Microbiome Awareness Month – Showering in Microbes!

What’s in your showerhead? We’re so glad you asked! Your showerhead might just be harboring bacteria, then blasting it onto your body, and possibly even into your lungs.

A study carried out at the University of Colorado in 2009 by Dr. Norman Pace, a professor of molecular, cellular, and developmental biology, studied how the microorganisms that can cause pulmonary (lung) disease can accumulate in the showerhead. His research showed that while these microbes may be present at levels of 0.1-1% in the water coming into the shower, it may make up to 70-80% of the biofilm in the showerhead itself.

In a 2009 interview, Dr. Pace suggested that breathing in this particular bacteria could cause a “low-grade cough that persists for months,” making you feel “lousy, weak,” and leading to, perhaps, “breathing difficulties.”
So, as you take stock this time of year, you may want to stock up on cleaners for your bathroom, or at least a new showerhead.

For more information on microbes, read our classic blog post.

If you are interested in learning more about your health and your microbiome come check out our clinical microbiome test SmartGut™.

Microbiome Awareness Month – TP: Under or Over?

This can be a reflective time of year for many of us as we take stock of the past year. In your deep reflective moments, have you considered that the way you use toilet paper is such a personal choice that scientists can identify who was in the loo based on which way the paper rolls?

Scientists at Japan’s Kobe University did research into a “personal identification system based on rotation of toilet rolls.” Essentially, they studied how to detect the identity of a toilet user by the way they pull the paper. Their study design allowed them to record what they termed “multiple pulling actions,” when someone “pulls, tears, and uses” several times between entering and exiting the stall.

The study began with known participants using the bathroom with specially rigged toilet paper rolls. Then, after the system had been trained to identify “signature styles,” a second stage aimed to accurately identify who was who, without the benefit of other forms of identification.

Among a five person group in a research setting, they managed a creditable 83.9% level of accuracy. There was apparently no significant difference in pulling action between men and women.

As you reflect on what you have accomplished this year and generally take stock of your life, don’t forget that you are unique and one-of-a-kind, all the way down to how you use TP.

For more on this topic, read our classic blog post.

If you are interested in learning more about your health and your microbiome come check out our clinical microbiome test SmartGut™.

Microbiome Awareness Month – To Handshake or Fist Bump?

Many find time this month to catch up with friends and family.  There has been interesting research on how many microbes are exchanged between people depending on the greeting – a handshake or a fist bump.

Research has studied whether a fist bump or handshake spreads more bacteria between individuals in order to determine which might be more hygienic.  In 2013, researchers at West Virginia University had two participants, both healthcare workers, shake hands with 20 colleagues, then got them to press their palms on specially prepared agar culture plates.  After thoroughly washing their hands, they went through a similar process, only this time using fist bumps.

Fist bumping resulted in a reduction in colony-forming units of around a quarter, compared to handshaking, a phenomenon the researchers said was mainly due to smaller areas of skin coming into contact.

So, as you catch up with old acquaintances, consider how you greet them, so you can get caught up on stories without catching microbes.

For more on microbes and hand contact, read our classic blog post.


If you are interested in learning more about your health and your microbiome come check out our clinical microbiome test SmartGut™.

Microbiome Awareness Month! Is the Future of Cars Poop as Fuel?

During this month of frenzied running from the office to home and events and back, stop to think of your mode of transportation.  Or, more to the point, the fuel it uses.  There have been some recent innovations resulting in vehicles running on human waste.

In 2010, the UK company GENeco converted a VW Beetle to run on biogas produced entirely from human waste.  Known as the Bio Bug, newspapers at the time excitedly reported that “excrement flushed down the lavatories of just 70 homes was enough to power the car for 10,000 miles.”

Just a few years later came another creatively fueled mode of transportation by the British which was called a “poo bus,” a 40-seater vehicle powered entirely by human and food waste.

The bus can travel 186 miles on one tank of gas, which can apparently be produced by recycling the waste of just five people.

Just some fuel for thought as you tool around town flitting from shopping to parties, about how your poop could one day be fueling your travels.

For more information on microbes and fuel, read our classic blog post


If you are interested in learning more about your health and your microbiome come check out our clinical microbiome test SmartGut™.

Microbiome Awareness Month – Eat Your Stinky Microbes!

This is often a time of year when we splurge on specialty foods, one of which are stinky cheeses – so let’s smell our way around the origins of some of these odorous treats.

Just four ingredients are needed to make cheese: milk, salt, rennet… and microbes.  The earliest cheeses were made around 7,000 years ago, largely by accident.

Traditional cheeses can include dozens of types of microbes which play a big part in how a cheese tastes and smells.  Once it has done its job, the majority of this bacteria dies naturally, but it can be inclined to survive in some Alpine and hard cheeses such as emmental, gruyere, and pecorino — contributing to their flavors.

There are microbes known as smear bacteria that are responsible for some of the cheese shop’s stinkier products like münster and limburger.

In fact, washed-rind cheeses have an odor like smelly feet because the bacteria they have, Brevibacter, can also be found on unwashed human skin.

At the next social gathering you attend, when you are presented with an array of stinky cheese treats, you will be able to appreciate their pungent odor and flavor, knowing just how microbes played a role in both.

For more information on microbes and cheese, read our classic blog post.

If you are interested in learning more about your health and your microbiome come check out our clinical microbiome test SmartGut™.

Meet SmartJane!

A couple of weeks ago, we announced SmartJane™— the world’s first doctor-ordered, sequencing-based, at-home vaginal health test.

SmartJane is the first test to combine human papillomavirus (HPV) genotyping, sexually transmitted infection (STI) testing, and microbial risk factors for common conditions like bacterial vaginosis and aerobic vaginitis. The test can also be used by trans and non-binary individuals who need to care for their vaginal health.

NOTE: The test is not intended to replace traditional Pap smears or well-woman visits and does not diagnose or treat any disease. SmartJane is only available with a valid lab test order from a healthcare provider. uBiome can work with your doctor or connect you with an independent external clinical care coordination network to review your test request.

Why did we make SmartJane?

Women’s health is important. We think it’s silly to even ask this question — why shouldn’t we make a test that will help women take better care of their health? Dozens of female scientists, engineers, and laboratory staff on our team (and some men too) have worked hard to make a product that would help women (and others with vaginas) to work with their doctors to better screen for HPV, STIs, and vaginal flora implicated in bacterial vaginosis and other conditions.

What’s new in SmartJane?

SmartJane can tell doctors and patients which type of HPV strain they have (genotyping), and how the microbiome interacts with HPV to increase or decrease risk. SmartJane tests for 14 high-risk HPV types which are associated with cervical cancer, squamous intraepithelial lesions, and cervicitis. SmartJane also tests for 5 low-risk HPV strains.

In a combined approach, SmartJane tests for four STIs as well as HPV and vaginal flora balance: Chlamydia trachomatis (chlamydia), Neisseria gonorrhoeae (gonorrhea), Treponema pallidum (syphilis) and Mycoplasma genitalium. Mycoplasma genitalium is a common STI that can be a cause of unexplained infertility. This bacterium has been recently implicated in cervicitis, pelvic inflammatory disease, and infertility in women. Mycoplasma genitalium was recently found to have a prevalence at least as high as that of Chlamydia trachomatis and Neisseria gonorrhoeae, but has not been included in standard STI tests, until now with SmartJane.

SmartJane includes testing for risk factors for ten conditions:

Vaginal conditions

Bacterial vaginosis
Aerobic vaginitis
Sexually transmitted infections

HPV and associated conditions

HPV infection
Cervical cancer
Squamous intraepithelial lesions
Genital warts


Idiopathic infertility
Pelvic Inflammatory Disease

Why self-sampling?

Self-sampling is common in most of the developed world. We’ve done a review of global self-sampling protocols (here in pre-print), and have found some really interesting facts:

How do I SmartJane?

Patients can request the test from your regular doctor or OB/GYN, or from an external clinical care coordination network through our website. Once the doctor order is placed, we’ll send you a kit.

Collecting the sample is simple and takes just two minutes at home. Once the sample is collected, it is then placed in a prepaid mailer and dropped in the mailbox for return to the uBiome CLIA-licensed (Clinical Laboratory Improvement Amendments) and CAP-accredited (College of American Pathologists) laboratory in San Francisco. After the sample is processed, uBiome sends a link to its HIPAA-compliant website. Here the patient and prescribing doctor can access the test report, which can then be used as a valuable resource for further treatment planning.

If you are a healthcare provider, please click here.

How does it work?

uBiome’s proprietary methods have exceptional sequencing accuracy for the detection of HPV infection (see our pre-print paper). On average, the sensitivity, specificity, precision, and negative prediction value for the microorganisms of the vaginal microbiome included on the test are 99.3%, 100.0%, 98.1%, 100.0% for the species, and 97.0%, 100.0%, 99.9%, 100.0% for the genera, respectively. Samples are processed in our CLIA-licensed and CAP-accredited laboratory in California.

Thank you!

SmartJane was made possible by citizen scientists who helped us make this groundbreaking test. We are so grateful to all of you and are very excited to make this test a reality with your help!

For those who also have gut issues…

SmartJane is the second in a series of ground-breaking clinical tests that are available through healthcare providers. The first in the series, SmartGut, the world’s first sequencing-based clinical microbiome test, was launched in the fall of 2016.

Further Reading

A new sequencing-based women’s health assay combining self-sampling, HPV detection and genotyping, STI detection, and vaginal microbiome analysis

Elisabeth M. Bik, Sara W. Bird, Juan P. Bustamante, Luis E. Leon, Pamela A. Nieto, Kwasi Addae, Victor Alegría-Mera, Cristian Bravo, Denisse Bravo, Juan P. Cardenas, Adam Caughey, Paulo C. Covarrubias, José Pérez-Donoso, Graham Gass, Sarah L. Gupta, Kira Harman, Donna Marie B. Hongo, Juan C. Jiménez, Laurens Kraal, Felipe Melis-Arcos, Eduardo H. Morales, Amanda Morton, Camila F. Navas, Harold Nuñez, Eduardo Olivares, Nicolás Órdenes-Aenishanslins, Francisco J. Ossandon, Richard Phan, Raul Pino, Katia Soto-Liebe, Ignacio Varas, Nathaniel A. Walton, Patricia Vera-Wolf, Daniel E.Almonacid, Audrey D. Goddard, Juan A. Ugalde, Jessica Richman, Zachary S. Apte

bioRxiv 217216; doi: https://doi.org/10.1101/217216


Self-Sampling for HPV Testing: Increased Cervical Cancer Screening Participation and Incorporation in International Screening Programs

Sarah Gupta, Christina Palmer, Elisabeth M. Bik, Juan P. Cardenas, Harold Nuñez, Laurens Kraal, Sara Bird, Jennie Bowers, Alison Smith, Nathaniel A. Walton, Audrey D. Goddard, Daniel E. Almonacid, Jessica Richman, Zachary S. Apte

Preprints 201711.0199: https://www.preprints.org/manuscript/201711.0199/

Microbiome Awareness Month – These Boots Are Made for Bacteria

This time of year, many of us will be stepping out quite often, whether for something as mundane as work or as glitzy as an annual party.  The next time you go out the door, you may want to pause and think of the potential unwanted bacteria you may be about to step in.

In 2008, a study at the University of Arizona found extraordinary amounts of bacteria on the bottoms of shoes.  The average sole harbored 421,000 bacterial units, each consisting of enough bacteria to reproduce and grow a new colony.

The study detected nasties like Escherichia coli (E. coli), Klebsiella pneumoniae (which can cause urinary tract infections), and Serratia ficaria (linked with respiratory infections) lurking on the bottoms of people’s shoes.

So, while this month you are stepping out maybe more than usual when returning to your humble abode, you may want to leave your shoes — and the many potential bacterial invaders that hitched a free ride on them — at the door.

For more information on shoes and bacteria, read our classic blog post

If you are interested in learning more about your health and your microbiome come check out our clinical microbiome test SmartGut™.