Citizen Science and the Microbiome: uBiome studies women’s health

Everyone that reads this blog has some stake in the human microbiome game, so I’m assuming that you would all be interested in exploring your own personal microbiomes!

If you haven’t heard of them by now, uBiome is a company started via a crowdsourcing effort in the San Francisco Bay Area back in 2012 with personal microbiomes in mind. They now provide sampling kits (internationally!) for you to test your own microbes at any of the five physical sites they currently study: skin, nasal, oral, gut, and genitals.  In addition to each sampling kit is a health survey.  The information uBiome gets in each of these surveys allows the data from the resulting microbiomes to be included in larger research projects (with your permission of course), both at uBiome and with various collaborators.

The latest project being pursued by uBiome is a women’s health initiative (sorry guys, this one’s for the ladies!).  The new study will make use of citizen science and the uBiome platform to delve into the changes in the vaginal microbiome throughout both the menstrual cycle and different phases of life.  Anyone that meets the criteria and wants to participate, anywhere in the world, can opt into the study.  Participating means that you not only get to learn about your own microbiome and how it stacks up against other women around the world, but you also get to be a part of a larger initiative towards advancing women’s health.  As an added incentive, uBiome provided the first 500 kits for free (all of which were claimed in under two days), and any kits beyond those initial 500 are being provided at a discounted price.

Between social media and word of mouth, innovative ventures like uBiome may be the most relevant new way to study broad topics like the microbiome.  Citizen science initiatives brings a whole new brand of participation in research studies to the field.  I for one can’t wait to see what they’ll do next.

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Does dysbiosis drive intestinal inflammation or is dysbiosis resulted from inflammation in IBD?

This Friday the 13th at 3:30pm we continue journal club to discuss: Lewis et al, 2015. Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn’s Disease.

Dysbiosis, a term that is often misused and over simplified as a reduction in diversity and altered bacterial composition, will be the highlight of our discussion this week. It is well documented that patients with Inflammatory Bowel Disease (IBD) have an altered microbial composition however, is this altered composition a result of inflammation or does it drive inflammation? This paper claims that dysbiosis is reduced when inflammation is reduced. Moreover, inflammation, antibiotic exposure, and diet independently influence specific taxa meaning the response of the gut microbiome depends on the environmental stressor.

Please join us for a great discussion at West End Pub @ 3:30pm!

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Microbiome Working Group is on a roll!


image by tommietheturtle

image by tommietheturtle

As the Microbiome Working Group picks up momentum we’ve needed to move to bigger rooms to facilitate more than one discussion at a time. I would like to congratulate everyone who participated so far and welcome you keep the momentum going by coming each week to either ask a question or answer one.

See the room schedule page here.

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Journal Club Resumes Friday, Sept 18

Just a reminder that last month’s journal club is rescheduled for this Friday, at West End Pub at 3:30 pm. We will be discussing this paper on gene copy number variation across different strains of the human gut microbiome. We hope you can join us!

PowerPoint Presentation

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Journal Club Postponed

Due to scheduling conflicts, tomorrow’s journal club will be postponed until Friday, September 18, at 3:30. I apologize if this inconveniences anyone but hope you get out there to enjoy the last few days of summer!

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The Microbiome Working Group Continues

After a successful summer, I’m happy to report that we will continue the Microbiome Working Group come September. We have had participation from multiple labs across many Departments, tackling big questions from laboratory contamination to large-scale bioinformatic analysis.

This Group is a weekly, drop-in hour with the goal of bringing microbiome researchers together from different laboratories and backgrounds to help and guide each other. This isn’t another meeting; bring your laptop to get advice where you’re stuck, or draw out your newest idea on the whiteboard to get some peer-review before the real peer-review.

Please note the new time and location: the Microbiome Working Group will occur Tuesdays at 3:30pm in the Farncombe Conference Room (enter the Farncombe Institute, follow the walkway around the cubicles to the very back of the area). Students, postdocs, PIs etc., human microbiome or otherwise, everyone is welcome!

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Strain-level copy number variation among human gut microbiome bacterial species

This month’s journal club will continue on the topic of increasing the resolution of human microbiome studies, through a novel metagenomics analysis pipeline developed by Greenblum et al. In the human microbiome, bacterial strains of the same species may possess different genes or different copy numbers of genes, which affects the functionality encoded by the entire community. However, this strain-level information is usually lost in 16S rRNA gene sequencing and metagenomic studies.

In this paper, the authors analyze the intra-species copy number variation from shotgun metagenomic data of 109 gut microbiome samples. They found that copy-number variation of genes was wide-spread across different species, with genes important for environmental adaptation more likely to be variable. Additionally, correlations were found between strain variation and host states, including IBD and obesity.

Please join us at 3:30pm on Friday, August 28 at West End Pub for a lively discussion on this novel method of determining strain-level copy number variability and the results obtained by the authors when this method was applied to microbiome data sets; the applicability of this analysis for other data sets, and any limitations of the overall study or method.

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Oligotyping to Achieve Increased Taxonomic Resolution of the Oral Microbiome

The development of novel bioinformatics tools has allowed for researchers to glean increasing amounts of information from next generation sequencing of 16S rRNA gene data. Current methods of sequence analysis have been limited to taxonomic identity up to genera or operational taxonomic units (OTUs). However, within these taxonomic classifications, numerous species can reside and play key roles in health and disease. One example of this can be seen within the oral microbiome where numerous Streptococci species cohabitate and are functionally diverse while sharing similar 16S rRNA sequences that are not distinguished between in routine taxonomic classification.

This week’s journal club at 3:30pm on Friday, July 31st at West End pub will discuss “Oligotyping Analysis of the Human Oral Microbiome” by Eren et al. This publication demonstrates the usage of oligotyping, a supervised computational approach designed to provide increased taxonomic resolution in the oral microbiome (such as distinguishing between the aforementioned Streptococci), to achieve a better understanding of the human microbiome.

I look forward to discussing:

  1. Their results on the spatial location of various oligotypes
  2. The application of oligotyping to other microbiome data
  3. Limitations of oligotyping

Relevant/ Related Publications:

For the original methods paper on oligotyping, click here.

For information on minimal entropy decomposition, or MED (‘unsupervised oligotyping’), click here.

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Summing up: Exploration of the Virome in Inflammatory Bowel Disease by Norman et al.

Last week we drew our attention to the virome as discussed in “Disease-specific alterations in the enteric virome in inflammatory bowel disease” (Norman et. al). Continuing on the thread of ‘other’ components of the microbiome from our discussion last month on the mycobiome, this paper’s exploration into the virome was particularly eye opening. Their demonstration of numerous correlations between virome and microbiome diversity and size in ulcerative colitis and Crohn’s disease enforced and echoed the role non-bacterial components of the microbiome play in health and disease.

In addition, numerous elements of the methodology used were of particular interest. The multi-centre approach utilized in this study – involving cohorts from Cambridge, Los Angeles and Chicago – strengthened and added depth to their findings. In addition, the authors’ use of household controls was appreciated by the group as it took into account various elements, such as the built environment, diet, and human behaviours, that regular healthy controls or familial controls might not.

One area of interest that was highlighted, however, was the usage of the number of Operational Taxonomic Units (OTUs), as the number by which samples were rarefied for alpha diversity, as we had not seen this done before. Furthermore, many were surprised that only 15% of sequences were identifiable although this did highlight the need for a comprehensive viral database if future work on the virome is to occur.

Conversation then transitioned into a discussion on whether the field at large was ready to foray into the virome. Challenges such as how one might capture and identify the incredibly large diversity of the virome without a viral analog to the bacterial 16S rRNA gene or the fungal ITS regions was discussed. For example, this paper’s methodology and findings largely focused on bacteriophages, although many other types of viruses exist and are part of the virome. Acquiring a complete virome could be difficult due to the challenge of extracting all viral genetic material (as viruses differ in nucleic acids, structure, etc. unlike bacteria or fungi). This challenge was further compounded by the possibility that current methods for viral genetic extraction protocols (such as the virus-like preparations in this paper) may either be losing genetic material or be skewed by contamination due to an apparent lack of benchmarking.

Overall, this month’s meeting of the HMJC was impressed by much of the findings and methods utilized by the authors and found their study served as an excellent and needed foray into the world of the virome that highlighted its potential and its infancy.

June 2015 Journal Club Paper:

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“Disease-specific alterations in the enteric virome in inflammatory bowel disease” [Norman et al, 2015]

Is IBD going viral? Pursuant to last month’s journal club discussion on the importance of examining the fungal mycobiome, a closer look at the intestinal virome seemed like the logical next step. Eukaryotic viruses have the ability to interact with IBD risk genes to potentially alter disease (Basic et al, 2014, Cadwell et al, 2010). Various environmental stimuli (nitric oxide, antibiotics) can modulate the relationship between virus and host, including bacteriophages and their hosts. Changes such as these may be inciting factors of disease onset or flare-ups, thus it is important to better understand the role of viruses in gut physiology.

This study published in Cell in January of 2015 examined the composition of viruses in multiple inflammatory bowel disease patient cohorts and also compared IBD patients to their household controls. The authors found a significant expansion of one group of bacteriophages that was reportedly not secondary to IBD-associated decreases in bacterial diversity. Increased richness of caudovirales was associated with both CD and UC. This was often accompanied by a decrease in the other predominant bacteriophage species, microviridae. Other viruses comprised less than 5% of all viral sequences that were detected.

We’ll meet again at West End pub at 3:30 pm. The primary objectives of this week’s discussion will be to discuss current and potential methods for reliably sequencing viral DNA, as well as the importance of doing so.

A few papers for relevant background information:

Bernstein et al, 2000. Viruses and inflammatory bowel disease: is there evidence for a causal association?

Breitbart et al, 2003. Metagenomic analyses of an uncultured viral community from human feces.

Perez-Brocal et al. Study of the viral and microbial communities associated with Crohn’s disease: a metagenomic approach.

Wagner et al, 2013. Bacteriophages in gut samples from pediatric Crohn’s disease patients: metagenomic analysis using 454 pyrosequencing.

Wang et al, 2015. Metagenomic analysis of microbiome in colon tissue from subjects with inflammatory bowel diseases reveals interplay of viruses and bacteria.

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