The microbial cloud

One of my favourite microbiologist is Jonathan Eisen, mostly because of the way he thinks about the microbial world around us and challenges conventions in science and elsewhere, but also because he’s creative and funny and outspoken in social media. Now he’s even dearer to my heart for sharing his personal experience with T1 diabetes in this compelling TED talk on the microbial world on and in us. It’s from about 6 months ago (sorry I’m a bit behind on my reading/viewing) but it’s still very topical. I especially related to his musing about what effect the “microbial cloud”, which physically covers each person, may have on the progression of autoimmune diseases such as T1 diabetes. He suggests that an imbalance in the microbial community could cause a miscommunication in a person’s immune response and possibly kick off an autoimmune reaction that ultimately kills the insulin producing beta cells. I would add that immune responses probably vary from one person to another, adding another level of complexity to this interaction and outcome. Anyhow, take a look, if you haven’t already…but watch out for the poo tea.

Microbe of the Week: Photorhabdus luminescens – a bug on the battlefield

I first came across Photorhabdus luminescens while listening to a TWiM podcast and became quite intrigued by the lifestyle of this microorganism in the environment and how it has made its mark in human history, making it one of my favourite microbes.

P. luminescens is a mutualistic bacteria that lives in the intestine of ‘entomopathogenic’ nematodes. These nematodes parasitize insects and use them to reproduce and acquire nutrients. When the nematode infects a new host, P. luminescens is regurgitated out of the nematode (video courtesy of Dr. Todd Ciche from Michigan State University here) and into the blood of the insect. Here, P. luminescens unveils its pathogenic side,  secreting toxins and hydrolytic enzymes that deteriorate the insect from the inside out and release nutrients that both the bacteria and nematodes metabolize. Once the lifecycle of the nematode is complete the nematode and bacteria reunite and leave the insect with a deadly fate, making this team a devilish duo. This switch from a mutualistic state in the nematode to a pathogenic state in the insect is a fascinating example of how microbes respond rapidly to different environments. A recent paper published in Science describes how a single promoter inversion controls these two lifestyles of P. luminescens (2).

A promoter switch inversion controls the pathogenic variant (P form) and mutualistic variant (M form) of P. luminescens as demonstrated by Somvanshi et al (Science 2012). The left panel depicts the M form (green) in the maternal nematode, while the P form (red) are visible outside the nematode. The right panel shows colonies of the P form (red) which outgrow the much smaller and slower growing M form (green). Images are courtesy of Dr. Ciche’s Microbial Symbiosis Laboratory at Michigan State University.

Now if you’re not already convinced that this two-faced microbe is worth remembering, perhaps a history lesson will lure you. During the American Civil War in 1862, the Battle of Shiloh claimed over 23,000 lives making it one of the bloodiest battles during the war. The bullets and bayonets left many soldiers with open wounds making them susceptible to lethal infections. Strangely, some of the soldiers’ wounds glowed at night and doctors and nurses noticed that the wounds that glowed healed faster (1). The eerie iridescence was termed “Angel’s Glow”, as the glow seemed to favour a soldier’s survival.

It wasn’t until 2001 that the mystery of “Angel’s Glow” was unraveled. In the midst of a bloody battleground open wounds were exposed to soil containing the nematodes that carry P. luminescens. The low temperatures at night resulted in many of the soldiers becoming hypothermic and a lower body temperature permitted growth of P. luminescens in the wounds. More unique features of P. luminescens are that it is bioluminescent and produces secondary metabolites, such as antibiotics, that kill other microbes. Thus, the supernatural glow was not a heavenly sign but rather a biomass of bacteria. Fortunately, P. luminescens is rather harmless to humans and its chemical warfare fended off other pathogens from infecting the tissue, likely saving lives during the Civil War.

A friend to humans and nematodes, a foe to insects, P. luminescens has a finesse for making the most of its host.

1. Bioluminescent bacteria and glowing wounds: Nealson, K. H., and J. W. Hastings. 1979. Bacterial bioluminescence: its control and ecological significance. Microbiol Rev 43:496-518.

2. Promoter inversion controls P and M form: Somvanshi, V. S., R. E. Sloup, J. M. Crawford, A. R. Martin, A. J. Heidt, K. S. Kim, J. Clardy, and T. A. Ciche. 2012. A single promoter inversion switches Photorhabdus between pathogenic and mutualistic states. Science 337:88-93.

RePOOPulate: Less sick and less “ick”

Hot off the press this week in the first issue of the open-source journal Microbiome is a paper demonstrating the proof of principle that synthetic stool is an effective alternative for donor stool used in fecal transplants for treating recurrent C. difficile infections. Dr. Emma Allen-Vercoe and her laboratory at the University of Guelph developed the “Robo-gut” to mimic the conditions in the intestine in order to grow a mixture of bacteria cultured from the stool of a healthy donor. They created a  probiotic mixture of diverse microorganisms, which they cleverly termed “rePOOPulate”, that restored regular bowel movement in two patients suffering recurrent C. diff associated diarrhea.

C. difficile is the leading cause of hospital-acquired diarrheal infections in Canada, particularly in the elderly. In recent years NAP1/BI/027 has emerged as a hypervirulent strain that is associated with increased disease severity (Quebec outbreak  2003, Niagara outbreak 2011), posing a continuous threat in the clinical setting. What’s worrying about C. diff infections are the number of individuals that suffer multiple relapsing infections. In these patients it is thought that dysbiosis of the intestinal microbiota prevents re-establishment of a healthy state. That’s where fecal transplants come in, the rationale being to restore the normal microbiota and eradicate infection. The first successful use of fecal transplant in treating C. diff was actually in 1958 (although at the time they were unaware it was a C. diff infection). Since then, over 500 patients have been treated with the achievement of a 95% success rate (see this review for list of published data).

Despite the evidence of success, fecal transplants are a last resort for many patients due to the “ick” factor, and because it is a difficult treatment to regulate. The development of synthetic stool not only removes the unpleasantness of the therapy, but it allows regulation of the bacteria transferred to the patient. The 33 species present in rePOOPulate were grown from healthy stool and screened for antibiotic susceptibility to improve the safety of the treatment.

What remains to be uncovered is the mechanism of how it works. Because the researchers knew what they were putting in they were able to monitor the presence of rePOOPulate bacteria over time in the two patients treated. The percentage of sequences that matched the rePOOPulate bacteria pre-treatment were <7% but between a period of 2 days to 2 weeks post-treatment it increased to 50-70%. After 6 months that proportion decreased to 25-36%. The findings that the recipient microbiome contained signatures of both the individual’s original microbiome and the rePOOPulate bacteria opens exciting new questions of how fecal transplants actually restore the intestinal microbiota to a healthy state that may be applied to other intestinal disorders, such as inflammatory bowel disease.

Naturally the media has fervently picked up the story – probably one of the only times you’ll see “poop” make headlines.

Back from hiatus…

Although things have been slow here on the HMjc site and it’s been a while since anyone presented a paper in journal club, my TO READ pile of human microbiome research papers continues to grow. It’s high time we got back to writing about and discussing the human microbiome! And what better way to start the new year than with a new HMjc schedule and list of upcoming events? Pick your favourite topic and sign-up to present a recently published paper. All kinds of hot topics are waiting, including antibiotic resistance in the environment and the clinic, the microbiome and autism, the influence of commensal bacteria on allergies, the microbiome and the mind, and how bacterial colonizers affect susceptibility to viral infection (and vice versa), to list a small few. I’ll be putting together a schedule for January so let me know if you’d like to be included.

We’re also looking for ideas for a new segment called “microbe of the week” where we’ll post a profile on an interesting organism. Nominate your favourite bacterium today! Another new initiative coming soon is the Micro.Bio program designed to get students involved in microbiome research and communication but more on that next year.

From FASTA file to microbiome profile: making sense of marker data

Find the slides here and my notes here. And here‘s a link to Mike’s blog

From FASTA file to microbiome profile: making sense of marker data

You’ve successfully turned your clinical or environmental DNA sample into a plethora of sequence information and you’re starting to analyze it with starry-eyed optimism. Or perhaps, you’re feeling a bit overwhelmed and aren’t sure where to start. Not to worry, help is on the way!

On Friday October 19^th Michael Lynch will present an overview of how to turn your FASTA file into a meaningful and informative microbiome profile. Find out how to turn your spaghetti factory of sequence into beautiful and meaningful figures. An outline is available here. Michael is a postdoctoral fellow at the University of Waterloo working to develop bioinformatics tools for microbial ecology research.

For those of you who would like a more detailed and technical look at the data analysis process there will be a tutorial specifically on the use of AXIOME and QIIME. If you would like to attend this second tutorial please RSVP with stearns@mcmaster.ca.  We’d like to make this as interactive as possible so please send us your specific questions and/or requests prior to the tutorial by email or by commenting on this post.

Join us on Friday October 19^th for a seminar at 10 am in MDCL 3022, light refreshments will be provided by the IIDR, and a tutorial at 2pm in the same room.

Sequencing Tutorial Slides

Last Friday Christine King led an informative tutorial on next generation sequencing of microbes. Thanks to all those who attended and who helped organize and support the event! For those who couldn’t make it or forgot to bring a pen and paper, Christine has kindly provided her slides for reference.

Stay tuned for details on future tutorials covering sequence analysis…

Microbial Sequencing 101: From bench-top to FASTA file

Are you itching to know what secrets lay in the nucleic acid of your favourite microbe? Are you curious in learning how to go from an environmental/clinical sample to revealing its microbial composition? On Friday July 13th from 12PM to 1PM in MDCL 3022, the HMBJC is hosting a tutorial lead by Christine King of the Farncombe Metagenomics Facility to explain the steps involved in sequencing microbial DNA. All are welcome to attend this methods tutorial which will cover the basics, from sequencing technology and terminology, to the steps involved in sample preparation for sequencing of whole bacterial genomes and mixed microbial communities.

Please join us and ready your questions for an interactive discussion to gain the knowledge to conduct your own sequencing project and/or the confidence to assess the validity of others’.

Pizza will be served! Hope to see you all there!

The Pros of Probiotics

We’ve all heard the claims of probiotic yogurts and their benefits for human health, but aside from improving our belly dancing skills, what exactly are probiotic bacteria doing?

An elegant study from the Jeffrey Gordon lab explored the effects of consuming fermented milk products (FMPs) containing probiotic bacteria on the human gut microbiota. They sequenced fecal samples from 7 pairs of monozygotic twins before, during, and after a 7-week period of consuming a FMP containing 5 probiotic strains to investigate if probiotic bacteria alter the composition of the microbiota. They conducted complimentary experiments in gnotobiotic mice harbouring a synthetic microbial community consisting of 15 strains whose genomes are sequenced and are considered functionally equivalent to the human gut microbiota. They then introduced 5 FMP strains and sequenced the model community to observe its dynamics over time. In both humans and mice, they observed that the community remained relatively stable during the period of exposure to FMP bacteria, an interesting finding suggesting that probiotics do not exert their effect by altering the proportions of microbial populations in the gut.

They then turned to RNA-seq to ask whether the bacterial community displayed functional changes. The transcriptional profile of the most dominant and persistent FMP strain revealed up-regulation of genes involved in catabolism of xylooligosaccharides in vivo in both mice and humans. They also found that the model community responded to the introduction of the FMP strains by altering expression of genes involved in metabolic pathways, primarily those associated with carbohydrate metabolism, and noted differences in carbohydrate metabolites in the urine of the mice. Perhaps the metabolic shift of the FMP bacteria and the resident microbiota is a key contributor to the benefits of FMPs on intestinal health.

Not only does this study provide insight as to how probiotics impact the gut microbiota, it also emphasizes that it’s not necessarily what microbes are there, but rather what they are doing that is relevant to our health. Our determination to uncover links between the microbiome and states of health and disease requires a global analysis, similar to this study, including techniques to study microbial communities at the genomic, transcriptomic, and metabolomic level. With this approach we will begin to understand the identity and functionality of our microbial ecosystem in a healthy stable state and further determine how divergence can positively or negatively impact our health.

Journal Club this week: switching things up.

This week I’m going to lead a discussion on the relationship between autism and the gut microbiota.  Instead of examining one paper in detail, I’d like to give a general review of the research going on in the field.  As a primer, take a quick read through this 2 page review found here.  For the truely keen, I’ll probably focus most on this paper detailing the abundance of clostridial species in children with autistic spectrum disorder compared to controls.

We’re going to try a new time this week, Friday June 1st at 12 noon in HSC-3N44A. Hope to see you out!