Review: Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota

 When people think about human evolution they usually consider big changes like multiple arms or extra eyes, but the reality is that there are many small changes long before any major change. These small changes occur in our genetic material and can have numerous effects, such as allowing us to process alcohol faster as is the case in alcohol dehydrogenase in peoples of European descent versus peoples of Asian descent. This paper is interesting because evolution is occurring and is opening new food sources to humans, but the thing changing is the genetic material of the microorganisms that live in our gut.
 So, a few words about microorganisms. They are single celled and the term "microorganism" can apply to archaea or bacteria, but for this paper it is bacteria. Humans have 23 chromosomes and two of each of them in each cell except for red blood cells, which don't have any genetic material. The totality of these chromosomes is the human genome. Bacteria only have one chromosome, but some, possibly many, can accept small pieces of DNA from other bacteria. These transferable pieces of DNA are called "plasmids." The transfer of plasmids is responsible for antibiotic resistant strains of Staphylococcus aureus which plague hospitals. This process of transferring plasmids is called "horizontal gene transfer." Many types of bacteria have an outer barrier which is composed of long strings of sugars usually D-galactose or some variation of it. Lastly, bacteria exist everywhere. Every square inch of everything has something growing on it or ready to grow on it should nutrients become available on aforementioned it.
 Now to the paper at hand. The researchers were initially interested in finding enzymes that can breakdown seaweed to its component sugars. By the way, seaweed is a collection of bacteria that grow together and their sugar barriers blend together. The researchers wanted to see what bacteria can eat that sugar barrier and what enzymes are used in that task. To do this they took the sequenced genome of Zobellia galactanivorans and used a computer program to search for genes which code for enzymes most likely to degrade the long sugar chains of seaweed. There search found five genes. Enzymatic analysis showed that only two could degrade seaweed, with Porphyra, commonly known as "nori," being preferentially degraded. These are the first "beta-porphyranases described so far" and represent "a new class of glycoside hydrolases."
 From here, the researchers crystallized those enzymes and identified the features that would allow them to find other enzymes that can degrade nori using the many publicly available sequence databases. During this data mining, they found that all beta-porphyranases were found in marine microorganisms except Bp1689, which is found in the human gut bacterium Bacteroides plebeius.  Curiously, all sequences of B. plebeius are from bacteria collected from Japanese individuals. Genomic sequences of B. plebeius strains collected from western people didn't contain the beta-porphyranase.
 I should give an additional word about microorganisms and their genetic material, they have operons. Operons are genes in very close proximity (<100 basepairs apart) that are part of a metabolic pathway. When studying bacteria, operons are very convenient because they can provide valuable clues about an enzyme's function. The paper, under discussion now, compared the operon of the beta-porphyranase from B. plebeius from Japanese individuals to B. plebeius from western individuals and found many of the former genes to be missing in the latter. Interestingly, the operon from B. plebeius from Japanese individuals is situated between conserved genes coding for "conjugative DNA transfer," suggesting horizontal gene transfer.
 Summing it all up, Z. galactanivorans evolved a beta-porphyranase to degrade nori. Nori is eaten by Japanese people who initially could not digest it. Over the years, the plasmid containing the operon that codes for nori degradation was transferred to B. plebeius in the gut of Japanese people. This allowed Japanese people to eat nori and get some nutritional value out of it. "Tax records from the eighth century list seaweeds as payments to the Japanese government" and since seaweed is not cooked this allows for live bacteria to enter the system.