Bacteria's family tree - Phylogenetic classification of bacteria

LUCA, our common ancestor

All life on Earth can be classified into three domains as the highest biological taxon: Bacteria, Archaea and Eukaryotes. All three domains share the same universal ancestor LUCA, the Last Universal Common Ancestor.


Archaea is a very old domain - from the outside very similar to bacteria but with very different genes and a distinct biochemistry. Currently 26 evolutionary groups (phyla) are known. They are mostly found in extreme ecosystems such as hot springs or salt lakes, but are probably found in ecological niches such as the gut or in the navel as well.


Eukaryotes are single-cell organisms with a nucleus and cell organelles and are the youngest domain. They are the building block for the complex, multi-cellular life which evolved 600 million years ago. Thus, some eukaryotes also belong to the microbes, as for example moulds or algae. Eukaryotes are distributed in five evolutionary groups (phyla).


The Bacteria domain is the largest of all three domains with currently 92 phyla.

Tree of life

Illustration: Hug et al., A new view of the tree of life, 2016

This great bacterial diversity can be illustrated as follows: when creating a tree of life, including all life on Earth, LUCA rests in the middle of a trunk with wide-reaching branches. If humans sat at the end of a branch at the 5 o´clock position, where would you expect the well-known herb basil to be? Well, it is right there next to us, on a branch at 5.01 am! So if herbs and humans are so close to each other in the phylogenetic tree, what else is seated within the rest of the tree??? It's the bacteria! They occupy around 80% of the tree! For example, if the well-known bacterium E. coli sat on a branch at 6 o'clock, Lactococcus lactis would be seated at 12 o'clock!

Classification of bacteria

bacteria cell


Bacteria can be classified by observable characteristics, the so-called phenotype…

First of all there is the Gram-staining which is the most important classification tool in microbiology. This staining distinguishes two different cell envelope types: the envelope which can be stained with the Gram-method and the ones that can´t. There are bacteria with a rigid, thick cell wall and a higher inner cell turgor – gram-positive bacteria. Gram-negative bacteria have a thinner cell wall but an additional protective outer membrane. The latter group could not be marked by the colorant, thus we now call them Gram-negative because they do not respond to the method of marking invented by Dr. Christian Gram.

Bacteria can also be classified through their colony morphology.

When growing bacteria in an environment they love with all the nutrients they need and the right temperature, a single bacterium can build colonies, which are conglomerates of millions of clones of that bacterium which you can see with the naked eye. These colonies look different: they may be slimy, dry, wrinkled, form towers and have different colours, always characteristic for a specific bacterium.

They can be classified by the way they move - if they are moving at all. They can swim, creep, crawl, swarm or move with gas vesicles.

By feeding bacteria with special supplements, or growing them at a special temperature or pH, one can distinguish them through their physiology. Either they grow on a special breeding ground or they release enzymes which effect a colour change of special chemical components…

…but since recently they are more often (and more precisely) classified by their genotype.

Here's just a quick detailed look into an excerpt of a few important evolutionary bacterial groups (phyla), to get a feeling for how they're classified and the relationships between bacteria. The highest order is the domain - here, bacteria - and the subsequent order is the phylum:

Phylum Firmicutes (Gram-positive):

Class: Bacilli or Firmibacteria

Order: Bacillales

  • Family: Bacillaceae
    Bacillus (commensal of the gut and environment)
  • Family: Listeriaceae
    Listeria (agent of Listeriosis)
  • Family: Staphylococcaceae
    Staphylococcus (agent of Atopic Dermatitis, MRSA)

Order: Lactobacillales

  • Family: Enterococcacae
    Enterococcus (commensal of the gut)
  • Family: Lactobacillaceae
    Lactobacillus (commensal of the gut and vagina)
  • Family: Streptococcaceae
    Streptococcus (commensal of the mouth)

Class: Clostridia

Order: Clostridiales

  • Family: Clostridiaceae
    Clostridium (commensal of the gut and agent of food poisoning)
Phylum Actinobacteria (Gram positive):

Class: Actinobacteria

Order: Actinomycetales

Suborder: Corynebacterineae

  • Family: Corynebacteriaceae
    Corynebacterium (commensal of the skin)
  • Family: Mycobacteriaceae
    Mycobacterium (agent of Tuberculosis)

Suborder: Propionibacterineae

  • Family: Propionibacteriaceae
    Propionibacterium (commensal of the skin, agent of acne)

Order: Bifidobacteriales

  • Family: Bifidobacteriaceae
    Bifidobacterium (commensal of the gut)
Phylum Bacteroidetes (Gram-negative):

Class: Bacteroida

Order: Bacteroidales

  • Family: Bacteroidaceae
    Bacteroides (commensal of the gut)
  • Family: Prevotellaceae
    Prevotella (commensal of the G.I. tract)

Class: Flavobacteria

Order: Flavobacteriales

  • Family: Flavobacteriaceae
    Flavobacterium (environmental bacterium)
Proteobacteria (Gram-negative):

Class: Alphaproteobacteria

Order: Rhizobiales

  • Family: Rhizobiaceae
    Rhizobacterium (nitrogen-fixating symbiont of plant-roots)

Class: Betaproteobacteria

Order: Neisseriales

  • Family: Neisseriaceae
    Neisseria (agent of gonorrhoea)

Class: Epsilonproteobacteria

Order: Campylobacterales

  • Family: Campylobacteriaceae
    Campylobacter (agent of food poisoning)
  • Family: Helicobacteraceae
    Helicobacter (commensal of the stomach)

Class: Gammaproteobacteria

Order: Enterobacteriales

  • Family: Enterobacteriaceae
  • Enterobacter (commensal of the gut)
  • Escherichia (commensal of the gut)
  • Klebsiella (dangerous hospital germ)
  • Salmonella (agent of food poisoning)
  • Shigella (agent of dysentery)

Order: Vibrionales

  • Family: Vibrionaceae
    Vibrio (agent of Cholera)

Order: Legionellales

  • Family: Legionellaceae
    Legionella (agent of Legionnaire's disease; found in warm-water-pipes)

Order: Pseudomonales

  • Family: Moraxellaceae
    Acinetobacter (dangerous hospital germ)
  • Family: Pseudomonadaceae
    Pseudomonas (agent of lung infections, highly abundant in CF-patients)

© Copyright 2018 - 2024 | MyMicrobiome
– The independent certification and research institute for our microbiome –

DISCLAIMER: Nothing on this site or blog is intended to provide medical advice, diagnosis or treatment.


By clicking "Accept all", you agree to cookies being stored on your local device. This improves navigation on the site, video content can be displayed and we can anonymously analyse whether the pages are being used as intended. All approvals are made in accordance with the provisions of the GDPR.

You are using an outdated browser. The website may not be displayed correctly. Close