You may have noticed a seeming oddity about science in that you often hear nothing about a topic for ages and then along come several new pieces of work more or less together — the London bus effect. There’s number of reasons for this, one being that scientists love gadgets — they’re really little boys and girls with licence to play with their toys for a living — so when a new method or piece of kit appears there’s usually something of a band wagon response. Another factor is that different labs quite often talk to each other and this can lead to collaborative efforts sometimes resulting in several, complementary publications. We’ve seen this recently with bugs and their effect on human cancers. In Secret Army: More Manoeuvres Revealed we saw how bacteria could drive lung cancer and in Mushrooming Secret Army how fungi are now established as players in at least in one type of cancer.
Now add to these a paper by Hila Sberro, Ami Bhatt and colleagues from Stanford, Berkeley and the Biomedical Sciences Research Center Alexander Fleming, Vari, Greece that reveals a huge pool of hitherto unknown proteins in the human microbiome.
What Sberro & Co did was to take tissue samples (1,773 of them) from humans (skin, vagina, gut and mouth) and look at the DNA sequences therein. What you get doing this is the ‘metagenome’ — i.e., the DNA of the whole community you pick up — and that type of study is therefore called ‘comparative genomics’.
Scheme showing how metagenomic analysis can identify thousands of small coding regions of DNA from microbiome sequences obtained from a range of human tissues. From Sberro et al., 2019.
They focused on ‘small’ proteins of 50 or fewer amino acids. The hormone insulin has 51 amino acids and proteins in the size range up to about 50 amino acids are often called ‘peptides’. Perhaps counter-intuitively, large proteins are easier to isolate than the little chaps who have for this reason been rather overlooked — until now that is.
Some over-sight because Sberro et al. discovered more than 400,000 of these potential mini-proteins lurking in the nooks and crannies of their human volunteers. This hitherto largely unknown horde (fewer that 5% had been identified before) turned out to be made up of about 4,500 ‘families’ — groups of proteins that are similar in size and amino acid content.
This is a really astonishing finding quite literally under our noses. At the moment we have no idea what most of these bacterial proteins do. As you might expect, some of the proteins appear to be involved in keeping cells alive (they’re ‘housekeeping genes’). You might also guess that some may not have any role at all — they’re just a kind of accidental by-product — but, by and large, Nature doesn’t waste energy and making proteins is a very expensive business in energetic terms. And if you’re in any doubt about the importance of ‘peptides’, give a moment’s thought to the human proteins oxytocin (9 amino acids that plays an important role in sexual reproduction and in childbirth) and — even smaller — the tripeptide (i.e. 3 amino acids) glutathione that protects most living things from damage by free radicals.
As some of the small, bacterial proteins are present in large amounts we can be confident they too do something useful — perhaps protect the bacteria themselves from their own toxins, made to kill viruses.
And, as ever, when we get to understand what these little guys are up to they may be useful in, for example, interventional medicine.
Sberro, H. et al., 2019. Large-Scale Analyses of Human Microbiomes Reveal Thousands of Small, Novel Genes. Cell 178, 1-15.