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

Other

Cervicitis
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! The 5-Second Rule?

During this month of frantic, frenzied days, as you are running out the door, noshing on something, what if your snack falls on the floor?  

You’ve probably come across the “Five-Second Rule,” a kind of working hypothesis that supposedly tells you whether it’s safe to eat an item of food you’ve dropped on the floor.  This rule was the subject of a rigorous study conducted by Rutgers University in New Jersey, published in the American Society for Microbiology journal.

The Rutgers researchers meticulously dropped watermelon, bread (buttered and unbuttered), and gummy candy, from a height of 5 inches onto four different surfaces that had been disinfected, inoculated with Enterobacter aerogenes, then allowed to dry.

Watermelon picked up the most contaminating bacteria, while the gummy candy acquired the least.

So, while this month is a busy one, remember that foregoing the 5-second rule and taking time to find something less bacteria-laden to eat may be the best time-saver for your health in the long run.

For more information on microbes and the five-second rule, 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™.

 

 

Extreme Dieting, and Meeces Who Eat Feces

Also: why it’s good to be cautious about study-based news stories.

As we noted last week, at this time of year, millions of Americans put themselves on diets, so it’s no big surprise to find books like Travis Stork’s The Lose Your Belly Diet, doing well on the New York Times Best Sellers list.

It’s also no surprise to see the media picking up on our fascination with losing weight, and part of this most recent onslaught of interest has come about through an intriguing paper published just last week in the journal Cell Host & Microbe. Continue reading “Extreme Dieting, and Meeces Who Eat Feces”

Friends for life: human microbiota

By E.M. Bik, Science Editor at uBiome
Translated from Dutch. Read the original publication in the December 2016 issue of the Dutch Journal of Medical Microbiology (Nederlands Tijdschrift voor Medische Microbiologie).

Abstract

The human body is home to large numbers of bacteria and other microbes, which are collectively known as the microbiome or microbiota, and which have important functions for our health, including for our digestive and immune systems. Recent innovations have resulted in better sequencing techniques and bioinformatics, resulting in a spectacular increase in studies of the human microbiome, particularly those of the intestines. This article gives a brief overview of the techniques used in microbiome research and provides new insights into this — until recently — invisible world. In addition, potential diagnostic and therapeutic applications will be discussed. Continue reading “Friends for life: human microbiota”

Are Your Genes Making It Hard To Get Into Your Jeans?

If you’re a regular reader of our weekly posts (and thank you so much if you are—it makes our very microbes merry) you’ll perhaps recall that last week we time-traveled back to the 13th century and Genghis Khan to explore and thoroughly debunk the Five Second Rule.

This week, however, we’d like to bring you back up-to-date by reporting on a fascinating study that was published on Monday (9/26/16) in the journal Genome Biology.

Its authors suggest that a dangerous kind of obesity may be associated with bacteria in the microbiome that can be “inherited.”

And, the paper’s authors say, this may partly explain why obesity can sometimes seem to run in families.

Like many studies, the story is slightly complicated, so we’ll do our best to interpret what it tells us, beginning with twins.

The focus of the study (led by scientists at King’s College London, with a team that also included researchers in the USA, Germany, and Belgium) was on approximately 1,800 pairs of twins, around 1,000 of whom were identical (monozygotic) and 800 who were fraternal, or non-identical (dizygotic).

They therefore studied 3,600 individuals in total, all members of a British twin registry known as Twins UK, where twins have volunteered to take part in scientific studies.

So-called twin studies are a staple of many areas of human science because identical twins not only look alike but are also almost (but not totally) genetically identical.

In many instances, twins are raised together, whether or not they are identical, so they develop in the same environment—with the same diet, for example.

Studying both monozygotic and dizygotic twins therefore enables researchers to investigate variances that may be associated with genetic similarities or differences.

In the research reported yesterday, the scientists set out to do two things:

They examined the bacterial composition of stool samples taken from the participants using 16S rRNA sequencing, the same methodology we use at uBiome, and they measured something called abdominal visceral fat, which health professionals regard as dangerous.

Unlike subcutaneous fat, which is, for example, what generally makes up a belly, visceral fat is buried deep in the body.

It often tends to be wrapped around major organs such as the kidneys, pancreas, and liver.

And experts say the reason it’s so hazardous is that it’s associated with a host of conditions, including coronary heart disease, cancer, stroke, dementia, and depression.

Unlike BMI— an inexact rating of obesity—visceral fat measurement is much more revealing, and it is determined using a process called Dual X-Ray Absorptiometry (DXA), which can divide soft tissue into lean and fat.

Previous work by some of the same researchers showed that the microbiomes of monozygotic twins are more similar than those of dizygotic twins, suggesting that, to some degree at least, we inherit the type of bacteria that inhabit our gut.

Until recently, it was believed that babies were born with a “sterile” gut, but we now know this isn’t so. They’re born with a smattering of bugs acquired while in the womb.

Probably, though, both monozygotic and dizygotic twins receive the same bacteria in utero.

Maybe it’s the genetic makeup of an individual that somehow either “attracts” or “repels” certain types of bacteria?

Or perhaps our genes somehow influence what we choose to eat in the first place?

It’s not easy to know, but further research may cast more light on the mechanisms involved.

But what were the two important takeaways from yesterday’s paper?

The first was that it confirmed the association between obesity and lower diversity in the fecal microbiome. The authors noted that obese individuals appeared to have fewer different bacterial species in their guts than lean individuals.

Secondly, the research identified a pretty big genetic component to visceral fat mass: heritability was responsible for 0.7 (or 70%) of the variance, so at least to some degree, it seems that you have a genetic predisposition to end up with a similar body shape to your parents, and this may be partly due to having a microbiome like Mom (or Dad).

As for increasing bacterial diversity, the study’s lead researcher, Dr. Michelle Beaumont, suggests that eating a broadly varied diet can help.

Five a day is good.

Varying your five a day is even better.


Further reading

Body fat link to bacteria in faeces

Difference Between Android and Gynoid Obesity

Dual-Energy X-Ray Absorptiometry for Quantification of Visceral Fat

Heritable components of the human fecal microbiome are associated with visceral fat

Heritable components of the human fecal microbiome are associated with visceral fat (paper)

How Gut Bacteria May Predict Belly Fat

Human Genetics Shape the Gut Microbiome

Study finds link between faecal bacteria and body fat

Twin

TwinsUK

Visceral Fat – What It Is and Why It’s So Dangerous

Why all body fat is NOT created equal…

Bacterium of the Month: Akkermansia muciniphila

We’re excited to bring you a new monthly series here at the uBiome Blog: Bacterium of the Month!

We hope you’ll join us as our laboratory team member, Akshaya Krishnan, shares her research with us. This month she focuses on a bacterium that has been getting a lot of attention lately.


Long live

Akkermansia muciniphila

Recent advances in microbiome sequencing and discovery technologies have resulted in a greater focus on the role played by different microorganisms in the human gut. Improper maintenance of one’s gut microbiota can lead to various diseases. One such microorganism that resides in the intestinal lining is Akkermansia muciniphila, a gram negative anaerobe [1].

Why does Akkermansia need your intestine?
Different regions of the intestine, although varying in their environmental conditions, have a mucous lining that covers the epithelial cells. Rich in mucin, this mucous layer acts as an adhesive surface for numerous microbes, facilitating host-microbe interactions. A. muciniphila, uses this mucin as its source of energy, thus colonizing the intestine and protecting the gut from pathogens by means of competitive exclusion [1]. This bacterium colonizes the human intestine at a very young age since it is found at low concentrations in breast milk and formula [2].

Utilizing mucin gives A. muciniphila an ecological advantage as it does not rely on the host for its nutrition, unlike many other microbes [1]. By utilizing the mucin reserves, they thrive even in the absence of nutrients in the gut (especially during fasting) [2]. 61 of the total genes in the Akkermansia genome are suggested to play a role in mucin degradation and gut environment adaptation [1].

Why do we need Akkermansia?
Akkermansia muciniphila is suspected to be involved in a mechanism that restores the intestinal mucin reserves, making them self-sufficient [2]. As mucin degrades, a variety of fermented products are released. Among these are Short Chain Fatty Acids (SCFA), known to serve as energy sources for neighboring bacteria. Acetate, a prominent SCFA released in the gut, is known to curtail weight gain by virtue of its anorectic effects. While the contribution of A. muciniphila towards acetate levels is unknown, published evidence suggests a strong correlation between its abundance and acetate levels [3]. This abundance in the intestine induces the expression of a protein FIAF (Fasting-Induced Adipose Factor) known to promote reduction of fat storage. Akkermansia also increases the expression of RegIII, a bactericidal lectin which specifically targets certain pathogenic species in the intestine [4].

Significance with respect to human health
A. muciniphila is considered to be the most abundant mucolytic (mucus degrading) bacteria in a healthy individual. A low concentration of this species in your gut could indicate a thin mucous layer, thereby resulting in a weakened gut barrier function, besides increased translocation of bacterial toxins. Patients suffering from Inflammatory Bowel Disease (IBD), obesity and Type II diabetes (T2D) tend to have lower concentrations of A. muciniphila [5]. Its concentration is also known to decrease with age [2]

Let’s have some Akkermansia for lunch!
It is understood that oral consumption of live Akkermansia spp. (tested on mice) may prevent diet-induced obesity by means of altering the adipose tissue metabolism and gut permeability without affecting appetite and food habits. As impressive as its properties are, the administration of this bacterium on humans is still under investigation owing to safety concerns [6].

An alternative to the direct intake of live A. muciniphila is the consumption of polyphenol-rich foods. Administration of polyphenol to obese mice has shown to reduce the detrimental effects of obesity and increase Akkermansia abundance. Cranberries contain Proanthocyanidins (PAC), a polyphenol, which has a prebiotic effect on Akkermansia. PAC facilitates the differentiation of goblet cells (found in the epithelial lining of certain organs) which in turn produce mucus, thus providing an environment for A muciniphila to thrive. PAC rich cranberries might be an excellent therapeutic alternative to improve Akkermansia abundance [7].

Not only does the existence of Akkermansia illustrate a thriving host-microbe relationship, its anti-obesity properties makes it an excellent candidate bacterium to be examined further in our fight to tame obesity and T2D.

Long live Akkermansia!

References:

1. Belzer, C., & de Vos, W. M. (2012). Microbes inside—from diversity to function: The case of Akkermansia. The ISME Journal, 6(8), 1449–1458. Article

2. Derrien, M., Belzer, C., & de Vos, W. M. (2015). Akkermansia muciniphila and its role in regulating host functions. Microbial Pathogenesis. Article

3. Dao, M. C., Everard, A., Aron-Wisnewsky, J., Sokolovska, N., Prifti, E., Verger, E. O., … Clément, K. (2015). Akkermansia muciniphila and improved metabolic health during a dietary intervention in obesity: relationship with gut microbiome richness and ecology. Gut, 1–11. Article

4. Anhê, F. F., Varin, T. V., Le Barz, M., Desjardins, Y., Levy, E., Roy, D., & Marette, A. (2015). Gut Microbiota Dysbiosis in Obesity-Linked Metabolic Diseases and Prebiotic Potential of Polyphenol-Rich Extracts. Current Obesity Reports, 389–400. Article

5. Brahe, L. K., Le Chatelier, E., Prifti, E., Pons, N., Kennedy, S., Hansen, T., … Larsen, L. H. (2015). Specific gut microbiota features and metabolic markers in postmenopausal women with obesity. Nutrition & Diabetes, 5(6), e159. Article

6. Shen, J., Tong, X., Sud, N., Khound, R., Song, Y., Maldonado-Gomez, M. X., … Su, Q. (2016). Low-Density Lipoprotein Receptor Signaling Mediates the Triglyceride-Lowering Action of Akkermansia muciniphila in Genetic-Induced HyperlipidemiaHighlights. Arteriosclerosis, Thrombosis, and Vascular Biology, 36(7), 1448–1456. Article

7. Anhê, F. F., Varin, T. V., Le Barz, M., Desjardins, Y., Levy, E., Roy, D., & Marette, A. (2015). Gut Microbiota Dysbiosis in Obesity-Linked Metabolic Diseases and Prebiotic Potential of Polyphenol-Rich Extracts. Current Obesity Reports, 389–400. Article


About the author:
Akshaya Krishnan is a member of the growing uBiome Laboratory Team. She firmly believes the next big revolution in healthcare will come from a personalized understanding of the human microbiome. She holds a MS in Biotechnology from the University of Melbourne and has an avid interest in microbiology and science communication. She is a die-hard Harry Potter fan and in her spare time, she loves to cook different cuisines. Find Akshaya on Twitter at @akshkrishnan.