Conserved signature inserts and deletions ( CSIs ) in protein sequences provide an important category of molecular markers for understanding phylogenetic relationships. CSIs, brought about by rare genetic changes, provide useful phylogenetic markers that are generally of defined size and they are flanked on both sides by conserved regions to ensure their reliability. While indels can be arbitrary inserts or deletions, CSIs are defined as only those protein indels that are present within conserved regions of the protein.
43-538: See text Enterobacteriaceae is a large family of Gram-negative bacteria . It includes over 30 genera and more than 100 species. Its classification above the level of family is still a subject of debate, but one classification places it in the order Enterobacterales of the class Gammaproteobacteria in the phylum Pseudomonadota . In 2016, the description and members of this family were emended based on comparative genomic analyses by Adeolu et al. Enterobacteriaceae includes, along with many harmless symbionts , many of
86-443: A 2 aa deletion in leucyl-tRNA synthetase was commonly present in the above orders of the class Gammaproteobacteria and in some members of the order Oceanospirillales. Another CSI-based study has also identified 4 CSIs that are exclusive to the order Xanthomonadales. Taken together, these two facts show that Xanthomonadales is a monophyletic group that is ancestral to other Gammaproteobacteria, which further shows that Xanthomonadales
129-486: A conserved insert or deletion is shared by several major phyla, but absent from other phyla. Figure 2 shows an example of 5aa CSI found in a conserved region that is commonly present in the species belonging to phyla X, Y and Z, but it is absent in other phyla (A, B and C). This signature indicates a specific relationship of taxa X, Y and Z and also A, B and C. Based upon the presence or absence of such an indel, in out-group species (viz. Archaea), it can be inferred whether
172-671: A few genera are nonmotile. Most members of Enterobacteriaceae have peritrichous, type I fimbriae involved in the adhesion of the bacterial cells to their hosts. They are not spore -forming. Like other Pseudomonadota, Enterobacteriaceae have Gram-negative stains, and they are facultative anaerobes , fermenting sugars to produce lactic acid and various other end products. Most also reduce nitrate to nitrite , although exceptions exist. Unlike most similar bacteria, Enterobacteriaceae generally lack cytochrome c oxidase , there are exceptions. Catalase reactions vary among Enterobacteriaceae. Many members of this family are normal members of
215-554: A lack of widespread consensus within the scientific community for extended periods. The continual publication of new data and diverse opinions plays a crucial role in facilitating adjustments and ultimately reaching a consensus over time. The naming of families is codified by various international bodies using the following suffixes: The taxonomic term familia was first used by French botanist Pierre Magnol in his Prodromus historiae generalis plantarum, in quo familiae plantarum per tabulas disponuntur (1689) where he called
258-496: A molecular means of distinguishing Enterobacteriaceae from other families within the order Enterobacterales and other bacteria. The following genera have been validly published, thus they have "Standing in Nomenclature". The year the genus was proposed is listed in parentheses after the genus name. The following genera have been effectively, but not validly, published, thus they do not have "Standing in Nomenclature". The year
301-429: A number of CSIs were found that are specific for different orders of Thermoproteota—3 CSIs for Sulfolobales , 5 CSIs for Thermoproteales , lastly 2 CSIs common for Sulfolobales and Desulfurococcales . The signatures described provide novel means for distinguishing Thermoproteota and Nitrososphaerota, additionally they could be used as a tool for the classification and identification of related species. The members of
344-787: A part of the Morganellaceae , a sister clade within the Enterobacterales . Several Enterobacteriaceae strains have been isolated which are resistant to antibiotics including carbapenems , which are often claimed as "the last line of antibiotic defense" against resistant organisms. For instance, some Klebsiella pneumoniae strains are carbapenem resistant. Various carbapenemases genes (blaOXA-48, blaKPC and blaNDM-1, blaVIM and blaIMP) have been identified in carbapenem resistant Enterobacteriaceae including Escherichia coli and Klebsiella pneumoniae . Family (biology) Family ( Latin : familia , pl. : familiae )
387-497: A particular clade or group of species, generally provide good phylogenetic markers of common evolutionary descent. Due to the rarity and highly specific nature of such changes, it is less likely that they could arise independently by either convergent or parallel evolution (i.e. homoplasy) and therefore are likely to represent synapomorphy . Other confounding factors such as differences in evolutionary rates at different sites or among different species also generally do not affect
430-406: A particular taxon (e.g. genus, family, class, order, phylum) but they are not present in other groups. These CSIs were most likely introduced in an ancestor of the group of species before the members of the taxa diverged. They provide molecular means for distinguishing members of a particular taxon from all other organisms. Figure 1 shows an example of 5aa CSI found in all species belonging to
473-461: Is absent in other ancestral bacterial phyla as well as Archaea . Similarly a large CSI of about 100 amino acids in RpoB homologs (between amino acids 919-1058) is present in various species belonging to Pseudomonadota, Bacteroidota , Chlorobiota , Chlamydiota , Planctomycetota, and Aquificota. This CSI is absent in other ancestral bacterial phyla as well as Archaea. In both cases one can infer that
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#1732788077931516-499: Is commonly referred to as the "walnut family". The delineation of what constitutes a family— or whether a described family should be acknowledged— is established and decided upon by active taxonomists . There are not strict regulations for outlining or acknowledging a family, yet in the realm of plants, these classifications often rely on both the vegetative and reproductive characteristics of plant species. Taxonomists frequently hold varying perspectives on these descriptions, leading to
559-517: Is enterobacterium with the suffix to designate a family (aceae)—not after the genus Enterobacter (which would be "Enterobacteraceae")—and the type genus is Escherichia . Members of the Enterobacteriaceae are bacilli (rod-shaped), and are typically 1–5 μm in length. They typically appear as medium to large-sized grey colonies on blood agar, although some can express pigments. Most have many flagella used to move about, but
602-1031: Is generally not used. Analyses of genome sequences from Enterobacteriaceae species identified 21 conserved signature indels (CSIs) that are uniquely present in this family in the proteins NADH:ubiquinone oxidoreductase (subunit M), twitching motility protein PilT, 2,3-dihydroxybenzoate-AMP ligase, ATP/GTP-binding protein, multifunctional fatty acid oxidation complex (subunit alpha), S-formylglutathione hydrolase , aspartate-semialdehyde dehydrogenase , epimerase , membrane protein , formate dehydrogenylase (subunit 7), glutathione S-transferase , major facilitator superfamily transporter, phosphoglucosamine mutase , glycosyl hydrolase 1 family protein, 23S rrna [uracil(1939)-C(5)]-methyltransferase, co-chaperone HscB, N-acetylmuramoyl-L-alanine amidase , sulfate ABC transporter ATP-binding protein CysA, and LPS assembly protein LptD. These CSIs provide
645-485: Is one of the eight major hierarchical taxonomic ranks in Linnaean taxonomy . It is classified between order and genus . A family may be divided into subfamilies , which are intermediate ranks between the ranks of family and genus. The official family names are Latin in origin; however, popular names are often used: for example, walnut trees and hickory trees belong to the family Juglandaceae , but that family
688-475: The Genera Plantarum of George Bentham and Joseph Dalton Hooker this word ordo was used for what now is given the rank of family. Families serve as valuable units for evolutionary, paleontological, and genetic studies due to their relatively greater stability compared to lower taxonomic levels like genera and species. Conserved signature indels The CSIs that are restricted to
731-432: The gut microbiota in humans and other animals, while others are found in water or soil, or are parasites on a variety of different animals and plants. Escherichia coli is one of the most important model organisms , and its genetics and biochemistry have been closely studied. Some enterobacteria are important pathogens, e.g. Salmonella , or Shigella e.g. because they produce endotoxins . Endotoxins reside in
774-423: The analyses still exhibited polyphyletic branching, indicating the presence of distinct subgroups within the family. In 2016, the order Enterobacteriales was renamed to Enterobacterales, and divided into 7 new families, including the emended Enterobacteriaceae family. This emendation restricted the family to include only those genera directly related to the type genus, which included most of the enteric species under
817-404: The cell wall and are released when the cell dies and the cell wall disintegrates. Some members of the Enterobacteriaceae produce endotoxins that, when released into the bloodstream following cell lysis, cause a systemic inflammatory and vasodilatory response. The most severe form of this is known as endotoxic shock, which can be rapidly fatal. Enterobacteriaceae was originally the sole family under
860-603: The class Gammaproteobacteria. A 2 aa deletion in AICAR transformylase was uniquely shared by all gammaproteobacteria except for Francisella tularensis . A 4 aa deletion in RNA polymerase b-subunit and a 1 aa deletion in ribosomal protein L16 were found uniquely in various species belonging to the orders Enterobacteriales, Pasteurellales, Vibrionales, Aeromonadales and Alteromonadales, but were not found in other gammaproteobacteria. Lastly,
903-718: The class or its different subgroups are known. A detailed CSI-based study was conducted to better understand the phylogeny of this class. Firstly, a phylogenetic tree based on concatenated sequences of a number of universally-distributed proteins was created. The branching order of the different orders of the class Gammaproteobacteria (from most recent to the earliest diverging) was: Enterobacteriales > Pasteurellales > Vibrionales , Aeromonadales > Alteromonadales > Oceanospirillales , Pseudomonadales > Chromatiales , Legionellales , Methylococcales , Xanthomonadales , Cardiobacteriales , Thiotrichales . Additionally, 4 CSIs were discovered that were unique to most species of
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#1732788077931946-429: The discovery and analyses of conserved indels (CSIs) in many universally distributed proteins have aided in this quest. The genetic events leading to them are postulated to have occurred at important evolutionary branch points and their species distribution patterns provide valuable information regarding the branching order and interrelationships among different bacterial phyla. Recently the phylogenetic relationship of
989-540: The family as a rank intermediate between order and genus was introduced by Pierre André Latreille in his Précis des caractères génériques des insectes, disposés dans un ordre naturel (1796). He used families (some of them were not named) in some but not in all his orders of "insects" (which then included all arthropods ). In nineteenth-century works such as the Prodromus of Augustin Pyramus de Candolle and
1032-407: The genus was proposed is listed in parentheses after the genus name. To identify different genera of Enterobacteriaceae, a microbiologist may run a series of tests in the lab. These include: In a clinical setting, three species make up 80 to 95% of all isolates identified. These are Escherichia coli , Klebsiella pneumoniae , and Proteus mirabilis . However, Proteus mirabilis is now considered
1075-482: The group Thermotogota was characterized based on the CSI approach. Previously no biochemical or molecular markers were known that could clearly distinguish the species of this phylum from all other bacteria. More than 60 CSIs that were specific for the entire Thermotogota phylum or its different subgroups were discovered. Of these, 18 CSIs are uniquely present in various Thermotogota species and provide molecular markers for
1118-418: The groups lacking the CSI are ancestral. A key issue in bacterial phylogeny is to understand how different bacterial species are related to each other and their branching order from a common ancestor. Currently most phylogenetic trees are based on 16S rRNA or other genes/proteins. These trees are not always able to resolve key phylogenetic questions with a high degree of certainty. However in recent years
1161-454: The indel is an insert or a deletion, and which of these two groups A, B, C or X, Y, Z is ancestral. Mainline CSIs have been used in the past to determine the phylogenetic relationship of a number of bacterial phyla. The large CSI of about 150-180 amino acids within a conserved region of Gyrase B (between amino acids 529-751), is commonly shared between various Pseudomonadota , Chlamydiota , Planctomycetota and Aquificota species. This CSI
1204-503: The interpretation of a CSI. By determining the presence or absence of CSIs in an out-group species, one can infer whether the ancestral form of the CSI was an insert or deletion and this can be used to develop a rooted phylogenetic relationship among organisms. CSIs are discovered by looking for shared changes in a phylogenetic tree constructed from protein sequences. Most CSIs that have been identified have been found to have high predictive value upon addition of new sequences, retaining
1247-399: The more familiar pathogens , such as Salmonella , Escherichia coli , Klebsiella , and Shigella . Other disease-causing bacteria in this family include Enterobacter and Citrobacter . Members of the Enterobacteriaceae can be trivially referred to as enterobacteria or "enteric bacteria", as several members live in the intestines of animals. In fact, the etymology of the family
1290-541: The number of CSIs that are commonly shared with other taxa is much smaller than those that are specific for Thermotogota and they do not exhibit any specific pattern. Hence they have no significant effect on the distinction of Thermotogota. Mesophillic Thermoproteota were recently placed into a new phylum of Archaea called the Nitrososphaerota (formerly Thaumarchaeota). However there are very few molecular markers that can distinguish this group of archaea from
1333-430: The order Pasteurellales are currently distinguished mainly based on their position in the branching of the 16srRNA tree. There are currently very few molecular markers known that can distinguish members of this order from other bacteria. A CSI approach was recently used to elucidate the phylogenetic relationships between the species in this order; more than 40 CSIs were discovered that were uniquely shared by all or most of
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1376-449: The order Enterobacteriales. The family contained a large array of biochemically distinct species with different ecological niches, which made biochemical descriptions difficult. The original classification of species to this family and order was largely based on 16S rRNA genome sequence analyses, which is known to have low discriminatory power and the results of which changes depends on the algorithm and organism information used. Despite this,
1419-445: The order. This classification was proposed based on the construction of several robust phylogenetic trees using conserved genome sequences, 16S rRNA sequences and multilocus sequence analyses. Molecular markers, specifically conserved signature indels, specific to this family were identified as evidence supporting the division independent of phylogenetic trees. In 2017, a subsequent study using comparative phylogenomic analyses identified
1462-692: The past to determine the phylogenetic relationship of a number of bacterial phyla and subgroups within it. For example a 3 amino acid insert was uniquely shared by members of the phylum Thermotogota (formerly Thermotogae) in the essential 50S ribosomal protein L7/L12 , within a highly conserved region (82-124 amino acid). This is not present in any other bacteria species and could be used to characterize members of Thermotogota from all other bacteria. Group-specific CSIs were also used to characterize subgroups within Thermotogota. Mainline CSIs are those in which
1505-458: The phylum Thermoproteota (formerly Crenarchaeota). A detailed phylogenetic study using the CSI approach was conducted to distinguish these phyla in molecular terms. 6 CSIs were uniquely found in various Nitrososphaerota, namely Cenarchaeum symbiosum , Nitrosopumilus maritimus and a number of uncultured marine Thermoproteota. 3 CSIs were found that were commonly shared between species belonging to Nitrososphaerota and Thermoproteota. Additionally,
1548-823: The phylum. Additionally there were many CSIs that were specific for various Thermotogota subgroups. Another 12 CSIs were specific for a clade consisting of various Thermotogota species except Tt. Lettingae. While 14 CSIs were specific for a clade consisting of the Fervidobacterium and Thermosipho genera and 18 CSIs were specific for the genus Thermosiphon . Lastly 16 CSIs were reported that were shared by either some or all Thermotogota species or some species from other taxa such as Archaea , Aquificota , Bacillota , Pseudomonadota , Deinococcota , Fusobacteriota , Dictyoglomota , Chloroflexota , and eukaryotes . The shared presence of some of these CSIs could be due to lateral gene transfer (LGT) between these groups. However
1591-405: The presence of 6 subfamily level clades within the family Enterobacteriaceae, namely the "Escherichia clade", "Klebsiella clade", "Enterobacter clade", "Kosakonia clade", "Cronobacter clade", "Cedecea clade" and an "Enterobacteriaceae incertae sedis clade" containing species whose taxonomic placement within the family is unclear. However, this division was not officially proposed as the subfamily rank
1634-575: The seventy-six groups of plants he recognised in his tables families ( familiae ). The concept of rank at that time was not yet settled, and in the preface to the Prodromus Magnol spoke of uniting his families into larger genera , which is far from how the term is used today. In his work Philosophia Botanica published in 1751, Carl Linnaeus employed the term familia to categorize significant plant groups such as trees , herbs , ferns , palms , and so on. Notably, he restricted
1677-431: The species. Two major clades are formed within this Pasteurellales: Clade I, encompassing Aggregatibacter , Pasteurella , Actinobacillus succinogenes , Mannheimia succiniciproducens , Haemophilus influenzae and Haemophilus somnus , was supported by 13 CSIs. Clade II, encompassing Actinobacillus pleuropneumoniae , Actinobacillus minor , Haemophilus ducreyi , Mannheimia haemolytica and Haemophilus parasuis ,
1720-434: The specificity for the originally identified clades of species. They can be used to identify both known and even previously unknown species belonging to these groups in different environments. Compared to tree branching orders which can vary among methods, specific CSIs make for more concrete circumscriptions that are computationally cheaper to apply. Group-specific CSIs are commonly shared by different species belonging to
1763-494: The taxon X. This is a distinctive characteristic of this taxon as it is not found in any other species. This signature was likely introduced in a common ancestor of the species from this taxon. Similarly other group-specific signatures (not shown) could be shared by either A1 and A2 or B1 and B2, etc., or even by X1 and X2 or by X3 and X4, etc. The groups A, B, C, D and X, in this diagram could correspond to various bacterial or Eukaryotic phyla. Group-specific CSIs have been used in
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1806-549: The use of this term solely within the book's morphological section, where he delved into discussions regarding the vegetative and generative aspects of plants. Subsequently, in French botanical publications, from Michel Adanson 's Familles naturelles des plantes (1763) and until the end of the 19th century, the word famille was used as a French equivalent of the Latin ordo (or ordo naturalis ). In zoology ,
1849-481: Was supported by 9 CSIs. Based on these results, it was proposed that Pasteurellales be divided from its current one family into two different ones. Additionally, the signatures described would provide novel means of identifying undiscovered Pasteurellales species. The class Gammaproteobacteria forms one of the largest groups of bacteria. It is currently distinguished from other bacteria solely by 16s rRNA -based phylogenetic trees. No molecular characteristics unique to
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