Happy Holidays

Hope everyone enjoys this time where we usually get to slow down for a day, or two, or three ... and appreciate all that most of us already have.

Merry Christmas!

I hope everyone has a Merry Christmas and a Happy New Year! Though I do intend on getting back to blogging* before 2009!


*Being able to set posting dates and times is a nice Blogger feature!

M

ycoplasma laboratorium. As much as it pains me to give props to Craig Venter (when I was in graduate school, he was "the enemy"), this is too cool to pass up. M. laboratorium is the name of the organism that has been planned to be "created" as part of the Minimal Genome Project. M. laboratorium is actually M. genitalium with bits and pieces removed. Essentially, if it was considered (and proven by transposon mutagenesis) to be a "non-essential gene", it was excluded from the final "blueprint". Once they have the base template/blueprint, they will synthesize the genome and then pop it into a cell so it can "take off" on its own. Venter has even filed a patent on this idea, and they've published on their efforts as far back as 2006 in PNAS (PDF, 6 pages). So, while this organism doesn't actually even exist (as far as I know), I'm going to put it at the top of my "Merry Christmas" list.

Hopefully everyone has enjoyed this little "series". It was definitely not intended to be a full-fledged repository for these organisms. Instead I hope that it exposes (excuse the pun) people to some organisms that they may not have heard of before. Even better if people have contributed additional information in the comment fields.

At any rate, I hope everyone has a great holiday season!

E

lizabethkingia meningoseptica (further referred to as Em). Em is a Gram negative bacillus from the phylum Bacteroidetes. It is ubiquitous in the environment, having been isolated from soil, as well as both fresh and salt water. The genus derives it's name from CDC bacteriologist Elizabeth O. King, who first identified this organism as having caused meningitis in infants. She originally named it Flavobacterium meningosepticum.

R

uminococcus albus. Three guesses as to where Ruminococcus can be frequently isolated. According to the MicrobeWiki (a neat little site hosted by Kenyon College), Ruminococcus can be isolated from ... yep, you guessed it ... the rumen of cattle, sheep, and goats. R. albus is a gram positive organisms, belonging to the phylum Firmicutes. It is anaerobic, does not produce spores, and is non-motile. They produce a number of cellulose degrading proteins, which is useful for the organisms they inhabit, as it allows them to obtain energy from cellulose which they cannot otherwise digest.

R

aphidiopsis curvata. This organism was first identified and classified in 1929, and it's been a problem ever since. R. curvata is a cyanobacteria and produces a number of toxins which can be lethal for certain animal species. Two identified toxins produced by R. curvata are cylindrospermopsin (CYN) and deoxy-cylindrospermopsin (deoxy-CYN), both are toxic to the liver and kidneys.

R. curvata

Y

ersinia enterocolitica. Y. enterocolitica (Ye for short) is one of the etiological agents of yersiniosis, and according to the CDC, Ye is the main cause here in the United States. The disease typically presents as fever, abdominal pain, and diarrhea and is often contracted by eating undercooked pork. It can often be confused as appendicitis. It's main target is children, though anyone is susceptible, especially those who suffer from hereditary hemochromatosis.

Yersinia enterocolitica

C

lostridium difficile. Lookie! A Gram positive organism! It's an anaerobe, which means it doesn't need oxygen. This is ideal for it's environment, which is your intestines. "C. diff" isn't the kind of organism you really want however. It is most closely associated with antibiotic-associated diarrhea. What happens is that, when you're given a dose of antibiotics to treat some other infection, it winds up killing a portion of your normal flora in your intestines. This normal flora typically keeps C. diff in check, however with it now gone, C. diff takes over. Given C. diff's arsenal of toxins, you can then wind up with some nasty diarrhea and severe complications.

There is a rather ... ummm... interesting treatment for people suffering recurrent infections with this organism. Fecal transplants. I only wish I was kidding.

Scanning Electron Micrograph of C. difficile

H

aemophilus ducreyi. This organism can be summed up by one word: Chancroid. When you hear that word, you should envision a painful ulcer on someones genitalia. H. ducreyi is a sexually transmitted disease (STD), and it's the #1 cause of genital ulceration in the world. Dubious distinction, eh?

If you have an ulceration on your private parts and suspect it's bacterial in origin, there is an easy way for you to figure out whether or not you have contracted H. ducreyi or syphilis. Poke it. If it hurts, it's H. ducreyi. If it doesn't hurt, it's syphilis.

Fortunately for everyone involved here, I won't be showing any pictures of genital ulcers. Of course, it'll be interesting to see how many people Google brings here due to the search for the words "genital" and "ulcer".

R

hizobium leguminosarum. Like with Aa below, we'll simply refer to this bug here as Rl, because I'm not typing that out every single time. Rl is a soil organism which was first identified in 1889. These organisms are interesting because they pair up with legumes in a symbiotic relationship -- residing within root nodules -- and fix nitrogen. A portion of this nitrogen remains in the soil after the legumes are harvested, which cuts down on fertilizer costs. Because of this, you'll see legumes often used in crop rotations, rotating with other plants which do not fix nitrogen.

The nodulation process (formation of root nodules) is very intricate. The legumes release chemicals (flavinoids) which are sensed by the bacteria. In turn, the bacteria secrete chemicals (nod factors) which force the legume roots to undergo cell division and direct root hair growth. Eventually (with a few more steps) this forms the nodules in which the rhizobia reside.

Root Nodule.

I

sosphaera pallida. Isosphaera pallida is a species within the phylum Planctomycetes. The Planctomycetes are unique in that while they don't have a true nucleus, typically their DNA is enclosed within a double membrane (though this feature seems to be absent in Isosphaera. I. pallida is phototactic*, reproduces by budding, and displays gliding motility. Unlike most eubacteria, I. pallida (and other Planctomycetes) lack muramic acid -- a key component of peptidoglycan -- in their cell wall. It is therefore believed that these organisms went on their merry evolutionary way before peptidoglycan was ever heard of.

*I. pallida moves towards light sources.

S

hewanella putrefaciens. S. putrefaciens is a member of the Proteobacteria (Gamma class). It is a facultative anaerobe, and uses can use either iron or manganese as the terminal electron acceptor in electron transport (most organisms use oxygen). This organism derives its name due to the fact that it produces trimethylamines, which means it takes on a rotten fish smell. Yummy. Growing this organism will reveal that it has a pinkish color upon isolation. Another interesting tidbit is that this organism can also generate electricity.

People have also been unfortunate enough to find themselves infected with S. putrefaciens, though electrocution is not something they need to worry about.

T

hermotoga neapolitana. Another organism which has garnered a fair amount of buzz in bioenergy research circles. This hyperthermophilic organism can produce large amounts of hydrogen under anaerobic conditions (typically at around 80 degrees C). Like other organisms which have had their 15 minutes of fame, T. neapolitana is currently having its genome sequenced. The hope is that carbohydrates (generated/recovered as waste from other processes) can be fed to this organism so it can produce hydrogen for a variety of purposes (maybe hydrogen-fueled cars).

M

ethylococcus capsulatus. M. capsulatus is a methanotroph, which means it's able to use methane as their sole source of carbon and energy. This is useful as methane is a GHG that is approximately 26 times more problematic on a mole:mole basis than carbon dioxide. M. capsulatus uses methane by oxidizing it in a two step process, first to methanol, then to formaldehyde. The enzyme responsible for the first step of this process is methane monooxygenase (MMO) which comes in two forms, a soluble form (sMMO) and a particulate membrane form (pMMO). Different organisms may carry one or the other, or both (the organism in question, M. capsulatus encodes for both). Multiple labs have spent time studying M. capsulatus in the hopes that it can be exploited for methanol production.

M. capsulatus (Bath) has had its 3.3 Mb genome sequenced. As it's name suggests, M. capsulatus does possess a polysaccharide capsule, perhaps a tool to help it survive long periods of time in arid conditions.

Methylococcus capsulatus

A

ctinobacillus actinomycetemcomitans, which we will refer to simply as Aa from now on (because I'm not typing that out every damn time) is one of the "HACEK" grouping of Gram negative organisms that are all part of the normal human orophayngeal and/or urogenital flora. This organism (and the others) can, given the right circumstances, be found in association with endocarditis, bacteremia, and wound infections. Aa is a slow bugger to grow, often taking 48 to 72 hours, and forget about growing it on anything but enriched media. The most common infection associated with Aa is subacute bacterial endocarditis, though it is also blazing a trail in the area of periodontal disease as well. Aa has a decent sized virulence factor arsenal, including a leukotoxin, a PMN chemotaxis-inhibiting factor, resistance to complement killing, and bone resorption-inducing toxin.

S

erratia marcescens. S. marcescens is a Gram negative organism which belongs to the family Enterobacteriaceae. It can be pathogenic, most often found as a UTI, though it does also pose problems for immunocompromised individuals, especially those in a hospital setting -- leading to nosocomial infections. To make matters worse, S. marcesens has a habit of being antibiotic resistant, making it a very hard organism to clear. One of its hallmarks is that most isolates produce a reddish pigment called prodigiosin (see below), which assists in identification of the pesky bug.

From a historical, and religious, point of view, S. marcesens has been theorized to be the culprit in Eucharistic miracles involving bleeding hosts. However I'm not aware of it being confirmed in any such cases, if there have been any cases recently (of which I am also not aware).

Serratia marcesens