Editing Gram-negative bacteria (section)

== Taxonomy ==
{{Main|Bacterial taxonomy}}
{{Further|Bacteria#Classification and identification}}
{{Technical|section|date=March 2014}}
{{Split section|Gram stain |discuss=Gram stain#Move Taxonomy sections here |date=November 2023}}
Bacteria are traditionally classified based on their [[Gram stain|Gram-stain]]ing response into the [[gram-positive]] and gram-negative bacteria. Having just one membrane, the gram-positive bacteria are also known as [[monoderm bacteria]], while gram-negative bacteria, having two membranes, are also known as '''diderm bacteria'''. It was traditionally thought that the groups represent lineages, i.e., the extra membrane only evolved once, such that gram-negative bacteria are more closely related to one another than to any gram-positive bacteria. While this is often true, the classification system breaks down in some cases, with lineage groupings not matching the staining result.<ref name="Guptab">{{cite journal|last=Gupta |first=RS |title=Protein phylogenies and signature sequences: A reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes |journal=Microbiol. Mol. Biol. Rev. |volume=62 |issue=4 |pages=1435–91 |date=December 1998 |pmid=9841678 |pmc=98952 |doi=10.1128/MMBR.62.4.1435-1491.1998}}</ref><ref name="Guptad">{{cite journal | author = Gupta RS | title = The natural evolutionary relationships among prokaryotes | journal = Crit. Rev. Microbiol. | volume = 26 | issue = 2 | pages = 111–31 | year = 2000 | pmid = 10890353 | doi = 10.1080/10408410091154219 | url = http://www.life.illinois.edu/govindjee/Part2/15_Gupta.pdf | citeseerx = 10.1.1.496.1356 | s2cid = 30541897 | access-date = 2017-10-24 | archive-date = 2018-07-20 | archive-url = https://web.archive.org/web/20180720153253/http://www.life.illinois.edu/govindjee/Part2/15_Gupta.pdf | url-status = live }}</ref><ref name="Desvaux et al., 2009">{{cite journal |vauthors=Desvaux M, Hébraud M, Talon R, Henderson IR | title = Secretion and subcellular localizations of bacterial proteins: a semantic awareness issue | journal = Trends Microbiol. | volume = 17 | issue = 4 | pages = 139–45 |date=April 2009 | pmid = 19299134 | doi = 10.1016/j.tim.2009.01.004 }}</ref><ref name="Sutcliffe, 2010">{{cite journal | author = Sutcliffe IC | title = A phylum level perspective on bacterial cell envelope architecture | journal = Trends Microbiol. | volume = 18 | issue = 10 | pages = 464–70 |date=October 2010 | pmid = 20637628 | doi = 10.1016/j.tim.2010.06.005 }}</ref> Thus, Gram staining cannot be reliably used to assess familial relationships of bacteria. Nevertheless, staining often gives reliable information about the composition of the cell membrane, distinguishing between the presence or absence of an [[bacterial outer membrane|outer lipid membrane]].<ref name="Guptab"/><ref name="Guptaa">{{cite journal | author = Gupta RS | title = What are archaebacteria: life's third domain or monoderm prokaryotes related to gram-positive bacteria? A new proposal for the classification of prokaryotic organisms | journal = Mol. Microbiol. | volume = 29 | issue = 3 | pages = 695–707 |date=August 1998 | pmid = 9723910 | doi = 10.1046/j.1365-2958.1998.00978.x | doi-access = free }}</ref>

Of these two structurally distinct groups of [[Prokaryote|prokaryotic]] organisms, monoderm prokaryotes are thought to be ancestral. Based upon a number of different observations, including that the gram-positive bacteria are the most sensitive to [[antibiotics]] and that the gram-negative bacteria are, in general, [[antimicrobial resistance|resistant]] to antibiotics, it has been proposed that the outer cell membrane in gram-negative bacteria (diderms) evolved as a protective mechanism against antibiotic [[Evolutionary pressure|selection pressure]].<ref name="Guptab"/><ref name="Guptad"/><ref name="Guptaa"/><ref name="Guptac">{{cite journal | author = Gupta RS | title = Origin of diderm (gram-negative) bacteria: antibiotic selection pressure rather than endosymbiosis likely led to the evolution of bacterial cells with two membranes | journal = Antonie van Leeuwenhoek | volume = 100 | issue = 2 | pages = 171–82 |date=August 2011 | pmid = 21717204 | pmc = 3133647 | doi = 10.1007/s10482-011-9616-8 }}</ref> Some bacteria such as ''[[Deinococcus]]'', which stain gram-positive due to the presence of a thick [[peptidoglycan]] layer, but also possess an outer cell membrane are suggested as intermediates in the transition between monoderm (gram-positive) and diderm (gram-negative) bacteria.<ref name="Guptab"/><ref name="Guptac"/> 

The conventional LPS-''diderm'' group of gram-negative bacteria (e.g., [[Pseudomonadota]], [[Aquificota]], [[Chlamydiota]], [[Bacteroidota]], [[Chlorobiota]], "[[Cyanobacteria]]", [[Fibrobacterota]], [[Verrucomicrobiota]], [[Planctomycetota]], [[Spirochaetota]], [[Acidobacteriota]]) are uniquely identified by a few [[conserved signature indel]] (CSI) in the [[HSP60]] ([[GroEL]]) protein. The presence of this CSI in all sequenced species of conventional lipopolysaccharide-containing gram-negative bacterial phyla provides evidence that these phyla of bacteria form a [[Monophyly|monophyletic]] [[clade]] and that no loss of the outer membrane from any species from this group has occurred.<ref name="Guptac"/> They have accordingly been assigned a kingdom [[Pseudomonadati]] (formerly "Hydrobacteria").<ref name="valid-dom-kingdom"/>

The difficulty lies in the other taxa that also have a diderm structure.
* The first group is [[Paraphyly|paraphyletic]]. It includes a number of taxa (including [[Negativicutes]], [[Fusobacteriota]], [[Synergistota]], and [[Elusimicrobiota]]) that are either part of the [[phylum]] [[Bacillota]] (a monoderm group) or branches in its proximity.<ref name="Sutcliffe, 2010"/><ref name="Guptac"/><ref name="pmid19667386"/> They lack the [[GroEL]] CSI signature, which is proof that they do not belong in the former group.<ref name="Guptac"/> Some members are likely monoderm, just with a very thin layer of LPS to not appear on the stain. Others have more convoluted structures.<ref name="pmid39162559">{{cite journal |last1=Choi |first1=JK |last2=Poudel |first2=S |last3=Yee |first3=N |last4=Goff |first4=JL |title=Deeply branching Bacillota species exhibit atypical Gram-negative staining. |journal=Microbiology Spectrum |date=3 October 2024 |volume=12 |issue=10 |pages=e0073224 |doi=10.1128/spectrum.00732-24 |pmid=39162559|pmc=11448272 }}</ref>
* The second group are the clinically-relevant ''[[Mycobacterium]]'', expanding to most of its encompassing order of [[Mycobacteriales]]. They do not have the CSI, and their cell wall is made of a different substance: [[mycolic acid]].<ref name=Gupta19myc/>

=== Example species ===
The [[proteobacteria]] are a major superphylum of gram-negative bacteria, including ''[[Escherichia coli|E. coli]]'', ''[[Salmonella]]'', ''[[Shigella]]'', and other [[Enterobacteriaceae]], ''[[Pseudomonas]]'', ''[[Moraxella catarrhalis|Moraxella]]'', ''[[Helicobacter]]'', ''[[Stenotrophomonas]]'', ''[[Bdellovibrio]]'', [[acetic acid bacteria]], ''[[Legionella]]'' etc. Other notable groups of gram-negative bacteria include the [[cyanobacteria]], [[spirochaete]]s, and [[green sulfur bacteria]].<ref>{{Citation |last=Castenholz |first=Richard W. |title=General Characteristics of the Cyanobacteria |date=2015 |work=Bergey's Manual of Systematics of Archaea and Bacteria |pages=1–23 |url=https://onlinelibrary.wiley.com/doi/10.1002/9781118960608.cbm00019 |access-date=2025-01-25 |publisher=John Wiley & Sons, Ltd |language=en |doi=10.1002/9781118960608.cbm00019 |isbn=978-1-118-96060-8|url-access=subscription }}</ref><ref>{{Citation |last=Cole |first=John R. |title=5 - Spirochetes |date=1990-01-01 |work=Diagnostic Procedure in Veterinary Bacteriology and Mycology (Fifth Edition) |pages=41–60 |editor-last=Carter |editor-first=G. R. |url=https://linkinghub.elsevier.com/retrieve/pii/B9780121617752500098 |access-date=2025-01-25 |place=San Diego |publisher=Academic Press |doi=10.1016/b978-0-12-161775-2.50009-8 |isbn=978-0-12-161775-2 |editor2-last=Cole |editor2-first=John R.|url-access=subscription }}</ref><ref>{{Cite book |last=Schmidt |first=Thomas M. |title=Encyclopedia of Microbiology |date=2019 |publisher=Elsevier Science & Technology |isbn=978-0-12-811737-8 |edition=4th |location=San Diego |pages=527–537}}</ref>

Medically-relevant gram-negative [[diplococci]] include the four types that cause a [[sexually transmitted disease]] (''[[Neisseria gonorrhoeae]]''<ref name=Yeshanew_2018>{{cite journal |last1=Yeshanew |first1=Addisu Gize |last2=Geremew |first2=Rozina Ambachew |date=2018-07-17 |title=MNeisseria Gonorrhoae and their antimicrobial susceptibility patterns among symptomatic patients from Gondar town, north West Ethiopia |journal=Antimicrobial Resistance and Infection Control |volume=7 |issue=85 |page=85 |doi=10.1186/s13756-018-0376-3 |doi-access=free |pmid=30026943 |pmc=6050735 }}</ref>), a [[meningitis]] (''[[Neisseria meningitidis]]''<ref name="CDC 2018 y478">{{cite web | title=Vaccine Preventable Diseases Surveillance Manual | website=CDC | date=April 3, 2018 | url=https://www.cdc.gov/vaccines/pubs/surv-manual/chpt08-mening.html | access-date=January 26, 2024}}</ref>), and respiratory symptoms (''[[Moraxella catarrhalis]]'',<ref name=Verduin_2002>{{cite journal |last1=Verduin |first1=Cees M. |last2=Hol |first2=Cees |last3=Fleer |first3=Andre |last4=van Dijk |first4=Hans |last5=van Belkum |first5=Alex |date=January 2002 |title=Moraxella catarrhalis: from Emerging to Established Pathogen |journal=Clinical Microbiology Reviews |volume=15 |issue=1 |pages=125–144 |doi=10.1128/CMR.15.1.125-144.2002 |pmid=11781271 |pmc=118065 }}</ref> A [[coccobacillus]] ''[[Haemophilus influenzae]]'' is another medically relevant coccal type.<ref name="CDC 2018 b143">{{cite web | title=For Clinicians: Haemophilus influenzae | website=CDC | date=February 13, 2018 | url=https://www.cdc.gov/hi-disease/clinicians.html#:~:text=Haemophilus%20influenzae%20is%20a%20pleomorphic,that%20have%20distinct%20capsular%20polysaccharides. | access-date=January 26, 2024}}</ref>

Medically relevant gram-negative [[bacillus (shape)|bacilli]] include a multitude of species. Some of them cause primarily respiratory problems (''[[Klebsiella pneumoniae]]'', ''[[Legionella pneumophila]]'', ''[[Pseudomonas aeruginosa]]''), primarily urinary problems (''[[Escherichia coli]]'', ''[[Proteus mirabilis]]'', ''[[Enterobacter cloacae]]'', ''[[Serratia marcescens]]''), and primarily gastrointestinal problems (''[[Helicobacter pylori]]'', ''[[Salmonella enteritidis]]'', ''[[Salmonella typhi]]'').{{cn|date=November 2023}}

Gram-negative bacteria associated with [[hospital-acquired infection]]s include ''[[Acinetobacter baumannii]]'', which cause [[bacteremia]], secondary [[meningitis]], and [[ventilator-associated pneumonia]] in hospital [[intensive-care unit]]s.