Enterobacteria


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Enterobacteria
Citrobacter freundii (secondary electron microscope image)

Citrobacter freundii (secondary electron microscope image)

Systematics
Domain : Bacteria (bacteria)
Department : Proteobacteria
Class : Gammaproteobacteria
Order : Enterobacteria
Scientific name
Enterobacterales
Adeolu et al. 2016

The Enterobacteria or the representatives of the Enterobacterales order established in 2016 are a large group within the Bacteria domain . According to the phylogenetic system, they belong to the class of Gammaproteobacteria in the Proteobacteria division ( Divisio , also called phylum among prokaryotes ) and form their own order there.

Before 2016, the name "Enterobacteriales" was used for this group of bacteria, but it was not valid according to the rules of the Bacteriological Code (ICBN). Furthermore, there was only one family - the Enterobacteriaceae - within the order. With the establishment of the Enterobacterales order, the previously known taxa are divided into several new families. The new systematics means , for example, that the genera Escherichia , Morganella and Yersinia belong to three different families (see section Systematics ).

The name enterobacteria is derived from enteron ( ancient Greek ἕντερον 'intestine') because many of them are typical intestinal inhabitants . However, many free-living and ubiquitous, non-colon-dwelling bacterial species also belong to this order.

features

Appearance

The cells are rod-shaped and usually 1 to 5  µm long and about 0.5-1.0 µm in diameter. No endospores are formed. Most can actively move with flagella , they are motile , but there are also species that cannot move actively. Since the cell wall consists of a few murein layers and a second, outer membrane of phospholipids and lipopolysaccharides , the enterobacteria are gram-negative .

metabolism

Their metabolism is facultatively anaerobic , so they can break down substances through oxidation in the presence of oxygen, and ferment under anaerobic conditions (no oxygen) . Two important anaerobic metabolic pathways which are used to differentiate the individual species are the 2,3-butanediol fermentation and the mixed acid fermentation ( mixed acid fermentation ). In mixed acid fermentation, the end products and by-products are mainly acids such as acetic acid , lactic acid and succinic acid (succinate), but no butanediol . In 2,3-butanediol fermentation, the fermentation of glucose results in smaller amounts of acids as end products and by-products, but above all in large amounts the alcohol 2,3-butanediol . Another characteristic of 2,3-butanediol fermentation is the intermediate product acetoin and the much higher gas production ( CO 2 ). One finds butanediol fermentation z. B. Enterobacter , Klebsiella , Erwinia and Serratia . Use mixed acid fermentation u. a. Genera such as Escherichia , Salmonella and Proteus .

A large number of diagnostic tests are used to determine the individual genera. For example, the intermediate product acetoin of 2,3-butanediol fermentation is detected with the help of the Voges-Proskauer test . The detection of the enzyme β-galactosidase is also often used to differentiate. Bacteria that have this enzyme can hydrolytically split the disaccharide lactose (milk sugar) into the monosaccharides glucose and galactose in order to use them in the metabolism.

Phylogenetics

By using phylogenetic methods, the tribal history and the relationships between the bacteria can be clarified. In the published 2016 Description of order Enterobacterales are five conserved characteristic indels (Engl. ' Conserved signature inserts and deletions ; details see the CSI Section Systematics and Taxonomy ) set that are typical of the members of the order, but not with other bacteria occurrence. The five CSI come to gene sequences before that for the proteins L - arabinose - isomerase , elongation factor -like protein -P YeiP , peptide ABC transporter permease , pyrophosphatase and a hypothetical protein coding .

Occurrence

Swarms of Proteus on blood agar

Many enterobacteria are part of the healthy intestinal flora of humans and animals; however, they also occur everywhere in the environment (soil, water). Some are pathogens in humans and animals. They often occur as nosocomial pathogens ("hospital germs") and attack people with a weak immune system .

Probably the most important representative of the enterobacteria is Escherichia coli , one of the most important model organisms in genetics , biochemistry and microbiology . The genus Proteus is also striking , where the so-called "swarm phenomenon" is observed. When growing colonies of these bacteria spread out on an agar plate, one sees a bacterial lawn with concentric rings.

Systematics and taxonomy

Methods used in phylogenetic systematics

With the representatives of the "Enterobacteriales", the results of phylogenetic methods of the last few years, which were based in particular on the investigation of 16S rRNA, a representative of ribosomal RNA typical for prokaryotes , did not lead to a satisfactory result. Therefore, it was the goal of several scientists ( Adeolu et al.) From McMaster University in Ontario, Canada to create a phylogenetic system based on the comparison of genetic characteristics of as many representatives of the group as possible. At the time of the investigation (2016), 14,000 genomes of 54 genera belonging to the enterobacteria were already available in the genome database of the National Center for Biotechnology Information (NCBI). 179 representative genome sequences were used for the analysis and various molecular markers were selected and compared in order to create a phylogenetic tree in each case that represents the evolutionary relationships between the representatives of the enterobacteria.

On the one hand, 1548 main proteins were used that are typical for the group and DNA sequences that code for the proteins were compared . Similarly, 53 ribosomal proteins (rProteins) were used and the DNA sequence analysis of several loci ( MLSA ) which code for four proteins was carried out. The proteins are GyrB ( Gyrase B), RpoB , AtpD and InfB . The three phylogenetic trees constructed in this way result in a uniform picture with seven clades each , which are called Enterobacter-Escherichia clade, Erwinia-Pantoea clade, Pectobacterium-Dickeya clade, Yersinia-Serratia clade, Hafnia-Edwardsiella clade, Proteus-Xenorhabdus -Klade and Budvicia -Klade. Based on this, the order Enterobacterales is defined with seven families (another family, the Thorselliaceae, was first described by another group of scientists ). The result of this phylogenetic analysis is supported by the results of the analysis of the genome relationship . This method is also carried out in silico (computer-based) as a replacement for DNA-DNA hybridization and is helpful for classifying taxonomically higher ranks.

Genome analysis also enables the discovery or definition of 'conserved (preserved) molecular properties' which do not or hardly differ from one another within a group of closely related organisms, while in organisms in another group they have changed significantly through evolution. For the phylogenetic systematics of the prokaryotes, ' conserved characteristic indels ' ( conserved signature inserts and deletions , CSI) are used. Group-specific CSIs are characteristic of a certain taxon (for example an order) because they appear in all representatives of this group and not in other groups. The original Indel of a group-specific CSI probably appeared before the split in the last common ancestor and was adopted by the resulting representatives of the group ("inherited"). Another important finding of the study by Adeolu et al. is the discovery of 71 CSI, including five, which are unique to all representatives of the order Enterobacterales and are therefore used for their description. The remaining 66 CSI are specific to the seven groups and can be used in future genome analyzes of newly discovered species of enterobacteria for their systematic classification.

Cladogram on the relationships within the Enterobacterales order (as of 2016)
 5 CSI 
 9 CSI 

Budvicia clade → Budviciaceae


   
 7 CSI 

Proteus Xenorhabdus clade → Morganellaceae


   
 4 CSI 

Hafnia Edwardsiella clade → Hafniaceae


   
 3 CSI 

Yersinia Serratia clade → Yersiniaceae


   
 4 CSI 

Pectobacterium Dickeya clade → Pectobacteriaceae


 6 CSI 
 12 CSI 

Erwinia Pantoea clade → Erwiniaceae


 21 CSI 

Enterobacter Escherichia clade → Enterobacteriaceae








Template: Klade / Maintenance / Style
The cladogram indicates the number of associated conserved characteristic indels (CSI). It does not include the Thorselliaceae family.

The result of the extensive genome-wide analyzes from 2016 is the systematics presented below.

Order nomenclature and taxonomy

The genus Enterobacter is not the type genus of the Enterobacteriacea family, this is the genus Escherichia . This deviates from the established nomenclature according to the Bacteriological Code ( International Code of Nomenclature of Bacteria ), which was established in 1958 in the Judicial Opinion 15 of the Judicial Commission (roughly "judicial or impartial commission") of the International Commission for the Systematics of Prokaryotes ( International Committee on Systematics of Prokaryotes , ICSP). According to the rules of the bacteriological code, an order with the type genus Escherichia would consequently have to be called “Escherichiales”, an order with the type genus Enterobacter would have to be called “Enterobacterales”, but not “Enterobacteriales”. In order to ensure the acceptance of the new system and to avoid possible confusion when naming the order as "Escherichiales", the name Enterobacterales ord. nov. with the type genus Enterobacter chosen.

Current system

Colonies of Enterobacter cloacae on a nutrient medium

The Enterobacterales order established in 2016 includes eight families with a total of around 60 genera. The type genus of the order that has been newly established and thus corresponds to the rules of the bacteriological code (ICBN) is the genus Enterobacter . The description of the order Enterobacterales Adeolu et al. 2016 ord. nov. corresponds to the description of the Enterobacteriaceae family in Bergey's Manual of Systematic Bacteriology from 2005, with the addition that the representatives of the order can be distinguished from all other bacteria by five CSIs.

The genus Phytobacter Zhang et al. 2017 emend. Pillonetto et al. 2018 has not yet been assigned to any family.

Below is a list of the associated families with most of the associated species (as of 2019).

Klebsiella pneumoniae
(secondary electron microscope image)
Secondary electron microscope image of Salmonella (colored red)
Colonies of Morganella morganii on blood agar
Light microscope image of Yersinia enterocolitica after Gram staining

Some synonyms and changes

  • All species from Levinea Young et al. In 1971 Werkman & Gillen were added to the genus Citrobacter in 1932
  • Various Erwinia TYPES were in the genera Pantoea , Enterobacter , Pectobacterium and Brenneria divided
  • Liquidobacterium is a synonym for Proteus

Reporting requirement

In Germany, the direct detection of Enterobacterales must be reported by name in accordance with Section 7 of the Infection Protection Act (IfSG), but only if there is evidence of a carbapenemase determinant or with reduced sensitivity to carbapenems, except in the case of natural resistance. The reporting obligation only applies in the event of infection or colonization. (Section 7, Paragraph 1, Sentence 1, No. 52 b) IfSG)

In addition, the occurrence of two or more nosocomial infections for which an epidemic connection is likely or suspected must not be reported by name. ( § 6 Paragraph 3 IfSG).

swell

literature

Individual evidence

  1. a b c d e f g h i M. Adeolu, S. Alnajar, S. Naushad, RS Gupta: Genome-based phylogeny and taxonomy of the 'Enterobacteriales': proposal for Enterobacterales ord. nov. divided into the families Enterobacteriaceae, Erwiniaceae fam. nov., Pectobacteriaceae fam. nov., Yersiniaceae fam. nov., Hafniaceae fam. nov., Morganellaceae fam. nov., and Budviciaceae fam. nov. In: International Journal of Systematic and Evolutionary Microbiology. No. 66 , December 2016, p. 5575-5599 , doi : 10.1099 / ijsem.0.001485 .
  2. Radhey S. Gupta, Emma Griffiths: Critical Issues in Bacterial Phylogeny. In: Theoretical Population Biology. No. 61 , June 2002, p. 423-434 , doi : 10.1006 / tpbi.2002.1589 , PMID 12167362 .
  3. ^ Jean Euzéby, Aidan C. Parte: Genus Enterobacter. In: List of Prokaryotic names with Standing in Nomenclature, Systematics of Bacteria (LPSN) . Retrieved December 20, 2019 .
  4. ^ SP Lapage, PHA Sneath, EF Lessel, VBD Skerman, HPR Seeliger, WA Clark (eds.): International Code of Nomenclature of Bacteria - Bacteriological Code, 1990 Revision . ASM Press, Washington (DC), USA 1992, ISBN 1-55581-039-X ( NCBI Bookshelf ).
  5. ^ P. Kämper, SP Glaeser, LKJ Nilsson, T. Eberhard, S. Håkansson, L. Guy, S. Roos, H.-J. Busse, O. Terenius: Proposal of Thorsellia kenyensis sp. nov. and Thorsellia kandunguensis sp. nov., isolated from larvae of Anopheles arabiensis, as members of the family Thorselliaceae fam. nov. In: International Journal of Systematic and Evolutionary Microbiology. No. 65 , February 2015, p. 444-451 , doi : 10.1099 / ijs.0.070292-0 .
  6. a b Jean Euzéby, Aidan C. Parte: Classification of domains and phyla - Hierarchical classification of prokaryotes (bacteria). In: List of Prokaryotic names with Standing in Nomenclature, Systematics of Bacteria (LPSN) . Retrieved December 20, 2019 .

Web links

Commons : Enterobacterales  - collection of images, videos and audio files
 Wikispecies: Enterobacterales  - Species Directory