bacteriology

BugsFeed: 4 bacteria that forgot how to bacteria

1. Mycoplasma - They are devoid of cell walls.

Yup. They lack cell wall precursors like muramic acid. No fixed shape or size. You could easily mistake mycoplasma for a virus, they even pass through bacterial filters!

2. Actinomycetes - They look like fungi!

I mean, the only reason we consider it as a bacteria is because it contains muramic acid in it’s cell wall. Otherwise, those branching filaments scream the word, fungi!

3. Chlamydiae - Obligate intracellular parasite. Are you a virus? 

They fail to grow in cell free media, they get filtered in bacterial filters. Why are you called a bacteria, anyway? Well, they do have DNA, RNA, ribosomes and replicate by binary fission.. So let’s count the poor energy parasite as a bacteria.

4. Mycobacteria - Here’s another rod shaped bacteria that sometimes shows filamentous forms resembling fungal mycelium.

So let’s call it ‘mycobacteria’, you know, fungus like bacteria!
Unlike you regular gram positive and gram negative bacteria, they are acid fast.

Related posts:
Cell wall of gram positive and gram negative bacteria mnemonic
Mycobacterial biochemical reactions mnemonic

Viruses Reconsidered

“The discovery of more and more viruses of record-breaking size calls for a reclassification of life on Earth.”

The theory of evolution was first proposed based on visual observations of animals and plants. Then, in the latter half of the 19th century, the invention of the modern optical microscope helped scientists begin to systematically explore the vast world of previously invisible organisms, dubbed “microbes” by the late, great Louis Pasteur, and led to a rethinking of the classification of living things.

In the mid-1970s, based on the analysis of the ribosomal genes of these organisms, Carl Woese and others proposed a classification that divided living organisms into three domains: eukaryotes, bacteria, and archaea. (See “Discovering Archaea, 1977,” The Scientist, March 2014) Even though viruses were by that time visible using electron microscopes, they were left off the tree of life because they did not possess the ribosomal genes typically used in phylogenetic analyses. And viruses are still largely considered to be nonliving biomolecules—a characterization spurred, in part, by the work of 1946 Nobel laureate Wendell Meredith Stanley, who in 1935 succeeded in crystallizing the tobacco mosaic virus. Even after crystallization, the virus maintained its biological properties, such as its ability to infect cells, suggesting to Stanley that the virus could not be truly alive.

Recently, however, the discovery of numerous giant virus species—with dimensions and genome sizes that rival those of many microbes—has challenged these views. In 2003, my colleagues and I announced the discovery of Mimivirus, a parasite of amoebae that researchers had for years considered a bacterium. With a diameter of 0.4 micrometers (μm) and a 1.2-megabase-pair DNA genome, the virus defied the predominant notion that viruses could never exceed 0.2 μm. Since then, a number of other startlingly large viruses have been discovered, most recently two Pandoraviruses in July 2013, also inside amoebas. Those viruses harbor genomes of 1.9 million and 2.5 million bases, and for more than 15 years had been considered parasitic eukaryotes that infected amoebas.

Now, with the advent of whole-genome sequencing, researchers are beginning to realize that most organisms are in fact chimeras containing genes from many different sources—eukaryotic, prokaryotic, and viral alike—leading us to rethink evolution, especially the extent of gene flow between the visible and microscopic worlds. Genomic analysis has, for example, suggested that eukaryotes are the result of ancient interactions between bacteria and archaea. In this context, viruses are becoming more widely recognized as shuttles of genetic material, with metagenomic studies suggesting that the billions of viruses on Earth harbor more genetic information than the rest of the living world combined. These studies point to viruses being at least as critical in the evolution of life as all the other organisms on Earth.

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E-Cigarette Vapor Boosts Superbugs and Dampens Immune System
In lab and mouse experiments, exposure promotes bacterial virulence and inflammation, while blocking the body’s ability to fight infection

Researchers at the University of California, San Diego School of Medicine and Veterans Affairs San Diego Healthcare System report data suggesting that e-cigarettes are toxic to human airway cells, suppress immune defenses and alter inflammation, while at the same time boosting bacterial virulence. The mouse study is published January 25 by the Journal of Molecular Medicine.

“This study shows that e-cigarette vapor is not benign — at high doses it can directly kill lung cells, which is frightening,” said senior author Laura E. Crotty Alexander, MD, staff physician at the Veterans Affairs San Diego Healthcare System and assistant clinical professor at UC San Diego School of Medicine. “We already knew that inhaling heated chemicals, including the e-liquid ingredients nicotine and propylene glycol, couldn’t possibly be good for you. This work confirms that inhalation of e-cigarette vapor daily leads to changes in the inflammatory milieu inside the airways.”

Crotty Alexander reported the preliminary results of this work at the American Thoracic Society annual meetings in 2014 and 2015. But now her team has also seen their findings hold up in mice. Inflammatory markers — signs of full-body inflammation — in the airways and blood of mice that inhaled e-cigarette vapors for one hour a day, five days a week, for four weeks were elevated by 10 percent compared to unexposed mice.

“We don’t know specifically which lung and systemic diseases will be caused by the inflammatory changes induced by e-cigarette vapor inhalation, but based on clinical reports of acute toxicities and what we have found in the lab, we believe that they will cause disease in the end,” Crotty Alexander said. “Some of the changes we have found in mice are also found in the airways and blood of conventional cigarette smokers, while others are found in humans with cancer or inflammatory lung diseases.”

Conversely, bacterial pathogens exposed to e-cigarette vapor benefited. Specifically, Staphylococcus aureus bacteria were better able to form biofilms, adhere to and invade airway cells and resist human antimicrobial peptides after exposure to e-cigarette vapor.

Read more here

BugsFeed: 7 reasons why Staphylococcus aureus should be your new favorite bacteria

1. It produces golden yellow colonies. 

Gold is royal.

2. They have the ability to develop resistance to every antibiotic you can think of.

Penicillin, methicillin, vancomycin. You name it.

3. It’s the bacteria you think of when you see a bunch of grapes.

Because, grape like clusters!

4. They turn pink due to lactose fermentation on MacConkey’s agar. 

Whoever said orange was the new pink was seriously disturbed!

5. TSST will leave you shocked. 

It’s called toxic shock syndrome toxin for a reason, duh!

6. Fastest enterotoxin ever.

Vomiting, diarrhea and nausea 2-6 hours after consuming contaminated food? Now that’s quick.

7. Catalase positive. 

Who doesn’t like cats? 

2

Streptococcus pyogenes

Streptococcus pyogenes (also known as the flesh eating bacteria) is a gram-positive bacterium that usually grows in pairs or chains. It has been classified as a beta-hemolytic streptococcus because when cultured on a blood agar plate all the red blood cells are ruptured by the bacteria. Furthermore, it has been classified using Lancefield serotyping as group A, because it displays antigen A on its cell wall. Therefore, this bacterium is commonly called the beta-hemolytic group A streptococcus, or GAS.

This bacterium is responsible for a wide array of infections. It can cause streptococcal sore throat which is characterized by fever, enlarged tonsils, tonsillar exudate, sensitive cervical lymph nodes and malaise. If untreated, strep throat can last 7-10 days. Scarlet fever (pink-red rash and fever) as well as impetigo (infection of the superficial layers of skin) and pneumonia are also caused by this bacterium. Septicaemia, otitis media, mastitis, sepsis, cellulitis, erysipelas, myositis, osteomyelitis, septic arthritis, meningitis, endocarditis, pericarditis, and neonatal infections are all less common infections due to S. pyogenes

There are at least 517,000 deaths globally each year due to severe S. pyogenes infections and rheumatic fever disease alone causes 233,000 deaths. 

Key characteristics: Gram(+), beta-hemolytic, bacitracin(+), PYR(+), facultatively anaerobic.

Today is a gross day at school.

- 8am lecture on pharmcologic treatment for barfing and all about barfing. Oh wait, I forgot to use my big fancy doctor words- I meant emesis.

- Gas gangrene infections by C. perfringens. If you are brave look it up.



- The treatment is maggots (Can you imagine being tasked with getting consent for that? “So you can see that your bloated, foul-smelling, horrifically infected wound is advancing at roughly 2cm/hr, what we want to do is put maggots in there… They will only eat the dead tissue, we promise… it’s science, just sign the damn form.”)

- C. difficile infections that destroy your colon because they can. Spoiler alert: yellow pseudomembranes are not like a pretty yellow sweater for your colon.

- A treatment for C. diff is a fecal transplant. We really didn’t need to see HOW it’s made. There’s a show for that if I was really curious. I did assure the Cute Boy that if he ever contracted a life-threatening C. diff infection I would give him some of my poo to save his life. No response yet.

- Pretty sure the whole point of these GI bacteriology lectures is some devious plot to turn me vegetarian. But my love for cheeseburgers is stronger than my fear of… well.. maybe not.

- It’s only 10am. Next up: Traveler’s diarrhea and medical parasitology. Goody.

BugsFeed: 7 bad ass organisms that can survive intracellularly in immune cells

1. Mycobacterium tuberculosis - Stops fusion!

Mycobacterium tuberculosis utilizes macrophages for its replication! (It uses the usual killer to expand it’s army :O ) How does tuberculosis bacilli survive in macrophages? M. tuberculosis has evolved a number of very effective survival strategies - It inhibits phagosome-lysosome fusion and inhibits phagosome acidification ensuring it’s survival inside the macrophage.

2. Brucella - Has chains, like Bruce Lee.

Brucella has a LPS O-chain. It ensures the Brucella containing vacuole (BCV) avoids fusion with lysosomes, prevents the deposition of complement at the bacterial surface and forms stable large clusters with MHC-II named macrodomians in the cell surface, interfering with MHC-II presentation of peptides to specific CD4+ T cells. Woah.

3. Listeria - It gets internalized in a vacuole and then runs away.

The pore-forming protein listeriolysin O mediates escape from host vacuoles. Once in the cytosol, the L. monocytogenes mediates efficient actin-based motility, thereby propelling the bacteria into neighboring cells. The cytosol is a favorable environment for listeria’s growth.

4. Mycobacterium leprae - Cholesterol and TACO!

Mycobacterium leprae is able to induce lipid droplet formation in infected macrophages. Cholesterol mediates the recruitment of TACO from the plasma membrane to the phagosome. TACO, also termed as coronin-1A (CORO1A), is a coat protein that prevents phagosome-lysosome fusion and thus degradation of mycobacteria in lysosomes. The entering of mycobacteria at cholesterol-rich domains of the plasma membrane and their subsequent uptake in TACO-coated phagosomes promotes intracellular survival.

5. Coxiella brunetti - The indestrucible

This hardy, obligate intracellular pathogen has evolved to not only survive, but to thrive, in the harshest of intracellular compartments: the phagolysosome. Following internalization, the nascent Coxiella phagosome ultimately develops into a large and spacious parasitophorous vacuole (PV) that acquires lysosomal characteristics such as acidic pH, acid hydrolases and cationic peptides, defences designed to rid the host of intruders.

6. Salmonella - TTSS

Salmonella have a specialized secretion system, termed the type III secretion system (TTSS), as well as proteins secreted by this system, are encoded in Salmonella pathogenicity island 1 (SPI1). TTSS are used by bacterial pathogens to inhibit their phagocytosis, induce eukaryotic cell death, and alter the host cell cytoskeleton. Salmonella species have at least one other TTSS encoded on SPI2 that appears to be involved in intracellular survival.

7. Human Immunodeficiency Virus - Tries to not attract attention

After infecting cells, HIV survives. Ever wondered why? It’s because the HIV protein, Nef plays a role in downregulating the expression of various proteins needed for recognition by potentially dangerous CD8 T cells. Nef lowers the surface expression of CD4, and several haplotypes of MHC-I by redirecting their transport from the trans-Golgi network. Another gene, Tat, appears to upregulate the expression of Bcl-2 during the early phase of cellular infection, increasing the likelihood that it will receive survival signals.

Many viruses can survive intracellularly, but I’ve included specifically HIV in this list because it survives in immune cells and it is an important virus to know.

For appropriate sources and references, click here.

How bacterial predators evolved to kill other bacteria without harming themselves

A joint study by the labs of Dr Andrew Lovering and Prof Liz Sockett, at the Universities of Birmingham and Nottingham, has shown how predatory bacteria protect themselves from the weapons they use in their bacterial killing pathway.

The research, published in Nature Communications, offers insights into early steps in the evolution of bacterial predators and will help to inform new ways of combatting antimicrobial resistance.

A useful predatory bacterium called Bdellovibrio bacteriovorus eats other bacteria (including important pathogens of humans, animals and crops).

It attacks them from inside out using enzymes (called DD-endopeptidases) that first loosen the cell walls of prey bacteria and then cause them to round up like a pufferfish, providing space as a temporary home for the predator.

However, Bdellovibrio also have similar cell walls so why don’t they fall victim of their own attack?

The project, funded by the Biotechnology and Biological Sciences Research Council (BBSRC), found that the bacterium uses an ankyrin-type protein called Bd3460 as a shield. It binds to the tip of the enzyme weapons, nullifying their action until they are safely secreted out of the Bdellovibrio and into the prey bacteria.

Dr. Andrew Lovering and Ian Cadby at the University of Birmingham determined the structure of the ankyrin protein using X-ray crystallography and found that that it attaches to two DD-endopeptidase weapons to temporarily deactivate them.

“When I first showed this to Liz, she hit the nail on the head by describing it as a decorative "quiff” on top of the endopeptidase" said Dr Lovering. “This covers up the active site of the enzymes that are used to cut cell walls and offers protection to the Bdellovibrio until these weapons are excreted into the prey.”

Carey Lambert, Rob Till and Prof Liz Sockett at The University of Nottingham confirmed the antidote protein’s use when the gene responsible for its production was deleted.

Prof Liz Sockett said: “When the Bd3460 gene responsible for antidote production was deleted, the Bdellovibrio had no way of protecting itself from its own weapons. When it attacked harmful bacteria with its cell-wall-damaging enzymes it also felt the effects.

"The Bdellovibrio bacteria lacking the Bd3460 gene tried to invade the bacteria but suddenly rounded up like pufferfish and couldn’t complete the invasion—the fatter predator cell could not enter the prey cell.”

This is the first paper to discover a ‘self-protection’ protein in predatory bacteria.

Prof Liz Sockett added, “Most bacteria are not predatory and so understanding these mechanisms gives us a glimpse of how predation evolved. In this case it seems that the Bd3460 gene was transferred into ancestors of Bdellovibrio, probably when they were beginning to develop as predators.”

Commenting on the potential impact of the study, Dr Andrew Lovering added: “If we are to use Bdellovibrio as a therapeutic in the future, we need to understand the mechanisms underpinning prey killing and be sure that any self-protective genes couldn’t be acquired by pathogens, causing resistance. Brilliantly, Liz and Carey have demonstrated this did not happen with the bd3460 antidote protein, and Ian and I showed how the mechanism works on predator enzymes only - this is a great inter-university collaboration.”

Image: Bdellovibrio Life Cycle. The Bdellovibrio attaches to a gram-negative bacterium after contact, and penetrates into the prey’s periplasmic space. Once inside, elongation occurs and progeny cells are released within 4 hours. 

Credit: Estevezj/Wikipeida

petrichor

petrichor—the pleasant smell of the first rain on dry rock.

In 1964, it was found that the smell coming off dry rocks or soil when they are wetted come ultimately from plants.  Vegetation gives off volatile chemicals which are adsorbed onto dry rock and released when water displaces them.   Petrichor is composed of many molecules such as terpenes released by the plants.

In the Indian village of Kannauj dry bricks are wetted and the petrichor scent is extracted.  The perfume, known as mitti attar—earth perfume, is infused in a base of sandalwood oil.

Dirt releases another odor, geosmin, that comes from soil-dwelling bacteria, called actinomycetes.  Beet roots also contain geosmin giving them the same earthy smell.  

 Word origin:  The word “petrichor” was coined by the Australian researchers Isabel Joy Bear and Richard Grenfell Thomas in a 1964 paper in Nature magazine.  They coined the word from the Greek petros, stone, and ichor, from the Greek word for the fluid that flows like blood in the veins of the gods. So the word means something like “essence of rock”. In the 1950s and 60s, the two Australian mineralogists, Bear and Thomas, set out to discover the source of the odor that had previously been called Argillaceous Odour.  The name change was needed because argillaceous refers to clay (from Latin, argilla, clay) and their research found that dry rocks other than clayey ones could also release the fragrance.

 More:

Indian Villagers make Perfume From the Rain

 The Chemical Compounds Behind The Smell Of Rain

Some earthy, wet perfumes you can buy

 Bear, I. J. & Thomas, R. G. (1964).  Nature of Argillaceous Odour.  Nature 201, 993 – 995.

Week 33: Streptococcus | 3D modelling (Cinema 4D)

Messing around with focal length and floatie bits to create a sense of depth :D

I wanted to make a scene for my mock editorial magazine cover that was cinematic. I’m far from done, and definitely still tweaking my colour palette… Escherichia coli (E coli) is next!

I’m also wondering about my choice of stream for 2nd year… I’m going to miss this sort of thing..

Molecular Homing Beacon Redirects Human Antibodies to Fight Pathogenic Bacteria
Bacteria-specific molecules attract pre-existing antibodies to help immune system clear infection

With the threat of multidrug-resistant bacterial pathogens growing, new ideas to treat infections are sorely needed. Researchers at University of California, San Diego School of Medicine and Skaggs School of Pharmacy and Pharmaceutical Sciences report preliminary success testing an entirely novel approach — tagging bacteria with a molecular “homing beacon” that attracts pre-existing antibodies to attack the pathogens. The study is published by the Journal of Molecular Medicine.

The molecular homing beacon is the brainchild of study co-author and Nobel Laureate Kary Mullis, PhD, who invented polymerase chain reaction (PCR), a now-common lab technique used to replicate DNA.

One end of the homing beacon is made up of a DNA aptamer, a small piece of DNA that can be selected from a pool of billions of candidates based on its ability to bind tightly to a particular target. In this test case, the aptamer specifically targeted group A Streptococcus, the bacteria that causes strep throat and invasive skin infections, while leaving human cells untouched. The other end of the homing beacon is alpha-Gal, a type of sugar molecule. Humans naturally produce antibodies against alpha-Gal. That’s because alpha-Gal is foreign to humans. Other mammals and some microbes produce it. Humans have evolved antibodies against it when we eat meat or are exposed to alpha-Gal-generating microbes in our environment.

To test the homing beacon — or “Alphamer” — against live strep bacteria, Mullis enlisted the help of Victor Nizet, MD, professor of pediatrics and pharmacy at UC San Diego, whose laboratory studies how pathogens interact with the human immune system. The research team found that Alphamers not only bind strep and recruit anti-Gal antibodies to the bacterial surface, they also helps human immune cells engulf and kill the Alphamer-coated bacteria.

The study offers the first proof-of-concept that Alphamers have the potential to specifically redirect pre-existing antibodies to bacteria and rapidly activate an antibacterial immune response.

“Our next step is to test Alphamers in animal models of infection with multidrug-resistant bacteria that pose a public health threat, such as MRSA,” said first author Sascha Kristian, PhD, visiting research scholar at UC San Diego and ‎associate research director at Altermune Technologies, a company Mullis founded to develop Alphamers into unique therapeutics. “Meanwhile, we’ll also be tweaking the Alphamer to make it more potent and more resistant to degradation by the body.”

If Alphamers continue to show promise, researchers might be able to apply the same concept to attack any type of bacteria or virus, or perhaps even cancer cells.

“We’re picturing a future in which doctors have a case full of pathogen-specific Alphamers at their disposal,” Nizet said. “They see an infected patient, identify the causative bacteria and pull out the appropriate Alphamer to instantly enlist the support of the immune system in curing the infection.”

An animation of the Alphamer technology is available at: https://youtu.be/5cfxhu3YqGs 

Pictured: Alphamers (purple) act as homing beacons, attracting pre-existing anti-alpha-Gal antibodies (green) to the bacterial surface. Credit: Altermune Technologies

Why you are more likely to get Lyme disease again

Here’s more reasons to be cautious of the pesky ticks during your summer outings.

UC Davis researchers have discovered that the Borrelia burgdorferi bacterium that causes Lyme disease hinders the immunity system from fighting the pathogen which may explain why some patients remain vulnerable to repeated infections.

The bacteria initially trigger a strong immune response in an infected animal, but findings from this study indicate that the bacteria soon cause structural abnormalities in “germinal centers” — sites in lymph nodes and other lymph tissues that are key to producing a long-term protective immune response.

For months after infection, those germinal centers fail to produce the specific cells — memory B cells and antibody-producing plasma cells — that are crucial for producing lasting immunity.

In effect, the bacteria prevent the animal’s adaptive immune system from forming a “memory” of the invading bacteria and launching a protective immune response against future infections.

The Borrelia burgdorferi bacteria are transmitted to humans and animals through bites from infected ticks.

Symptoms of the disease include fever, headache, fatigue and a characteristic skin rash. If left untreated, the infection can spread to the joints, heart and nervous system. About 300,000 cases of Lyme disease are diagnosed annually in the United States, and cases have grown the last few decades.

Read more about the study

Scientists pinpoint when harmless bacteria became flesh-eating monsters

Bacterial diseases cause millions of deaths every year. Most of these bacteria were benign at some point in their evolutionary past, and we don’t always understand what turned them into disease-causing pathogens. In a new study, researchers have tracked down when this switch happened in a flesh-eating bacteria. They think the knowledge might help predict future epidemics.

The flesh-eating culprit in question is called GAS, or Group A β-hemolytic streptococcus, a highly infective bacteria. Apart from causing flesh-eating disease, GAS is also responsible for a range of less harmful infections. It affects more than 600m people every year, and causes an estimated 500,000 deaths.

These bacteria appeared to have affected humans since the 1980s. Scientists think that GAS must have evolved from a less harmful streptococcus strain. The new study, published in the Proceedings of the National Academy of Sciences, reconstructs that evolutionary history.

James Musser of the Methodist Hospital Research Institute and lead researcher of the study said, “This is the first time we have been able to pull back the curtain to reveal the mysterious processes that gives rise to a virulent pathogen.”

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