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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Response to May 29, 2015 Journal Club: “Modulation of Post-Antibiotic Bacterial Community Reassembly and Host Response by Candida Albicans” [Downward et al, 2013]

Although this is a slightly older paper, the role of fungi in the gut microbiota is becoming an increasingly prevalent topic of discussion among microbiome groups, making this discussion a timely one. This group also previously published two papers on the role of antibiotics and fungal microbiota in allergic airway disease (Noverr et al 2004 & Noverr et al 2005). The primary finding of the paper at hand was that the introduction of C.albicans following antibiotic treatment causes marked changes in the reassembly of the microbiome, even in the absence of inflammation.

As discussed in journal club, there were several positive aspects to the study. First, the authors demonstrated the importance of the role of fungi in the gut despite relatively small numbers compared to that of bacteria. This is an aspect of the microbiome that has largely been neglected in recent years but fungi are large organisms and as illustrated, possess a significant ability to impact community reassembly following a disturbance. The inclusion of a multiplex qPCR array was helpful in examining changes to gene expression in response to various microbiome disturbances, although many aspects of this data were not addressed in the discussion. Finally, the relative abundance graphs were a good way to summarize taxonomic distribution, though we did discuss the challenges of pooling this type of data when samples are vastly different from one another.

There were a few other suggested areas for improvement to the study and paper that were discussed as well. For example, it was difficult to compare the bands from the graphs in Fig. 7 as their relative abundances may have been different (ie. Graph C: band for undisturbed ~10% versus band for disturbed + C.albicans ~1%). As a result some of the graphs were difficult to interpret with accuracy. The practice of using a log scale to demonstrate relative abundance followed by a non-log scale to plot taxa is also misleading. In addition, the authors’ use of rarefaction curves was not ideal. Finally, the title of Fig. 7 should read Day 21, not Day 7. Overall there were no major issues with the study or its findings.

We found this paper helpful in demonstrating the need for addressing fungi in microbiome analyses. However, there are still many obstacles to overcome in this area, such as limited fungal databases.

May 2015 Journal Club Paper:

Previous Work:

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Should we care about fungi? The mycobiome: an emerging field of the human microbiome research

penici2With the advancement of next-generation sequencing in the last decade, our knowledge about the trillions of microbes that the human body harbours has exponentially increased. Microbiome research has mostly been focused on the study of bacteria notwithstanding that the classical definition of the microbiome includes viruses and fungi. Despite the numerous microbiome publications, we know only little about the impact of fungi on health and disease. That said, with the increased evidence demonstrating the importance of host bacterial communities on host physiology and their involvement in health, research groups are interested in looking at the impact of fungi as well.

I have selected this publication because it demonstrates the potential effect of fungal colonization on the bacterial composition in vivo. In this study, Downward and colleagues demonstrated that the introduction of C.albicans in a disturbed microbiota was sufficient to alter the reassembly of the bacterial population.

During our journal club Friday, May 29th at 3:30pm, Westend Pub I hope to discuss:
(a) The underappreciated impact of fungi in microbiome research
(b) The feasibility and significance of including a mycobiome component in our research
(c) The limitation of the ITS sequencing

Relevant reviews for people interested to read more on the topic include:

The mycobiota: interactions between commensal fungi and the host immune system:

The human mycobiome in health and disease:

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Going beyond 16S rRNA gene sequencing to examine the functionality of the gut microbiome.

As the technology advances, so does our ability to probe and profile human microbiomes. Next week, I will lead a discussion of the recent paper entitled Functional Dynamics of the Gut Microbiome in Elderly People during Probiotic Consumption.” by Emiley Eloe-Fadrosh et al. This paper combines together many aspects that we’re interested in here at McMaster, including the inclusion of techniques beyond 16S rRNA gene sequencing to gain a more complete understanding of how the elderly gut community is affected by the popular probiotic, Lactobacillus rhamnosus GG (LGG).

During our journal club Friday, May 1st at 3:30pm, Westend Pub I hope to discuss:
(a) the combined use of 16S rRNA gene sequencing and RNAseq
(b) their conclusions regarding the effect of LGG on the gut microbiota
(c) on the more philosophical: discuss their use of data visualizations, and how we can apply their methods to our own datasets

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