Research on gut bacteria has turned up some interesting and somewhat unexpected results.
Certain bacteria are necessary for humans to digest food. But we don't all have the same bacteria. Although the research found people possessed the "same core group of bacterial genes" needed for digestion, those genes in common were provided by different ranges of bacteria species.
The study also found people who were related shared a similar set of species of gut bacteria. There are several possible explanations for that including, I presume, inheritance via shared environment.
Analysis also indicated that obese people had a greater proportion of bacterial genes for digesting fat, protein and carbohydrates - ie they were better able to extract and store energy from food. If this proves significant, it has strong ramifications for the management of obesity.
The study, written up in Nature, was headed by Jeffrey Gordon of Washington University School of Medicine (Missouri), reported in New Scientist, 8-Dec-08.
Showing posts with label bacteria. Show all posts
Showing posts with label bacteria. Show all posts
Monday, February 16, 2009
Sunday, September 14, 2008
The DNA of NY air
A bloke is sampling New York's air to extract the DNA from its microbes.
A 'microbe' is a rather generic term for a microscopic organism. The sample would encompass bacteria and fungal spores in particular, as well as a few other stray strands. Report here.
The scientist is Craig Ventner, who competed against the publicly funded project to sequence the human genome. He states that only about 1% of the organic matter in the air could be cultivated in a laboratory.
A fascinating experiment for one of the most urban centres in the world. Most of the answers would veer into the mundane, but there may be a few surprises, particularly for bacterial DNA, where mutation can be rapid relative to large-scale organisms.
Ventner has apparently uncovered about a million new "genes" from a similar exercise run in the Sargasso Sea (a mass of seaweed in the middle of the Atlantic). That's not too surprising: it is a unique ecosystem. The NY experiment is unlikely to be as productive, but it strikes me as a useful mission.
A 'microbe' is a rather generic term for a microscopic organism. The sample would encompass bacteria and fungal spores in particular, as well as a few other stray strands. Report here.
The scientist is Craig Ventner, who competed against the publicly funded project to sequence the human genome. He states that only about 1% of the organic matter in the air could be cultivated in a laboratory.
A fascinating experiment for one of the most urban centres in the world. Most of the answers would veer into the mundane, but there may be a few surprises, particularly for bacterial DNA, where mutation can be rapid relative to large-scale organisms.
Ventner has apparently uncovered about a million new "genes" from a similar exercise run in the Sargasso Sea (a mass of seaweed in the middle of the Atlantic). That's not too surprising: it is a unique ecosystem. The NY experiment is unlikely to be as productive, but it strikes me as a useful mission.
Tuesday, September 02, 2008
Evolution: Bacterial DNA exchange
DNA refers to complex molecules that contain genetic data for all living organisms. The most commonly understood locus for that data is the genomic DNA in the nucleus of each cell in an organism - or in the nucleoid (a somewhat nucleus-like region), in the case of prokaryotes (less complex, mostly single-celled organisms that lack a nucleus per se).
There are various other loci for that genetic data, beyond the core genomic DNA in cell nuclei - for example, mitochondria, viruses and plasmids, for example.
DNA is typically transmitted direct by direct inheritance, sexual reproduction in most more complex organisms, binary fission in more elemental organisms such as bacteria. Yet we see evidence that as well as that "vertical" data transmission, some "horizontal" exchange of genetic data takes place. I noted here that Bdelloid rotifers somehow acquire DNA from a number of sources outside the species.
Bacteria apparently exchange DNA too. A recent paper in the journal Science discusses this (also reported in New Scientist). Two species of bacteria, Campylobacter jejuni and Campylobacter coli, share about 87% of their genetic material, suggesting they diverged about 100 million years ago (by contrast, humans and chimpanzees share about 94%, having diverged about 6 million years ago). These bacterial species don't normally run into each other in the wild, as they inhabit different animals. But the artificial environment of farms has brought their environmental niches together, where they have both been able to infect chickens and cattle.
Samuel Shepherd and colleagues from Oxford University found one variety of C. coli was carrying more genes from C. jejuni than others studied; in nearly all cases, the genetic sequence in question was unchanged between species. This suggested they were exchanging DNA recently; the scientists' analysis indicated they were converging more quickly than mutation was diverging them.
This is said to be the first concrete evidence that speciation of bacteria is affected by environment in a similar fashion to more complex animals. I find it very surprising that it is a first; intuitively, it makes good sense that environment influences evolution in bacteria just as much as in other living things.
Further, I would be very reluctant to call this species convergence, as the report's authors do. The bacteria's genetic driftage would be a trend, but it would be hard to call it an absolute. I reckon it would be particularly unlikely for species to perfectly converge such that their genetic material is cleanly lined up identically at all points. I'm happy to be proven wrong, but I don't think this will happen. I would posit a randomness to the exchange, similar to the randomness of mutation. (However, at this stage we don't know the speed of the exchange: whether environment or proximity can hasten it to the point of a blur.)
Aside from the exchange of genetic material, the article makes the point that there remains disagreement over the nature of speciation in bacteria, and how the boundaries of species are maintained. My understanding of this issue would related to the nature of species stability in more complex organisms: the fact that sexual reproduction necessitates an exchange of genetic material at each generation would inherently stabilise species, whereas surely binary fission would normally destabilise. Mutations in sexual reproduction have only a 50% chance of being carried forwards, whereas in binary fission (perfect replication or no), any mutations are carried forward at each generation.
So why would bacterial species ever maintain stability? Two possibilities are the DNA exchange mechanism (a stabiliser in the immediate term), and environmental factors over the longer term.
All this is a mere curtain raiser for the role in DNA propagation of... viruses.
There are various other loci for that genetic data, beyond the core genomic DNA in cell nuclei - for example, mitochondria, viruses and plasmids, for example.
DNA is typically transmitted direct by direct inheritance, sexual reproduction in most more complex organisms, binary fission in more elemental organisms such as bacteria. Yet we see evidence that as well as that "vertical" data transmission, some "horizontal" exchange of genetic data takes place. I noted here that Bdelloid rotifers somehow acquire DNA from a number of sources outside the species.
Bacteria apparently exchange DNA too. A recent paper in the journal Science discusses this (also reported in New Scientist). Two species of bacteria, Campylobacter jejuni and Campylobacter coli, share about 87% of their genetic material, suggesting they diverged about 100 million years ago (by contrast, humans and chimpanzees share about 94%, having diverged about 6 million years ago). These bacterial species don't normally run into each other in the wild, as they inhabit different animals. But the artificial environment of farms has brought their environmental niches together, where they have both been able to infect chickens and cattle.
Samuel Shepherd and colleagues from Oxford University found one variety of C. coli was carrying more genes from C. jejuni than others studied; in nearly all cases, the genetic sequence in question was unchanged between species. This suggested they were exchanging DNA recently; the scientists' analysis indicated they were converging more quickly than mutation was diverging them.
This is said to be the first concrete evidence that speciation of bacteria is affected by environment in a similar fashion to more complex animals. I find it very surprising that it is a first; intuitively, it makes good sense that environment influences evolution in bacteria just as much as in other living things.
Further, I would be very reluctant to call this species convergence, as the report's authors do. The bacteria's genetic driftage would be a trend, but it would be hard to call it an absolute. I reckon it would be particularly unlikely for species to perfectly converge such that their genetic material is cleanly lined up identically at all points. I'm happy to be proven wrong, but I don't think this will happen. I would posit a randomness to the exchange, similar to the randomness of mutation. (However, at this stage we don't know the speed of the exchange: whether environment or proximity can hasten it to the point of a blur.)
Aside from the exchange of genetic material, the article makes the point that there remains disagreement over the nature of speciation in bacteria, and how the boundaries of species are maintained. My understanding of this issue would related to the nature of species stability in more complex organisms: the fact that sexual reproduction necessitates an exchange of genetic material at each generation would inherently stabilise species, whereas surely binary fission would normally destabilise. Mutations in sexual reproduction have only a 50% chance of being carried forwards, whereas in binary fission (perfect replication or no), any mutations are carried forward at each generation.
So why would bacterial species ever maintain stability? Two possibilities are the DNA exchange mechanism (a stabiliser in the immediate term), and environmental factors over the longer term.
All this is a mere curtain raiser for the role in DNA propagation of... viruses.
Thursday, August 07, 2008
Evolution experienced - on a bacterial scale
A fascinating experiment written up in PNAS brings to life - and helps quantify - evolutionary theory that is usually only induced or deduced from widely scattered evidence.
Richard Lenksi, at Michigan State University, has been running a meticulous experiment on the common bacteria Escherichia coli, aka E coli (below).
Starting with a single bacterium in 1988, he cultivated its descendents (daughters, as they grow to a certain length, then reproduce asexually through binary fission, splitting) into twelve populations in an identical medium. That medium was glucose-limited, and contained a secondary nutrient, citrate (based on citric acid), which E coli cannot use.
Those populations have evolved through 44,000 generations over the past 20 years; every 500 generations, Lenski extracted and froze samples of each strain. In this way, he could test mutations in the populations, even to the extent of "replaying" the evolutionary clock from given points.
In general, each of the 12 samples evolved in these lab conditions larger cells, faster growth rates, and lower peak population densities.
And there evolved a population of E coli that could metabolise (and thus feed on) citrate. This happened in only one of the 12 populations, from around the 31,500th generation.
Lenski calculated that within this time, all "simple" mutations would have appeared at some point in each population. He reasoned that citrate-metabolising must be either a particularly unusual mutation, or one that required several mutations to accumulate in a rare sequence - no E coli strain had been found with this trait outside his lab.
So he extracted some of the frozen samples for testing. The finding was that the special trait evolved only when the population of that one-in-twelve strain was replayed from at least the 20,000th generation - no earlier. This demonstrated that a crucial precursor to the citrate-metabolising trait had occurred around that point.
And with the additional nutrient available, the citrate-metabolising strain yielded a greater population size and variety.
Thus far, the experiment adds little of significance to general evolutionary theory, apart from adding some numbers to the pace of change at a macro level - and then yet, further similar experimentation could better quantify the statistical variance involved.
But the experiment is a very neat, clean illustration of a significant trait evolving via a series of smaller and insignificant steps. And of the randomness inherent in evolutionary change. Beneficial changes are contingent, and can rely on key chance developments. Then once a crucial point has been crossed, certain outcomes are much more easily achieved.
Richard Lenksi, at Michigan State University, has been running a meticulous experiment on the common bacteria Escherichia coli, aka E coli (below).
Starting with a single bacterium in 1988, he cultivated its descendents (daughters, as they grow to a certain length, then reproduce asexually through binary fission, splitting) into twelve populations in an identical medium. That medium was glucose-limited, and contained a secondary nutrient, citrate (based on citric acid), which E coli cannot use.
Those populations have evolved through 44,000 generations over the past 20 years; every 500 generations, Lenski extracted and froze samples of each strain. In this way, he could test mutations in the populations, even to the extent of "replaying" the evolutionary clock from given points.
In general, each of the 12 samples evolved in these lab conditions larger cells, faster growth rates, and lower peak population densities.
And there evolved a population of E coli that could metabolise (and thus feed on) citrate. This happened in only one of the 12 populations, from around the 31,500th generation.
Lenski calculated that within this time, all "simple" mutations would have appeared at some point in each population. He reasoned that citrate-metabolising must be either a particularly unusual mutation, or one that required several mutations to accumulate in a rare sequence - no E coli strain had been found with this trait outside his lab.
So he extracted some of the frozen samples for testing. The finding was that the special trait evolved only when the population of that one-in-twelve strain was replayed from at least the 20,000th generation - no earlier. This demonstrated that a crucial precursor to the citrate-metabolising trait had occurred around that point.
And with the additional nutrient available, the citrate-metabolising strain yielded a greater population size and variety.
Thus far, the experiment adds little of significance to general evolutionary theory, apart from adding some numbers to the pace of change at a macro level - and then yet, further similar experimentation could better quantify the statistical variance involved.
But the experiment is a very neat, clean illustration of a significant trait evolving via a series of smaller and insignificant steps. And of the randomness inherent in evolutionary change. Beneficial changes are contingent, and can rely on key chance developments. Then once a crucial point has been crossed, certain outcomes are much more easily achieved.
Wednesday, July 09, 2008
Evolution: DNA part 2: DNA exchange at the periphery
As mentioned before, human DNA is the familiar double helix shape, wrapped up inside the nucleus of each cell. The physical molecule is referred to as DNA; packaged up (with proteins) it constitutes a chromosome; normal human cells have 23 pairs of chromosomes. Each DNA molecule contains a number of base pairs (the unit of genetic information, somewhat akin to a byte in digital information). The human genome of 46 chromosomes has about three billion base pairs.
But the narrative is not nearly as neat as that. We have to understand bacterial DNA, mitochondrial DNA, plasmids, and how they all interact and exchange information.
The basics of human genetic inheritance are relatively simple: sex-specific cells, the sperm and egg gametes, are haploid, only containing one copy of each chromosome pair, pending unification which results in the full complement.
Mitochondrial DNA is one of the complications. This is not a part the human genome located in the nucleus: it's genetic information located in mitochondria, cell elements outside the nucleus that generate chemical energy for the cell to operate. Each cell can contain from one to thousands of mitochondria, depending on the organism type and cell type. When gametes unite, the sperm's mitochondrial DNA is tagged for deletion, so allowing mtDNA to be a marker of matrilineal descent.
Mitochondrial DNA is small (in the order of 15,000 base pairs) and circular - which is pretty much the description of bacterial DNA. In fact, it is generally agreed that mitochondria are bacterial in origin, once endosymbiotic - that is, symbiants located inside the cell that came to be part of the cell's structure. How? A somewhat harder question to answer.
Bacteria are prokaryotic - that is, they lack a cell nucleus. Their DNA consists of a single continous loop. But bacteria, too, have strands of DNA that are separate from their chromosomes. These are called plasmids, rings of DNA that are capable of reproducing independently of bacterial reproduction. Plasmids could be seen as independent symbiotic life-forms in bacteria, similar to viruses except more useful, for example conveying antibiotic res
Bacteria reproduce through binary fusion: that is, they divide into two daughter cells. In the process, the bacterial chromosome is duplicated, one copy for each daughter.
This inheritance mechanism sounds simple, as if each bacterium could be uniquely traced to an ancestor. However, there is an additional mechanism for DNA change: horizontal gene transfer (HGT).
HGT can be seen as a counterpoint to inheritance mechanisms, which could be called vertical gene transfer. HGT, as the name suggests, involves the transfer of genetic information between organisms. This too can result in the spreading of drug resistance - in fact, this was how it was first noted, as far back as 1959. There are three mechanisms for this: transformation involves the absorption of foreign DNA; transduction occurs when a bacterial virus transfers genetic information from one bacterium to another; and in bacterial conjugation, bacteria that are touching can under certain circumstances exchange DNA.
HGT is common in prokaryotic bacteria, and even happens in some unicellular eukaryotes. It would be harder to say that this mechanism impacts on multicellular eukaryotes (having cells with nuclei), the evidence does suggest this has happened. It is suggested that this would have happened in the early stages of eukaryotic evolution.
However, this story is not complete. I noted in May a study of bdelloid rotifers (small marine animals), which found they had absorbed genetic material from a wide range of organisms: animals, plants, fungi and bacteria. The mechanism is not well understood, but it must have been relatively recently in evolutionary terms - in the order of tens of millions of years, maybe.
There are a number of gaps which need explaining, in particular how these mechanisms take place, and how they evolve. I hope to fill in some of the gaps in time, as far as scientific research and my learning permit.
So it would seem that bacteria play an important role in the spreading and exchanging of genetic information - even as far as humans.
But the narrative is not nearly as neat as that. We have to understand bacterial DNA, mitochondrial DNA, plasmids, and how they all interact and exchange information.
The basics of human genetic inheritance are relatively simple: sex-specific cells, the sperm and egg gametes, are haploid, only containing one copy of each chromosome pair, pending unification which results in the full complement.
Mitochondrial DNA is one of the complications. This is not a part the human genome located in the nucleus: it's genetic information located in mitochondria, cell elements outside the nucleus that generate chemical energy for the cell to operate. Each cell can contain from one to thousands of mitochondria, depending on the organism type and cell type. When gametes unite, the sperm's mitochondrial DNA is tagged for deletion, so allowing mtDNA to be a marker of matrilineal descent.
Mitochondrial DNA is small (in the order of 15,000 base pairs) and circular - which is pretty much the description of bacterial DNA. In fact, it is generally agreed that mitochondria are bacterial in origin, once endosymbiotic - that is, symbiants located inside the cell that came to be part of the cell's structure. How? A somewhat harder question to answer.
Bacteria are prokaryotic - that is, they lack a cell nucleus. Their DNA consists of a single continous loop. But bacteria, too, have strands of DNA that are separate from their chromosomes. These are called plasmids, rings of DNA that are capable of reproducing independently of bacterial reproduction. Plasmids could be seen as independent symbiotic life-forms in bacteria, similar to viruses except more useful, for example conveying antibiotic res
Bacteria reproduce through binary fusion: that is, they divide into two daughter cells. In the process, the bacterial chromosome is duplicated, one copy for each daughter.
This inheritance mechanism sounds simple, as if each bacterium could be uniquely traced to an ancestor. However, there is an additional mechanism for DNA change: horizontal gene transfer (HGT).
HGT can be seen as a counterpoint to inheritance mechanisms, which could be called vertical gene transfer. HGT, as the name suggests, involves the transfer of genetic information between organisms. This too can result in the spreading of drug resistance - in fact, this was how it was first noted, as far back as 1959. There are three mechanisms for this: transformation involves the absorption of foreign DNA; transduction occurs when a bacterial virus transfers genetic information from one bacterium to another; and in bacterial conjugation, bacteria that are touching can under certain circumstances exchange DNA.
HGT is common in prokaryotic bacteria, and even happens in some unicellular eukaryotes. It would be harder to say that this mechanism impacts on multicellular eukaryotes (having cells with nuclei), the evidence does suggest this has happened. It is suggested that this would have happened in the early stages of eukaryotic evolution.
However, this story is not complete. I noted in May a study of bdelloid rotifers (small marine animals), which found they had absorbed genetic material from a wide range of organisms: animals, plants, fungi and bacteria. The mechanism is not well understood, but it must have been relatively recently in evolutionary terms - in the order of tens of millions of years, maybe.
There are a number of gaps which need explaining, in particular how these mechanisms take place, and how they evolve. I hope to fill in some of the gaps in time, as far as scientific research and my learning permit.
So it would seem that bacteria play an important role in the spreading and exchanging of genetic information - even as far as humans.
Monday, February 11, 2008
Evolutionary oddities 2: Giant tube worm
Riftia pachyptila, the Giant tubeworm, is a marine annalid (the phylum, or body type, most familiar to us as the earth worm).
These creatures appears to be sessile, which means they latch on to a rock (or somesuch) and stay there (in the adult form at least). They live near black smokers, geothermal vents in the ocean floor. The emissions of these vents are particularly hot and acidic.
They have no digestive system as such: no mouth, no gut, no anus. They do, however, have specialised bacteria inside them, which make up perhaps 35% of the tubeworm's weight. The red plume you see is an organ used for absorbing a number of chemicals, including oxygen, carbon dioxide, and hydrogen sulphide. These chemicals are fed to the bacteria, which then metabolises them into nutrients for the worm.
I'd note that this is one of the few food cycles that doesn't rely on the sun's emissions, directly or indirectly. Such cycles will typically involve bacteria.
My research thus far hasn't been able to answer a few questions: are the juvenile forms of the tubeworm non-sessile? (that is frequently the case.) How does it excrete waste products? (if there are any.) And how do the bacteria get inside them in the first place? (in the juvenile stage?)
It's likely this worm was able to adapt to a niche that was otherwise unoccupied. It would have few predators either, so over time it was probably able to strip back its organs to the bare essentials.
The other thing of note is that whenever an evironment is found on earth that is hostile to life, you're likely to find bacteria adapted to it.
Evolution oddity #1 was: the anglerfish.
Subscribe to:
Posts (Atom)