Importance of Microbiomes: how they are formed (Introduction)

by David Turell , Wednesday, January 17, 2024, 20:11 (101 days ago) @ David Turell

Each species has different roles in different microbiomes:

https://www.quantamagazine.org/the-quest-for-simple-rules-to-build-a-microbial-communit...

"Each bacterial city has an origin story. A vat of wine fermenting for months, a biofilm in the lungs of a cystic fibrosis patient and a sulfur-rich hot spring all started with a set of founder cells that proceeded to form a robust network of interacting species. These communities can perform biochemical functions that no single species can do on its own. It takes a quorum of Lactococcus and Streptococcus strains working together to give cheddar cheese its texture and tang. Different combinations of gut microbiota can enhance or blunt the effectiveness of a pill.

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“'There is redundancy — like, two species can perform the same function — and the same species can perform different functions depending [on] if you change the environment,” said Otto Cordero, a microbiologist at the Massachusetts Institute of Technology. “Taxonomy is not as informative as function.”

"Last year in Cordero’s lab, research led by the microbiologist Matti Gralka identified a set of microbial functions that could be predicted without species information. After characterizing the metabolisms of 186 different bacterial strains collected from the Atlantic Ocean, he found that he could predict a given microbe’s basic food preferences based on its genome alone.

"This pattern allows researchers to bypass the gene sequences involved in breaking down one food source or another. Gralka’s team discovered that they could predict the preferred food merely by measuring the molecular composition of the genome. The findings were published in Nature Microbiology.

"While the field is in its infancy, the microbial ecologists are looking for ways to quickly assess and describe naturally occurring microbial communities, whether in a wild environment or in a hospital. By developing a theory of microbial assembly, they hope they can learn to see the largely invisible and rapidly shifting microscopic ecologies unfolding all around us.

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"In 2009, fewer than 1,000 bacterial genomes had been completely sequenced. By 2014, there were more than 30,000. That figure has since ballooned: At the end of 2023 there were 567,228 complete bacterial genomes, easily browsable and available for cross-reference. Today bacteria account for nearly 80% of all available genomic data.

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"For the study, his lab grew wild bacteria cultured from dead leaves and soil around New Haven, Connecticut. They found that given the same set of environmental conditions — the same carbon sources, temperature, acidity and so on — any microbial community will arrive at roughly the same functional composition, no matter how it started. In his experiments, with every population, the same niches appeared and were filled over and over, though not necessarily by the same species of bacteria.

"The research changed how microbiologists looked at community. When Sanchez compared communities sampled from the same environment, the names of the bacteria were always different, D’Souza said. “But if you look at the functional gene content, like who does what? That is surprisingly similar,” he said. “So it doesn’t matter who you are; what you do matters.”

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"The chemistry of a bacterium’s DNA predicted its niche in the community. Gralka could identify whether a species primarily ate sugars or acids based on the content of its genome alone, without examining its genes at all. Statistics and genomics found simple order where taxonomy didn’t see any.

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"Microbial communities are key players in every ecological cycle on Earth. When a tree falls in a forest, a litany of fungi and bacteria assemble to eat and decompose it, returning the tree’s components to global nutrient cycles. With the concepts introduced by Gralka, Sanchez, Cordero and other microbial ecologists, this new community’s niches are predictable. Wood is mostly composed of cellulose and hemicellulose, which are glucose polymers; therefore, a functioning community ripe for participating in woodland decomposition would host sugar-eating bacteria, be abundant in sugar-digesting genes, and have genomes composed of a lower proportion of GC molecules. A sudden and mysterious spike in acid-eaters could be a sign of something amiss, Gralka suggested.

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"In a sense, these scientists are ecologically mapping microbial communities for the very first time. Their work proposes a new view into what a microbial community actually is — showing that what microbes are is best defined as what they do."

Comment: a bright new way to look at biomes at work. Throughout all of evolution the bacteria remained to be an essential part of life. They most have had their own form of evolution to prepare for the job.