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I can understand everything from this article except one single word that causes me trouble in getting the complete meaning of the following sentence:

The dietary swaps appeared to cause significant changes to the cells lining the gut as well as the bacteria that live in the bowel - with the US volunteers faring better.

I understand that the new diet caused important changes to the cells, modifying their structure, but what exactly happened to the gut by lining it and also to the bacteria (were they lined too or what?) I quite can't get.

Checking The Free Dictionary for the verb to line, I couldn't find an appropriate sense for the context in question.

So, please let me know which one of the following dictionary definitions matches:

v. lined, lin·ing, lines

v.tr.

  1. To mark, incise, or cover with a line or lines.
  2. To represent with lines.
  3. To place in a series or row.
  4. To form a bordering line along: Small stalls lined the alley.
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The closest match is the fourth definition. What "lining the gut" refers to is cells in the body whose location is the inside of the gut. They are spread around the gut's walls creating a bordering protective layer of cells. For instance, we often refer to the lining of the stomach, which is a layer of mucous cells which produce mucus to protect the stomach from its own secretions. As such, the first definition of the noun "lining" may help you more than the definition of the verb.

The key part of the phrase in doubt when parsed is "cells that line the gut", so they should be understood to be spread along the inside of the gut in such a way as to create a layer of protection as described in the definition I linked above. The bacteria simply "live" in the bowel, so I imagine them to be "floating around" and not providing a protective layer in the way the cells in the gut do.

As a final source of help, my mother used to "line her frying pan with butter" before she put it on the heat so as to protect it (and the foodstuffs inside) from immediately burning. We also talk about "lining our stomachs" (not to be confused with the noun use above) before we go to the pub and imbibe quantities of alcohol. This means eating some food which is intended to soak up/absorb some of the alcohol and reducing the chances of ill-effect from the impending alcohol.

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    I'd consider adding comparison with such as a jacket lining, preventing wear on the inside of the 'main' material. – Tetsujin Apr 30 '15 at 8:57
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    An excellent point. Yes, it should be noted that we often have lining on the inside of our clothes to protect the outer material, or, depending on the garment, to provide a nicer feel against our skin. Grab a jacket and compare the outside to the inside. The material that is stitched on the inner side is the lining. – JMB Apr 30 '15 at 10:52
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The misunderstanding here is the sentence structure: "lining the gut" describes the cells, not the effects of the diet.

Here's a trimmed-down version of the sentence.

The dietary swaps caused changes to the cells lining the gut.

There are cells ("cells lining the gut"), and the diet caused changes to them. (A slightly clearer alternative would be "...cells that line the gut...", but that's not what this author chose, perhaps because journalists habitually use shorter ways of saying things.)

Now, as for the meaning of "lining", your fourth dictionary definition is the appropriate one here. Your gut is lined with cells; the cells are lining (verb) the gut; they are its lining (now a noun). Check your dictionary for a professional version, but I would define "lining" (noun) as "a layer that covers the inside of something".

Lastly, because "lining the gut" describes the cells, it has nothing to do with the bacteria, so you don't need to ask what "lining the bacteria" means!

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Compare:

Commuters taking the subway are delayed whenever the electrical power fails.

The monks living in silence meditate and work all day.

The cells lining the gut are affected by diet.

These are modifying clauses not introduced by relative pronouns; they could be restated:

who take the subway
who live in silence
which line the gut

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