Editing Gram-positive bacteria (section)

== Importance of the outer cell membrane in bacterial classification ==
{{Split section|Gram stain |discuss=Gram stain#Move Taxonomy sections here |date=November 2023}}
[[File:Mureine.svg|thumb|240px|The structure of peptidoglycan, composed of [[N-acetylglucosamine]] and [[N-acetylmuramic acid]]]]
Although bacteria are traditionally divided into two main groups, gram-positive and gram-negative, based on their Gram stain retention property, this classification system is ambiguous as it refers to three distinct aspects (staining result, envelope organization, taxonomic group), which do not necessarily coalesce for some bacterial species.<ref name="Gupta B">{{Cite journal |last=Gupta |first=R.S. |date=1998 |title=Protein phylogenies and signature sequences: A reappraisal of evolutionary relationships among archaebacteria, eubacteria and eukaryotes |journal=Microbiology and Molecular Biology Reviews |volume=62 |issue=4 |pages=1435–1491 |doi=10.1128/MMBR.62.4.1435-1491.1998 |pmc=98952 |pmid=9841678}}</ref><ref name="Gupta D">{{Cite journal |last=Gupta |first=R.S. |date=2000 |title=The natural evolutionary relationships among prokaryotes |url=http://www.life.illinois.edu/govindjee/Part2/15_Gupta.pdf |url-status=live |journal=Critical Reviews in Microbiology |volume=26 |issue=2 |pages=111–131 |citeseerx=10.1.1.496.1356 |doi=10.1080/10408410091154219 |pmid=10890353 |s2cid=30541897 |archive-url=https://web.archive.org/web/20130625170008/http://www.life.illinois.edu/govindjee/Part2/15_Gupta.pdf |archive-date=2013-06-25}}</ref><ref name="Desvaux et al., 2009">{{Cite journal |last1=Desvaux |first1=M. |last2=Hébraud |first2=M. |last3=Talon |first3=R. |last4=Henderson |first4=I.R. |date=2009 |title=Secretion and subcellular localizations of bacterial proteins: A semantic awareness issue |journal=Trends in Microbiology |volume=17 |issue=4 |pages=139–145 |doi=10.1016/j.tim.2009.01.004 |pmid=19299134}}</ref><ref name="Sutcliffe, 2010">{{Cite journal |last=Sutcliffe |first=I.C. |date=2010 |title=A phylum level perspective on bacterial cell envelope architecture |journal=Trends in Microbiology |volume=18 |issue=10 |pages=464–470 |doi=10.1016/j.tim.2010.06.005 |pmid=20637628}}</ref> The gram-positive and gram-negative staining response is also not a reliable characteristic as these two kinds of bacteria do not form phylogenetic coherent groups.<ref name="Gupta B" /> However, although Gram staining response is an empirical criterion, its basis lies in the marked differences in the ultrastructure and chemical composition of the bacterial cell wall, marked by the absence or presence of an outer lipid membrane.<ref name="Gupta B" /><ref name="Gupta A">{{Cite journal |last=Gupta |first=R.S. |date=1998 |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=Molecular Microbiology |volume=29 |issue=3 |pages=695–707 |doi=10.1046/j.1365-2958.1998.00978.x |pmid=9723910 |s2cid=41206658}}</ref>

All gram-positive bacteria are bound by a single-unit lipid membrane, and, in general, they contain a thick layer (20–80&nbsp;nm) of peptidoglycan responsible for retaining the Gram stain. A number of other bacteria—that are bound by a single membrane, but stain gram-negative due to either lack of the peptidoglycan layer, as in the [[mycoplasma]]s, or their inability to retain the Gram stain because of their cell wall composition—also show close relationship to the gram-positive bacteria. For the bacterial cells bound by a single cell membrane, the term ''monoderm bacteria'' has been proposed.<ref name="Gupta B" /><ref name="Gupta A" />

In contrast to gram-positive bacteria, all typical gram-negative bacteria are bound by a cytoplasmic membrane and an outer cell membrane; they contain only a thin layer of peptidoglycan (2–3&nbsp;nm) between these membranes. The presence of inner and outer cell membranes defines a new compartment in these cells: the [[periplasmic space]] or the periplasmic compartment. These bacteria have been designated as [[diderm bacteria]].<ref name="Gupta B" /><ref name="Gupta A" /> The distinction between the monoderm and diderm bacteria is supported by conserved signature indels in a number of important proteins (viz. DnaK, GroEL).<ref name="Gupta B" /><ref name="Gupta D" /><ref name="Gupta A" /><ref name="Gupta C">{{Cite journal |last=Gupta |first=R.S. |date=2011 |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=171–182 |doi=10.1007/s10482-011-9616-8 |pmc=3133647 |pmid=21717204}}</ref> Of these two structurally distinct groups of bacteria, monoderms are indicated to be ancestral. Based upon a number of observations including that the gram-positive bacteria are the major producers of antibiotics and that, in general, gram-negative bacteria are resistant to them, it has been proposed that the outer cell membrane in gram-negative bacteria (diderms) has evolved as a protective mechanism against [[antibiotic]] selection pressure.<ref name="Gupta B" /><ref name="Gupta D" /><ref name="Gupta A" /><ref name="Gupta C" /> Some bacteria, such as ''[[Deinococcus]]'', which stain gram-positive due to the presence of a thick peptidoglycan layer and also possess an outer cell membrane are suggested as intermediates in the transition between monoderm (gram-positive) and diderm (gram-negative) bacteria.<ref name="Gupta B" /><ref name="Gupta C" /> The diderm bacteria can also be further differentiated between simple diderms lacking lipopolysaccharide, the archetypical diderm bacteria where the outer cell membrane contains lipopolysaccharide, and the diderm bacteria where outer cell membrane is made up of [[mycolic acid]].<ref name="Desvaux et al., 2009" /><ref name="Gupta C" /><ref name="pmid19667386">{{Cite journal |last1=Marchandin |first1=H. |last2=Teyssier |first2=C. |last3=Campos |first3=J. |last4=Jean-Pierre |first4=H. |last5=Roger |first5=F. |last6=Gay |first6=B. |last7=Carlier |first7=J.-P. |last8=Jumas-Bilak |first8=E. |date=2009 |title=Negativicoccus succinicivorans gen. Nov., sp. Nov., isolated from human clinical samples, emended description of the family Veillonellaceae and description of Negativicutes classis nov., Selenomonadales ord. nov. and Acidaminococcaceae fam. nov. In the bacterial phylum Firmicutes |journal=International Journal of Systematic and Evolutionary Microbiology |volume=60 |issue=6 |pages=1271–1279 |doi=10.1099/ijs.0.013102-0 |pmid=19667386 |doi-access=free}}</ref>

=== Exceptions ===
In general, gram-positive bacteria are monoderms and have a single [[lipid bilayer]] whereas gram-negative bacteria are diderms and have two bilayers. Exceptions include:
* Some taxa lack peptidoglycan (such as the class [[Mollicutes]], some members of the [[Rickettsiales]], and the insect-endosymbionts of the [[Enterobacteriales]]) and are [[Gram stain#Gram-variable and gram-indeterminate bacteria|gram-indeterminate]].
* The [[Deinococcota]] have gram-positive stains, although they are structurally similar to gram-negative bacteria with two layers.
* The [[Chloroflexota]] have a single layer, yet (with some exceptions<ref>{{Cite journal |last1=Yabe |first1=S. |last2=Aiba |first2=Y. |last3=Sakai |first3=Y. |last4=Hazaka |first4=M. |last5=Yokota |first5=A. |date=2010 |title=''Thermogemmatispora onikobensis'' gen. nov., sp. nov. And ''Thermogemmatispora foliorum'' sp. nov., isolated from fallen leaves on geothermal soils, and description of Thermogemmatisporaceae fam. nov. and Thermogemmatisporales ord. Nov. Within the class Ktedonobacteria |journal=International Journal of Systematic and Evolutionary Microbiology |volume=61 |issue=4 |pages=903–910 |doi=10.1099/ijs.0.024877-0 |pmid=20495028 |doi-access=free}}</ref>) stain negative.<ref>{{Cite journal |last=Sutcliffe |first=I.C. |date=2011 |title=Cell envelope architecture in the Chloroflexi: A shifting frontline in a phylogenetic turf war |journal=Environmental Microbiology |volume=13 |issue=2 |pages=279–282 |bibcode=2011EnvMi..13..279S |doi=10.1111/j.1462-2920.2010.02339.x |pmid=20860732}}</ref> Two related phyla to the Chloroflexi, the [[TM7]] clade and the Ktedonobacteria, are also monoderms.<ref name="TM7">{{Cite journal |last1=Hugenholtz |first1=P. |last2=Tyson |first2=G.W. |last3=Webb |first3=R.I. |last4=Wagner |first4=A.M. |last5=Blackall |first5=L.L. |date=2001 |title=Investigation of Candidate Division TM7, a Recently Recognized Major Lineage of the Domain Bacteria with No Known Pure-Culture Representatives |journal=Applied and Environmental Microbiology |volume=67 |issue=1 |pages=411–419 |bibcode=2001ApEnM..67..411H |doi=10.1128/AEM.67.1.411-419.2001 |pmc=92593 |pmid=11133473}}</ref><ref name="Kt">{{Cite journal |last1=Cavaletti |first1=L. |last2=Monciardini |first2=P. |last3=Bamonte |first3=R. |last4=Schumann |first4=P. |last5=Rohde |first5=M. |last6=Sosio |first6=M. |last7=Donadio |first7=S. |date=2006 |title=New Lineage of Filamentous, Spore-Forming, Gram-Positive Bacteria from Soil |journal=Applied and Environmental Microbiology |volume=72 |issue=6 |pages=4360–4369 |bibcode=2006ApEnM..72.4360C |doi=10.1128/AEM.00132-06 |pmc=1489649 |pmid=16751552}}</ref>

Some Bacillota species are not gram-positive. The class Negativicutes, which includes ''[[Selenomonas]]'', are diderm and stain gram-negative.<ref name="pmid19667386" /> Additionally, a number of bacterial taxa (viz. [[Negativicutes]], [[Fusobacteriota]], [[Synergistota]], and [[Elusimicrobiota]]) that are either part of the phylum Bacillota or branch in its proximity are found to possess a diderm cell structure.<ref name="Sutcliffe, 2010" /><ref name="Gupta C" /><ref name="pmid19667386" /> However, a conserved signature indel (CSI) in the [[HSP60]] ([[GroEL]]) protein distinguishes all traditional phyla of gram-negative bacteria (e.g., [[Pseudomonadota]], [[Aquificota]], [[Chlamydiota]], [[Bacteroidota]], [[Chlorobiota]], "[[Cyanobacteria]]", [[Fibrobacterota]], [[Verrucomicrobiota]], [[Planctomycetota]], [[Spirochaetota]], [[Acidobacteriota]], etc.) from these other atypical diderm bacteria, as well as other phyla of monoderm bacteria (e.g., [[Actinomycetota]], [[Bacillota]], [[Thermotogota]], [[Chloroflexota]], etc.).<ref name="Gupta C" /> The presence of this CSI in all sequenced species of conventional LPS ([[lipopolysaccharide]])-containing gram-negative bacterial phyla provides evidence that these phyla of bacteria form a monophyletic clade and that no loss of the outer membrane from any species from this group has occurred.<ref name="Gupta C" />