Lactobacillus and Bifidobacteria metabolism

[StringJunky]

What do these bacteria have that can use oligosaccharides but we can't? What are the chemical pathways and byproducts?

[CharonY]

Actually many bacteria are able to utilize oligo- and even polysaccharides, so it is not necessarily a special feature of these genera. Also, humans can also digest certain poly- as well as oligosaccharides.

 

The basic requirement is to have enzymes that can break down the long chain sugars into monosaccharides that then can be fed to the respective sugar metabolism pathways. So there is not a general pathway for oligosaccharides but it depends on the type carbohydrate chain you start out with. Or in other words, if you lack those enzymes, the respective oligo- or polysaccharides become indigestible.

 

For example, sucrase hydrolyses sucrose (a disaccharide) into fructose and glucose. The latter can then be utilized directly.

Edited March 22, 2017 by CharonY

[StringJunky]

Actually many bacteria are able to utilize oligo- and even polysaccharides, so it is not necessarily a special feature of these genera. Also, humans can also digest certain poly- as well as oligosaccharides.

 

The basic requirement is to have enzymes that can break down the long chain sugars into monosaccharides that then can be fed to the respective sugar metabolism pathways. So there is not a general pathway for oligosaccharides but it depends on the type carbohydrate chain you start out with. Or in other words, if you lack those enzymes, the respective oligo- or polysaccharides become indigestible.

 

For example, sucrase hydrolyses sucrose (a disaccharide) into fructose and glucose. The latter can then be utilized directly.

Yeah, I thought other micro-organisms could use them but i'm interested in those two in particular as commensal organisms.Do they secrete the enzyme then absorb the glucose so their is competition for what they produce? Are hydrogen and methane byproducts of their metabolism ?

 

I find myself interested in the gut flora; about the symbiotic relationships between them and their hosts. Also, how they affect the immune system. I thought understanding their metabolism and ecological niches would the place to start. I've just chosen those two organisms arbitrarly because they are populous in the gut and seem to be major players in human-bacteria symbiosis.

 

Do you know any resources or books that would get me started? I have a basic level of carbon chemistry knowledge and could learn more.

Edited March 22, 2017 by StringJunky

[CharonY]

A few general pointers first. The initial degradation often occurs in an extracellular space, though smaller oligosaccharides can be transported into the cells first. These intial degradation steps tend to be hydrolysis reactions, and thus generally do not release byproducts other than the cleaved sugars.

Sugar metabolism itself does not release methane per se, though. It is more closely connect to respiration, in which a carbon body (rather than O2) is used as terminal electron acceptor.

Methanogens in the human gut include (IIRC) are mostly arachaea including Methaninobrevibacter and Methanospaera species. Overall, methanogenesis is, in a way, a bit of a niche metabolic pathway.

 

An excellent overview on bacterial species and metabolism is the Brock Biology of Microorganisms. Based on your questions I note that you are actually interested in many levels of bacterial interactions, which is very difficult to put into a simple view due to the intrinsic complexity. Ultimately basically all metabolic possibilities are somehow realized in bacteria and even in a limited niche there are complex metabolite flows. So it can be difficult to find your way through. Do not be discouraged, though as it is a fascinating topic.

Edited March 22, 2017 by CharonY

[StringJunky]

A few general pointers first. The initial degradation often occurs in an extracellular space, though smaller oligosaccharides can be transported into the cells first. These intial degradation steps tend to be hydrolysis reactions, and thus generally do not release byproducts other than the cleaved sugars.

Sugar metabolism itself does not release methane per se, though. It is more closely connect to respiration, in which a carbon body (rather than O2) is used as terminal electron acceptor.

Methanogens in the human gut include (IIRC) are mostly arachaea including Methaninobrevibacter and Methanospaera species. Overall, methanogenesis is, in a way, a bit of a niche metabolic pathway.

 

An excellent overview on bacterial species and metabolism is the Brock Biology of Microorganisms. Based on your questions I note that you are actually interested in many levels of bacterial interactions, which is very difficult to put into a simple view due to the intrinsic complexity. Ultimately basically all metabolic possibilities are somehow realized in bacteria and even in a limited niche there are complex metabolite flows. So it can be difficult to find your way through. Do not be discouraged, though as it is a fascinating topic.

Thanks. Your comments are good pointers. I know the area I'm interested in but I appreciate I need the fundamentals first. Hopefully, that book will get me started. Forty to fifty quid, after a casual browse, seems about right for a book like that.

 

I'm kind of seeing humans and their commensal organisms as subsets of higher organism... we can't function optimally without them... if I can put it that way. What we call humans is the totality of everything that resides and functions as a unit in the space that is a person.

 

I've found a copy to download. If it's up my street I'll buy the physical book as it looks to be a definitive first year student text going by reviews.... not surprising, coming from you.

Edited March 22, 2017 by StringJunky

[StringJunky]

 

....An excellent overview on bacterial species and metabolism is the Brock Biology of Microorganisms. Based on your questions I note that you are actually interested in many levels of bacterial interactions, which is very difficult to put into a simple view due to the intrinsic complexity. Ultimately basically all metabolic possibilities are somehow realized in bacteria and even in a limited niche there are complex metabolite flows. So it can be difficult to find your way through. Do not be discouraged, though as it is a fascinating topic.

Just thought I'd mention that the book is super and will be getting a hard copy. I've read the first 50 pages or so and the style is very accessible to me. Thanks. I thought about getting a microscope, but looking into it, it's pretty expensive for a phase-contrast job and I'd need an aseptic environment and methodology which I don't have, so, I'll make do with the pictures. I couldn't better stock images anyway.

 

I'm confused by 'aerobic anoxygenic bacteria'. does this mean they require oxygen (aerobic) and don't produce it (anoxygenic)?

[CharonY]

Unfortunately getting decent images from bacteria typically requires relatively high-end equipment as they are so darn small...

 

I think you may have left a thing out. Maybe it refers to aerobic anoxygenic phototrophes? You are basically correct. The aerobic refers to the the fact that they require oxygen for respiration. The anoxygenic means they do not preoduce O2. However, that would only be expected if they do something that actually produces oxygen, such as during phototrophy.

 

Also, am glad you like the book. It is a nice and easy read and provides a nice overview of what these buggers are up to.

Edited March 26, 2017 by CharonY

[StringJunky]

Unfortunately getting decent images from bacteria typically requires relatively high-end equipment as they are so darn small...

 

I think you may have left a thing out. Maybe it refers to aerobic anoxygenic phototrophes? You are basically correct. The aerobic refers to the the fact that they require oxygen for respiration. The anoxygenic means they do not preoduce O2. However, that would only be expected if they do something that actually produces oxygen, such as during phototrophy.

 

Also, am glad you like the book. It is a nice and easy read and provides a nice overview of what these buggers are up to.

Thanks, yes, I meant phototrophes. Still learning the lingo.

 

It was nice to read that some of my medical heros as a child, like Pasteur, Koch and Lister, are given a good overview in the historical perspective. In retrospect, I'm resuming an interest I had 40-odd years ago... it feels familiar. Hopefully, I can work through the book and have a fairly good basic understanding of the principles of the subject by the end.

[StringJunky]

Any ideas on what accessible organic chemistry book I can use to support my learning bacterial biochemical processes in the Brock's book as an adjunct to it? It seems to assume one already has a certain level of knowledge, I think, which I don't have.

Edited March 31, 2017 by StringJunky

[CharonY]

My guess is that a biochemistry book is what you are looking for? OC may be a bit broad. The issue is that many good biochem books with a biological focus (which contextualize pathways better) have a primary focus on eukaryotic metabolism (which is fairly limited). One book that is fairly good with regard to bacterial metabolism (Gottschalk: Bacterial Metabolism).

[StringJunky]

My guess is that a biochemistry book is what you are looking for? OC may be a bit broad. The issue is that many good biochem books with a biological focus (which contextualize pathways better) have a primary focus on eukaryotic metabolism (which is fairly limited). One book that is fairly good with regard to bacterial metabolism (Gottschalk: Bacterial Metabolism).

Right. Thanks. That's good to know because I want to keep my learning sphere reasonably compact, manageable and as specific to bacteriology as possible. I'll see if I can find the Gottschalk.

[CharonY]

In some areas it is slightly advanced, though, if memory serves.

[StringJunky]

In some areas it is slightly advanced, though, if memory serves.

I'm sure some of it will be but, hopefully, I'll get some useful stuff from it. I'm expecting to stutter and start quite bit until I've got a better view of the landscape.

[CharonY]

Another thing to note is that often not all steps are clearly elucidated (because we just don't know) and some bacteria do things surprisingly and we are not sure why. As such much what you read will be limited to model bacteria (which may or may not be good models).

 

One helpful way to dissect bacterial metabolism is to look at certain aspects in a somewhat isolated way and generalize across genera. For example, start with respiration, but focus only on NADPH to the terminal acceptor and look at the variations at the back end. This will help you understand why they are formed like that and what limitations exist, independent on the specific niche (things such as redox potentials) without getting bogged down by the variety of potential pathways to producing those reducing equivalents. It is very difficult to try to understand all the various aspects as it is just too broad and interconnected.

[StringJunky]

Another thing to note is that often not all steps are clearly elucidated (because we just don't know) and some bacteria do things surprisingly and we are not sure why. As such much what you read will be limited to model bacteria (which may or may not be good models).

 

One helpful way to dissect bacterial metabolism is to look at certain aspects in a somewhat isolated way and generalize across genera. For example, start with respiration, but focus only on NADPH to the terminal acceptor and look at the variations at the back end. This will help you understand why they are formed like that and what limitations exist, independent on the specific niche (things such as redox potentials) without getting bogged down by the variety of potential pathways to producing those reducing equivalents. It is very difficult to try to understand all the various aspects as it is just too broad and interconnected.

I'll try to follow that path. Thanks. My aim, up to now is to get a good grasp of the Brock's then, if I'm up to it, specialise and go a bit deeper in specifically focused areas and, perhaps, just on one or two species, like the two mentioned, That's a fair way off yet. i'll just try and enjoy the journey for now until I hit a brick wall. My knowledge of science, in general, is fairly superficial and I've wanted to go to in-depth in an area that interests me for some time. I'm in autodidact mode and not on prescribed course, so, I've no massive expectations of myself; I'll go as far as I can go and be content with that.

 

I found and ordered the Gottschalk 2nd Edition for about $9 secondhand in "good condition" on Amazon with no dust cover and in the UK too. Seems like a bargain when a new copy is well over $100.

[CharonY]

The book is very good to get a decent foundation. It is a bit old now and will be missing a lot of newer findings, but as a basic read it is fairly accessible and, more importantly, it tells you a lot about principles rather than getting bogged down in unnecessary details.

[StringJunky]

The book is very good to get a decent foundation. It is a bit old now and will be missing a lot of newer findings, but as a basic read it is fairly accessible and, more importantly, it tells you a lot about principles rather than getting bogged down in unnecessary details.

Cool. Principles is what I need and want. As you say but in another way, I'm looking for the branches on the tree, not the leaves

 

The book might be old but it's still bloody dear for one written in the eighties. There's a shop online, that happens to be in my city, that's selling it with a "poor" condition hardcover for $35.

Edited April 1, 2017 by StringJunky

[CharonY]

Oh for 9$ it is an absolute steal, no doubt about it. Generations of students have spent a significant time copying parts out for exam preparation.