Companion planting is one of the most common and effective planting methods in modern agriculture. White clover (Trifolium repens L.) and orchard grass (Dactylis glomerata L.) are two typical pastures planted together to promote each other's growth. However, the detailed biological foundations of companion planting remain unclear. In this study, we screened typical microbiome profiles under separate and combination planting conditions using 16s RNA gene sequencing techniques. We identified the typical distinctive microorganism subtypes based on the microbiome profiles and recognized the enriched functions of top abundant microorganisms in soil using different planting strategies with the help of Kyoto Encyclopedia of Genes and Genomes and Clusters of Orthologous Groups annotation. This analysis confirmed that the optimal microorganisms and screened functional annotations are correlated with nitrogen fixation; thus, companion planting may improve the yield and efficacy of plants by improving the efficiency of nitrogen fixation.

Gut microbiomes are integral microflora located in the human intestine with particular symbiosis. Among all microorganisms in the human intestine, bacteria are the most significant subgroup that contains many unique and functional species. The distribution patterns of bacteria in the human intestine not only reflect the different microenvironments in different sections of the intestine but also indicate that bacteria may have unique biological functions corresponding to their proper regions of the intestine. However, describing the functional differences between the bacterial subgroups and their distributions in different individuals is difficult using traditional computational approaches. Here, we first attempted to introduce four effective sets of bacterial features from independent databases. We then presented a novel computational approach to identify potential distinctive features among bacterial subgroups based on a systematic dataset on the gut microbiome from approximately 1,500 human gut bacterial strains. We also established a group of quantitative rules for explaining such distinctions. Results may reveal the microstructural characteristics of the intestinal flora and deepen our understanding on the regulatory role of bacterial subgroups in the human intestine.