( ( ( ( ( ( ( ( The protein ) ( of ( ( ( both ( the bacteria ) ) and ) ( plant material ) ) ) ) ( is digested ) ) , ) ( ( the ( digestion products ) ) ( passing ( into ( ( the ( small intestine ) ) ( where ( assimilation ( takes place ) ) ) ) ) ) ) ) and ) ( they ( enter ( the bloodstream ) ) ) ) . )
(ROOT (S (S (NP (NP (DT The) (NN protein)) (PP (IN of) (NP (NP (PDT both) (DT the) (NNS bacteria)) (CC and) (NP (NN plant) (NN material))))) (VP (VBZ is) (VP (VBN digested)))) (, ,) (S (NP (DT the) (NN digestion) (NNS products)) (VP (VBG passing) (PP (IN into) (NP (NP (DT the) (JJ small) (NN intestine)) (SBAR (WHADVP (WRB where)) (S (NP (NN assimilation)) (VP (VBZ takes) (NP (NN place))))))))) (CC and) (S (NP (PRP they)) (VP (VBP enter) (NP (DT the) (NN bloodstream)))) (. .)))
The protein of both the bacteria    and plant material is digested, the digestion products passing into the    small intestine where assimilation takes place and they enter the    bloodstream.
(ROOT (S (PP (IN In) (NP (DT the) (NN body))) (, ,) (NP (NN chemical) (NN digestion)) (ADVP (RB mainly)) (VP (VBZ takes) (NP (NP (NN place)) (PP (IN in) (NP (DT the) (JJ small) (NN intestine))))) (. .)))
In the body, chemical digestion mainly takes place in the small intestine.