffering assistant:
“Alimentary, my dear Watson, alimentary.”

Have a great week!
Alexandra 🙂

Alexandra Carmichael
Director of Product, Community, and Growth
uBiome


 

Further reading

Deputy UN chief calls for urgent action to tackle global sanitation crisis

Distinctive thanatomicrobiome signatures found in the blood

Identifying personal microbiomes using metagenomic codes

In Forensics, Microbiome May Become Next Fingerprint

Introducing the Thanatomicrobiome

Paging ‘CSI’- Microbiome analysis may be the new fingerprint

Personal microbiomes shown to contain unique ‘fingerprints’

The Death Microbiome Could Inform Forensic Science And Medicine

The Dirty World of Body Farm Microbes

The Future of Microbiome Forensics

Microbial communities associated with human decomposition and their potential use as postmortem clocks

Your death microbiome could catch your killer

How People Influence Their Microbiomes

The human microbiome begins forming at birth then steadily evolves during an individual’s lifetime. Different areas of the body have their own individual microbial profiles. A child’s microbiome reaches a stable configuration at around 2-3 years of age, with its species and strain composition generally maintained throughout the individual’s life. However, although there tends to be relative stability within individuals, the composition of any one person’s microbiome is likely to differ substantially from any other’s. Genetics may play a part in the microbiome’s development, since a study of monozygotic twins showed that twins’ microbiomes resemble each other to a significantly greater degree than those of pairs of unrelated individuals.

influence
The host and his or her microbiome influence one another, and in this short article we’ll look at three ways in which the host affects the microbiome:

1.  Reductions in NOD-like receptors increase presence of commensal bacteria

Human tissue cells have the ability to sense molecules which may threaten infection. They do so through pattern recognition receptors expressed in a cell’s cytosol (intra-cellular fluid), known as nucleotide-binding oligomerization domain receptors, in short NOD-like receptors (NLRs). NLRs play an essential role in controlling the intestine’s commensal bacteria, so an NLR deficiency can cause an increasing abundance of normally helpful microbes, resulting in a disequilibrium and a reduced capacity to eliminate newly colonizing bacteria. This is because NLRs regulate the bactericidal (bacteria destroying) ability of antimicrobial peptides secreted by the ileal crypt (a kind of ‘pocket’ in the wall of the small intestine) affecting microbiota composition and abundance. Several studies suggest that mutations of a type of NOD called NOD2, a protein coding gene associated with Crohn’s disease and Inflammatory bowel disease, can affect the interaction between host and microbiome through changes in antimicrobial activity.

2.  Immunomodulation leads to microbiome change

Microorganisms involved in inflammatory disease are capable of modulating the immune system’s response to their presence, allowing them to either establish or consolidate an infection. Either as a result of this process (known as immunomodulation) or through immunodeficiency, the composition of the microbiome can change, reciprocally influencing the disease process. Many examples of this are known, including graft-versus-host disease (a condition occurring when donor bone marrow or stem cells attack the recipient), problems in kidney transplantation, hepatitis, cirrhosis, psoriasis, Inflammatory bowel disease, and arthritis. Furthermore immunosuppressive drugs, used to prevent a recipient’s body from rejecting a transplant, generally affect the microbiome-immune system balance.

3.  Changing gene expression correlates with microbial diversity

Variations in a host’s gene expression have been found to correlate with changes in taxa distribution (microbial diversity) in the host’s microbiome. For example, differences in the expression of the lactase enzyme had a resultant impact on the abundance of Bifidobacteria in the gastrointestinal tract, probably since some bacterial strains appear to prefer lactose to glucose. In another case, enrichment of genes involved in the leptin-signaling pathway correlated with changes in the microbiota found in the nose, oral cavity, and skin. Leptin is a hormone which is among the best known markers for obesity, and the associated microbiome changes involved, for example, changing levels of: Veillonella (found in the anterior nares, the external part of the nostrils); Lachnospiraceae, and Haemophilus (located in the attached keratinized gingiva, part of the gum); Clostridium (in the right antecubital fossa, the part of the arm inside the elbow); Bacteroides (behind the ear); and Propionibacterium (in subgingival plaque, dental plaque formed under the gums).


References

Host genetic variation impacts microbiome composition across human body sites.
Ran Blekhman, Julia K. Goodrich, Katherine Huang, Qi Sun, Robert Bukowski, Jordana T. Bell, Timothy D. Spector, Alon Keinan, Ruth E. Ley, Dirk Gevers, and Andrew G. Clark.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4570153/

Metagenomic cross-talk: the regulatory interplay between immunogenomics and the microbiome.
Maayan Levy, Christoph A. Thaiss, and Eran Elinav.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4654884/

Host genetic architecture and the landscape of microbiome composition: humans weigh in.
Andrew K Benson.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4578423/


Written and researched by: Francisco & Daniel of the Data Science Team