1. A method of improving the intestinal microbiota population, which comprises administering to the subject a composition to increase the first intestinal microbiota population while reducing the second intestinal microbiota population in said subject, wherein the first intestinal microbiota population includes a short-chain fatty acid producing bacterium (SCFA) and a second population intestinal microbiota includes an endotoxin producing bacterium. 2. The method of claim 1, wherein the composition comprises a natural medicament, a natural product, an herbaceous plant, or an extract of herbs. The method of claim 1, wherein the composition comprises berberine, a derivative of berberine, or an anisoquinoline alkaloid. The method of claim 1, wherein the composition comprises a plant or an extract thereof, the plant comprising Berberis vulgaris, Coptischinensis, Scutellariabaicalensis, Phellodendri Chinensis, Momordicacharantia, Ilex kudingcha, Sophoraflavescens, Gentianascabra, Anemarrhenaasmathemabides, Anemarrhenaaspha mémoides, and Anemarrhenaaspha mélodes, combinations. 5. The method of claim 1, wherein the composition comprises a plant or its extract, the plant being Berberis, Coptis, Scutellaria, Phellodendron, Momordica, Ilex, Sophora, Gentiana, Anemarrhena, Gardenia, Rheum or Taraxacum. The method of claim 1, wherein the composition comprises a plant or its extract, the plant being Berberidaceae, Ranunculaceae, Lamiaceae, Rutaceae, Cucurbitacea, Aquifoliaceae, Leguminosae, Gentianaceae, Agavaceae, Rubiaceae, Polygonaceae, Asteraceae, Menispermaceae or Cucurbit. The method according to claim 1, wherein the first intestinal microbiota population includes Alistipes, Allobaculum, Bacteroides, Barnesiella, Blautia, Butyricicoccus, Butyricimonas, Dorea, Helicobacter, Hespellia, Holdemania, Lawsonia, Oscillibacter, Parabacterooterides, Pharabacterobides, Phobacterobides, Phocactoboides, Phobacterobides, Phocobacterides, Phocobacterides, Phocobacterides, Phasobacteride
