Due to the progress of science and technology, it is now possible to directly sequence all the DNA in the sample and piece together the genomes of different organisms. Therefore, even microorganisms that cannot be cultivated or even previously unknown have the opportunity to be discovered by new methods.
The same concept can also be used in ancient samples to understand ancient living microorganisms. Recently, two papers were published, which discussed the oral and intestinal bacteria born in ancient humans.
Do Neanderthals eat grass? Mauricio Anton obtained ancient oral microorganisms from dental calculus.
It is easier to study the microorganisms in the ancient people's mouth than to study other parts such as skin and intestine. This is because soft tissue is difficult to preserve, and even if there is soft tissue, it is difficult to leave traces of microorganisms in it except in a few cases such as Oz the Iceman. In contrast, various components in the mouth often enter dental calculus and remain with the teeth to this day.
There have been some studies on dental calculus of ancient Homo sapiens before, and several samples were published by Neanderthals tens of thousands of years ago.
In these two new papers, in addition to 15 known samples, 109 new dental calculus were obtained. This is a total of *** 124 samples, which are from howler monkeys in America, gorillas and chimpanzees in Africa, Neanderthals and Homo sapiens tens of thousands of years ago, and more recently Homo sapiens. [ 1, 2]
Ancient and modern intellectuals who contributed dental calculus samples. Excerpted from [References 1]
There are some microbial patterns in various primates, from which it can be inferred that some microorganisms should have a long-term relationship with primates, perhaps more than 10 million years. Microorganisms in the oral cavity mainly include Streptococcus, Actinomyces, Fusobacterium and Corynebacterium.
The difficulty in studying microorganisms is that there are too many changes in close relatives and many unknown patterns. According to genetic differences, oral microorganisms obtained from human dental calculus can be divided into 27 genera, but three of them don't even have names.
That is to say, although they used to be the main microorganisms in human mouth, all of them have no known information. There are too many unknowns about living microorganisms.
Neanderthals who contributed dental calculus samples. Homo sapiens and Neanderthals from Europe [Reference 1], did they enjoy the microorganisms in the oral cavity?
The earliest sample obtained this time is Neanderthals about 654.38 million+years ago, from Serbian Pe in Eastern Europe. Turina site is the remains of Neanderthals tens of thousands of years ago, located in Spanish, Belgian and Italian.
Interestingly, the oral microbial composition of Homo sapiens and Neanderthals was similar as early as 6.5438+0.4 million years ago. Homo sapiens in Europe, which was later than 1.4 million years ago, was obviously different and close to the later Homo sapiens. It is known that many immigrants entered Europe after10.4 million years ago. It seems that different people also carry different oral microorganisms.
Is the oral microorganism of Homo sapiens in Europe directly related to Neanderthals? The formation of oral microorganisms is related to the baby's caregivers. Therefore, the researchers concluded that Homo sapiens who first entered Europe and met Neanderthals had children and also obtained oral microorganisms from Neanderthals. [3]
More than 40,000 years of European Homo sapiens (with Zlat? k？ Genetic relationship with later Europeans and Asians. Homo sapiens outside Africa had gene communication with Neanderthals before branching; However, the later Homo sapiens in Europe was not directly related to the earlier Homo sapiens immigrants. From bumpy driving to rediscovery of zlat? k？ ň
The problem is that the above inference is inconsistent with the known evidence. Homo sapiens inherited Neanderthal DNA from the stage before the separation of peoples outside Africa more than 50 thousand years ago. Homo sapiens who entered Europe more than 40 thousand years ago did meet Neanderthals, and some people exchanged more genes; But they all disappeared later, and it has nothing to do with later European Homo sapiens. [4, 5]
Homo sapiens in Europe, with oral microbes similar to those of Neanderthals, probably entered Europe after the disappearance of Neanderthals from 1.4 to more than 30,000 years ago, but actually did not have a chance to meet each other. I think the similarity of oral microorganisms between the two sides comes not from direct communication, but from other reasons
Even without agriculture, Homo sapiens and Neanderthals ate a lot of starch?
Another discovery worth mentioning is that both Neanderthals and Homo sapiens had various types of streptococcus that could digest starch. If there is no starch in the diet, such microorganisms are unlikely to be so rich; It can be inferred that Homo sapiens, even Neanderthals, who did not invent agriculture, probably consumed a lot of starch at ordinary times.
The diet of homo sapiens in ancient and modern times can be described as ever-changing. Even if there are no crops such as rice, wheat and corn, a large amount of starch can be obtained only by collecting tubers, tubers, fruits and other foods without relying on agriculture.
In Utah, USA, wild potato eggplant is rich in starch. Archaeological research found that the local people had already eaten this plant 10,000 years before the emergence of agriculture. It is taken from starch granules, which proves that potatoes were first used in North America.
As for what Neanderthals ate, our understanding is still limited. Some studies believe that Neanderthals mainly ate meat, especially the meat of large herbivores. The large amount of starch put forward this time is still an argument that needs textual research.
My personal thought is that even without agriculture, the diet of Homo sapiens is very different in different time and space according to the so-called gathering, hunting and fishing, and so is Neanderthals. Some staple foods eat meat, and some eat a lot of starch, which may be closer to the actual situation. So far, the sampling is very limited, so it is difficult to evaluate the dietary diversity of Neanderthals.
/kloc-intestinal bacteria of ancient Americans more than 0/000 years ago
Microorganisms living in the intestine will affect digestion, immunity and other functions. In recent years, their popularity has increased greatly, and even the trees under the banyan tree may know it.
Another recently published study obtained intestinal bacteria of several ancient Americans from 1000 to 2000. Sampling intestinal bacteria usually does not go deep into the intestine, but samples from feces. The same is true of this new study. Rare samples come from fecal fossils from three locations in the southwestern United States. [6, 7, 8, 9, 10]
The researchers tried 15 samples, and 8 of them succeeded. After sequencing all the DNA, they pieced together the genomes of 498 kinds of bacteria. The objects to be discussed here are "ancient times" and "intestinal bacteria". After excluding the suspected non-ancients, there were 209 samples, of which only 18 1 came from the intestine, and the most likely was the intestinal bacteria of the ancients.
From Phil Madden
There are many microorganisms, many mutations, and ever-changing strains, most of which are not within the scope of human cognition; This research method relies on piecing together DNA to speculate, and does not obtain complete real bacteria. Therefore, the "species" here is not completely equivalent to the general species, but refers to the genome bin at the species level, abbreviated as SGB. For convenience, this paper is written directly as a.
18 1 39% of the ancient intestinal bacteria, that is, 6 1 species, have never been seen before. They may have disappeared, or they are unique styles of the ancient southwestern United States. When exploring ancient microorganisms, it is normal to find unknown microorganisms.
The relationship between intestines echoes the great history of mankind.
Compared with the ancient 789 modern people, most kinds of intestinal bacteria are still * * * connected, but there are some genetic differences. Two kinds of Brevibacterium methanogenes were pieced together from ancient specimens, which were called Brevibacterium Smith in Chinese. Brevibacterium methanogenes is often found in the intestine. They are not bacteria, but archaea.
Brevibacterium Smith in ancient and modern times, an evolutionary tree constructed according to genomic differences. Red is a sample of ancient Americans. Excerpted from [Reference 6]
The two strains of Brevibacterium smithii have a history of 1000 years. They are most similar to each other in genetics and belong to the DNA variation of modern samples. It is estimated that the ancestral age of these archaea * * * is the same, ranging from 5 1 to128,000 years ago, with an average of 85,000 years ago. It seems to be one of the intestinal bacteria that Homo sapiens ancestors took away in their stomachs when they left Africa.
Interestingly, the age of separation between archaea and its recent congeners ranged from 1.6 to 40,000 years ago, with an average of 27,000 years ago. If the estimate is correct, it is likely to fall in the era when Homo sapiens immigrated to America and gradually separated from Asia.
These coeval microorganisms also hide the clues of migration and immigration history.
Before industrialization, there were no antibiotics.
Living environment and daily diet are the main reasons that affect the composition of intestinal bacteria. Compared with 789 modern people, the intestinal bacteria of the ancients were closer to the non-industrialized society, which was obviously different from the industrialized society, which was in line with expectations.
Under PCA, ancient Americans are more similar to modern people in non-industrialized society than modern people in industrialized society. Excerpted from [Reference 7]
At the gene level, there are many genes (endo -4-O- sulfatase, SusD-like protein) that decompose glycans in the intestinal bacteria of modern people in industrialized society.
In contrast, the intestinal bacteria of ancient people and non-industrialized modern people have more carbohydrate active enzymes (CAZYME); Decomposition of starch and glycogen. In addition, they also have more movable geic components (such as transposons), which may help to increase their adaptability in the changing environment.
However, whether modern people in industrialized society or non-industrialized society, intestinal bacteria are equipped with more anti-antibiotic genes than the ancients. Let's take a look at the influence of antibiotics on intestinal bacteria after they are widely used.