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, an ...

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 ha ...

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 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 microorganism ...

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

plant sludge rainforest soil, human saliva, 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 throug ...

cockroach Cockroaches (or roaches) are a Paraphyly, 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 we ...

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-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 characteris ...

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 ...

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 process is carried out which involves organisms or biochemically active substances ...

sludge revealed the presence of a Gram-positive bacteria, gram-positive cell envelopes and several Polymorphism (biology), morphotypes: a sheathed Filamentation, filament (abundant), a Bacillus (shape), rod occurring in short chains, a thick filament and coccus, cocci; the former may be the cause of Eikelboom type 0041 (bulking problems of activated sludges). The majority of bacterial phyla are Gram-negative bacteria, Gram-negative Gram-negative bacteria#Taxonomy, diderms, whereas only the Bacillota, the Actinomycetota and Chloroflexota are Gram-positive bacteria#Importance of the outer cell membrane in bacterial classification, monoderms. Using a polycarbonate membrane as a growth support and soil extract as the substrate, microcolony, 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 Lab-on-a-chip, 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 phylotypes 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 of TM7, built using List of phylogenetic tree visualization software#Online software, jsPhyloSVG, allows for quick access to GenBank sequences and distance matrix calculations between tree branches. Stable-isotope probing studies have found that some members of this phylum can degrade toluene.

Taxonomy

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) and National Center for Biotechnology Information (NCBI) * Class "Saccharimonadia" 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. Lifemap is an interactive tool to explore NCBI taxonomy. Damien M. de Vienne
environmental samples - candidate division WS5
NCBI Lifemap, University of Lyon. 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