Small Things Considered

What’s the Score on the Microbiome?

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by Elio

Just for kicks, let’s count up recent papers that say the microbiome is a good thing and those that say otherwise.

Just count titles.

For instance:

Socially transmitted gut microbiota protect bumble bees against an intestinal parasite

Drosophila Microbiome Modulates Host Developmental and Metabolic Homeostasis via Insulin Signaling

Successful Transmission of a Retrovirus Depends on the Commensal Microbiota

Intestinal Microbiota Promote Enteric Virus Replication and Systemic Pathogenesis

So, right now, the score is 2 to 2. It will change soon.

Especially if you send us some to add to the list.

Retrospective, December 2011

We’ve prepared this quick tour for you, with brief visits to all the major articles we posted since our May, 2011, retrospective.

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Microbial Behavior

Are You Me or Am I You?  Proteus mirabilis is one sentient bug: it can distinguish itself from its parents and relatives.

Ringing a Microbial Dinner Bell.  Bacteria make smelly stuff, some of which provides appetizing cues for insects. Associate blogger Mark Martin explains.

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Structure and Function

Hard Biology.  How do diatoms make their glass-hard shells? Well, they assemble subunits within the cells, then export them and insert them into preformed structures.

Some Like It Curved.  How do bacteria make curves in their cell wall? It turns out that cardiolipin is a curved and curve-inducing lipid molecule found in the curvilinear cell poles of rod-shaped bacteria.

Rafting Through Time.  Do bacteria have lipid rafts in their membranes, a la eukaryotic cells? Possibly.

Vital or Not Vital: That Is the Question.  Guest Gemma Reguera clarifies the confusion about what is viable and what is vital, including what ‘vital dyes’ tell us about such states.

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Viruses

Virus Hacks Intercellular Communications Network.  Cells of our immune system talk to each other when mobilizing a defense, but vaccinia has many clever ways to tamper with those messages for its own benefit.

Is a Good Offense the Best Defense? Yeasts have to choose between having RNAi to defend against incoming viruses and such, or hosting killer viruses that eliminate the competition.

Phage Lambda’s Polar Expedition.  Are all regions on the surface of an E. coli equally inviting to an adsorbing lambda phage, or does lambda have a preference?

Phage DNA: Going with the Flow.  To launch an infection, a phage needs to transfer its DNA into the host cell, but a phage is not a hypodermic needle.

And We Thought We Knew What CRISPRs Do!  Here’s a new twist. A prophage in Pseudomonas aeruginosa inhibits biofilm formation and the host’s CRISPRs are required.  

Now That's Using Your Head!  We thought all tailed phages use their tails to recognize and attach to their host cells, but here’s one that uses its head instead.

Viruses that Infect Parasites that Infect Us: The Matryoshka Dolls of Human Pathogens.  Graduate student Jamie Schafer takes us, layer by layer, through two stories of viruses that infect parasites that infect us, both with possible clinical implications.

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Pathogenesis

A Pestis from the Past.  Associate blogger Marvin Friedman recounts the history of the Great Plague, as illuminated by recent genomic studies of old bones.

The Lyme Disease Spirochete Feasts on Tick Antifreeze.  A fellow blogger, Microbe Fan, allowed us to use his article on how borrelias use of antifreeze in ticks as a nutrient. Who would have thought?

The Janus Bug.  And you thought that Helicobacter pylori  was a bad bug, causing ulcers and cancer! Well, it may also stimulate the immune response to protect people from asthma.

Going Next Door Without Getting Your Feet Wet.  By using novel techniques, Daniel Portnoy’s lab can introduce Burkholderia into a cell, thus bypassing early stages of infection and isolating later ones. New pathogenesis mechanisms are now revealed.

A Clever Bug That Is Difficile to Control.  Marvin Friedman discusses how Clostridium difficile adenylates its teichoic acids to ward off the action of host defensive peptides.

How We Tell The Good Bacteria From The Bad.  MD/PhD student Micah Manary tells us how the inflammasome (which some of us need to look up) is involved in selecting members of the intestinal microbiome.

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Genomics and Evolution

The Façade of E. coli K-12.  Nothing was thought to be less dangerous than the K-12 strain of E. coli. Guess again. It’s full of genes encoding factors that can be turned on in HU protein mutants.

Fine Reading:  Microbial Evolution.  On the 150^th anniversary of publication of On the Origin of Species, 34 microbiologists met in the Galapagos to discuss the role of microbes in evolution.

Bacteria Activate Fungal Gene Clusters.  Cross-talk among very different organisms are the rage. Marvin Friedman presents another exciting example.

What’s Old is New: Genome Wide Manipulation of the Bacterial Chromosome in Vivo.  Guest Michael Schmidt discusses a novel and clever way of manipulating the bacterial chromosome on genome-wide basis.

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Ecology

Shipwreck Microbiology.  One shipwreck can devastate a coral reef for decades. The culprit? Iron leached from the wreckage.

One Size Sometimes Can Fit All.  And this is of great concern when it is one antibiotic resistance factor that can counter every antibiotic in our arsenal.

Some Like it Cold.  Marvin Friedman explains that the trigger factor protein (a chaperone involved in keeping nascent peptides from folding prematurely) is selectively upregulated in the cold.

Taking Bugs Out For a Spin.  Graduate students Linh Truong and Shabana Din describe the unexpected resistance of bacteria to very high g forces.

A Microbe By Any Other Name Would Smell As Sweet…  Mark Martin waxes eloquent on the subject of smells emanating form bacteria and their uses.

Symbiosis

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A Bug in a Bug in a Bug.  Bacteria living inside bacteria? Astounding as this sounds, you find them as nested endosymbionts of mealy bugs.

Wolbachia: The Difference Between a Nuisance and a Threat?  Graduate student Jamie Shafer tells a great story about a phage altering how the endosymbiont Wolbachia affects its insect host.

A Wormful of Bugs.  Here’s another example of an animal that considers a gut obsolete. Instead, it employs a sack of densely packed bacteria that feed it by oxidizing sulfur.

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Fungi

The King of the Fungi.  Imagine a fungus half the size of a bowling alley growing from a fallen tree. A big tree.

Fungi That Spit Like Baseball Players.  Guest Gemma Reguera reveals new insights on how mushrooms shed their spores. Fast! Very fast!

How to Escape a Deadly Embrace.  There lurk fungi in soils that can trap nematodes. Aha! The nematodes have evolved an escape tactic.

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Miscellanea

How to Improve Vaccines (or Not), 1912 Style.  Antibodies, it turns out, make a toxic vaccine less toxic. So it was thought 100 years ago, and now we find out that this holds up.

Fine Reading: Microbial Genomics and Infectious Diseases.  We call attention to a seminal paper by David Relman on this topic.

Preaching to a Prokaryotic Choir.  Mark Martin directed some probing questions about the microbial world to students in his undergraduate micro class and shares with us the results.

Of Terms in Biology: Riboswitch.  Twenty classes of these talented RNAs are known, and they do interesting and diverse jobs.

The Microbial Weltanschauung. Elio muses on the effect of knowing that there are so many prokaryotic cells on this planet.

Talmudic Question #82

Are there any surface structures or components on bacteria that are NOT used as receptors by some phage?

A Wormful of Bugs

by Elio

Paracatenula cf. polyhymnia. Light microscope
micrograph. The light portion is the ‘head’ or
rostrum, the dark portion the trophosome.
Source.

 

Let’s start out with a little quiz. What examples can you name of endosymbiotic bacteria so tightly packed that they’re nearly wall-to-wall within cells of their host? If you said legume root nodules, you can claim a prize. (Ask someone else for it, as we don’t have any.) You would get bonus points if you also mentioned the bacteria-filled bacteriocytes of certain insects or the celebrated giant tube worms found near the deep sea black smokers. By the way, the root nodule symbioses, though not mandatory, are highly beneficial to the host, but the other two are obligatory.

Here is another recently described example to add to this thought-provoking repertoire. In the sandy bottoms beneath shallow ocean waters one finds worms that have neither a mouth nor a gut. Although such areas seem sparse in life, in fact they’re home to a rather rich biota. Microbes, both pro– and eukaryotic, are present in abundance and so are animals, such as the worms we’re talking about here. So, how can animals be mouthless and gutless? Taking a page from the giant tube worms, a group of investigators found that indeed these worms are filled with a sack of bacteria. As in the tube worms, these bacteria provide food for the host by oxidizing H₂S using oxygen as the electron acceptor. This kind of biochemical endowment is widespread in nature and is found in groups as diverse as ciliates, arthropods, mollusks, and other kinds of worms. There is even a giant archaeon that is covered with sulfur oxidizing bacteria. Despite this huge variety of hosts and the many other sites where sulfur metabolism takes place in nature, the great majority of the bacterial sulfide-reducers are either Gamma- or Epsilonproteobacteria. Here, the symbionts are Alphas. The Alphaproteobacteria include others prone to intracellular life such as the nitrogen-fixing rhizobia and the rickettsiae (from which the mitochondria appear to be derived). Should we expect more examples of symbionts in this class?

The Astonishingly Rich Smorgasbord of New Methods for Light Microscopy

by Elio

A replica of a Leuwenhoek microscope. Source.

The two age-old problems of the light microscope are resolution and contrast. Resolution is a function of the wavelength of light, so that in the visible it is, at best, about 200 nm. (It also depends on the lenses, but they have been pretty good for a long time.) This means that if you were looking at, say, a virus 100 nm across, you could possibly see it, but you couldn’t tell if you were looking at a single particle or several stuck together. An irreducible problem, it seemed. Besides, that is if you could see it at all. Most biological objects have little contrast, thus are practically invisible. This was countered early on by staining the object with deep-hued dyes, but most of the time the cells were killed in the process.

One tactic for enhancing the contrast in living cells was the advent in the 1930’s of the phase contrast microscope. By taking advantage of small differences in refractive index between object and background, it could make a nearly transparent object visible. That was about it, until recently. Regarding resolution, an important breakthrough in the early 1950s was the introduction of fluorescence in microscopy (although other uses of this technique have made this a secondary point). Think about it. You are now looking at emitted light, which means that you can see the object as long as it gives off enough light. Size does not matter. Think of a very distant star, which can be seen even though, to the eye, it’s insignificant in size.

Lynn

by Elio

Lynn Margulis, a preeminent figure in modern biology, died suddenly at the age of 73. She was a good and an old friend of mine. When we were both living in Newton, Massachusetts, our spouses wanted nothing better than for us to take the kids out of the house on Sunday mornings. So, we went on countless walks together, the little ones running ahead of us. We talked about lots of topics, most of which I have forgotten. Now, I would dearly love to recall what they were. We have been friends ever since.

Her major contribution, as is widely known, was to cause the endosymbiotic theory of the origin of eukaryotic cells to become accepted as a central tenet in Biology. Although this idea had been proposed earlier, it laid fallow as a neglected and nearly forgotten notion that had little impact. Lynn broke through all the barriers explosively. I have mused about when this revolution would have happened had she not done this. Surely, in time, perhaps 10 or 20 years later, the bacteria-like properties of mitochondria and plastids would have compelled its acceptance. The clincher, of course, would have been the indisputable genomic homology between mitochondria and rickettsiae, and likewise between plastids and cyanobacteria.

What makes it hard to write about Lynn is not only the personal loss I feel. In addition to praising her, I feel obligated to point out that she repeatedly proclaimed views that were not only unorthodox but that seemed indefensible. As one example, she believed that AIDS is caused not by HIV but by some spirochete. Through the years, I've tried to explain this strange devotion to untenable beliefs. Was this the same tenacity that enabled her to fight the endosymbiotic theory battle so successfully? She was one of the most intelligent people I have ever known and therefore I cannot readily dismiss my puzzlement.

She was also one of the best informed biologists going. Her font of knowledge, especially of the protists (which, characteristically, she insisted in calling the Protoctista), was astounding. She knew the old 19th century literature inside and out, including hard-to-find Russian papers. This knowledge she put to use in the numerous books she wrote, some together with her son, Dorion Sagan. Most of these are well worth reading.

I cannot think of anyone more stimulating, more bewildering, more exasperating than Lynn. But, to me, what really matters is that she was a most caring person and a devoted friend. I will miss her.

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If you want to read several dozen other reflections and obituaries on Lynn in various languages, visit the blog of Mercé Piqueras, La Lectora Corrent, for her post About Lynn Margulis.

Our Sixth Year Is Starting

by Elio

Five years and over 500 posts behind us, I would like to share with you a bit of the history of this blog. How did it start? I had retired officially in 1995 from Tufts University in Boston and came to San Diego. I arrived with the intention of staying involved in matters microbiological, but how? Basically, I think of myself as a commentator and I knew that there was a lot to comment about. Since I like to write, I started looking for publications. I found very few where I could park my prose. I had heard of a thing called a blog, but as is generally true of my age group, I did not take kindly to such a fresh invention with an unfamiliar name. However, I thought I should look into it and I called Chris Condayan, manager for Public Outreach at the ASM for advice. For all I knew, I could have asked it in a foreign language,  e.g., Qu'est-ce que c'est, un blog? The time could not have been more propitious because Chris told me that ASM had just decided that what they wanted was a blog! So, with his help, I timorously started posting a few snippets. Surprisingly, I felt comfortable doing it, so I kept it up.

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Our first post.

 

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Soon, I had the encounter with my partner, Merry, a defining event in this endeavor. Merry approached me early on saying that she was interested in blogging in microbiology and could she help. We proceeded with some caution, not knowing each other, but I soon found out that she was not only a remarkable editor (she knew how to get into my brain and pick out what I wanted to say), but also that she had a luminous writing style. She had not spent most of her life in microbiology, so this was doubly impressive. Merry and I decided to share the work, much to my immense gratification. You’ve got to be lucky sometime!

 

What I had in mind at the beginning was to share with readers interesting and exciting stories, perhaps some that would otherwise escape the attention of many in microbiology. I knew fully that astounding discoveries were being made at the level of basic phenomena. But besides that, the microbial world is full of dazzling phenomena that pop up from all sides, some of ineffable beauty or mind-boggling cunning. They kept knocking on my door! I have a particular liking for symbiosis, perhaps in the belief that if one genome is exciting, two interacting are even more exciting. Plus, I love the intricate choreography of microbes and their environment.

Week after week we have posted a major piece on Monday and a “minor” piece on Thursdays, which is a pretty demanding endeavor. And except for stated vacation periods, we have not missed a single one of these posting in all these years. We have come up with a few innovations. Chief among them are our Talmudic Questions, questions with no definite answer but that make for thinking along unconventional tracks. We also have a few other hallmarks, one being our Terms of Biology, another our Fine Reading posts where we point to articles that we think are either particularly well written or a good review of an area.

Most gratifying is that material from the blog has been used in teaching, from high-school to advanced studies, or so I’m told. The reason this matters to me has to do with the powers of less structured scientific writing. When writing for our blog, I think in conversational terms, picturing how I would tell a story if I were talking to someone. That is one way to teach, and not a bad one at that.

From the beginning, we encouraged others to contribute, and so they did. In time, we agreed that the blog could be an opportunity for students to try their hand at telling scientific stories. I offered this to a number of graduate students in a course I teach, and many accepted the invitation, succeeding in fine style in most cases. I like to think that they all benefited from our exacting and sometimes brutal editing. A number of other people have shown up spontaneously, expressing an interest in contributing an article. All of this has been a great pleasure to us. Three colleagues, Marvin Friedman, Welkin Johnson, and Mark Martin, have become part of the family and so we call them our associate bloggers.

Our intention is to continue in this endeavor. We're told that we're doing well. On that assumption, we’ll try to improve.

Why Blog?

by Merry

Euplotidium. Credit: Giovanna Rosati.

After five years, you’d think I’d have an answer to that question, a coherent and satisfying answer that I could share. Well, I dug around inside for a bit and this is what I came up with.

Picture a Rip van Winkle with a recent Ph.D. in biology who fell asleep late in 1970 and remained comatose until the 21^st century was well underway, then woke up and looked around to see what was new in biology. That sums up several decades of my life, scientifically speaking. When I woke up I was still working as a tech writer preparing computer software user’s manuals. I purchased a few used textbooks—microbiology, cell biology, virology, genetics. They’re very cheap if you don’t need the latest edition, and I didn’t. I started reading. What I found was truly stunning. A few years later I finally gained access to e-journals online—heaven indeed. And when I realized that, despite my ignorance, people would actually pay me to edit research papers, grant proposals, and other microbiology-related materials, it was bye-bye software manuals.

The now known microbial world is far more amazing than I ever imagined. I love exploring it. Blogging provides a structure for that exploration. Writing a post requires, at least for one like me so lacking in background, reading a lot of papers and covering much new terrain. Instead of just wandering around in a daze, this reading now has a specific goal—to find and assemble the pieces needed to tell a story. Eventually a post is written, giving me a sense of completion, and then it is on to the next post.

Why blog about viruses in particular, as is my habit? Don't they deserve it? These ‘simple’ entities are often disparaged as not being ‘alive,’ just as often denied a place in the Tree of Life, yet they possess more complexity than I can wrap my human mind around. They embody the evolutionary creativity that characterizes all life, and more of it than any other life form due to their numbers and rate of replication. They make the living world go round. Some people are filled with a sense of awe when they stand amongst the giants in an old-growth redwood forest, some when they muse about the viruses.

Fortunately I enjoy not only writing, but also editing. Both Elio and I spend much time editing each others posts as well as everything that comes in from our associate bloggers and over-the-transom. Give us a page, any page, and we can’t help but set to editing. Except for our brief winter and summer vacations, the pace has been non-stop, a post every Monday and Thursday. It seems worth the effort, even without adding in the pleasure and the learning we derive. I found that blog posts are not as ephemeral as I had thought when this began. The majority of our visitors each day don’t come to read the latest article, but rather arrive looking for information on a particular topic. If you Google “euplotidium” as I did almost five years ago, you’ll find that STC is still one of the top hits, #3 for me just now.

There are many reasons why I am still blogging with Elio after all these years. A lot of them have to do with the sort of person he is. (I can’t say more about that here because he keeps editing it out.) But there is one aspect in particular that brought me to STC originally and that keeps me here. That concerns his raison d’être for the blog: to share my appreciation for the width and depth of the microbial activities on this planet. There are many microbiology blogs out there, some very excellent ones indeed. Many of them, however, have a decidedly anthropocentric point of view, focusing on the organisms that we can exploit or that exploit us. Others cover only the current hot news items, emphasizing the scary or the bizarre. In contrast, both Elio and I delight in the Small Things and in sharing their stories.

And as soon as I complete one story, more are clamoring for attention. It just goes on and on…

 

A Gathering of Comments on a Talmudic Question

by Elio

First it may be appropriate to repeat what we mean by Talmudic Questions (and therefore Talmudic Answers). We use the term loosely to denote questions that may lack definitive answers but that open the door to ingenuity and dialectic. These questions embody the musings: “I have often wondered about…” We are fond of saying that answers to such questions are not likely to be found by a Google search.

Our Talmudic Question #81 (Given that most mutations are deleterious, why does the mutation rate not evolve to zero?) elicited especially lucid comments. Here we summarize a few only (and apologize to those whose comments are not mentioned).