A network based approach to longitudinal analysis of the microbiota

tileshopAnalysis of the microbiome over time is hard. You can treat the abundance of each bacterial taxa as a separate outcome and look at them all individually but then you lose interactions between them. Worse yet, you can treat each measurement time point as separate, to get a picture of the interactions, but lose the connections between time points.

This week in journal club we will explore an alternative to longitudinal gut microbiome modeling – Network-based methods. After a simple introduction to longitudinal modeling and the different types of network methods we will look at a new implementation of one network method for longitudinal microbiome analysis from McGeachie et al. 2016 called Dynamic Bayesian Networks. In this paper they present the method and try it out on real data (16S rRNA gene profiles) from infants sampled every day in a neonatal intensive care unit. It’s important that you attempt the paper and google some of the terms before attending but I’ll do my best to explain the concepts used so that we can have a lively discussion.

Journal club will be this Friday April 29th from 3 – 4 pm in MUMC 3N10A. Afterward we will retire to the pub for a pint and to talk about a new view of the tree of life or maybe What Is the Tree of Life?

McGeachie MJ, Sordillo JE, Gibson T, Weinstock GM, Liu YY, Gold DR, Weiss ST, Litonjua A. (2016) Longitudinal Prediction of the Infant Gut Microbiome with Dynamic Bayesian Networks. Scientific Reports 6.

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April journal club: genomes from metagenomes.

Research into the composition and effect that the human microbiome can have on its host has advanced significantly with the application of 16S rRNA gene sequencing techniques and improvements in next generation sequencing technology. Using this marker gene, we can get a pretty good picture of “who” is there using standard, easy-to-use techniques.

However, in order to move forward with mechanistic, functional research, we need to know more than the coarse outline of the bacteria that are present in these communities. First, 16S studies only allow for the identification of the bacterial portion of the microbiome (though we have looked at ways of assessing fungal communities as well in past JCs). Additionally, 16S sequencing does not have the ability to differentiate between bacterial strains, and at the length that most high-throughput methods are currently optimized for, sequencing of specific regions of the 16S rRNA gene generally can only identify bacteria accurately to the genus level.

Inevitable advances in the biology and sequencing will improve 16S sequencing in the coming years; however, another interesting avenue for studying the composition of the (human) microbiome is by whole genome shotgun metagenomics. This method is advantageous in that they give us more biological information about a sample by identifying the genes that are present, and non-bacterial components such as viruses, phage, and fungi. However, if we do not have the computational tools to be able to re-assemble the metagenomic jigsaw puzzle into individual genomes, mechanistic and functional research will still be difficult.

This Friday, we will be examining a semi-recent paper entitled “Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes” where Nielsen et al. design a bioinformatic approach for sub-dividing the jigsaw puzzle of metagenomics into neat little piles, each representing a genome present within the sample.

Together we’ll investigate:

-the what of this algorithm (for a non-bioinformatic audience): what it is, and how it works to disentangle the input information into pseudo-genomes

-the howhow the authors applied this algorithm to a set of gut microbiome samples from which they identified and assembled 238 microbial genomes

For those who stick around to philosophize over beer, we can discuss the future of metagenomic technologies, how it might interact with 16S sequencing for the microbiome centre-stage, and how algorithms like these could be used to explore the human microbiome further.

Details: I will give a short presentation with discussion Friday, April 1st (no joke) at 3:00pm in HSC-3N10A (just outside of the Farncombe Institute). Following, all are welcome to continue discussions at the Phoenix.

Note: You MUST read the paper! This is a more technical paper than we usually pick, but you must make an honest effort to go through the manuscript to attend HMBJC. Highlight areas you are unsure of, and we’ll go through them together!

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Sign up now for the human microbiome journal club

Journal club continues this year with a powerpoint presentation and discussion from 3 – 4 pm in MUMC 3N10A, then continuing the discussion at the Phoenix for those who are interested. See the schedule here and sign up for empty spots! A blog post introducing each paper will go up one week before the presentation and notes on each journal club discussion will be turned into a brief post on the pros and cons of the research discussed. See you all there!

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Working Group: updated room information

Hello fellow microbiome-explorers!

Our drop in, bring-your-data&questions style, working group format is still kicking every Tuesday from 3:30pm on. Our room booking moves around a bit, so I would just like to update you that we will be in MUMC 2v7 from now until May 3rd 2016, when we move to MUMC 4N55A.

See you next week!

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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 https://www.flickr.com/photos/tommietheturtle1/14466902505/in/photostream/

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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