the tertiary amine trimethylamine ( tma ) is a volatile compound which has a characteristic fishy odor , and is formed by bacterial reduction of trimethylamine oxide ( tmao ) . this alkylamine is detected as unpleasant by the human olfactory system at even very low levels , thereby preventing humans from ingesting rotting fish . ironically , this molecule is also endogenous in humans , being synthesized in the gut and sometimes in the vagina by the endogenous microbiota . the microbiome of the gastrointestinal tract is better characterized than that of other body sites , so only this niche will be discussed here , although relevant metabolic processes in the vagina are probably similar . in the gut , tma is formed by microbial conversion of dietary ingredients and is further absorbed before being oxidized into tmao in the liver ( see fig .  1 ) . such tma precursors include tmao ( in abundance in seafood ) , and choline ( eggs , soybean , cauliflower ) , which is likely the most important tma source . recent data also show that l - carnitine found in red meat ( and in some energy drinks and dietary supplements ) is converted into tma . the metabolic pathways leading to tma are thought to be exclusively microbial in humans : the mechanism of conversion of choline by an anaerobic mammalian gut desulfovibrio has recently been identified and relies on the cut ( choline utilization ) operon , in which cutc encodes a glycyl radical enzyme with a choline trimethylamine - lyase activity . choline is an important factor for human health , with an adequate intake for adults of 425 mg and 550 mg per day being recommended for women and men respectively in the us . choline depletion resulting from a choline - deficient diet causes clinical consequences such as non - alcoholic fatty - liver disease ( nafld ) and muscle damage . dietary lecithin ( phosphatidylcholine , pc ) also feeds into plasma tmao levels by gut conversion into choline ( and then to tma ) , as shown by mouse studies . thus , limiting intake of choline or its precursors to reduce tma production is not feasible . however such a reduction of tma levels is highly desirable because tma is related to at least two disorders . figure  1 . origin and fate of tma in the human gut , and the archaebiotics concept . gut microbiota synthesis of tma is realized from tmao , choline , pc and l - carnitine . the tma is then absorbed and goes to the liver , routes ( a or ( b ) . in the case of route ( a ) , a partial or total defect in fmo3-oxidation into tmao when fmo3 liver oxidation is functional ( b ) , the increase of tmao in blood is associated with atherosclerosis . therefore , converting tma directly in the gut using archaebiotics belonging to the seventh methanogenic order , naturally - occurring in the gut , route ( c ) should be envisaged . interestingly , these archaea are only able to perform methanogenesis using methyl compounds ( see fig . 2 ) , because the two other pathways are absent ( co2 reduction with h2 and aceticlastic pathway ) : this would increase the efficiency of tma conversion . trimethylaminuria ( tmau ) is caused by a metabolic anomaly whereby sufferers emit a pervasive fishy odor caused by the excretion of tma in their breath , sweat and urine . as tmau is still under - recognized and often goes undiagnosed , those affected often suffer from psychological problems and social stress . although no large prevalence studies are currently available , people with compromised ability to n - oxidize trimethylamine into the odorless tmao are probably common . tmau can be classified into a primary genetic form and an acquired ( or secondary ) form . the genetic form is now well characterized with approximately 15% of single nucleotide polymorphisms ( snps ) in the fmo3 gene ( encoding a flavin - containing monooxygenase ) associated with either lack of or diminished enzymatic oxidation in the liver of tma into tmao . in the healthy individual , more than 95% of tma is oxidized into tmao in this way , while genetic defects in fmo3 result in accumulation of tma in blood , and then in breath , sweat and urine ( fig .  1 , pathway a ) . acquired tmau , sometimes transient , includes conditions featuring elevated urinary levels of tma due to dietary and hormonal factors in combination with enzymatic activity and metabolism in the gut . important examples include transient menstrual tmau , overload of dietary precursors of tma ( see above ) , and impaired hepatic function . treatment relies mainly on an empirical dietary approach , or several complementary therapeutic adjuncts , including soaps which limit the volatility of tma from the skin , together with brief courses of antimicrobials ( neomycin , metronidazole ) which are not always effective . this last approach limits the bacterial load , and in extenso , gut conversion of tmao , choline and derivatives into tma . gut microbiota metabolism of phosphatidylcholine ( pc ) and l - carnitine can promote atherosclerosis . this is because their plasma metabolites ( choline , betaine and tmao ) are risk factors for cardiovascular disease ( cvd ) in humans . experimentally , dietary choline supplementation has been shown in a seminal paper to significantly enhance aortic lesion area in mice genetically prone to atherosclerosis , as did supplementation of the diet with tmao . furthermore , gut microbiota depletion by antibiotics led to inhibition of the dietary choline - induced cardiovascular effects . mice with depleted gut microbiota did not experience increased tmao plasma levels ( fig .  1 , pathway b ) nor did humans . human gut microbiota is also required to form tmao from l - carnitine , and plasma tmao is likely the primary driver of cardiovascular risks rather than l - carnitine itself . it is important to stress that , in this instance , tma does not originate from urine , but rather from in situ production of tma by the vaginal microbiota through a process similar to that which occurs in the gut . we were prompted by recent microbiology studies to ask if tma could be depleted in vivo by bioconversion into a molecule with no undesirable properties . the underlying biochemistry was described more than 35 y ago in the rumen of cows , where choline is metabolized via tma and onwards into methane . rumen microbes like the methanogenic archaea methanosarcina barkeri metabolize methyl compounds , including tma , to methane for growth . a distinct archaeal group ( the rumen cluster c ; rcc ) was subsequently identified as being putatively able to convert methyl compounds including tma and methylamines into methane . half the human subjects examined to date also produce methane , usually by harboring the methanogen methanobrevibacter smithii , or less frequently , methanosphaera stadtmanae ( reviewed in ref . we thus asked if methylotrophic methanogens would be able to survive and deplete tma in the human gut ( or in the vagina ) , a notion that would be greatly supported if methanogens that naturally occur in the human gut could metabolize tma . the trigger for proposing this hypothesis now is that , until recently , only the methanogens m. smithii and m. stadtmanae were recognized as residents of the human gut . they belong to the order methanobacteriales , one of the six known orders of methanogens . however in 2008 , the existence of a seventh order inhabiting the human gut ( hereafter referred to as the mx - lineage ) was proposed , particularly common in older subjects , and methanomassiliicoccus luminyensis , the first and unique isolated member of this order metabolizes methanol with hydrogen for methane production . genomic sequences of three of these unusual methanogens are currently available , that of m. luminyensis , and genome sequences that we recently determined for  candidatus 
 methanomethylophilus alvus  and  candidatus 
 methanomassiliicoccus intestinalis  grown in an enrichment culture from human stool .  ca . belongs to the rcc cluster that was recently highlighted for its putative involvement in tma consumption in the rumen , while m. luminyensis and  ca . these three genomes have all of the genes necessary for reduction of methanol using hydrogen , but also for the reduction of tri- di- and monomethylamine with hydrogen ( fig . 2 ) , while the two other possible pathways for methanogenesis ( co2 reduction with h2 and acetoclastic methanogenesis ) are genetically incomplete . whereas the capacity of these strains to reduce methanol with hydrogen was previously demonstrated , their ability to grow on tma with hydrogen has not been investigated . we therefore tested this hypothesis on the sole strain of this group available in pure culture , m. luminyensis b10 , and thus confirmed for the first time that this strain is able to grow on tma with hydrogen ( fig . m. luminyensis b10 was also able to grow on the by - products of tma catabolism , dimethylamine and then monomethylamine , both being used with hydrogen for methanogenesis ( data not shown ) . these results are in agreement with the annotated genetic complement of this strain and strongly suggest the same metabolic capacity in  ca . m. intestinalis  because they harbor orthologs of all the relevant m. luminyensis genes involved in these pathways . collectively this suggests to us that natural methanogenic inhabitants of the human gut will be able to metabolize tma , and could deplete this metabolite as it is formed by bacterial elements of the microbiota . metabolic pathway of tma conversion deduced from genomic data from species of the 7th order of methanogens . the pathway of tma conversion involves a trimethylamine : corrinoid methyltransferase ( mttb ) which contains a pyrrolysine , an unusual amino - acid . the synthesis of this amino - acid and its transfer on a trna to form a pyrrolysyl - trna , and its insertion during the translation of mttb are presented in the green part . the pathway of trimethylamine ( tma ) conversion , involving the pyrrolysine containing mttb , is presented in the orange part . the dotted arrows indicate steps that are not detailed for the clarity of the scheme . recognized enzyme names ( see kegg map 00680 ) are provided , flanked by the corresponding protein accession numbers in the  ca . only accession numbers of enzymes specifically involved in the depletion of tma are presented , some being shared with dimethylamine ( dma ) and monomethylamine ( mma ) depletion ( not shown here ) . growth of methanomassiliicoccus luminyensis strain b10 on trimethylamine ( tma ) and hydrogen ( h2 ) . ( a ) the growth of m. luminyensis b10 on methanol ( m , 50 mm ) and h2 ( previously described by dridi et al . ) was used as a positive control for growth and maximal cell density . ( b ) we now show that m. luminyensis b10 also grows on tma ( 15 mm ) in the presence of h2 ( filled diamonds ) but not on tma in the absence of h2 ( open diamonds ) . accordingly , tma is depleted in presence of h2 ( filled triangles ) and not in the absence of h2 ( open triangles ) . the composition of the gas phase was measured at the end of the experiment ( c ) and revealed the production of methane ( ch4 ) and the depletion of h2 in presence of either m or tma . no ch4 was produced in the absence of h2 and ch4 was not produced nor h2 depleted in the absence of the methylated compound substrate ( m or tma ) . 25720 ) and cultivated in dsmz medium 119 , with rumen fluid replacing the sludge fluid . when h2 was present , initial atmosphere composition was : n2/h2/co2 ( 55:35:10 ) , and in absence of h2 : n2/co2 ( 75:25 ) . drawing together these ecological and biochemical strands , we now propose the archaebiotics concept viz . the intestinal application of specific archaeal strains for the treatment of human diseases including cardiovascular disease and tmau ( fig .  1 ) . the fishy - odor aspect of some vaginal conditions could be addressed using pessary delivery . methane , the tma - metabolite produced by these archaea is usually considered biologically inert in humans . the pathway and relevant coding sequences for catalyzing tma conversion to methane by  ca . methanomassiliicoccus intestinalis  based on annotation of the genomes we recently sequenced is shown in figure  2 ; a similar pathway is inferred from the m. luminyensis genome . as for other methanogenic archaea , it includes a methyltransferase mttb with a predicted pyrrolysine residue , which is associated with its synthetic machinery . m. luminyensis like m. smithii is susceptible to bacitracin , metronidazole , ordinazole and squalamine , providing the reassurance of contingency eradication . an alternative to administering live cells might be therapeutic administration of the relevant enzymes ( fig . 2 ) , all of which are also encoded by m. luminyensis . paralleling the experience with the development of probiotic bacterial strains for human consumption , it has been shown that particular archaeal methanogen strains are likely to be more suitable for clinical use in this application . for example , we established that some strains seem to be evolutionarily more adapted to the human gut ecosystem , harboring genes predicted to confer resistance to bile salts ( bile salt hydrolases occur in  ca . consideration of factors other than tma depletion alone is thus appropriate ( see also below ) . technological hurdles to overcome will include establishing the best way to deliver oxygen - sensitive microorganisms into the human gut , and whether or not this administration will lead to cell levels that are sufficient to allow clinically relevant tma depletion . there are additional biological challenges ; will these strains be able to effectively deplete tma in the gut ? are the ensuing risk reductions for cardiovascular disease achieved , as they were by antibiotic therapy to limit tma production ? it is also important to concede that archaeal abundance is not uniformly associated with increased health in mammals ; for example , bacteroides thetaiotaomicron - m . archaea in general appear to be more abundant in native africans than in african americans , likely indicating dietary influences on the microbiota . diet could conceivably be controlled or modulated to promote methanogen levels in recipients of archaebiotics . we can not currently explain why the mx - lineage of archaea appears from the literature to be more abundant in older subjects , so we are determining fecal archaeal levels in the eldermet cohort subjects , that are well phenotyped for diet , health and bacterial microbiota . a possible factor is the trophic interaction with other microbiota elements , and that a more favorable ecology emerges in some older subjects . this raises the provocative issue of what the effects of introducing a methanogenic archaea might be on the microbiota of the recipient . the mx - methanogens are very likely not acetoclastic but would compete with other hydrogenotrophic archaea and bacteria , so the downstream effects on microbiome , metabolome and host physiology would need detailed exploration in vitro , in animal models , and ultimately in humans . although the application of archaebiotics as proposed here faces significant challenges , we contend that the anticipated benefit of their use to mitigate the life - time risk of cvd and to treat tmau warrants a concerted research effort in this area by the scientific community .
trimethylamine ( tma ) is produced by gut bacteria from dietary ingredients . in individuals with a hereditary defect in flavin - containing monooxygenase 3 , bacterial tma production 
 is believed to contribute to the symptoms of trimethylaminuria ( tmau ; fish - odor syndrome ) . 
 intestinal microbiota tma metabolism may also modulate atherosclerosis risk by affecting trimethylamine oxide ( tmao ) production levels . 
 we propose that reducing tma formation in the gut by converting it to an inert molecule could be used to prevent or limit these human diseases , while avoiding the major drawbacks of other clinical interventions . 
 reducing tma levels by microbiological interventions could also be helpful in some vaginoses . 
 particular members of a recently discovered group of methanogens , that are variably present in the human gut , are unusual in being apparently restricted to utilizing only methyl compounds including tma as substrates . 
 we confirmed experimentally that one of these strains tested , methanomassiliicoccus luminyensis b10 , is able to deplete tma , by reducing it with h2 for methanogenesis . 
 we therefore suggest that members of this archaeal lineage could be used as treatments for metabolic disorders .