Saccharibacteria, formerly known as ''TM7'', is a major bacterial lineage. It was discovered through

16S rRNA 16S rRNA may refer to: * 16S ribosomal RNA 16 S ribosomal RNA (or 16 S rRNA) is the RNA component of the 30S subunit of a prokaryotic ribosome ( SSU rRNA). It binds to the Shine-Dalgarno sequence and provides most of the SSU structure. The g ...

sequencing . TM7x from the human oral cavity was cultivated and revealed that TM7x is an extremely small

coccus A coccus (plural cocci) is any bacterium or archaeon that has a spherical, ovoid, or generally round shape. Bacteria are categorized based on their shapes into three classes: cocci (spherical-shaped), bacillus (rod-shaped) and spiral ( of whi ...

(200-300 nm) and has a distinctive lifestyle not previously observed in human-associated microbes. It is an obligate

epibiont An epibiont (from the Ancient Greek meaning "living on top of") is an organism that lives on the surface of another living organism, called the basibiont ("living underneath"). The interaction between the two organisms is called epibiosis. An ep ...

of various hosts, including ''

Actinomyces ''Actinomyces'' is a genus of the Actinomycetia class of bacteria. They all are gram-positive. ''Actinomyces'' species are facultatively anaerobic and they grow best under anaerobic conditions. ''Actinomyces'' species may form endospores, and ...

odontolyticus'' strain (XH001) yet also has a

parasitic Parasitism is a close relationship between species, where one organism, the parasite, lives on or inside another organism, the host, causing it some harm, and is adapted structurally to this way of life. The entomologist E. O. Wilson has c ...

phase thereby killing its host. The full genome sequence revealed a highly reduced genome (705kB) and a complete lack of amino acid biosynthetic capacity. An

axenic In biology, axenic (, ) describes the state of a culture in which only a single species, variety, or strain of organism is present and entirely free of all other contaminating organisms. The earliest axenic cultures were of bacteria or unicellul ...

culture of TM7 from the oral cavity was reported in 2014 but no sequence or culture was made available. Along with Candidate Phylum TM6, it was named after sequences obtained in 1994 in an environmental study of a soil sample of peat bog in Germany where 262 PCR amplified 16S rDNA fragments were cloned into a

plasmid A plasmid is a small, extrachromosomal DNA molecule within a cell that is physically separated from chromosomal DNA and can replicate independently. They are most commonly found as small circular, double-stranded DNA molecules in bacteria; how ...

vector, named TM clones for ' ( lit. peat, middle layer). It has been found in several environments since such as from

activated sludge The activated sludge process is a type of biological wastewater treatment process for treating sewage or industrial wastewaters using aeration and a biological floc composed of bacteria and protozoa. It uses air (or oxygen) and microorganisms ...

water treatment Water treatment is any process that improves the Water quality, quality of water to make it appropriate for a specific end-use. The end use may be drinking water, drinking, industrial water supply, irrigation, river flow maintenance, water recrea ...

plant sludge

rainforest Rainforests are characterized by a closed and continuous tree canopy, moisture-dependent vegetation, the presence of epiphytes and lianas and the absence of wildfire. Rainforest can be classified as tropical rainforest or temperate rainfores ...

soil, human

saliva Saliva (commonly referred to as spit) is an extracellular fluid produced and secreted by salivary glands in the mouth. In humans, saliva is around 99% water, plus electrolytes, mucus, white blood cells, epithelial cells (from which DNA can be ...

, in association with

sponge Sponges, the members of the phylum Porifera (; meaning 'pore bearer'), are a basal animal clade as a sister of the diploblasts. They are multicellular organisms that have bodies full of pores and channels allowing water to circulate through t ...

cockroach Cockroaches (or roaches) are a paraphyletic group of insects belonging to Blattodea, containing all members of the group except termites. About 30 cockroach species out of 4,600 are associated with human habitats. Some species are well-known as ...

es,

gold mines Gold mining is the extraction of gold resources by mining. Historically, mining gold from alluvial deposits used manual separation processes, such as gold panning. However, with the expansion of gold mining to ores that are not on the surface, ...

acetate An acetate is a salt (chemistry), salt formed by the combination of acetic acid with a base (e.g. Alkali metal, alkaline, Alkaline earth metal, earthy, Transition metal, metallic, nonmetallic or radical Radical (chemistry), base). "Acetate" als ...

-amended

aquifer An aquifer is an underground layer of water-bearing, permeable rock, rock fractures, or unconsolidated materials (gravel, sand, or silt). Groundwater from aquifers can be extracted using a water well. Aquifers vary greatly in their characterist ...

sediment, and other environments (bar

thermophilic A thermophile is an organism—a type of extremophile—that thrives at relatively high temperatures, between . Many thermophiles are archaea, though they can be bacteria or fungi. Thermophilic eubacteria are suggested to have been among the earl ...

), making it an abundant and widespread phylum. Recently, TM7 rDNA and whole-cells were detected in activated sludge with >99.7% identity to a human skin TM7 and 98.6% identity to the human oral TM7a, suggesting metabolically active TM7 isolates in environmental sites may serve as model organisms to investigate the role TM7 species play in human health.

Properties

TM7 specific

FISH Fish are aquatic, craniate, gill-bearing animals that lack limbs with digits. Included in this definition are the living hagfish, lampreys, and cartilaginous and bony fish as well as various extinct related groups. Approximately 95% of li ...

probes identified species from a

bioreactor A bioreactor refers to any manufactured device or system that supports a biologically active environment. In one case, a bioreactor is a vessel in which a chemical reaction, chemical process is carried out which involves organisms or biochemistry, ...

sludge revealed the presence of a

gram-positive In bacteriology, gram-positive bacteria are bacteria that give a positive result in the Gram stain test, which is traditionally used to quickly classify bacteria into two broad categories according to their type of cell wall. Gram-positive bacte ...

cell envelopes and several morphotypes: a sheathed filament (abundant), a rod occurring in short chains, a thick filament and

cocci A coccus (plural cocci) is any bacterium or archaeon that has a spherical, ovoid, or generally round shape. Bacteria are categorized based on their shapes into three classes: cocci (spherical-shaped), bacillus (rod-shaped) and spiral ( of whi ...

; the former may be the cause of Eikelboom type 0041 (bulking problems of activated sludges). The majority of

bacterial phyla Bacterial phyla constitute the major lineages of the domain ''Bacteria''. While the exact definition of a bacterial phylum is debated, a popular definition is that a bacterial phylum is a monophyletic lineage of bacteria whose 16S rRNA genes ...

are

Gram-negative Gram-negative bacteria are bacteria that do not retain the crystal violet stain used in the Gram staining method of bacterial differentiation. They are characterized by their cell envelopes, which are composed of a thin peptidoglycan cell wall ...

diderms Gram-negative bacteria are bacteria that do not retain the crystal violet stain used in the Gram staining method of bacterial differentiation. They are characterized by their cell envelopes, which are composed of a thin peptidoglycan cell wall s ...

, whereas only the

Bacillota The Bacillota (synonym Firmicutes) are a phylum of bacteria, most of which have gram-positive cell wall structure. The renaming of phyla such as Firmicutes in 2021 remains controversial among microbiologists, many of whom continue to use the earl ...

, the

Actinomycetota The ''Actinomycetota'' (or ''Actinobacteria'') are a phylum of all gram-positive bacteria. They can be terrestrial or aquatic. They are of great economic importance to humans because agriculture and forests depend on their contributions to soi ...

and

Chloroflexota The Chloroflexota are a phylum of bacteria containing isolates with a diversity of phenotypes, including members that are aerobic thermophiles, which use oxygen and grow well in high temperatures; anoxygenic phototrophs, which use light for photo ...

are

monoderm In bacteriology, gram-positive bacteria are bacteria that give a positive result in the Gram stain test, which is traditionally used to quickly classify bacteria into two broad categories according to their type of cell wall. Gram-positive bacte ...

s. Using a

polycarbonate Polycarbonates (PC) are a group of thermoplastic polymers containing carbonate groups in their chemical structures. Polycarbonates used in engineering are strong, tough materials, and some grades are optically transparent. They are easily work ...

membrane as a growth support and soil extract as the substrate, microcolonies of this clade were grown consisting of long filamentous rods up to 15 μm long with less than 50 cells or short rods with several hundred cells per colony, after 10 days incubation. Thanks to a microfluidic chip allowing the isolation and amplification of the genome of a single cell, the genome of 3 long filament morphology cells with identical 16S rRNA were sequenced to create a draft sequence of the genome confirming some previously ascertained properties, elucidating some of its metabolic capabilities, revealing novel genes and hinting to potential pathogenic abilities. Over 50 different

phylotype In taxonomy, a phylotype is an observed similarity used to classify a group of organisms by their phenetic relationship. This phenetic similarity, particularly in the case of asexual organisms, may reflect the evolutionary relationships. The term ...

s have been identified and it has a relatively modest intradivision 16S rDNA sequence divergence of 17%, which ranges from 13 to 33%. An interactive

phylogenetic tree A phylogenetic tree (also phylogeny or evolutionary tree Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA.) is a branching diagram or a tree showing the evolutionary relationships among various biological spec ...

of TM7, built using jsPhyloSVG, allows for quick access to

GenBank The GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations. It is produced and maintained by the National Center for Biotechnology Information (NCBI; a part ...

sequences and distance matrix calculations between tree branches. Stable-isotope probing studies have found that some members of this phylum can degrade

toluene Toluene (), also known as toluol (), is a substituted aromatic hydrocarbon. It is a colorless, water-insoluble liquid with the smell associated with paint thinners. It is a mono-substituted benzene derivative, consisting of a methyl group (CH3) at ...

Taxonomy

The currently accepted taxonomy is based on the

List of Prokaryotic names with Standing in Nomenclature List of Prokaryotic names with Standing in Nomenclature (LPSN) is an online database that maintains information on the naming and taxonomy of prokaryotes, following the taxonomy requirements and rulings of the International Code of Nomenclature ...

(LPSN) and

National Center for Biotechnology Information The National Center for Biotechnology Information (NCBI) is part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health (NIH). It is approved and funded by the government of the United States. The ...

(NCBI) * Class "Saccharimonadia" corrig. McLean et al. 2020 corrig._McLean_et_al._2020;_"Nanosyncoccia"_corrig._McLean_et_al._2020.html" ;"title="Nanoperiodontomorbia" corrig. McLean et al. 2020; "Nanosyncoccia" corrig. McLean et al. 2020">Nanoperiodontomorbia" corrig. McLean et al. 2020; "Nanosyncoccia" corrig. McLean et al. 2020** Order "Saccharimonadales" McLean et al. 2020 ["Nanogingivalales" corrig. McLean et al. 2020; "Nanoperiodontomorbales" corrig. McLean et al. 2020; "Nanosynbacterales" McLean et al. 2020; "Nanosyncoccales" McLean et al. 2020] *** "''Ca.'' Chaera" corrig. Lemos et al. 2019 **** "''Ca.'' C. renei" corrig. Lemos et al. 2019 *** "''Ca.'' Minimicrobia" Ibrahim et al. 2021 **** "''Ca.'' M. naudis" Ibrahim et al. 2021 **** "''Ca.'' M. vallesae" Ibrahim et al. 2021 *** "''Ca.'' Mycosynbacter" Batinovic et al. 2021 (JR1) **** "''Ca.'' M. amalyticus" Batinovic et al. 2021 *** "''Ca.'' Nanosynsaccharibacterium" corrig. McLean et al. 2020 *** Family "Nanogingivalaceae" McLean et al. 2020 **** "''Ca.'' Nanogingivalis" McLean et al. 2020 (CMJM_G6_1_HOT_870; UMGS1907) ***** "''Ca.'' N. gingivitcus" McLean et al. 2020 *** Family "Nanoperiodontomorbaceae" corrig. McLean et al. 2020 **** "''Ca.'' Nanoperiodontomorbus" corrig. McLean et al. 2020 (EAM_G5_1_HOT_356; UBA1103) ***** "''Ca.'' N. periodonticus" corrig. McLean et al. 2020 *** Family "Nanosynbacteraceae" McLean et al. 2020 **** "''Ca.'' Nanosynbacter" McLean et al. 2020 (TM7x) ***** "''Ca.'' N. lyticus" McLean et al. 2020 *** Family "Nanosyncoccaceae" McLean et al. 2020 **** "''Ca.'' Nanosyncoccus" McLean et al. 2020 (G3_2_Rum_HOT_351B; UBA2866) ***** "''Ca.'' N. alces" McLean et al. 2020 ***** "''Ca.'' N. nanoralicus" McLean et al. 2020 *** Family "Saccharimonadaceae" McLean et al. 2020 **** "''Ca.'' Saccharimonas" Albertsen et al. 2013 ***** "''Ca.'' S. " Albertsen et al. 2013 *** Family UBA1547 **** "''Ca.'' Microsaccharimonas" corrig. Lemos et al. 2019 (AMD02; UBA6175) ***** "''Ca.'' M. sossegonensis" corrig. Lemos et al. 2019

Phylogeny

References

Fredrik Bäckhed, Ruth Ley, Justin L Sonnenburg, Daniel A. Peterson, Jeffrey I. Gordon
Host‐Bacterial Mutualism in the Human Intestine
In: Science 307(5717): 1915-1920. April 2005. doi:10.1126/science.1104816. Michael A. Dojka, Philip Hugenholtz, Sheridan K. Haack, Norman R. Pace
Microbial diversity in a hydrocarbon- and chlorinated-solvent-contaminated aquifer undergoing intrinsic bioremediation
In: ASM Appl. Environ. Microbiol. 64(10): 3869-3877. 29 October 2020. doi:10.1128/AEM.64.10.3869-3877.1998. PMID 9758812. Damien M. de Vienne
Parcubacteria group
NCBI Lifemap,

University of Lyon The University of Lyon (french: Université de Lyon), located in Lyon and Saint-Étienne, France, is a center for higher education and research comprising 11 members and 24 associated institutions. The three main universities in this center are: ...

. Lifemap is an interactive tool to explore NCBI taxonomy. Damien M. de Vienne
environmental samples - candidate division WS5
NCBI Lifemap,

. Lifemap is an interactive tool to explore NCBI taxonomy. C. L. Schoch, Sayers ''et al''.
Parcubacteria groupParcubacteria group
(clade/superphylum, syn. candidate division OD1); C. L. Schoch, Sayers ''et al''.
candidate division WS5candidate division WS5
(clade, syn. candidate division Wurtsmith 5);

External links

Ultra-Small, Parasitic Bacteria Found in Groundwater, Dogs, Cats — And You
on: SciTechDaily; July 21, 2020; source: Forsyth Institute * Jeffrey S. McLean, Batbileg Bor, Kristopher A. Kerns, Kelly Wrighton, Wenyuan Shi, Xuesong He, ''et al.''
Acquisition and Adaptation of Ultra-small Parasitic Reduced Genome Bacteria to Mammalian Hosts
in: CellRep 32, 107939; July 21, 2020; doi:10.1016/j.celrep.2020.107939 * Jeffrey S. McLean, Batbileg Bor, Thao T. To, Quanhui Liu, Kristopher A. Kerns, Lindsey Solden, Kelly Wrighton, Xuesong He, Wenyuan Shi
Evidence of independent acquisition and adaption of ultra-small bacteria to human hosts across the highly diverse yet reduced genomes of the phylum Saccharibacteria
on: bioRxiv; February 02, 2018; doi:10.1101/258137 (PrePrint) {{Taxonbar, from=Q5031741 Bacteria Bacteria phyla Candidatus taxa

Properties

Taxonomy

Phylogeny

See also

References

External links