Talk:Obligate anaerobe

Are all obligate anaerobes killed by oxygen?

It's clear that oxygen inhibits growth of obligate anaerobes, but it's not clear if oxygen does kill them.

At the beginning of the article is written:

Obligate anaerobes are microorganisms that live and grow in the absence of molecular oxygen; some of these are killed by oxygen.

But below the picture it says:

2: Obligate anaerobes are poisoned by oxygen, so they gather at the bottom of the tube where the oxygen concentration is lowest.

So are all obligate anaerobes killed by oxygen or not?? In other words: Are there any existing obligate anaerobes that just stop growth but aren't killed?

Thanks for your help and for correcting the article. --178.197.226.131 (talk) 13:35, 8 November 2013 (UTC)

Hi. All obligate anaerobes are killed by atmospheric concentrations of oxygen (ie. ~20% oxygen). Some can survive in up to 8% oxygen, others won't survive unless the concentration of oxygen is less than 0.5%. I don't have a supporting reference for this at hand, but will dig one out as soon as possible and modify the opening sentence. Thanks for your patience. Active agent (talk) 14:59, 8 November 2013 (UTC)

I do not know the answer to this question but it is essential to realise that it is a question of semantics and not science. We need to find sources which use the term 'obligate anaerobe' and note how the term is used and to what organisms it is applied. If the sources differ in their usage then we should explain that fact here. Martin Hogbin (talk) 12:06, 9 November 2013 (UTC)

Hi Martin. Could you clarify what you mean when you say this is a question of semantics and not science? It's my understanding that all of the different O₂ requirements can be explained scientifically. Organisms vary in how they metabolise energy (eg. fermentation, anaerobic respiration) and they vary in their sensitivity to oxygen (eg. due to differing levels of superoxide dismutase production, different levels of catalase production). This combination of factors results in the five classifications of obligate aerobe, obligate anaerobe, facultative anaerobe, microaerophile, and aerotolerant. Where does semantics enter into it? Active agent (talk) 16:17, 9 November 2013 (UTC)

Perhaps 'a question of terminology' would have been better. I do not doubt the science and that organisms vary in their sensitivity to oxygen. I would expect that some organisms cannot grow (but survive) in the presence of oxygen and that some are killed by oxygen. Let us call these type A and type B. The question that we need to answer is whether the term 'obligate anaerobe' is normally used for type A or type B organisms. Martin Hogbin (talk) 19:20, 9 November 2013 (UTC)

Hi Martin. Obligate anaerobes are 'type B' ie. killed by normal atmospheric concentrations of oxygen, with the rare exception of endospore-forming microorganisms like the Clostridium species. I think most people would accept that these definitions refer to vegetative bacteria, rather than dormant bacteria though. This subject can be difficult enough for students without throwing red herrings into the opening paragraph. A sub-section later in the article describing spore-forming obligate anaerobes may be warranted. Active agent (talk) 03:21, 10 November 2013 (UTC)

Active agent, do you know of any sources that show the term 'obligate anaerobe' cannot be used to refer to endospore-forming microorganisms. Martin Hogbin (talk) 16:08, 10 November 2013 (UTC)

A quick Google search shows some disagreement between reliable sources:

One source says: 'Exposure to atmospheric levels of oxygen is lethal to obligate anaerobes'.

This source says: 'Obligate anaerobes - need environments where there is no oxygen as they cannot grow in its presence. Some obligate anaerobes are even harmed by oxygen' [My italics].

Hi Martin,

In answer to your first question, the term 'obligate anaerobe' can certainly be used to refer to endospore forming microorganims. Clostridium spp. form endospores, and they are considered obligate anaerobes. The fact that they produce spores does not change the fact that vegetative bacteria are killed by normal atomospheric concentrations of oxygen though. The bacteria are only able to survive if they happen to be in endospore form when they are exposed to oxygen. As I stated above, I think this is a red herring. If it's mentioned in the opening paragraph of the Article, I suspect it will confuse rather than enlighten readers.

In answer to your second question, I've seen quotes like 'Some obligate anaerobes are even harmed by oxygen' before. However, I've also seen microbiology books use the terms fermentation and anaerobic respiration interchangeably. I would argue that this is quite a complex topic, that mistakes are unfortunately inevitable, and that readers need to be quite discerning. When reading quotes like 'Some obligate anaerobes are even harmed by oxygen', for example, readers should look to see if the author provides the names of any genera/species of microbes that are inhibited but not killed by atmospheric concentrations of oxygen. It's sometimes worth chasing up supporting references too. All writers modify the original wording of their source material to avoid plagiarism, and these changes can inadvertently change the meaning of the source material.

Enough of my yakking though. I'm sure there must be other Wikipedians with an opinion on this. Many thanks for the questions.

All the best,

Active agent (talk) 07:51, 11 November 2013 (UTC)

If you'd like another opinion, here's mine ---

First, the terms fermentation and anaerobic respiration can overlap -- fermentation does not require oxygen, so it is an anaerobic process. Many organisms that perform fermentation are perfectly comfortable in oxygen, and can switch from aerobic to anaerobic metabolism. They are 'facultative anaerobes.' So fermentation might be done by an organism that is a facultative or an obligate anaerobe.

Here are some other citations that might be added to this article:

"Obligate anaerobes cannot grow in the presence of atmospheric concentrations of oxygen. It is likely that this deficit is due, in part, to the presence of oxygen-labile targets within the cell. Despite the inability to grow under anaerobic conditions, many obligate aerobes can survive transient exposure to O2 and reactive oxygen species."

"There are two important groups of anaerobic bacteria. these groups are the oxygen-tolerant (aerotolerant) and the oxygen-intolerant (obligate) anaerobic bacteria. The oxygen tolerant anaerobes can survive in the presence of free molecular oxygen. Oxygen tolerant anaerobes may or may not be active in the presence of free molecular oxygen. Obligate anaerobes such as the methane-forming bacteria die in the presence of free molecular oxygen. Obligate anaerobes are not killed by free molecular oxygen. They are killed by superoxide (O2-) and hydrogen peroxide (H2O2). These products are formed when oxygen enters the bacterial cell." [p. 30] Note that this book, on the page cited, has a version of the test tube diagram already featured on this page.

"The facultative anaerobes are able to grow and reproduce in an aerobic or an anaerobic environment. ... The growth of facultative anaerobes does not necessarily need oxygen, but if the oxygen is supplied to the culture, there is better growth. ...Obligate anaerobes can only survive in the environment without the presence of free oxygen. Obligate anaerobes have a series of physiological characteristics, such as the lack of the intracellular respiratory enzyme system, superoxide dismutase, catalase, and cytochrome oxidase, and this show high sensitivity to oxygen."

So it sounds like the best formulation might be:

"Obligate anaerobes lack all ability to perform respiratory metabolism using free oxygen. They also lack enzymes such as superoxide dismutase, which protect aerotolerant organisms from the harmful effects of free oxygen. As a consequence, obligate anaerobes cannot survive anything more than transient exposure to free oxygen at atmospheric concentrations."David.thompson.esq (talk) 02:45, 12 November 2013 (UTC)

Hi David,

I would disagree with you on a few points there. There is no overlap between fermentation and anaerobic respiration. Anaerobic respiration describes the metabolism of energy via the TCA cycle and then the electron transport chain. Fermentation uses neither.

It's also untrue to say that all obligate anaerobes lack superoxide dismutase and catalase. One of the reasons the oxygen tolerance (ability to survive in the presence of oxygen) of obligate anaerobes varies from <0.5% to 8% is that some obligate anaerobes produce small amounts of these enzymes eg. Bacteroides fragilis.

Lastly, I would argue against opening the Article with the sentence "Obligate anaerobes lack all ability to perform respiratory metabolism using free oxygen". If you consider the two defining features of obligate anaerobes, the fact that they don't use oxygen to metabolise energy has to be less important than the fact that they are poisoned by oxygen.

Respectfully,

Active agent (talk) 07:59, 12 November 2013 (UTC)

You may be right about fermentation vs. anaerobic respiration, but you were also right when you said above that there are quite a number of scientific works that say that the two are equivalent, e.g. I don't think it matters particularly to the question that was originally posed, which was whether or not anaerobic organisms are killed by oxygen. My main goal in my comment was to provide citations that can be used to derive and support truthful statements about the question that was posed. I don't have any particular stake in how this is carried out -- your suggested order/emphasis is fine with me. And you are right to point out that absolute generalizations about the bacterial world are nearly always wrong. There also seemed to be plenty of sources available in Google Books if needed, should the citations I provided not be what's required. I wandered onto this page for reasons that I now forget; I think I'll go back to editing pages about Brazilian singers now.... David.thompson.esq (talk) 02:42, 13 November 2013 (UTC)

By the way, a cite for your 2-8% number can be found here: http://books.google.com/books?id=qkLibW2ZikYC&pg=PT384&dq=anaerobic+organisms++oxygen+8%25&hl=en&sa=X&ei=qeiCUs_CN7DgsASCtIHIDw&ved=0CC0Q6AEwAA#v=onepage&q=anaerobic%20organisms%20%20oxygen%208%25&f=false or here http://books.google.com/books?id=np_iQG2GWkMC&pg=PT428&dq=anaerobic+organisms++oxygen+8%25&hl=en&sa=X&ei=qeiCUs_CN7DgsASCtIHIDw&ved=0CDIQ6AEwAQ#v=onepage&q=anaerobic%20organisms%20%20oxygen%208%25&f=false David.thompson.esq (talk) 02:53, 13 November 2013 (UTC)

Hi David, Many thanks for all the reference material... it'll be really useful. I don't have a lot of spare time at the moment, so I'd been editing the pages on oxygen requirements of microbes a little bit at a time. I was focusing on correcting obvious errors in the first place with a view to adding supporting references at a later point. My rationale was that it was better to have something that was correct and unsupported, than to have something that was incorrect and unsupported. Your literature search will save me a lot of time. Many thanks, Active agent (talk) 05:13, 13 November 2013 (UTC)

A suggestion

How about you chaps, who obviously know far more about the subject than I do, write some reasonably detailed and technically accurate material for the body of the article and I summarise it in less technical language for the lead. Martin Hogbin (talk) 10:06, 12 November 2013 (UTC)

Hi Martin,

I'm happy to help, but am afraid it'll only be a little bit at a time. Family and worklife are both kind of busy.

By the way, I've noticed there are Wikipedia articles on aerobic organisms and anaerobic organisms. It might be a good idea to migrate information from these two pages to the pages on obligate aerobes, facultative anaerobic organisms, obligate anaerobes, microaerophiles, and aerotolerant organisms. Wikipedia could then have a disambiguation page for the search 'aerobic organism' and a disambiguation page for the search 'anaerobic organism' each directing to the appropriate sub-category (ie. 'obligate aerobe', 'facultative anaerobic organism', 'obligate anaerobe', 'microaerophile', and / or 'aerotolerant organism'). Do you know how to propose such a merge/change?

Thanks,

Active agent (talk) 05:41, 13 November 2013 (UTC)

* Comment 1) Someone debated whether this might be a matter of semantics or terminology. Those two terms are not clearly separable; the usual dismissive sense of semantics as dealing with quibbles is an illiteratism; sematics is the branch of semiotics dealing with the relationships between signs and meanings, and the concept of terminology is either equivalent to, or a subset of the discipline. Why this is important here is because the point at issue is being debated partly on points of semantics.

2) Up to a point this is reasonable, but we cannot hope to find a definitive terminology based on any one source because various authorities (or, to be more precise, assorted authors) have used the term in various ways and on various whims. We cannot ignore published definitions, but in general we also cannot favour one source against a rival citable source.

3) The points raised in the discussion all are reasonable in their respective contexts, and it follows that the appropriate response is not to claim the greater correctness of one rather than the others, but to present the various concepts in turn, probably in separate sections, together with an introductory overview (not in the lede!) of the various contexts.

4) We must bear in mind that the general concept of (obligate) anaerobic metabolism deals with several forms of metabolism in their relevance to the organisms' biological strategies. The differences between many of the textbook definitions reflect this. The fact that oxygen and many oxidising chemicals are lethal to many organisms does not imply that if others can survive the presence of oxygen, whether by means of spore formation or not, those others therefore are not obligate anaerobes. Any organism that cannot by any means complete its life cycle or metabolise nutrients to propagate successfully in the presence of oxygen can very validly be regarded as an obligate anaerobe; the continuous presence of oxygen or the like prohibits its long-term survival. If anyone argues that the difference between metabolic strategies is material to the terminology, s/he should be able to explain what that difference is, together with citations of course, and why it is important to the terminology. It might be desirable to define or adopt distinct terms for distinct categories, so as to distinguish between for example types of fermentation and obligate anaerobic metabolism.

5) If this proves too tall an order for this article (which seems very possible) then we might find it best to coordinate a few articles dealing with related concepts, together with proper cross-linking. Topics that spring to mind are facultative anaerobiosis, aerobic metabolism, fermentation etc.

$0.02... JonRichfield (talk) 11:01, 13 November 2013 (UTC)

Just to be clear, I was just pointing out that there was no argument about biology but about terminology or classification. The biological facts do not seem to be in dispute the question is simply one about how to classify different types of organism. That does not make the matter trivial or unimportant.

Regarding your later points. I agree that we should aim for a level of consistent nomenclature within WP but we must base that on current usage as shown reliable sources (which is pretty much my original point). We must not invent our own terms. Martin Hogbin (talk) 13:23, 13 November 2013 (UTC)

Hi Jon,

Regarding your comments 'We cannot ignore published definitions' and 'we also cannot favour one source against a rival citable source', I would agree up to a point. I think if someone publishes a definition but fails to back that definition up with suitable examples, it is reasonable to ignore it. For example, if someone defines the Homo genus as 'a group of 4- and occasionally 5-limbed vertebrates' and fails to provide an example of any 5-limbed species, I'd suggest it's reasonable to ignore that definition. Otherwise, Wikipedia would just become a collection of published mistakes. The beauty of Wikipedia is that it's information is constantly evolving anyway, so if somebody does discover the fossil of a 5-limbed Homo species, then that information can be added at a later point.

Lialono (talk) 05:27, 14 November 2013 (UTC)

PS. Just changed my username... hope this doesn't cause any confusion. 'Active agent' sounded too much like a toilet disinfectant.

Well, strictly speaking, if a reliable source referred to 5-limbed vertebrates of the genus Homo, that would be what we have to say here but I am not against a modicum of common sense. Martin Hogbin (talk) 13:53, 14 November 2013 (UTC)

Hi Martin,

Surely, a reliable source ceases to be a reliable source if it fails to provide supporting evidence/examples. Unless.... Unless... Unless, of course, its a book on 'Theoretical Microbiology', 'Theoretical Biochemistry', 'Theoretical Biology' etc. Hmmmmmm... I'm beginning to think you were correct from the start. This is a question of semantics. Hats off to you, sir. I stand corrected.

Lialono (talk) 05:13, 15 November 2013 (UTC)

PS. Thanks, chaps! You've really brightened my week.

Well, one way or another this has been an unusually sane and civilised RFC, leaving me with good hopes for a practical and useful outcome. JonRichfield (talk) 08:15, 15 November 2013 (UTC)

Present state

In its present state, the article is perfectly clear that all obligate anaerobes are killed by oxygen. The article also discusses the varying sensitivities of different obligate anaerobes, and distinguishes them from microaerophiles; both points are made clearly.

I'm here commenting by invitation. As a reader with no prior knowledge of the topic, I find the article is admirably clear and succinct. As far as I can tell, there is no [longer a] problem with the article's clarity. yoyo (talk) 16:28, 22 November 2013 (UTC)

References

Wrong word?

Should the word "can" in the first line of text under the test tubes image be "in"? And, in either case, should there be a space between the word and thioglycollate?

I started to correct this, but I don't know enough about the field to be confident in my correction.

Would somebody scientifically competent please take this on? KC 18:25, 28 March 2016 (UTC) — Preceding unsigned comment added by Boydstra (talk • contribs)