Information

Do bacteria die of old age?


I know that the cells of mammals at least stop dividing when they are old, and then die a programmed cell death. Then other cells have to replace them.

But in a bacterial colony, each cell replicates for itself. Obviously, if a division of a bacterial cell of generation N were to produce two new cells of generation N+1, and all bacteria died of old age at generation M, there would be no bacteria left around.

So how is it regulated in bacteria? Are their divisions simply unlimited? Does a cell never die and just divide forever?


This is a interesting question and for a long time it was thought that they do not age. In the meantime there are some new papers which say that bacteria do indeed age.

Aging can be defined as the accumulation of non-genetic damages (for example oxidative damage to proteins) over time. If too much of these damages are accumulated, the cell will eventually die.

For bacteria there seems to be an interesting way around this. The second paper cited below found that bacteria do not divide symmetrically into two daughter cells, but seem to split into one cell which receives more damage and one which receives less. The latter one can be called rejuvenated and seems to make sure that the bacteria can seemingly divide forever. Using this strategy limits the non-genetic damage to relatively few cells (if you consider the doubling mechanism) which could eventually die to save the others.

Have a look at the following publications which go into detail (the first is a summary of the second but worth reading):

  1. Do bacteria age? Biologists discover the answer follows simple
    economics
  2. Temporal Dynamics of Bacterial Aging and Rejuvenation
  3. Aging and death in an organism that reproduces by morphologically symmetric division.

Bacteria: Fossil Record

It may seem surprising that bacteria can leave fossils at all. However, one particular group of bacteria, the cyanobacteria or "blue-green algae," have left a fossil record that extends far back into the Precambrian - the oldest cyanobacteria-like fossils known are nearly 3.5 billion years old, among the oldest fossils currently known. Cyanobacteria are larger than most bacteria, and may secrete a thick cell wall. More importantly, cyanobacteria may form large layered structures, called stromatolites (if more or less dome-shaped) or oncolites (if round). These structures form as a mat of cyanobacteria grows in an aquatic environment, trapping sediment and sometimes secreting calcium carbonate. When sectioned very thinly, fossil stromatolites may be found to contain exquisitely preserved fossil cyanobacteria and algae.

The picture above is a short chain of cyanobacterial cells, from the Bitter Springs Chert of northern Australia (about 1 billion years old). Very similar cyanobacteria are alive today in fact, most fossil cyanobacteria can almost be referred to living genera. Compare this fossil cyanobacterium with this picture of the living cyanobacterium Oscillatoria:

The group shows what is probably the most extreme conservatism of morphology of any organisms.

Aside from cyanobacteria, identifiable fossil bacteria are not particularly widespread. However, under certain chemical conditions, bacterial cells can be replaced with minerals, notably pyrite or siderite (iron carbonate), forming replicas of the once-living cells, or pseudomorphs. Some bacteria secrete iron-coated sheaths that sometimes fossilize. Others may bore into shells or rocks and form microscopic canals within the shell such bacteria are referred to as endolithic, and their borings can be recognized all through the Phanerozoic. Bacteria have also been found in amber -- fossilized tree resin -- and in mummified tissues. It is also sometimes possible to infer the presence of disease-causing bacteria from fossil bones that show signs of having been infected when the animal was alive. Perhaps most amazing are the fossils left by magnetobacteria -- a group of bacteria which form tiny, nanometer-sized crystals of magnetite (iron oxide) inside their cells. Magnetite crystals identifiable as bacterial products have been found in rocks as old as two billion years -- at a size of a few hundred millionths of a meter, these hold the record for the smallest fossils.

NEWS FLASH!One of the hottest science news stories of the decade is the discovery of possible remains of bacteria-like organisms on a meteorite from Mars. But are they really fossils? How would we be able to find out whether or not they are real? And what could they tell us about the history of Mars -- and of life on our own planet? Paleontologists are working together with space scientists to try and answer some basic questions about the possible "Martian bacteria." There will eventually be an exhibit on this server dealing with the "Martian microbes." Until it's ready, you can view photographs and news articles about the find, or learn more about Mars meteorites courtesy of the NASA Jet Propulsion Laboratory. --> Read a UCMP Research Report: "Bacteria and protozoa from middle Cretaceous amber of Ellsworth County, Kansas." Find out more about fossilized filamentous bacteria and other microbes, found in Cretaceous amber -- a unique mode of preservation. This report was originally published in PaleoBios 17(1): 20-26. Dr. Raul Cano, at California Polytechnic State University at San Luis Obispo, has succeeded in isolating and reviving bacteria taken from inside fossilized insects trapped in amber. Read all about it!

Bitter Springs chert fossil image provided by J. William Schopf. The image of Oscillatoria was provided by Alejandro Lopez-Cortes (CIBNOR, Mexico), Mark Schneegurt (Wichita State University), and Cyanosite.


Scientists expose fascinating 'compartments' in bacteria

Credit: CC0 Public Domain

Bacteria—tiny and in some cases deadly single-celled organisms—are far more complex than commonly thought.

A review paper by Monash Biomedicine Discovery Institute (BDI), published in the high-impact journal Nature Reviews Microbiology, casts light on organelles, the internal compartments in bacterial cells that house and support functions essential for their survival and growth.

The BDI's Professor Trevor Lithgow and Associate Professor Chris Greening, experts in bacterial cell biology and physiology, were invited to review the available scientific literature worldwide to consolidate the latest knowledge of organelles.

"There was an age-old truism until recently that bacteria were simply a bag of enzymes, the simplest type of cells," Professor Lithgow said. "New developments in nanoscale imaging have shown that internal compartments—organelles—make them very complex."

Cryoelectron microscopy and super-resolution microscopy have allowed scientists to fathom the workings of bacterial organelles, which typically have a diameter 10,000 times smaller than a pinhead. The BDI has been at the forefront in Australia in adopting and developing the use of these technologies, Professor Lithgow said.

"It's been a rewarding experience doing this scholarly review and being able to showcase the broad swathe of work that demonstrates the complexity of bacterial cells," he said.

Organelles enable bacteria to do extraordinary things. They help bacteria photosynthesise in dimly lit environments, break down toxic compounds like rocket fuel or even orientate themselves relative to the Earth's magnetic field by lining up magnetic iron particles. Some bacteria use gas collected within organelles to control buoyancy to let them rise or go deeper in water, allowing optimal access to light and nutrients for growth and division.

Exploring and understanding the intricacies of bacterial cells is not only important for scientific knowledge, but also for biotechnological applications and for addressing global issues of human health.

"Organelles enable many bacteria to perform functions useful for us, from supporting basic ecosystem function to enabling all sorts of biotechnological advances. But a few pathogens use organelles to cause disease," Associate Professor Greening said. "The deadly pathogen that causes tuberculosis, for example, scavenges fatty molecules from our own bodies and stores them as energy reserves in organelles, helping the pathogen to persist for years in our lungs, compromising treatment and making the emergence of drug resistance likely."

Countering drug-resistant infections are key 21st century problems for humans, Professor Lithgow said. "In these times of COVID-19 the death tolls we're seeing for viral infections are terrible, but the projection is that by 2050 at least 22,000 Australians (and 10 million people worldwide) will die every year due to infections caused by drug-resistant bacteria," he said.


Results

Cells were grown from one cell into a monolayer microcolony that contained up to 500 cells, and time-lapse images (see Video S1 for an example film) were analyzed with custom automated software designed for this purpose. We followed 94 such colonies, resulting in the complete record from division to division, of 35,049 cells. As the history and physical parameters of each cell in the microcolony are known, and the identity of each pole is tracked, the complete lineage can be determined. The resulting lineages from each film were averaged by each unique cell position within the lineage. This can be represented as a single, bifurcating tree, where each branch point is an average cell for that position in the lineage, and the length of the lines connecting cells to their progeny are proportional to the growth rate of the cell (Figure 2). At each division in the tree, the cell inheriting the old pole of the progenitor cell is represented on the right branch of the sibling pair (in red), while the cell inheriting the new pole is on the left branch (in blue).

The first division in the microcolonies is not represented, as the identity of the poles is not known until after one division (hence each initial cell gives rise to two lineages that are tracked separately, and subsequently combined from all films to create the single average lineage shown here). The lengths of the lines connecting cells to their progeny are proportional to the average growth rate of that cell a longer line represents a higher growth rate for that cell. At each division, the cell inheriting the old pole is placed on the right side of the division pair, and shown in red, while new poles are placed on the left side of each pair, and shown in blue (note that this choice of orientation is not the same as that of Figure 1, to compare more easily old and new pole lineages). Because the position of the start of the growth line for each new generation is dependent on the generations that preceded it, the difference in growth rates is cumulative. Green lines indicate the point at which the first cell divides in the last four generations. Nine generations from 94 films encompassing 35,049 cells are included in this tree. The average growth rate of all the cells corresponds to a doubling time of 28.2+/−0.1 min. The data used to generate the average lineage are provided in Dataset S1.

The pattern of fast and slow growth rates in this average lineage gives striking evidence for reproductive asymmetry between the progeny cells, as the cells that show a cumulatively slowed rate of growth (shorter lines) are those cells that have more often inherited an old pole during their ancestry. To verify that this pattern in the average lineage is actually due to a difference in growth rate between new and old pole cells, we performed a pairwise comparison of every set of sister cells that was produced at the eighth generation in each of the films. As sister cells share temporal and spatial surroundings, this comparison controls for potential environmental variation within the microcolony. The comparison (two-tailed t-test) includes cells of all division ages and shows that the average growth rate of the old pole progeny cell is 2.2% (+/−0.1%) slower than that of the new pole cell. This analysis, performed on 7,953 cell pairs, conclusively demonstrates (p < 0.00001, t = 14.40, df = 7952) that the cell that inherits the old pole grows slower than the new pole cell produced in the same division. Two factors from this same dataset demonstrate the lack of a juvenile phase in E. coli. First, comparison of the progeny cells shows that the new pole cell is slightly larger on average (0.9+/−0.1% p < 0.00001, t = 5.62, df = 7952) than the old pole cell (the contrary would be expected in the presence of a juvenile phase). Second, the young pole cell is marginally more likely to divide sooner than the old pole cell (in about 15% of the cases cells divide within the same 2-min time point of those where the two cells divide in different time points, 54% of the time the new pole cell divides first [significant p < 0.00001, t = 5.02, df = 4812]), which is also not consistent with a phase where the young cell must grow or differentiate before reproduction. These differences are consistent for all generations during steady-state growth (data not shown). Therefore, while a juvenile phase is absent, there is a consistent functional asymmetry between the two progeny cells that is disadvantageous to the old pole.

Each cell is defined not just by its preceding division, however, but also by all previously recorded divisions, back to the initial cell in the analysis. Therefore, each old pole cell can be categorized by the number of consecutive, final old pole divisions that occurred to produce the current cell (thus giving the age in divisions of its old pole). Equivalently, each new pole cell can be assigned a number of divisions that it sequentially divided as the new pole cell. Comparing these values with the growth rates of the cells, we find that the older the old pole of a cell is, the slower the growth rate of that cell, while cells with more consecutive new pole divisions exhibit increasing growth rates (Figure 3A). Furthermore, a pairwise comparison shows that the difference in the growth rate between the old pole sibling (the mother cell) and the new pole sibling (daughter cell) increases with the increasing age of the mother (Figure 3B). Therefore, the difference between pairs of progeny cells, as well as the pattern seen in the average lineage, is not only due to a decrease in growth rate of cells that have inherited the old pole, but also to an increase in the growth rate (for at least three divisions subsequent divisions do not detectably improve) of cells that have repeatedly inherited the new pole.

(A) The cellular growth rate, represented on the y-axis, is normalized to the growth rate of all cells from the same generation and geography in each film. On the x-axis consecutive divisions are seen as either a new pole (open circles), showing rejuvenation, or an old pole (closed circles), showing aging. Cells represented at each point: new pole divisions 1–7: 7,730 3,911 1,956 984 465 211 89 old pole divisions 1–7: 4,687 3,833 1,933 956 465 213 75.

(B) Pair comparison of the growth rates of sibling cells. The division age of the old pole sibling (the mother cell) is shown on the x-axis. The percentage difference between the growth rate of the new pole sibling (the daughter cell) and this cell is shown on the y-axis. A positive difference corresponds to a faster growth rate for the new pole cell. Cell pairs represented at each point, ages 1–7: 9,722 4,824 2,409 1,202 601 282 127.

In both graphs, cells are from all 94 films. The error bars represent the standard error of the mean. The old and new pole growth rates in (A) and the pair differences in (B) are fitted to a line to show the trend however, the actual progressions may not be linear (R 2 old poles = 0.97, new poles = 0.83, pair difference = 0.94).

To determine the longer-term effect of inheriting the old pole, we performed a second pairwise analysis, comparing the total length of offspring produced by sister cells from the fifth generation until the end of tracking (this generation was chosen as each cell has the opportunity to progress through about three divisions). As the bacteria are rod shaped, the total length of cells produced is proportional to the biomass of the offspring. The results show that old pole cells produce less offspring biomass compared to their new pole sisters (3.1+/−0.3% less, p < 0.00001, t = 9.29, df = 1565). Therefore, it appears that the slower growth rate of the old pole cells also results in a longer-term decreased ability to produce offspring biomass. Another long-term effect of aging is the probability of survival of the organism over time. During the growth of the microcolonies, sixteen cells were observed to cease growing these cells never resumed growth during the course of the experiment. We have defined these cells as potentially dead cells and have analyzed their locations in the lineages. While these apparent deaths may ultimately be due to stochastic events, they show a statistically significant bias (p = 0.01 see Materials and Methods) toward increased divisions spent as an old pole (over the total observation history). This observation is consistent with the hypothesis that aged cells are more susceptible to harmful events and/or less likely to survive them. It is unlikely that these cells represent a growth arrested “persister” state, as it has recently been demonstrated that persister cells that arise during exponential growth occur at a frequency of approximately 1.2 × 10 −6 [14] the appearance of apparently dead cells in our study (about 4.6 × 10 −4 ) is almost 400 times more frequent.


In Bacteria, Some Daughters Are Born Old

(Inside Science) -- When bacteria reproduce, they divide into two equal daughters. At least, that's the traditional view. For decades, differences between the two daughter cells were put down to random chance.

In fact, research over the past 15 years has revealed that each division of an Escherichia coli bacterium produces one "old daughter" who gets most of the age-related damage, and one "new daughter" who gets a relatively fresh start. Camilla Rang, an evolutionary microbiologist at the University of California, San Diego, views the old daughter as the remnant of the mother cell -- a being that is in one sense sacrificing herself for her youthful offspring.

"It's not just noise," said Rang. "It's a rule -- more to say, like, 'I'm going to keep this to give you a better life.'"

Of course, Rang isn't saying that bacteria make conscious decisions or experience maternal emotions. But the differences between the daughters appear to be systematic, and they may result in more progeny for the mother in the long run. Rang and her colleagues have been studying this process for years, and their new paper in the journal Proceedings of the Royal Society B reveals new details of how it works.

New cells, same old parts

E. coli are shaped like rods with rounded ends called poles. When they divide, each daughter gets one old pole that used to be on the end of the mother cell, and one new pole that forms where the mother cell splits down the middle.

Now imagine one of those daughters dividing. You can think of the original mother as the grandmother. Both of the "granddaughters" will have an old and a new pole. But in one case, the old pole formed from her grandmother's middle. She's called the "new daughter." The other one's old pole will be at least a generation older, since it was her grandmother's pole as well. She's called the "old daughter."

Diagram showing how old poles from the outside of a mother cell are passed down through generations.

Credits: Abigail Malate, staff illustrator. Based on a diagram in "Allocation of gene products to daughter cells is determined by the age of the mother in single Escherichia coli cells," published in Proceedings of the Royal Society B.

Rights: This image may only be reproduced with this Inside Science article.

Over time, some of a cell's proteins are damaged by oxidative stress. As a result, they fold into the wrong shapes and stick together in clumps. These damaged proteins tend to be more concentrated in the cell's old pole. Past research has shown that old daughters receive about 63% of the mother cell's damaged proteins.

If you trace the original oldest pole down through the generations, each cell that receives it tends to grow more slowly than the one that had it before. You can think of the old pole as belonging to a single old cell that gives birth to new daughter after new daughter. No one has yet proven that damaged proteins cause the slow growth rates, but the two tend to go together, noted Ariel Lindner, a systems and synthetic biologist at INSERM, the French National Institute of Medical Research, and the Center of Research Interdisciplinary at the University of Paris. Lindner was not involved in the new study, but his team conducted much of the early work in the field.

If the old mother cell is raised in a bacteria's paradise with lots of food and no toxins, she reaches an equilibrium after several generations, and she no longer grows more slowly each time she divides. But eventually, the old cell will die. In groups of such old cells, the death rates continue to increase over time, suggesting that aging damage continues to snowball down the family tree.

Fresh proteins for new daughters

To better understand why the new daughters grow faster, the researchers engineered E. coli cells to produce a protein that shines fluorescent green when exposed to light. New daughters shone brighter than old daughters, indicating either that they were producing more of the fluorescent proteins, or that they received more from their mothers. Proteins are the major building blocks of cells, so the findings suggest that new daughters are richer in materials needed for growth.

Furthermore, pairs of daughters formed from new mothers were more similar to each other in brightness than pairs of daughters formed from old mothers. That's probably because the old mothers had more damage to start with, so more of it got shunted to their old daughters, said Rang.

Both Rang's and Lindner's teams had seen this pattern years earlier, but they couldn't demonstrate it conclusively until Rang's graduate student Chao Shi developed a way to track the output of fluorescent light from individual cells.

Why do mother E. coli cells give one daughter more advantages than the other? According to Lindner, it might be a side effect of the size and structure of the bacteria. Damaged proteins naturally clump together into large balls that can't easily diffuse through the tight confines an E. coli cell, so they tend to build up in the old pole. In larger cells such as yeast, you would need an active transport mechanism to move the damaged proteins. "In E. coli, it turns out that you do not need such a system. Physics gives it to you for free," said Lindner.

Still, if such asymmetry were harmful to the cells, they likely would have evolved a way to change it, said Lindner. Mathematical models have suggested that dividing the damage unequally could increase the colony's total growth.

To explain why, Rang uses a banking analogy. Imagine investing $1,000 at an interest rate of 8%, or $500 at 6% and $500 at 10%. Splitting the investment into two accounts with different interest rates leaves you richer as the interest compounds over time -- just as splitting the advantages of youth unevenly between two daughters eventually yields more progeny.

Once, scientists believed E. coli were immune to aging, reborn fresh at each cell division, said Rang. Now, they know that's not true. The new study helps show how mother bacteria carry the burden of age across generations -- findings that hint at the universal toll of time.

"If you think of bacteria almost like our first living organism on Earth," said Rang, "they do age. Which means that aging is [probably] as old as life itself."


Do Lobsters Die?

Most living organisms grow old and eventually die. However, there are a few plant and animal species that appear not to feel the pressure of time, and not exhibit the signs of aging that much. These organisms are the so-called “biologically immortal” organisms.

However, quite contrary as it might seem, these organisms have actually finite lifespan. A lot of factors like natural catastrophes, disease, or predation can kill them. But unlike other organisms, they do not die simply because of senility.

To grow, lobsters undergo a process called molting where they shed their exoskeleton from time to time. In general, a larger body means an older lobster. The video below depicts the life cycle of lobsters.

Scientific studies showed that in the wild, an average male lobster could live up to 31 years while a female one can survive up to 54 years. However, some tough species like the American lobster (Homarus americanus) can live up to 140 years!

  • The age of these lobsters was approximated through the measurement of the amounts of neuro lipofuscin, a pigment that is gradually deposited in the lobsters’ brain.
  • Scientists also are looking at the possibility of approximating the age of these lobsters via their exoskeleton growth band deposits.


Lecture 32: Infectious Disease, Viruses, and Bacteria

This lecture covers microorganisms and some of the threats they pose to human health, such as infectious diseases. Professor Imperiali also discusses antibiotics and the mechanisms by which bacteria become resistant.

Instructor: Barbara Imperiali

Lecture 1: Welcome Introdu.

Lecture 2: Chemical Bonding.

Lecture 3: Structures of Am.

Lecture 4: Enzymes and Meta.

Lecture 5: Carbohydrates an.

Lecture 9: Chromatin Remode.

Lecture 11:Cells, The Simpl.

Lecture 16: Recombinant DNA.

Lecture 17: Genomes and DNA.

Lecture 18: SNPs and Human .

Lecture 19: Cell Traffickin.

Lecture 20: Cell Signaling .

Lecture 21: Cell Signaling .

Lecture 22: Neurons, Action.

Lecture 23: Cell Cycle and .

Lecture 24: Stem Cells, Apo.

Lecture 27: Visualizing Lif.

Lecture 28: Visualizing Lif.

Lecture 29: Cell Imaging Te.

Lecture 32: Infectious Dise.

Lecture 33: Bacteria and An.

Lecture 34: Viruses and Ant.

Lecture 35: Reproductive Cl.

PROFESSOR: OK. Let's get going here. So this week I'll be talking about bacteria and viruses. And these are really significant topics, because I think it's something that we often don't think about the magnitude of the problems and what kind of crises we're approaching with respect to the therapeutic treatment of infectious disease.

So what I want to try and get home to you this week is the variety of different microorganisms that threaten our health, and just talk to you about the sorts of issues that are really prominent in the news concerning resistance to therapeutic agents. But in order to do that, we've got to meet some bacteria, meet some viruses, and understand that some of their lifestyles, their mechanisms, so that we can understand what kinds of agents are used and developed to try to mitigate these diseases, because it's only through a molecular mechanistic understanding of the life cycles of viruses and bacteria that we can understand how many of these therapeutic agents work and what may be happening in resistance development.

Now I find this particular slide a little daunting, but I want to point out to you that it concerns the world's deadliest animals. So we worry a lot about tigers, and sharks, and things like that, nasty poisonous snakes, bites from dogs with rabies, and so on. I'm going to leave this black bar here, sort of unmentioned. I don't know what year this is, but if we talk about daunting, that's pretty serious. And then the biggest killer on this screen is the mosquito. But it isn't actually the mosquito, it's the protozoal microorganisms that the mosquito carries from one person to another that really make that such a serious consideration.

But what's not here are all the bacteria and viruses that actually are far more serious. And the numbers on the next stage will show you just quite how shocking these numbers are. If you're interested in infectious disease as a field, because I think anyone going towards MD, MD/PhD infectious diseases, it really is a critical area that we have to get to grips with. There are not enough vaccines in the world. There is not enough treatment with a very microbe specific anti-infective agents.

So I encourage you to look at the CDC. There's a few other places where there's loads of information collated, such as the NIAID, which is the NIH Center for Infectious Disease, and the World Health Organization. So there's lots of places where you can find stuff out.

So what we're going to be talking about in the next three classes are our smallest enemies, things like bacteria, fungal infections from things like yeast or Aspergillus, which would cause candida and aspergillosis. Protozoal disease we won't mention, but those are the types of diseases that are carried by things like ticks, mosquitoes, tsetse flies. We think of those as the infectious agent, but it's really what those organisms carry and cause the spread of disease that's important there. And we won't either talk about prion diseases, which are the diseases that don't involve an infectious microorganism, but are believed to be spread from protein to protein through the nucleation of new prions from existing prions.

What we'll focus on in the first class is bacteria and in the other two on viruses, with an eye to looking at antibiotics and antiviral agents, how they work, where they go wrong. And this is where the numbers get fairly shocking. So for example, bacterial infections of the lower respiratory tract, that's deep in the lungs, cause 4 million deaths a year. Think back to the numbers you just saw on that first slide. These are things like strep pneumoniae, Klebsiella pneumoniae. They're called pneumonias because they're infectious diseases of the lung, but the organisms that cause them are of the Streptomyces, and Klebsiella, and Staphylococcus aureus specifically.

But there are others that cause lung infections and lower respiratory disease. These are particularly troublesome in areas where the atmosphere is bad. In big cities where there's a lot of insult from emissions and such that make the lungs weaker, then these sorts of organisms can really take a hold more readily, so they are more serious. There are many, many microorganisms that cause pneumonias. And sometimes it's a real problem to track down the precise microorganism, which makes the issue of treatment really difficult, really challenging. So I'm going to talk in a minute about absolute identification of infectious agents, so we can do better jobs of specifically targeting the causative agents.

Diarrheal disease-- 2 million deaths. These are organisms like Campylobacter jejuni and Salmonella enterica. We tend to have these crises, because romaine my is contaminated with infection. There are very few deaths in the developed world. We get down to that very quickly, say stop eating Romaine lettuce until we figure out what's going on here-- very, very few.

But once again, in the developing world, these can run rampant. And they can grab small children and older people who are already compromised, already a little bit not quite with strong immune systems, and people generally die of dehydration, because these diseases really hit the GI tract. It causes leaking us in the GI tract and really, really serious diarrheal disease. So those are the bad boys there. But once again, there are many others.

Tuberculosis is yet another really serious infectious disease caused by Mycobacterium tuberculosis, that's the main one of the mycobacteria that is a threat. It used to be called consumption in the old days, because people almost looked consumed by the disease. They would just get thinner and thinner. Literally it was a wasting disease. People would be sent up into the mountains of Switzerland to try to recover from consumption, to where the air is clearer and cleaner, and maybe hope that they can recuperate.

But TB-- look at these numbers. In 2015 there were almost 10 million new cases. There are about 1.2 million deaths from TB. A serious situation with TB is that it's often found co-infecting with the HIV virus, where you just can't fight the TB. So eventually, if you're infected with the HIV virus, it's the TB that gets you due to the weakening caused by the infection with TB.

So these numbers are shocking in light of the numbers I showed you on the previous slide, right. Look at these numbers if you go to snakes and things like that. They're meaningless numbers compared to infectious diseases.

So now, and I'm going to talk to you about the origins of this, many, many infectious agents that we thought we had conquered-- we thought we could take care of it. You just take this course of antibiotics and you're off, you're set. But now, because of the rapid mutation rates in bacteria and viruses, certain pathogens have completely worked out mechanisms to escape therapeutic agent. And I'm going to talk to you about those mechanisms towards the end of this class.

So basically you can dose a person one day with a normal dose of an antibiotic agent, and then 10 months later that normal dose or 10 times or 100 times that dose stops working. Why is that? It's due to resistance acquisition due to rapid cell division and mistakes made on replication and transcription, that then may one in a million times confer an advantage on the microorganism. All of a sudden the drugs don't work anymore.

The WHO and various community notice boards call this set of infectious agents the escape pathogens. It helps us remember which ones these are, because these are pathogens that escape treatment, because they've developed resistance to multiple drug cocktails. So commonly, when someone has a particular disease they don't take one drug, they take two or three to hit lots of pathways at once in the hope that resistance won't develop fast. But the escape pathogens have collectively acquired resistance to several antibiotics, meaning there's no good treatment. So the letters of escape stand for Enterococcus faecium, Staph aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and some of the Enterobacter species.

Some of these infectious agents are what result from-- I always say this wrong-- nosocomial infections. Does anyone know what those are? These are infections that people get in hospitals. So Tom Brady had a knee operation. He got an infection in his knee that came from the surgery, right. These are hospital acquired infections, because you can't sometimes clear an area enough, and there's infectious agents around.

So Acinetobacter baumannii was dubbed the Iraqi Bug for many, many years, because the vets coming back from Iraq were going to military hospitals, and these were abundant with cases of Acinetobacter baumannii. So that moved on to the escape pathogen list. So these are things to watch out for.

It's the reason that nosocomial infections-- I hope I'm saying it right, otherwise you're going to go off and Google it and realize I said it wrong. It's the reason why old school physicians wore bow ties and not ties. Can you imagine why? So if you're wearing a tie, which I seldom wear to be honest, and you're working over a patient, the tie can be the thing that carries the infection, because it gets closer to infected areas. This is old school stuff. And so originally the physicians wore bow ties in order to distinguish themselves as important people, but not to wear ties that might carry infectious agents. That's sort of a scary thing.

So with all this said, let me just lead you in to talk about bacteria antibiotics and resistance development. So we often name bacteria somewhat by their shape. So the long rod shaped ones are cocci. The round ones are cocci. The rod ones, whatever they are, come on one of you. And then what did the rod shape ones? Bacilli. I had a blank moment. So the rod shaped ones are bacilli. And then there's some others that have a different morphology like Campylobacter jejuni that have kind of a corkscrew shape. And that's thought to be important in their motility, digging through the mucous layers in the epithelial layers. So here I show you several shapes of bacteria.

And I'm just going to, once again, reinforce what diseases some are associated with and some other diseases that you might be surprised by. So yes, we know about salmonella and the E. coli and food poisoning. But Helicobacter pylori, which is one of these flagellated bacteria, can infect the stomach. It's often the cause of ulcers. So it's a causative agent of stomach ulcers, but that has in turn led to a considerable risk factor in stomach cancer. So what we thought was just an infection causes a constellation of other problems, including cancers. And more and more microbial agents are now associated with cancers, in particular the viruses.

Neisseria, these come along with the sexually transmitted diseases such as gonorrhea. Neisseria meningitidis is the one that causes meningitis. It is a very, very often fatal infection of the meninges. Staph aureus lots of infections around the body, just gruesome things like cellulitis, wound infections, toxic shock. Streptococcal bacteria, I've already mentioned-- the pneumonias, and then Campylobacter.

And now another complicated factor of infection-- so I talked to you about stomach ulcers and stomach cancer. Another thing that seems to be coming along with infections is autoimmunity. So in the last section of the class you heard about immunity and you also heard about tolerance, that we don't react to things that are ourselves, otherwise we'd be in deep trouble. Autoimmunity can suddenly pop up from certain bacterial infections, because bacteria tend to cloak themselves with unusual sugar polymers and other kinds of structures that the body doesn't really know what to do with.

And in some cases they kind of mimic things that are in the human body. So they they are mimetics of normal structures in the human body. And the body just doesn't notice them at all. And then there are incidences where certain bacterial infections later on cause autoimmune disease. So a bacteria may come along. It may have something that looks kind of like something human, but not quite. The human body responds, develops antibodies, and then they cross talk back to aspects of our physiology.

So Campylobacter jejuni is often a contaminant in poultry. It's a severe GI infection. But later on people get diseases such as Guillain-Barre, which is a neuropathy where the ends of your limbs become numb and non-functional. So there was a famous football player, the one they called "The Refrigerator," who had a serious case of Guillain-Barre resulting from very much an infectious disease, which converted into autoimmunity.

So let's now look at antibiotic targets. And to look at antibiotic targets, I think the first clear place to look is at the bacterial cell wall. Now when we first started talking about prokaryotes, things that include bacteria, we talked about the fact that these single celled organisms have to have a robust cell wall to prevent osmotic shock. They have to have some kind of thing to keep them from taking up too much water and basically exploding because of osmosis. Water floods in to balance the salt concentrations. So they have a complex cell wall, which is made of a macro molecule called peptidoglycan And it's usually one word, but I want to just underline peptidoglycan because it's a fascinating polymer that's made up of peptides and linear carbohydrate polymers.

So if you look at this typical bacterium, this is just a cartoon of the peptidoglycan. So it's a cross-linked polymer, we in one direction it has repeating carbohydrate units. I'm not drawing those complex hexose structures there. I'm just drawing it in cartoon form.

And those are carbohydrates known as NAG and NAN. NAG is N-Acetyl Glucosamine. It's a hexose sugar. NAN is N-AcetylMuramic acid. It's another modified sugar.

And on the one of those sugars, there is a reactive site that allows you to basically cross-link these polymers into a mesh work. So it's a feat of engineering to build this amazing polymer. It starts being built on the inside, on the cytoplasm. And then the components get flipped onto the other side of the cytoplasm of bacteria. Then they get polymerized in place to make this complex mesh work of a polymer that creates the rigidity of the bacterial cell wall.

It's generically known as a peptidoglycan. Different bacteria have different peptidoglycans. There are several modifications that might be specific to particular bacterial sera But this is the generic structure, where you have a polymer that's built of sugars. You can recognize the sugar structure there going in one direction and the peptide component that cross-links across in order to make this mesh.

And bacterial wall have different amounts of this, but it'll build up to a really strong, rigid mesh work that's permeable to things, small molecules and water. There is holes, and so on. But it creates a mechanical rigidity so that osmotic shock doesn't occur on the bacteria. Any questions about that? Does that makes sense? So that, in a sense, it's their exoskeleton, if you want to think about it like that.

So the properties are rigid. Without it, the bacteria would suffer osmotic shock. And it's plenty permeable to allow 2-nanometer type pores in order for nutrients and water to go into the structure.

- --have E. coli growing here. And it's living. You can see it start to grow. Here we add penicillin. We're going to see these bacteria--

PROFESSOR: These are bacteria, rod-shaped bacteria.

- There wasn't any microphone on this, so--

PROFESSOR: And I'm going to ask you to just keep watching this kind of carefully.

- There goes another one, boop, boop.

- Poking holes in the cell wall, boom, bacteria is dead.

PROFESSOR: Look at some of the bacteria disappearing. All right, I guess

So we're going to leave it.

Let's go back one. OK, now what was that? OK, so I've told you bacteria would suffer osmotic shock without peptidoglycan. Those are bacteria that you see popping, as the person who was talking said, because the peptidoglycan cannot be made. There is an antibiotic that's added. It is penicillin that's added to the bacteria.

And it stops-- as bacteria grow, they have to make a bunch more peptidoglycan, because if you're doubling, you've got to make twice as much peptido-- you've got to double the amount of peptidoglycan. If you have something that inhibits the peptidoglycan being made, you have a bacterium that's trying to stretch out what it has, it's not resistant to osmotic shock. And what you saw was the bacteria basically undergoing cell death via osmotic shock, pretty graphic, pretty visual.

So penicillin was one of the first antibiotics that was described for the treatment of bacterial infections. And we'll go to the timeline of that in a moment. So when we talk about bacteria, the original definition of bacteria is in three different subtypes, gram-negative, gram-positive, and mycobacterial.

This is actually the first way that people would take a look at your cell-- at the bacterial cells and diagnose roughly what kind of bacteria they were. Did they fall-- which of these broad families did they fall into? Because it would help in defining how you would treat the infectious disease.

So I want to show you the difference between the cell wall of these various types of bacteria. And the truth is, if you have an infectious disease, your wish is, if you had to pick one of the three, that you have a gram-positive disease. And I'll explain why that is in a moment, because it's all to do with how drugs can get into the bacteria to inhibit vital functions in order that they die and they don't take over your system.

So let's look first at gram-positive bacteria. They're shown here. This is a section of a bacterium. Gram-positive have a single cell wall. And they also have a thick layer of peptidoglycan.

So they gain rigidity by basically having an extracellular thick layer of peptidoglycan coating them. There is a schematic of it here. So here would be the inner cell wall. And here would be the peptidoglycan, shown in orange and pale, buff-colored circles. So that would be where their peptidoglycan is.

And then there are some other glyco conjugates that actually stick out beyond that. But there is only one cytoplasmic membrane. That's the standard double bilayer.

And the peptidoglycan is quite thick, relatively, 20 to 80 nanometers across. So that's how wide it is. And you can, if you've got a-- if you've stain a bacterium under a microscope, you would see that, the thickness of that wall, but the absence of a double wall.

The gram-negative bacteria have a double wall. The inner membrane is pretty standard. It's just typical phospholipids. It looks like the inner cytoplasmic membrane of the gram-positive bacteria. And then it has an outer wall.

So the inner membrane is typical. And then the outer wall has one leaflet that looks kind of normal. And then it has a second leaflet that's sort of decorated, honestly, like a Christmas tree.

There is all kinds of things sticking out there that interact with hosts that they infect, and so on. And the space between the two walls is called the periplasmic space, because it's between. It's not the cytoplasm. It's what's called the periplasm.

Now, what's interesting about these, the gram-negative bacteria, is they have quite a bit less peptidoglycan, only about 7 to 8 nanometers. So that's pretty interesting. But they sort of gain robustness from that second wall structure that's coating on the outside.

Now, their challenge with gram-negative bacteria relative to gram-positive bacteria is any drugs you develop have to make a pretty-- if they're targeted at intracellular sites, they have to get through two walls, not just one wall. So they are harder to treat. And they also have a lot of characteristics that make them more prone to resistance development.

So I want to point out to you, on this electron micrograph, you can actually see the double wall, the dark band of space and then another dark band, whereas here you see a thin single wall, but you see a lot of junk on the outside. Is everyone seeing the differences just to look at them?

OK, so what's this gram thing about? What does this stand for? It simply stands for a chemical dye that stains peptidoglycan. And it was invented or discovered by Professor Gram. That was his name. So when someone says you got a gram-positive infection, gram-negative infection, it's how those cells look when they've been treated with this stain.

Gram positives show up very positive to the stain because there is a lot of peptidoglycan on the outside that absorbs the dye and shows a strong color. The gram-negatives don't show very well with a Gram stain, because the peptidoglycan is tucked in the periplasm, not on the outside of the cell. So if someone does a quick check on a bacterial streak or an infection that you have, they might treat it with the Gram stain and say gram-positive or gram-negative just based on that simple color analysis. And so in one case, the peptidoglycan is abundant and accessible. In the other case, it's very, very much thinner and less accessible to the dyes.

Now, this probably looks like stone-age stuff to you, because how much can you learn by these simple colorimetric stains? We're certainly moving in very, very different directions. But let me just finish off with the third type of bacteria, the mycobacteria, which include Mycobacterium tuberculosis.

And they have a different kind of wall, again. And they're pretty unusual. And they are really, really hard to treat, because it's almost impossible to get therapeutic agents into mycobacteria.

I used to work on a team with Novartis in Singapore. And they said, doing anything with mycobacteria was like trying to do biochemistry on a wax candle, literally. You just can't work with it, because they have a thick additional wall that's kind of different again. Did you have a question? No. Sorry, I thought I saw your hand up.

So what they have is a typical cell wall then some peptidoglycan, but then they have this thick mycobacterial layer which comprises what are known as mycolic acids, which basically add this thick layer of greasy hydrophobic material on the outside of the mycobacteria that's pretty impenetrable. The cell wall is quite different. It doesn't have an outer coat. It's like gram-positives in that respect.

But it doesn't stain very strongly. So it has a weak, what's known as Gram stain. So sometimes if you've got something that gives a sort a so-so response to the Gram stain, you might say, oh, it looks like a mycobacterium because of what's happening.

Now, mycobacteria TB is a huge threat, because its treatment, its current treatment-- and it's the same treatment that's been around for, like, 30 years or something-- is a treatment with four different antibacterial agents that hit a bunch of different sites in the lifecycle of the bacteria. It includes these compounds shown here which are isoniazid, rifampicin, ethambutol, and pyrazinamide. And it's a six-month treatment with those medications, so handful, four different medications for six months.

So what they were realizing in the developing world is that there was terrible compliance. The drugs are cheap, but there was no compliance. People just were not taking the pills, because they're like, I'm tired of taking these pills every day for six months.

So what was developed was what's known as the DOTs program. Has anyone never heard of this? Is anyone interested in infectious disease? It was a situation where it was a social system set up in order to make sure people took these drugs every day for six months in order to comply.

So social workers would go to the villages in remote areas and watch people take the medications. So it's directly observed treatment to make sure they followed through, because if they had regular TB, not very resistant TB, you could overcome it, provided that you took these medications. But still, it's a hugely debilitating thing to have to deal with these treatments.

Now, there are two strains of TB. One is called MDR-TB. And the other ones called XMDR-TB You'll occasionally hear of these on TV programs. MDR is resistant to three of the four medications. And XMDR, which stands for extremely MultiDrug Resistant, is resistant to every single one of those medications. New medications, different mechanisms of action are sorely needed.

All right, this is just what things look like with the Gram stains. So here you see gram-positive Bacillus anthracis. That's the deep purple rods. You know that's a gram-positive because it's a deep purple stain.

The other cells in this picture are white cells. So you can really pick out the gram-positive. This is the structure of the chemical dye that stains peptidoglycan through absorbing into the peptidoglycan. It's a very sort of physical interaction of the dye with the polymer.

And over on this slide, it's a mixture of gram-positive and gram-negative. And you can pick up the gram-positive and differentiate them from the gram-negative, which just stains sort of kind of weakly pink. And then mycobacteria, which are formerly gram-positive, don't stain very well because of that thick mycolic acid hydrophobic wall.

So what would you do nowadays? Would you pull out a stain and drop it on bacteria and get some vague response? What's open to you now in the 21st century? You have a tiny sample of a bacterium. Grow it up. What would you do? You could tell exactly what it is.

PROFESSOR: Yeah, you'd PCR up the genomic DNA and then go match it, because the thing that we, in addition to the human genome, there are thousands of pathogenic bacteria sequences that are completely annotated, known. The [INAUDIBLE] has a massive compilation of these sequences. And you just go and you find out what the bacterium is based on the sequence.

So now rapid sequencing efforts-- maybe they're just a few number of key places in a genome that you would go towards and just do a really fast array and figure out what's there and within what bacterium it is, which gives you a much better clue as to how to treat it than the vague, ambiguous stains. So even though stains keep going, there is now other ways.

Unfortunately, not everyone has the instrumentation to do rapid sequencing. So nowadays, there is a lot, lot, lot of interest in faster dipstick sorts of tests that can distinguish between different bacterial strains by, for example, interrogating that coat of glyco-conjugates that's on the outside of the bacteria, dipstick paper tests that can give you an idea of what organism and what serotype so you can move forward and do a much more rational treatment of those organisms.

OK, let's see what's-- yes. All right, so where did the antibiotics first come from? Any questions so far? OK, so where did the first antibiotics come from? From a couple of accidental discoveries. Who has heard of the Fleming experiment? Who knows about that discovery of penicillin?

Yeah, so there was an original observation that predated that which sort of suggests that Pasteur was a pretty smart guy, because he contributed in a lot of different areas. He discovered that some bacteria tend to release substances that kill other bacteria. That was in the 1870s.

Then later on, there was another sort of spread of antibiotic agents. And it came with the discovery that we had things like arsenic derivatives actually showed some value in treating the organism that causes syphilis. So talk about the treatment being-- the cure being worse than the infection. People were being treated, seriously, with these arsenic derivatives in the hope of wiping out the infectious agent that caused syphilis. But you know, sometimes it was a mixed bag.

But where things started to get a lot more interesting was that in 1928, there was this sort of famous historic story of Fleming discovering that some bacteria seemed to be inhibited by a particular agent that came from a fungus. And this was the origin of penicillin. So he would have a Petri dish where he was growing bacteria. And he noticed that in some of his samples, there was inhibition of bacterial growth due to an exogenous agent that had somehow contaminated the plates.

So in that story, that was the substance that was named as penicillin. The mold from the-- mold is the fungus-- actually inhibited the growth of staphylococcus bacteria. And it was called penicillin. And then a lot more time went by.

But in the 1940s, the active ingredient was discovered. So 1940s is sort of slap bang about, I would say, a couple of years into the Second World War. And they were able to mobilize the production of this agent.

Towards the later end of the war, people had penicillin available to them. And it's basically pretty well believed that, if it wasn't for the antibiotic agents that emerged-- you know, the war ended in 1945. If it wasn't for those agents that emerged, there would have been way way, way more deaths from the war. As it was, there were way too many.

So penicillin was the first antibiotic that was discovered with a discreet mechanism of action. And it was discovered at a very, very important time. So that was all great news. Penicillin was produced widely. Some of you may be allergic to penicillin. There are other options nowadays. But it's the cheapest and most viable of the first-line antibiotics.

Here we go. And this thing, this pointer has a mind of its own. It sort of changed its mind.

But the problem was the bacterial species started to survive treatment due to development of resistance. And all of a sudden, something that worked really well wasn't working anymore. So let's try and think about peptidoglycan, what penicillin looks like and what it does, and how penicillin resistance emerges. Those are the three things I'm going to cover here.

OK, so what does penicillin do? Penicillin stops the formation of this big macromolecular peptidoglycan polymer by stopping the last cross-link, stopping the chemistry that happens to join the peptide chains to make a cross-linked polymer. And anyone who is in the mechanical engineering area will know that polymers that are just strands are much weaker than polymers that are crossed-linked structures which have tensile strength in both directions.

So the uncross-linked peptidoglycan was weak. And what penicillin specifically did was inhibit forming that cross-link. What does penicillin look like? Here it is. It's a cool structure. It's what's known as a natural product, five ring, four ring, an interesting structure. And what it would do is it would interact with the enzyme the cross-linked the peptidoglycan and basically stop it dead in its tracks.

What did the bacteria do? The key part of this structure is this four-membered ring within amide bond in it. The bacteria evolved an enzyme to chop it open basically making it completely inactive. So beta lactamase was evolved in the bacterial populations.

It was probably derived from some other enzyme that did some useful function, but not targeted to the penicillins. But the bacteria started to survive because they made a ton of an enzyme called beta lactamase. And then it completely stopped working.

So the chemists came up with other options, because they said, well, you know, if that doesn't work, we've got other antibiotics in our arsenal. And there is a compound that was used for years as a last line of resort antibiotic known as vancomycin. It was very, very important, so very serious infections, and really preserved for that use. And they thought that vancomycin might be a drug that just couldn't be defeated.

This big molecule here is vancomycin. This little piece of peptide is actually the peptide that's in that cross-link. And vancomycin basically, like a glove, sat on that piece of peptide and stopped it being cross-linked. And what did the bacteria do? They evolved a set of enzymes to completely change that little piece of peptide into something that bound more poorly, giving you resistance to vancomycin as well.

So when there is one drug involved, it's pretty easy to get resistance quite quickly. You just mutate one enzyme and you get a resistant strain. And the enzyme that can beat the antibiotic will win.

If you've got a compound that takes five different enzymes or an antibiotic that has a very complex mechanism of action, you might say, well, this is never going to be defeated. It took five additional enzymes to evolve to make the peptidoglycan a different structure. And it's not that within every bacterium, you mutate five different enzymes and get them all working as a team. What was happening in these infections is that a plasmid with the set of enzymes was being passed around amongst bacteria. So a new bacterium could acquire resistance to this compound without evolving a whole bunch of new enzymes, but rather by lateral transfer of plasmids encoding the genes that it took to make the vancomycin inactive.

All right, so let me just tell you a few of the targets. And then there is one movie I want to show you that's kind of cool. So currently, when we inhibit bacteria with antibiotics, there are a number of essential processes that are targeted with common antibiotics.

So this would be a typical bacterium. One target of action is DNA synthesis and DNA polymerase. And the enzyme that is targeted is one we've talked about, topoisomerase. And that is inhibited by the fluoroquinolones such as ciprofloxacin that actually targets specifically the bacterial polymerase. So that's one way, inhibit DNA replication, bacteria can't divide.

Another set of antibiotics are those that inhibit protein synthesis. So in particular, you know the tunnel that comes out of the ribosome where the growing polypeptide chain emerges after reading the messenger RNA and translating the messenger into protein? There are antibiotics to basically stick in that tunnel and stop protein synthesis. And those are things like the aminoglycosides. And they block exit from the ribosome. But you could imagine that mutating.

There are the ones that inhibit cell wall biosynthesis that I've already talked to about, the penicillins, the vancoymcin. And then there are others that inhibit folate synthesis. And then there is a lot of synthetic drugs, but also a lot of natural product drugs. So both nature and chemistry have teamed up to inhibit all of these essential steps.

OK, so how do you test for antibiotic resistance? You use plates where you're growing particular strains of bacteria on a plate. This would be a colony. And it's growing outwards.

Where there is a colony but there is no growth around it, it means there is something in that plate that is inhibiting bacterial growth. So these are very clear types of ways that people check to see if bacteria have become resistant to drugs. You would look for that zone of inhibition. Does it disappear with some of the resistant strains, for example? And these get pretty sophisticated now where you can test a bunch of antibiotics in one go, where each of these colored dots represents an area where there is treatment with one antibiotic or another.

So what's the problem? The problem is this graph, that as soon as an antibiotic is introduced, just a few years go by. And there is resistance to that antibiotic.

So resistance basically is the gradual acquisition of machinery to somehow inactivate the antibiotic treatment. So if you take a look, here on the top is where the drug is introduced. And on the bottom is when resistance was developed.

So let's go to something we're familiar. Here is penicillin, people introduced about 1940 to the general population. By about '47, there was resistance to penicillin. And you can see, this is really just a really serious sort of series of events.

So what I want to show you was resistance in action. And that'll be the last thing I talk about today, because I just want to give you a feel for what does resistance look like. So this was an experiment that was done at Harvard on just a visualization of resistance development.

I think what's so fascinating is you could then go back to the plate and pluck the first pioneers who crossed that line and find out what that was. What was that mutation that let the population expand, and so on? So you could really map out the entire evolution of very, very strong resistance.

So in the next class, I'll talk to you about resistance mechanisms. And then we'll talk about viruses and resistance to antivirals.


The Normal Gut Microbiota: An Essential Factor in Health

Basic Definitions and Development of the Microbiota

The term microbiota is to be preferred to the older term flora, as the latter fails to account for the many nonbacte-rial elements (eg, archea, viruses, and fungi) that are now known to be normal inhabitants of the gut. Given the relatively greater understanding that currently exists of the role of bacteria, in comparison with the other constituents of the microbiota in health and disease, gut bacteria will be the primary focus of this review. Within the human gastrointestinal microbiota exists a complex ecosystem of approximately 300 to 500 bacterial species, comprising nearly 2 million genes (the microbiome). 1 Indeed, the number of bacteria within the gut is approximately 10 times that of all of the cells in the human body, and the collective bacterial genome is vastly greater than the human genome.

At birth, the entire intestinal tract is sterile the infant’s gut is first colonized by maternal and environmental bacteria during birth and continues to be populated through feeding and other contacts. 2 Factors known to influence colonization include gestational age, mode of delivery (vaginal birth vs assisted delivery), diet (breast milk vs formula), level of sanitation, and exposure to antibiotics. 3 , 4 The intestinal microbiota of newborns is characterized by low diversity and a relative dominance of the phyla Proteobacteria and Actinobacteria thereafter, the microbiota becomes more diverse with the emergence of the dominance of Firmicutes and Bacteroidetes, which characterizes the adult microbiota. 5 – 7 By the end of the first year of life, the microbial profile is distinct for each infant by the age of 2.5 years, the microbiota fully resembles the microbiota of an adult in terms of composition. 8 , 9 This period of maturation of the microbiota may be critical there is accumulating evidence from a number of sources that disruption of the microbiota in early infancy may be a critical determinant of disease expression in later life. It follows that interventions directed at the microbiota later in life may, quite literally, be too late and potentially doomed to failure.

Following infancy, the composition of the intestinal microflora remains relatively constant until later life. Although it has been claimed that the composition of each individual’s flora is so distinctive that it could be used as an alternative to fingerprinting, more recently, 3 differ-ent enterotypes have been described in the adult human microbiome. 10 These distinct enterotypes are dominated by Prevotella, Ruminococcus, and Bacteroides, respectively, and their appearance seems to be independent of sex, age, nationality, and body mass index. The microbiota is thought to remain stable until old age when changes are seen, possibly related to alterations in digestive physiology and diet. 11 – 13 Indeed, Claesson and colleagues were able to identify clear correlations in elderly individuals, not only between the composition of the gut microbiota and diet, but also in relation to health status. 14

Regulation of the Microbiota

Because of the normal motility of the intestine (peristalsis and the migrating motor complex) and the antimicrobial effects of gastric acid, bile, and pancreatic and intestinal secretions, the stomach and proximal small intestine, although certainly not sterile, contain relatively small numbers of bacteria in healthy subjects. 15 Interestingly, commensal organisms with probiotic properties have recently been isolated from the human stomach. 16 The microbiology of the terminal ileum represents a transition zone between the jejunum, containing predominantly aerobic species, and the dense population of anaerobes found in the colon. Bacterial colony counts may be as high as 10 9 colony-forming units (CFU)/mL in the terminal ileum immediately proximal to the ileocecal valve, with a predominance of gram-negative organisms and anaerobes. On crossing into the colon, the bacterial concentration and variety of the enteric flora change dramatically. Concentrations of 10 12 CFU/mL or greater may be found and are comprised mainly of anaerobes such as Bacteroides, Porphyromonas, Bifidobacterium, Lactobacillus, and Clos-tridium, with anaerobic bacteria outnumbering aerobic bacteria by a factor of 100 to 1000:1. The predominance of anaerobes in the colon reflects the fact that oxygen concentrations in the colon are very low the flora has simply adapted to survive in this hostile environment.

At any given level of the gut, the composition of the flora also demonstrates variation along its diameter, with certain bacteria tending to be adherent to the mucosal surface, while others predominate in the lumen. It stands to reason that bacterial species residing at the mucosal surface or within the mucus layer are those most likely to participate in interactions with the host immune system, whereas those that populate the lumen may be more relevant to metabolic interactions with food or the products of digestion. It is now evident that different bacterial populations may inhabit these distinct domains. Their relative contributions to health and disease have been explored to a limited extent, though, because of the relative inaccessibility of the juxtamucosal populations in the colon and, especially, in the small intestine. However, most studies of the human gut microbiota have been based on analyses of fecal samples, therefore representing a major limitation. Indeed, a number of studies have already shown differ-ences between luminal (fecal) and juxtamucosal populations in disorders such as inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS). 17 , 18

In humans, the composition of the flora is influenced not only by age but also by diet and socioeconomic conditions. In a recent study of elderly individuals, the interaction of diet and age was demonstrated, firstly, by a close relationship between diet and microbiota composition in the subjects and, secondly, by interactions between diet, the microbiota, and health status. 14 It must also be remembered that nondigestible or undigested components of the diet may contribute substantially to bacterial metabolism for example, much of the increase in stool volume resulting from the ingestion of dietary fiber is based on an augmentation of bacterial mass. The subtleties of interaction between other components of diet and the microbiota are now being explored and will, undoubtedly, yield important information. For example, data indicating a potential role of certain products of bacterial metabolism in colon carcinogenesis have already provided strong hints of the relevance of diet-microbiota interactions to disease. Antibiotics, whether prescribed or in the food chain as a result of their administration to animals, have the potential to profoundly impact the microbiota. 19 In the past, it was thought that these effects were relatively transient, with complete recovery of the microbiota occurring very soon after the course of antibiotic therapy was complete. However, while recent studies have confirmed that recovery is fairly rapid for many species, some species and strains show more sustained effects. 20

Host-Microbiota Interactions

Gut-commensal microbiota interactions play a fundamental role in promoting homeostatic functions such as immunomodulation, upregulation of cytoprotec-tive genes, prevention and regulation of apoptosis, and maintenance of barrier function. 21 The critical role of the microbiota on the development of gut function is amply demonstrated by the fate of the germ-free animal. 22 , 23 Not only are virtually all components of the gut-associated and systemic immune systems affected in these animals, but the development of the epithelium, vasculature, neu-romuscular apparatus, and gut endocrine system also is impaired. The subtleties of the interactions between the microbiota and the host are exemplified by studies that demonstrate the ability of a polysaccharide elaborated by the bacterium Bacteroides fragilis to correct T-cell deficien-cies and Th1/Th2 imbalances and direct the development of lymphoid organs in the germ-free animal. 24 Intestinal dendritic cells appear to play a central role in these critical immunologic interactions. 24 , 25

How does the gut immune system differentiate between friend and foe when it comes to the bacteria it encounters? 26 At the epithelial level, for example, a number of factors may allow the epithelium to tolerate commensal (and thus probiotic) organisms. These include the masking or modification of microbial-associated molecular patterns that are usually recognized by pattern recognition receptors, such as Toll-like receptors, 27 and the inhibition of the NF㮫 inflammatory pathway. 28 Responses to commensals and pathogens also may be distinctly different within the mucosal and systemic immune systems. For example, commensals such as Bifidobacterium infantis and Faecalibacterium prausnitzii have been shown to differentially induce regulatory T cells and result in the production of the anti-inflammatory cytokine interleukin (IL)-10. 29 Other commensals may promote the development of T-helper cells, including TH17 cells, and result in a controlled inflammatory response that is protective against pathogens in part, at least, through the production of IL-17. 30 The induction of a low-grade inflammatory response (physiologic inflammation) by commensals could be seen to prime the host’s immune system to deal more aggressively with the arrival of a pathogen. 31

Through these and other mechanisms, the microbiota can be seen to play a critical role in protecting the host from colonization by pathogenic species. 32 Some intestinal bacteria produce a variety of substances, ranging from relatively nonspecifc fatty acids and peroxides to highly specific bacteriocins, 33 , 34 which can inhibit or kill other potentially pathogenic bacteria, 35 while certain strains produce proteases capable of denaturing bacterial toxins. 36

The Microbiota and Metabolism

Although the immunologic interactions between the microbiota and the host have been studied in great detail for some time, it has been only recently that the true extent of the metabolic potential of the microbiota has begun to be grasped. Some of these metabolic functions were well known, such as the ability of bacterial disac-charidases to salvage unabsorbed dietary sugars, such as lactose, and alcohols and convert them into short-chain fatty acids (SCFAs) that are then used as an energy source by the colonic mucosa. SCFAs promote the growth of intestinal epithelial cells and control their proliferation and differentiation. It has also been known for some time that enteric bacteria can produce nutrients and vitamins, such as folate and vitamin K, deconjugate bile salts, 37 and metabolize some medications (such as sul-fasalazine) within the intestinal lumen, thereby releasing their active moieties. However, it is only recently that the full metabolic potential of the microbiome has come to be recognized and the potential contributions of the microbiota to the metabolic status of the host in health and in relation to obesity and related disorders have been appreciated. The application of genomics, metabolomics, and transcriptomics can now reveal, in immense detail, the metabolic potential of a given organism. 38 – 41

It is now also known that certain commensal organisms also produce other chemicals, including neurotrans-mitters and neuromodulators, which can modify other gut functions, such as motility or sensation. 42 – 44 Most recently and perhaps most surprisingly, it has been proposed that the microbiota can influence the development 45 and func-tion 46 of the central nervous system, thereby leading to the concept of the microbiota-gut-brain axis. 47 – 49


Do labradors hold the key to successful aging in humans?

Following Vicki Adams and her colleagues’ publication in Acta Veterinaria Scandinavica today, in this blog she explains more about their research findings and how dogs may provide an insight into understanding successful aging in humans.

As a veterinary epidemiologist my interest and passion lies in the investigation of causes of disease in companion animals and how to prevent them from occurring. One clear benefit of an epidemiological study such as a prospective cohort study is that the knowledge gained can be used to help members of the target population extend their healthspan, defined as the number of years in which an individual is generally healthy and free from serious disease.

Unlocking the secrets of successful aging

In 2015 I was invited to be part of a team to evaluate the results of 10+ years observation of a group of 39 Labrador retrievers almost one-third (28%) of these Labradors achieved an exceptional age, reaching or exceeding 15.6 years. This exceptional age was defined by taking the breed`s average age of 12 and extending it by 30%. We were interested in trying to unlock some of the secrets of successful ageing as increasing the healthspan of dogs will benefit both the pet and their owners.

Could our ‘oldest of the old’ canine companions give us some clues to how we can age successfully?

But why should these Labradors be of interest to humans and our ageing process? The interest lies in the fact that a 15.6 year-old Labrador represents ̴95 years in human physiological age. The oldest dog, a male called Utah, died 5 weeks before his 18 th birthday, a human equivalent age of ̴109 years, making him almost a supercentenarian in human terms (meet Utah and some of the other dogs). Could our ‘oldest of the old’ canine companions give us some clues to how we can age successfully?

Aiming to understand the process

A leading veterinary gerontologist, Professor David Waters, from Purdue University College of Veterinary Medicine, Indiana, USA, is well known for his work on the subject of extending human healthspan.

He has studied highly successful ageing in the domestic dog, Canis lupus familiaris, particularly in the Rottweiler breed. The ultimate goal is to fully understand the process of highly successful ageing, including cancer resistance, in both our domestic dogs and people this has been captured in a 13-minute talk by Professor Waters on YouTube, shown below.

What did we find?

For an epidemiologist, this observation of longevity in Labradors, published today in Acta Veterinaria Scandinavica, produced some exciting results. Almost 90% of the Labradors exceeded the breed`s expected average age of 12 and five dogs went on to become 16 or 17 years of age.

Why did some Labradors live to 16 or 17 and others only reached their expected average age of 12 or even below?

When compared to other groups of Labradors, this group showed a significant increase in their lifespan. Why did some Labradors live to 16 or 17 and others only reached their expected average age of 12 or even below? Could their experience help in developing strategies that increase the healthspan of humans?

For humans, the ‘oldest of the old’ (centenarians) demonstrate a compression of morbidity they have ‘compressed’ diseases into the last few years of their 100+ life that would have typically caused illness and death at a younger age. Our 16-17 year old Labradors represent 99-104 year old humans. What ‘compressions’ did they achieve and what can we learn about highly successful ageing?

We found that the longest lived Labradors, the 28% that became exceptionally aged (≥15.6 years old), had a significantly slower rate of body fat mass accumulation over their first 13 years of life compared to Labradors that lived only to their expected average age of 12 or less.

They also had a significantly slower loss of lean body mass compared to those with the shortest lifespan. An important component of lean body mass is muscle mass loss of muscle mass and strength in the absence of disease is called sarcopenia.

In humans, age-related sarcopenia fits the current definition of a geriatric syndrome: conditions that result from incompletely understood interactions of disease and age on multiple body systems, producing a collection of signs and symptoms. Sarcopenia is associated with an increased risk of adverse outcomes such as physical disability, poor quality of life and death.

Do dogs hold the key?

We are now interested to further evaluate the changes in body fat and lean body mass to see if they could hold the key as to why some dogs did, and some did not, reach an exceptional age.

We are now interested to further evaluate the changes in body fat and lean body mass to see if they could hold the key as to why some dogs did, and some did not, reach an exceptional age. Such knowledge could be applied to the human ageing model and aid in the development of strategies to improve our chance of healthy ageing and to extend healthspan.

It must be noted that the Labradors included in the longevity observations were fed to maintain a body condition score of between 2 and 4 on a 5-point scale in order to avoid excessive weight gain that has been previously linked to musculoskeletal disease and decreased longevity. Interestingly, just this week an obesity gene (POMC) has been identified in Labradors by Dr Eleanor Raffan and other scientists at Cambridge University.

So, the next time you stroke your ageing dog and look lovingly into their eyes, just think that they could hold the keys to some of the secrets as to how we could also age successfully.


Are Human Beings Just Intelligent Bacteria?

By Rain Noe - July 28, 2016

Following the Tools & Craft reference to Burning Man, I rewatched this time-lapse videos shot there a few years ago:

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I remember finding this video pretty when I first viewed it, but something about it bothered me this time around. The perfect semicircle of the "town" taking shape atop the more organic canvas of the sand, interrupted by little dust storms, didn't seem beautiful to me instead it seemed almost…grotesque. As the lasers kicked in and the illuminated vehicles began moving back and forth, we humans look, as we always do from afar and in fast motion, insectoid.

The entire scene reminded me of a Joe Rogan rant from years ago:

Redditor Nesshie91 provided the above transcription in a thread there. The subsequent discussion is illuminating, touching on everything from Carl Sagan's Pale Blue Dot to a 1934 scientific paper by Russian biologist Georgii Frantsevich Gause called "The Struggle for Existence," which explains what happens when bacteria reaches its limits.

If the theory above strikes a chord in you, the thread is worth the read and it's right here.