The human microbiome is a highly complex community of microorganisms that conveniently does good for our health while we provide it with a cozy place to live. With the advent of sequencing technology, scientists have taken the opportunity to explore this ecosystem in detail to find the story behind these microbes. They have been asking who’s there, where are they located, and what exactly are they doing? Although we’ve made quite some progress in answering these questions, one that has received relatively less attention is, when do we acquire our microbiome?
The current dogma is that the human fetus is sterile and that colonization with microbes begins during exit from the birth canal. The vaginal microbiota is therefore a primary source of microbes for the infant gut microbiota and contribute to the newborn’s health (babies born by C-section are at higher risk of developing allergic disease (1)).
In previous posts we’ve looked at breast milk as an additional source of microbes and also questioned whether the human fetus is indeed sterile. In a recent review published in PLoS Biology (2), Lisa Funkhouser and Seth Bordenstein discuss these internal and external modes of microbial transmission in greater detail. In an added bonus to summarizing the current literature for humans/mice, they consider an evolutionary perspective of symbiotism and feature examples of microbial transmission in marine invertebrates, terrestrial invertebrates, and vertebrates. It’s an insightful look at the mechanisms that different species uses to make sure offspring get their dose of essential microbes.
The review reads like an episode of Planet Earth and is sure to be both entertaining and educational.
We’re starting the year off by discussing a new paper out this month on metagenomic data analysis (Darling et al. 2014 PeerJ 2:e243). Members of the Matsen and Eisen labs came together to explore methods for phylogenetic-based microbial community analysis and the result is their open-source software package PhyloSift. Bring your low-tech paper and pen to discuss this high-tech article at the Phoenix pub next Monday, January 20th, at 3 pm. The highlights of the paper include:
- Studying microbial communities with metagenomes (i.e. entire genomes of all the microbes in the sample) instead of the amplicon-based single gene methods (i.e. PCR amplification of the 16S rRNA genes from all microbes in the sample).
- The software incorporates 37 marker genes as well as all other gene families.
- They use a phylogenetic methods for studying microbial communities – we’ll talk about what this means and how it’s different from OTU-based taxonomies.
- Bayesian hypothesis testing, edge PCA over PCoA or CA based on UniFrac, alpha diversity based on phylogenetic methods versus OTU-based methods, and much more…
We’ll talk about the pros and cons of their method, how this applies to us and metagenome analysis in general and about how they show the taxonomic ambiguities in their data instead of ignoring it. PeerJ is even set up to accept comments and question on the article website, so if we have some burning questions remaining we might even post them. Great, see you there.
Fecal microbiota transplants (FMT) work when it comes to treating Clostridium difficile colitis as it restores alterations in the intestinal microbiota. But is dysbiosis responsible for intestinal inflammation in inflammatory bowel dieases such as ulcerative colitis (UC)? This question has created a lot of buzz and is the focus of next week’s human microbiome jounal club! As I learned this week (courtesy of my lab mate Julie Kaiser @jukais), many people with UC do think FMT is the answer and has taken it upon them to create and administer a home made stool cocktail – a movement now dubbed DIY fecal transplants http://bit.ly/12iRb93 .
Join us Thursday August 29 at 3 pm at the Phoenix to discuss Kump et al., 2013 – a study that concludes intestinal dysbiosis in UC patients does not cause inflammation but is a result of inflammation.
Some points we could discuss:
- Is dysbiosis in UC a cause of inflammation or a result?
- Are 6 patients enough to make a statistically significant conclusion?
- How big a role do donors play in UC FMT success? Could sex, age and environment play a role in a donor’s success?
- The authors used a single application of donor stool – why does it work for C. Diff but not UC
- DIY FMT – good idea?
BACKGROUND:In patients with ulcerative colitis (UC), alterations of the intestinal microbiota, termed dysbiosis, have been postulated to contribute to intestinal inflammation. Fecal microbiota transplantation (FMT) has been used as effective therapy for recurrent Clostridium difficile colitis also caused by dysbiosis. The aims of the present study were to investigate if patients with UC benefit from FMT and if dysbiosis can be reversed.
METHODS:Six patients with chronic active UC nonresponsive to standard medical therapy were treated with FMT by colonoscopic administration. Changes in the colonic microbiota were assessed by 16S rDNA-based microbial community profiling using high-throughput pyrosequencing from mucosal and stool samples.
RESULTS:All patients experienced short-term clinical improvement within the first 2 weeks after FMT. However, none of the patients achieved clinical remission. Microbiota profiling showed differences in the modification of the intestinal microbiota between individual patients after FMT. In 3 patients, the colonic microbiota changed toward the donor microbiota; however, this did not correlate with clinical response. On phylum level, there was a significant reduction of Proteobacteria and an increase in Bacteroidetes after FMT.
CONCLUSIONS:FMT by a single colonoscopic donor stool application is not effective in inducing remission in chronic active therapy-refractory UC. Changes in the composition of the intestinal microbiota were significant and resulted in a partial improvement of UC-associated dysbiosis. The results suggest that dysbiosis in UC is at least in part a secondary phenomenon induced by inflammation and diarrhea rather than being causative for inflammation in this disease.
Two pitchers later we’d only gotten through the first figure. Here are the notes but I spent more time discussing than typing so they’re incomplete. Does anyone have a suggestion for the next paper?
The work of Dr. Gordon and colleagues has generated a lot of excitementabout the gut microbiome and its impact on health and disease, and their recent work is no different. After a first read, this substantial Science paper (see link in Mendeley) seems to actually be both a method and a study wrapped into one convenient package. We’ll dive into the nitty gritty of both the methods and the findings, this Thursday at 3 pm at the Phoenix, to determine:
- How the LEA-Seq method works and how it stacks up to current sequencing protocols
- How direct sequencing of 16S rRNA genes compares to whole genome sequencing of cultured bacterial isolates for displaying stability of the gut microbiota over time
- What data filtering is recommended, for as they say: “…without filtering the microbiota appears much more diverse and much less stable.”
- What fraction of the microbiota is persistent within an individual over time and after a perturbation like dieting
- Which members of the microbiota are shared among family members
Abstract: A low-error 16S ribosomal RNA amplicon sequencing method, in combination with whole-genome sequencing of >500 cultured isolates, was used to characterize bacterial strain composition in the fecal microbiota of 37 U.S. adults sampled for up to 5 years. Microbiota stability followed a power-law function, which when extrapolated suggests that most strains in an individual are residents for decades. Shared strains were recovered from family members but not from unrelated individuals. Sampling of individuals who consumed a monotonous liquid diet for up to 32 weeks indicated that changes in strain composition were better predicted by changes in weight than by differences in sampling interval. This combination of stability and responsiveness to physiologic change confirms the potential of the gut microbiota as a diagnostic tool and therapeutic target.
Scientists recently described a new form of symbiosis at our mucosal sites with an unassuming partner: bacteriophage. In a paper published in PNAS, Jeremy Barr and colleagues noticed that phage are enriched at mucosal surfaces compared to surrounding surfaces and demonstrated that a specific interaction between Ig-like domains on the phage capsid and mucin glycans is what holds them in place. Their findings suggest that the presence of phage in mucin protects the underlying epithelial cells from bacterial infection, a good reason for us to have evolved to keep them there. The relationship benefits the phage too – mucosal sites are a buffet of bacteria for the phage to infect and multiply within.
Join us at the Pheonix next Friday May 31st at 1 PM for a discussion over drinks about our friendly phage.
Here are some reasons we chose this paper and a few things to think about for discussion:
• It’s important to consider the diversity of microorganisms in our microbiome and their interactions with each other and the host in order to understand the ecosystem. Given phage specificity for certain bacterial species, does our virome change with fluctuations in bacterial communities? How does this alter community dynamics? (Interesting read on virome research: The other microbiome)
• We’ve coerced bacteriophage to act as our microscopic army against invading pathogens. It’s a strategy that not only humans, but also other metazoans with mucosal sites use as a strategy to defend against infection. But bacteria are smart too and aren’t content with the short end of the stick. They have their own defense against phages – the CRISPR/Cas systems. Recently this system is also implicated in bacterial virulence and immune evasion. Have our friendly phage contributed to pathogen evolution?
If you’re not able to make it, but are equally as fascinated with our inner viromes as we are, check out these links for more info and check back for a follow-up post on our discussion.
Carl Zimmer, The Loom: Meet your new symbionts: Trillions of Viruses
Ed Yong, Nature News: Viruses in the gut protect from infection
Story behind the paper by Jeremy Barr, The Tree of Life
Bacteriophage Paper: Barr, J. J. et al. Proc. Natl. Acad. Sci. USA http://dx.doi.org/10.1073/pnas.1305923110 (2013)
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.
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.
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.