[3] Microbial phylogenetics emerged as a field of study in the 1960s, scientists started to create genealogical trees based on differences in the order of amino acids of proteins and nucleotides of genes instead of using comparative anatomy and physiology.
[4][5] One of the most important figures in the early stage of this field is Carl Woese, who in his researches, focused on Bacteria, looking at RNA instead of proteins.
Biologists tried to overcome this limitation by sequencing rRNA genes obtained from DNA isolated directly from the environment.
[17] HGT explains why similarities and differences in some genes have to be carefully studied before being used as a measure of genealogical relationship for microbial organisms.
[18] Studies aimed at understanding the widespread of HGT suggested that the ease with which genes are transferred among bacteria made impossible to apply ‘the biological species concept’ for them.
Nonetheless, due to the great role that HGT plays for microbes some evolutionary microbiologists suggested abandoning this classical view in favor of a representation of genealogies more closely resembling a web, also known as network.
[22] PICRUSt is a computational approach capable of prediction functional composition of a metagenome with marker data and a database of reference genomes.
[27] Phylofactorization is a dimensionality-reducing tool used to identify edges in the phylogeny from which putative functional ecological traits may have arisen.
[23] It is possible for microbial traits to be unrelated due to horizontal gene transfer causing the taxonomic composition to reveal little about the function of a system.