Filifactor alocis: Difference between revisions

From MicrobeWiki, the student-edited microbiology resource
(Created page with "{{Uncurated}} <b>This Funk Microbial Biorealm <i>Genus </i>template page is a guide for each student when creating and adding an entirely new species to MicrobeWiki. COPY...")
 
No edit summary
 
Line 8: Line 8:
Domain; Phylum; Class; Order; family; genus, species [Others may be used.  Use [http://www.ncbi.nlm.nih.gov/Taxonomy/ NCBI] link to find]
Domain; Phylum; Class; Order; family; genus, species [Others may be used.  Use [http://www.ncbi.nlm.nih.gov/Taxonomy/ NCBI] link to find]


Bacteria; Firmicutes, Clostidia, Clostridiales, Peptostreptococcaceae, Filifactor, alocis  
Bacteria; Firmicutes, Clostridia, Clostridiales, Peptostreptococcaceae, Filifactor, alocis  
===Species===
===Species===


{|
Filifactor alocis
| height="10" bgcolor="#FFDF95" |
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=2&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]'''
|}


''Genus species''
''Genus species''


==Description and significance==
==Description and significance==
a. Give an introduction to the organism.  Indicate the full name of the organism, what the name means, when and where it was first isolated/described, and by whom. Correctly write the binomial species name and the taxonomic designation (enter information above, including the link to the correct NCBI page(s). Abbreviate the genus name after the first usage.
Filifactor alocis, formally named Fusobacterium alocis 1,  is a bacterium that is best known for being associated with periodontal and gingivitis disease. After much review of the literature the year 1985 is considered the year of discovery 2, however, the individual who discovered it is unknown. The classification of F. alocis was determined by genus similarity and species function. The meaning behind alocis is furrow, named from the common habitat of this species in the sulcus of the gums1.  
b.  Give the morphological characteristics (cells, colonies), Gram stain (or cell wall equivalent), cellular appendages and any extracellular matrix that it secretes as well as whether or not it is motile.


 
.  F. alocis is characterized as rod shaped, gram negative, and grouped alone, in pairs, or in chains1. F. alocis is a none spore forming bacteria. The optimal temperature of the bacteria is 37℃ and is an obligate anaerobe1. F alocis is also characterized as being nonmotile due to the lack of a flagella1. Although they are characterized as nonmotile, they have been observed as having twitching and end over end movement1. F. alocis forms small, circular, entire, and low to convex colonies1.  
Include a link if there is an existing microbewiki page for this genus (Ex. [[Salmonella]]).


==Genome and genetics==
==Genome and genetics==
a. To what major branch of the prokaryotes do they belong? (see textbook or Bergey’s). List 2-3 closely related but separate species or genera of bacteria.   
According to Bergey’s Manuel F. alocis belongs to the prokaryotic branch bacteria. F. alocis shares the genus Filifactor with one other species, F. villosus. F. alocis is also very similar to Fusobacterium. For a long time F alocis was confused as belonging to the genus Fusobacterium for many years because of the similar characteristics.   


b. Briefly describe any extra-chromosomal elements or genetic tools that are used to study the bacterium:  viruses, plasmids, transposons that allow genetic manipulation and analysis. 
F. alocis has been completely sequenced. 16s rRNA has been a common means of classifying and comparing bacteria like F. alocis. In resent research probes such as EUB338 have been used in combination with species-specific probes to identify bacteria2. EUB338 is such a domain specific probe that is characteristic of bacteria5 fluorescence in situ hybridization (FISH) is commonly used with EUB338 analysis, both of which have been used to identify important characteristics of F. alocis, specifically biofilm formation2. FISH is used to target specific aspects of DNA or RNA that 16s rRNA sequence satisfies2,3


c. Has the genome or genomes been sequenced?  If so, include the website for the database and one or two highlights of the genome.  Also indicate genome size (base pairs), %G+C (nucleotide base composition) and number of genes, and specific genes or gene regions that are unique to this organism. If it has not been sequenced, give its closest relative that has been sequenced, its website, and some general information about the related sequence.
The complete genome of F. alocis has been sequenced. The exact strain number is ATCC 358964. The genome was last updated 01/27/20114. Characteristics of the sequence show the chromosome length being 1,931,012 base pairs long4. 35.4% of the base pairs are G+C while 64.6% are A+C base pairs. Within the genome of F. alocis are 1,729 differing genes and 25 pseudogenes4. F. alocis has a proteome consisting of 1644 different proteins that have been identified4.  




Example: The sequence of ''Haemophilus influenzae'' was determined using whole genome shotgun sequencing (Fleischmann et al. 1995).
==Nutrition and metabolism==
Resent studies on F. alocis have used rich non selective media in an anaerobic condition for incubation5. As of right now there is not a lot of research on nutrition and metabolism on the F. alocis.  


==Nutrition and metabolism==
== Pathology==
a.Describe the growth characteristics of your bacterial species; sources of C, N, electrons; respires/ferments, uses O2, etc.
F. alocis is most commonly known for its suggested influence on periodontitis. The microbe is suggested to be involved in a numerous number of functions such as biofilm formation, immune invasion, oxidative stress resistance and triggering epithelial cell death6. Although the exact function Filifactor alocis contributes to the microbiota is unknown, it is thought of as being a great identifier for being associated with the presence of other pathogens, such as Pseudomonas gingavalis6


b.What kinds of culture conditions (temp, pH, media) are needed for laboratory study? 


c.What kinds of waste, by-products, volatile compounds are generated?


==Ecology / Pathology==
==Current Research==
Ecology:  How is your microorganism important in the ecosystem where it is found?  How does it impact other organisms in the environment (could be positive or negative impact)? 


Pathology:  How does the microbe cause disease as it interacts with the host? Describe any specific toxins or pathways that are used for invading and causing disease in the host. What treatment is used to inhibit or kill the microbe?
Current research has shown that F. alocis is a marker for periodontitis and influences the microbiota6. Research has also shown that F. alocis colonization is reliant on a tecendent inhabitant of microbial communities7.   


==Current Research==


Describe recent research and findings that have been done with this organism. The research can be clinical, applied or basic research.  This section should be based on 2 recent papers (10 years or less) and summarized in your own words.


==References==
==References==
The format for citations and for the “References” list will follow the “Citation—Name” Council of Science Editors (CSE) format, as the suggested formatting method listed on the MicrobeWiki Home page. The reference list will be numbered based on an alphabetical list of the first author’s last name.
 
A style guide for the CSE format can be found here: http://writing.wisc.edu/Handbook/DocCSE_CitationSystems.html.<br><br>
1 https://books.google.com/books?id=0-VqgLiCPFcC&pg=PA1013&lpg=PA1013&dq=filifactor+alocis+bergey's+manual&source=bl&ots=kGFav0Lo1A&sig=_k_9GgA3JtVF3Yi0Mx44qO-3x10&hl=en&sa=X&ved=0ahUKEwjigoq65MHTAhWqxYMKHZRVCWUQ6AEIKTAB#v=onepage&q=filifactor%20alocis%20bergey's%20manual&f=false
 
2 https://bmcmicrobiol.biomedcentral.com/articles/10.1186/1471-2180-10-66
 
3 https://www.nature.com/scitable/topicpage/fluorescence-in-situ-hybridization-fish-327
 
4 https://www.ncbi.nlm.nih.gov/genome/?term=Filifactor alocis
 
5 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4321760/
 
6 https://www.ncbi.nlm.nih.gov/pubmed/24898946
 
7 https://www.ncbi.nlm.nih.gov/pubmed/24098460




Latest revision as of 16:13, 26 April 2017

This student page has not been curated.

This Funk Microbial Biorealm Genus template page is a guide for each student when creating and adding an entirely new species to MicrobeWiki. COPY AND PASTE this entire template (below) to set up a new page for a new species entry, then begin to fill in and edit the page. State at the bottom of the page that the page is "Authored by [your Student Name]" in front of "a student of CJ Funk at John Brown University".

Classification

Higher order taxa

Domain; Phylum; Class; Order; family; genus, species [Others may be used. Use NCBI link to find]

Bacteria; Firmicutes, Clostridia, Clostridiales, Peptostreptococcaceae, Filifactor, alocis

Species

Filifactor alocis

Genus species

Description and significance

Filifactor alocis, formally named Fusobacterium alocis 1, is a bacterium that is best known for being associated with periodontal and gingivitis disease. After much review of the literature the year 1985 is considered the year of discovery 2, however, the individual who discovered it is unknown. The classification of F. alocis was determined by genus similarity and species function. The meaning behind alocis is furrow, named from the common habitat of this species in the sulcus of the gums1.

. F. alocis is characterized as rod shaped, gram negative, and grouped alone, in pairs, or in chains1. F. alocis is a none spore forming bacteria. The optimal temperature of the bacteria is 37℃ and is an obligate anaerobe1. F alocis is also characterized as being nonmotile due to the lack of a flagella1. Although they are characterized as nonmotile, they have been observed as having twitching and end over end movement1. F. alocis forms small, circular, entire, and low to convex colonies1.

Genome and genetics

According to Bergey’s Manuel F. alocis belongs to the prokaryotic branch bacteria. F. alocis shares the genus Filifactor with one other species, F. villosus. F. alocis is also very similar to Fusobacterium. For a long time F alocis was confused as belonging to the genus Fusobacterium for many years because of the similar characteristics.

F. alocis has been completely sequenced. 16s rRNA has been a common means of classifying and comparing bacteria like F. alocis. In resent research probes such as EUB338 have been used in combination with species-specific probes to identify bacteria2. EUB338 is such a domain specific probe that is characteristic of bacteria5 fluorescence in situ hybridization (FISH) is commonly used with EUB338 analysis, both of which have been used to identify important characteristics of F. alocis, specifically biofilm formation2. FISH is used to target specific aspects of DNA or RNA that 16s rRNA sequence satisfies2,3

The complete genome of F. alocis has been sequenced. The exact strain number is ATCC 358964. The genome was last updated 01/27/20114. Characteristics of the sequence show the chromosome length being 1,931,012 base pairs long4. 35.4% of the base pairs are G+C while 64.6% are A+C base pairs. Within the genome of F. alocis are 1,729 differing genes and 25 pseudogenes4. F. alocis has a proteome consisting of 1644 different proteins that have been identified4.


Nutrition and metabolism

Resent studies on F. alocis have used rich non selective media in an anaerobic condition for incubation5. As of right now there is not a lot of research on nutrition and metabolism on the F. alocis.

Pathology

F. alocis is most commonly known for its suggested influence on periodontitis. The microbe is suggested to be involved in a numerous number of functions such as biofilm formation, immune invasion, oxidative stress resistance and triggering epithelial cell death6. Although the exact function Filifactor alocis contributes to the microbiota is unknown, it is thought of as being a great identifier for being associated with the presence of other pathogens, such as Pseudomonas gingavalis6


Current Research

Current research has shown that F. alocis is a marker for periodontitis and influences the microbiota6. Research has also shown that F. alocis colonization is reliant on a tecendent inhabitant of microbial communities7.


References

1 https://books.google.com/books?id=0-VqgLiCPFcC&pg=PA1013&lpg=PA1013&dq=filifactor+alocis+bergey's+manual&source=bl&ots=kGFav0Lo1A&sig=_k_9GgA3JtVF3Yi0Mx44qO-3x10&hl=en&sa=X&ved=0ahUKEwjigoq65MHTAhWqxYMKHZRVCWUQ6AEIKTAB#v=onepage&q=filifactor%20alocis%20bergey's%20manual&f=false

2 https://bmcmicrobiol.biomedcentral.com/articles/10.1186/1471-2180-10-66

3 https://www.nature.com/scitable/topicpage/fluorescence-in-situ-hybridization-fish-327

4 https://www.ncbi.nlm.nih.gov/genome/?term=Filifactor alocis

5 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4321760/

6 https://www.ncbi.nlm.nih.gov/pubmed/24898946

7 https://www.ncbi.nlm.nih.gov/pubmed/24098460



For an example, see this entry: https://microbewiki.kenyon.edu/index.php/Bacillus_anthracis


Authored by [Ryan Alexander], a student of CJ Funk at John Brown University

[[Category:Pages edited by students of CJ Funk at John Brown University]

Retrieved from "https://microbewiki.kenyon.edu/index.php?title=Filifactor_alocis&oldid=129981"