Tara A. Gianoulisa, et al., PNAS

In the Origin, the Darwin believes the environment will affect the characteristics of individual. These are always interesting questions: Do the different species have similar effect in the same environment? Is there any common effect in the similar environment? Above questions only can study [...]]]> Quantifying environmental adaptation of metabolic pathways in metagenomics

Tara A. Gianoulisa, et al., PNAS

In the Origin, the Darwin believes the environment will affect the characteristics of individual. These are always interesting questions: Do the different species have similar effect in the same environment? Is there any common effect in the similar environment? Above questions only can study from metagenomics aspect. The authors focus on not common functions but pathways across the species. They try to find the common and different pathway within the environment to describe the environment. They propose two methods, regularized canonical correlation analysis (CCA) and discriminative partition matching (DPM). These two methods can correlate different features and different environment to find the similar pathway across the samples.

There are three cases have been analyzed. Firstly, the metabolic pathways associated with amino acid and cofactor transport and metabolism have significant variation with the environmental features. The species can uptake and recycle the exogenous amino acid, and the uptake is related to the light availability. They observed variation in different location from the north to the south. The temperature and chlorophyll have the same principal axis along with light availability.

Secondly, the amino acid synthetic pathways are not related to the energetic cost of synthesizing a particular amino acid. Instead, it has highly correlation between the structural correlation of the amino acid pathways and their dependence on potentially limiting cofactors. It means the species may be more favorable to uptake outside amino acid than synthesis it.

Thirdly, there is an essential amino acid, methionine, in oceanic microorganisms. The methionine synthesis, salvage, and degradation pathways are related to the environment. When methionine degradation and amino acid transporters increase the synthesis of methionine and cobalamin will decrease. This result shows methionine has a significant role in shaping the adaptations.

The authors also take a look on lipid and glycan metabolism. Those components are important in the extracellular, so it might reflect the change of environment. The glycan can modify the lipid to enable or disable the function on the lipid. They do find a strong correlation between environment and features.

The authors claim these finding can be good biosensors when there is no other indicator of the certain environment. I am thinking whether these can be used as the environment evolution index or not. If we can use these as the evolution indicator, we can describe these environment changes by looking at the lineage of the microorganism within this environment.

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