What Do Your Results Mean? Go In Depth With A uBiome Data Scientist.

Some of you might be wondering…

What do my results mean?
What can I learn from this test?
What is a firmicutes, anyway?

At long last, here’s your chance to find out.

Book your exclusive 20-minute Skype or phone session with one of our data scientists here at uBiome to help you understand the specifics of your microbiome test results.

For example, you could be talking one-on-one with:

We look forward to answering your questions and helping to make meaning from your data! We’re offering this for a limited time at $149.

Schedule your spot now at http://ubiome.com/products/data-help

 

Why Your Microbiome is Older Than You Are.

Now we know. A baby’s microbiome starts developing in the womb.

You probably wonʼt remember this, but the very first poop you popped out as a baby was pretty extraordinary.

So extraordinary, in fact, that it even had a name.

Meconium.

A babyʼs first bowel movement consists of stuff that was already in the gut before the first meal.

And Meconium is like no other stool youʼll ever pass.

Itʼs kind of dark olive-green with a tarry, viscous consistency, barely any smell, and made up of stuff you ingested when you were in the womb, including skin cells and “lanugo” – that thin downy hair often found on an infantʼs body.

Delightful, right?

But thatʼs not all meconium is made up of.

Researchers at the University of Florida discovered in 2010 that new-born babiesʼ meconium contains a diversity of bacteria, and that came as something of a shock.

You see, back in 1900 a French pediatrician called Henry Tissier had confidently declared that unborn babies were bacteria–free.

So according to popular myth, a baby was effectively sterile until the moment of birth.

Now to be fair to Tissier, he also isolated and named a bacterium called Bifidus that went on to play an important part in the world of probiotics, but thereʼs no doubt that he caused over 100 years of microbial misunderstandings with his sterile baby theory.

However, while itʼs certainly true that babies are born with a certain amount of bacteria, most of their microbiome builds up over time, with the first few minutes of life being especially important.

If a baby is delivered vaginally, she receives a dose of bacteria from her mother as she passes through the birth canal, getting covered in a microbial film that includes species which will help her digest her first meal.

But what happens if she enters the world as a result of a Cesarean section?

Well then her first dose of bacteria is likely to come from her motherʼs skin rather than her vagina, an observation supported by a Swedish study which showed that babies born via C-section have gut bacteria which show significantly less resemblance to their mothers compared to those delivered vaginally.

Some parents restore the balance after C-sections by “inoculating” their babies with a vaginal swab: incubating a piece of gauze in the vagina for an hour prior to delivery, then wiping it over the mouth, face, and body of the infant after delivery, in a process sometimes called “seeding”.

Quite a wake-up call.

A babyʼs microbiome continues developing after birth, resembling that of an adult by the age of three.

In fact babies pick up microbes from every single person and thing they touch, which in general is A Good Thing.

Humans tend to do best when they play host to a diverse microbial community.

A University of Idaho study found that there are even important bacteria in breast milk, meaning that the guts of babies given formula differ from those fed on breast milk.

All in all thereʼs no doubt about it.

Your bacteria play a vital part in your health, and always have.

Ever since you passed that rather outlandish first poop.

Have a great week!
Alexandra 🙂

Alexandra Carmichael
Director of Community, Product, and Growth
uBiome

Further reading

Your Changing Microbiome

Nurturing A Babyʼs Microbiome, Before And After Birth

The Maternal Microbiome

Maturation of the Infant Microbiome

Human Microbiome May Be Seeded Before Birth

The infant gut microbiome: New studies on its origins and how it’s knocked out of balance

The Human Microbiome, Diet, and Health: Workshop Summary

How to seed your baby with a healthy microbiome to last a lifetime

Mothers facing C-sections look to vaginal ‘seeding’ to boost their babies’ health

Microbirth: Why ‘Seeding Baby’s Microbiome’ Needs to Be on Every Birth Plan

Intestinal Microbial Ecology in Premature Infants Assessed Using Non-Culture Based Techniques

Characterization of the Diversity and Temporal Stability of Bacterial Communities in Human Milk

Your Monthly Gut Check: 50% Off Today Only

A monthly checkup for your gut microbiome. For less than $45.

The bacteria in and on your body are constantly shifting in response to your diet, lifestyle, and health status.

Why not check in on them once a month to see how they’re doing?

We’re happy to report that until tonight, subscriptions on uBiome kits are 50% off.

Get yours started today, and watch the snapshots shift. Like if your bacteria had Instagram.

What Do I Do With My Raw Data?

We’ve had this question so many times, that I finally had to put a post together to answer it for all of you. Calling in our great friend Richard Sprague again, to help explain:

If you only submit one or two samples, the standard uBiome web page (at http://app.ubiome.com) offers plenty of information about your microbiome. You can look at the percentage breakdown of different bacteria, compare them with other users or to yourself over time, and dig deeper with descriptions of the most common organisms and what they do. But if you really want to understand your microbiome, uBiome offers much more: full access to all the raw data, literally millions of snippets of genetic information ready to analyze.

I recently wrote a detailed description for the July 2015 issue of O’Reilly’s Biocoder magazine (available as a free download here:http://www.oreilly.com/biocoder/ ) and I encourage you to read the whole thing for more details, but here’s a short summary. Three steps to get more from your data:

STEP 1

First, click the “Download taxonomy” button on the web page for your sample.

DownloadSample

Although it will look like gobbledygook, you can turn this into an Excel spreadsheet easily enough. Select the info on the page and copy/paste it into a site that will convert it automatically into a CSV file of Comma-Separated Values. (I use http://konklone.io/json/ orhttp://www.convertcsv.com/json-to-csv.htm). Open the CSV file from Excel and ignore everything but these three columns: tax_rank, tax_name and count_norm.

ExcelSnippet

Now it’s a simple matter of running some standard Excel filtering operations on the data. Filter tax_rank by “phylum”, “species” or whatever other taxonomic rank you care about and then sort the count_norm field from largest to smallest. The count_norm numbers correspond to parts per million; divide by 10,000 to convert to percentages of that sample.

By the way, a big bonus awaits you in the taxonomy file that you can’t get from the standard uBiome web page: species information. Most scientists trust the 16S rRNA technology down to the genus level, but there is more uncertainty at the species level, so uBiome doesn’t publish it to the web page. Drag it into Excel, though, and you can make up your own mind about whether you trust the species info or not. (And as always, keep in mind that you should never treat uBiome results as medical information; if you’re sick, see a doctor.)

STEP 2

Head to the new uBiome open source microbiome-tools GitHub page and download ubiomeCompare.py. If you have the Python language on your computer you can run this file without installing anything extra. (All Macs come with it built-in; Windows users download it for free).

Let’s say your spouse has the sample in a file called Wife1.JSON and yours is in Husband1.JSON. On a Mac, open Terminal and run the following command:

> python ubiomeCompare.py –u Husband1.JSON Wife1.JSON > HusbandUnique.CSV

The new file, HusbandUnique.CSV contains just those organisms that are unique to the Husband1 sample, i.e. are found in the husband’s microbiome and not the wife’s.

Similarly, the following command will give you a file that contains the relative differences between every organism in Husband1 and Wife1:

> python ubiomeCompare.py –c Husband1.JSON Wife1.JSON > HusbandWifeCompare.CSV

Read HusbandWifeCompare.CSV into Excel, sort and filter it, and you’ll see something like this:

ExcelCompare

Positive numbers indicate more in the Wife1 sample; negative numbers are more in Husband1. Armed with this information, you can try to understand the reasons behind the differences. Follow the uBiome Blog for some examples of how I’ve done this.

STEP 3

Finally, if you’re really into serious number crunching, uBiome gives you the raw output from a state-of-the-art Illumina NextSeq 500 in the form of FASTQ files. If you know what that is, you probably already know how to read them, but if not please look at the BioCoder article for an introduction. With a little work, the FASTQ files will let you see precisely which genes were detected in your sample. Since so much of the microbiome is still unexplored, you may find pieces that are missing from the regular uBiome output, so this is your chance to go straight to the underlying genetic information for more.

For example, I was able to compute the following measure of diversity from my most recent sample. It’s a measure I’ll track for all of my samples:

AlphaDiversity

Going Even Further

I’ve barely scratched the surface of what’s possible when you use your raw uBiome data. Please look at the BioCoder article for more step-by-step instructions, and contact me if you have other questions.

Why You’re Probably Not Eating Enough Fiber, and Why It Should Bother You.

Fail to feed your bacteria properly and they’ll start eating you.

I donʼt want to frighten you, but right now there are around 100 trillion bacteria chomping away in your gut.

Itʼs a hungry job being a microbe.

Thereʼs something like three pounds of bacteria lining your intestinal tract,
probably made up of about 500 different species.

I say probably, because everyoneʼs different. Although you and I share around 99.5% of the same DNA,
our microbiomes almost certainly vary widely, one of the reasons itʼs so fascinating to explore yours
with a uBiome test.

The thing is, a lot of your bacteria keep you healthy – theyʼre helping you digest
food and synthesize vitamins, for instance.

Doesnʼt it therefore make sense, in return, to keep them healthy too?

One way to do that is to ensure theyʼre properly fed, and hereʼs where things
get interesting and actually pretty serious.

You see, a prime source of bacterial nutrition comes from fiber, but most
peopleʼs diets are vastly underrepresented in this respect.

An average individual in the West gets roughly 15 grams of fiber a day, which
is nowhere near enough. In fact, The Institute of Medicine recommends
women should get 25 grams per day, while men should consume 38 grams.

Does this matter much?

Well, yes.

Actually it matters enough for the U.S. governmentʼs dietary guidelines to label
dietary fiber as a “nutrient of concern”. A public health issue, no less.

Itʼs long been accepted that having enough fiber in your diet can contribute to
a feeling of fullness (so you know when to stop eating) and what
gastroenterologists politely call “healthy laxation” (regularity in the bowel
movement department).

More seriously, a low fiber diet may also be associated with the risk of
developing various conditions, including heart disease, diabetes, diverticular
disease, and constipation.

But now studies are showing that failing to provide enough fiber to the gutʼs
bacteria may lead to them feeding on the gut itself.

Researchers at the University of Michigan Medical School found that when
mice were placed on a fiber-free diet, their microbes began to eat away at the
gutʼs protective mucus lining, potentially triggering inflammation and disease.

So fiberʼs important.

How easy is it to get enough, then?

Well since most of us are only getting around half as much as we should,
clearly not very. Eating a salad every night, for instance, would only provide
two or three grams of fiber.

Dieticians say itʼs best to get fiber as part of your regular diet, but supplements
can help.

In a small study at the University of Illinois at Urbana Champaign, adults ate a
fiber-enriched snack bar containing 21 grams of fiber once a day for three
weeks.

The good news?

Their gut bacteria composition shifted from a profile similar to that found in
obese individuals to one which was more like the microbial make-up of lean
people.

The bad news?

The minute the experiment was over, participantsʼ microbiomes returned to the
way theyʼd been before the experiment began.

So to keep your gut healthy, itʼs vital to eat a high fiber diet every day.
Whole grains, legumes, vegetables, and fruits. Raspberries, bran, split peas, artichokes.
Whatever roughage you like.

Your bacteria will thank you for it.

Split peas for dinner tonight, anyone?

Have a great week!
Alexandra

Further reading
Fiber-Famished Gut Microbes Linked to Poor Health

Shift in gut bacteria observed in fiber supplement study may offer good news for weight loss

Fiber supplementation influences phylogenetic structure and functional capacity of the human intestinal microbiome: follow-up of a randomized controlled trial

Think Globally, Act Locally: Regulated Deployment of Polysaccharide Degradation Abilities by our Symbiotic Gut Bacteria

 

uBiome Extends Reach of Microbiome Testing Through Global Ambassador Program

Screen Shot 2015-09-09 at 5.33.56 AM

We’ve worked with citizen scientists around the world since inception, with almost 40 percent of our participants living outside the US, in countries ranging from Canada to Romania to Ghana. To support our international users, uBiome is now launching its Global Ambassadors Program for thought leaders and innovators in microbiome research around the world.

uBiome Global Ambassadors will have access to:

1. Speaking opportunities and invitations for conferences, symposia, and other events around the world
2. Commissions on kits you sell (50% in September!)
3. Opportunity to vote on our Global Citizen Scientist Award
4. Grants — up to $100k total in microbiome kits for exceptional research proposals based in a specific country
5. A FREE uBiome kit!

Prospective Ambassadors can learn more about the program here: http://ubiome.com/pages/global-ambassador

The human microbiome describes the rich community of microbes that live in tandem with the body, supporting – and sometimes interfering with – health. An average human has around ten times more bacterial cells than human cells, with their bacteria weighing between three and five pounds, enough to fill a large soup can. Bacteria in the gut play a supporting role in digestion and the synthesis of vitamins, but more pathogenic bacteria are associated with a range of conditions such as autoimmune disorders, diabetes, heart conditions, Inflammatory Bowel Disease and skin conditions. There may even be bacterial connections with anxiety and depression.

Every human being has a microbiome, but its makeup and diversity can vary substantially from person to person. Global, environmental, and cultural factors mean that microbiomes may also vary from country to country, with diet playing a part, for instance. Researchers have shown, just as one example, that Japanese people are uniquely likely to have an enzyme in their gut bacteria which specializes in degrading algal cell walls, making it possible to digest the nori seaweed around sushi rolls. Most Western guts cannot process this.

uBiome wants its new Ambassadors to be part of ground-breaking research which may identify other such global microbial differences. They aim to amass a truly representative microbiome data set of the world. This means engaging individuals in all countries, including under-served populations and rural communities, with limited access to cutting edge technology.

Jessica Richman, co-founder and CEO of uBiome, says: “We’ve been happily surprised at the volume of samples arriving at our labs each day from all over the planet, and we’re delighted to help research on the microbiome spread around the world to citizen scientists everywhere. The uBiome Global Ambassador program is a great way for citizen scientists to be recognised for their expertise, excellence, and experience.”

Kevin Corkum, a current Canadian Ambassador for uBiome believes that engaging his community in microbiome research will increase the pace of scientific discovery. He notes, “I think it’s amazing that a company like uBiome exists to assist quantifying my experiments and allowing me to be part of a global community. It’s also important for me to get the message out to my local community. By contributing to the research and the conversation about the cultivation of our microbiome, I’m assisting in acceleration of those breakthroughs”

Dr. Zachary Apte, CTO and co-founder of uBiome adds: “uBiome’s sequencing service builds on this pioneering work, enabling us to cut the cost of microbiome sequencing from millions of dollars ten years ago to just $89 today, making it accessible to every citizen scientist around the world.”

uBiome was founded in 2012 by UCSF and Stanford technologists after a crowdfunding campaign raised more than $350,000 from citizen scientists, triple its initial goal. uBiome is now backed by Andreesen Horowitz, Y Combinator, and other leading investors. The company’s mission is to use big data to understand the human microbiome by giving consumers the power to learn about their bodies, perform experiments, and see how current research studies apply to them.

To learn more about how to become a uBiome Ambassador for your country, visit http://ubiome.com/pages/global-ambassador