insertion sequences ( is ) are short prokaryote transposable elements ( tes ) characterized by a simple structure , often consisting of a single transposase - encoding open reading frame flanked by terminal inverted repeats . because their proliferation can induce variation in genome size , activate and inactivate gene expression and trigger various types of genomic rearrangements , is have a profound influence on prokaryote genome evolution . the general lack of congruence between is and host phylogenies , together with their overall patchy distribution among hosts , suggest that is distribution among prokaryotes is strongly shaped by horizontal transfer . unlike is , bacteriophages and plasmids encode the enzymatic machinery allowing them to move between cells . these two types of mobile genetic elements ( mges ) have traditionally been considered as the main vectors of is horizontal transfer . however the relative contribution of phages and plasmids to is horizontal transfer has never been thoroughly evaluated . we recently reported a comprehensive survey of the abundance and distribution of is elements integrated in 900 phage and plasmid annotated genomes available in the aclame database . this study revealed that while over half of plasmids contain at least one is ( with a density of one copy every 19 kb on average ) , the vast majority ( 92% ) of phages are completely devoid of is insertion ( one copy every 346 kb on average ) . we further showed that the density of deleterious insertion sites is significantly higher in phages than in plasmids . consequently , acquisition of is elements is more strongly counter - selected in phages than in plasmids . based on these results , we concluded that phages are less tolerant to is insertions than plasmids , i.e. , phages have a lower cargo capacity than plasmids . therefore , while our analysis confirmed the classically held view that plasmids are efficient vectors of is horizontal transfer , we concluded that phages may be rather poor vectors of is horizontal transfer among prokaryotes . if phages indeed do possess a lower cargo capacity than plasmids do , then we expect the distribution pattern observed for is elements to also hold for other tes . transposons are certainly the most thoroughly studied bacterial tes . they comprise elements with various modes of mobility : ( 1 ) composite ( formerly class i ) transposons are genetic sequences flanked by is elements which use the is transposase for their mobility , ( 2 ) unit transposons ( formerly type ii / tn3 family ) which use specific transposase / resolvase genes for their mobility , and ( 3 ) conjugative transposons / ices which can transfer from a bacterial cell to another through conjugation . transposons are often found in plasmids . on the contrary , to our knowledge , there has been no report of a transposon being carried by an active bacteriophage . the distribution of transposons in plasmids and phages therefore seems fully consistent with higher selective constrains on phages compared with plasmids . mobile introns are other bacterial tes which are able to self - splice from the transcript they are inserted in . they include two unrelated types of elements : group i introns ( which move through a homologous recombination process termed homing ) and group ii introns ( which move through reverse - transcription and integration of an rna intermediate in a process termed retrohoming ) . group ii introns are widespread in the bacterial world and frequently observed within plasmid sequences . to our knowledge , the distribution of group ii introns in plasmids and phages thus apparently reflects that of is elements . recent studies suggest that group ii intron insertions may be deleterious for hosts despite their splicing ability . while the greater tolerance of plasmids to group ii introns is likely due to lower selective constraints acting on their genomes compared with phages genomes , the presence of some group ii introns in plasmids may also be explained by their insertional preferences . for example , the well - studied group ii intron ll.ltrb performs specific retrohoming into relaxase genes , which are parts of the plasmid mobility machinery . analogously , members of the giic - attc intron class target integrons themselves often integrated within plasmids . finally , the targeting of is elements by various group ii introns may also account for group ii intron preferential presence in plasmids compared with phages . in contrast with group ii introns , group i introns are preferentially found in phages rather than plasmids . many group i introns have indeed been detected in phage sequences but to our knowledge , only two copies have been reported in a plasmid . furthermore , these two plasmid - borne group i introns are inserted within a prophage which is itself inserted into the plasmid genome . therefore , there is as yet no evidence that a group i intron has jumped into a plasmid genome . the pattern of group i intron distribution in mges is puzzling as it is contradictory to that observed for other tes , but it may be explained by the specific mobility mechanism used by group i introns . indeed , group i introns move from an intron - containing locus to a highly similar intron - free locus ( generally another allele of the same locus ) through a recombination - mediated process . the break is then repaired by the host homologous recombination machinery , which uses the intron - carrying allele as a template . as homologous recombination proceeds only on highly similar regions , the spread of group i introns relies on their ability to invade conserved regions . accordingly , chromosomal group i introns are usually found in trna and rrna genes or other essential genes , while most phage - borne group i introns are found in genes important for phage biology . in this context , the absence of group i intron in plasmids might simply reflect the fact that these site - specific elements never evolved to target plasmid genes . in sum , this brief overview of the distribution of the main bacterial tes in plasmids and phages globally supports our previous observations on is elements . it is fully consistent with higher selective constraints applying to phage genomes compared with plasmid genomes . in addition to the density of deleterious insertion sites , other factors may also contribute to the basis for strong negative selection against te insertions in phages and plasmids , and thus their cargo capacity . for example , growth rates of plasmid - carrying bacteria are negatively correlated with plasmid genome size . however , the decrease in growth rate induced by plasmid genome size increase is negligible compared with that induced by highly expressed genes . thus , a small plasmid with a single highly expressed gene may be much more counter - selected than a large plasmid with many lowly expressed tes . by contrast , genome size is a much more salient constraint in phages because capsids ( i.e. , phage container particles ) can not package more than 105106% of the wild type genome size . with a median size of 42 kb for phage genomes , this means that half of phage genomes can not package more than 2.5 kb of additional sequence , which translates into a couple of is elements or one group ii intron , at most . thus , constraints on genome size also argue for a larger cargo capacity for plasmids relative to phages . however , whatever its strength , purifying selection has to be efficient in order to effectively purge mge genomes from deleterious te insertions . population genetics theory indicates that selection efficiency depends on effective population size : the higher the effective population size , the more efficient the selection . phages are the most numerous organisms on earth and their effective population size is presumably enormous . thus , in addition to the fact that their genome contains a higher proportion of deleterious sites , the efficiency of purifying selection in phages is likely to be much higher than in plasmids : for an equally deleterious insertion site , purifying selection is expected to remove a te quicker from a phage population than from a plasmid population . on the other hand , many more low - frequency neutral te insertions are expected in ( large ) phage populations than in ( smaller ) plasmid populations . even though the lifespan of individual insertions is very short , they may collectively represent a dynamic reservoir of tes that might be transferable between bacterial cells . the magnitude of such a phenomenon is currently difficult to estimate , but the availability of an increasing amount of metagenomic data is likely to provide new insights into this question in the near future . if this hypothesis was verified , it would argue for a potentially more important role of phages in the horizontal transfer of tes than the current evidence suggests . nevertheless , another population genetics parameter to keep in mind for a horizontal transfer to be successful is not only vector fitness , but also bacterial host fitness . indeed , a large number of potential transfers initiated by phages simply can not lead to successful te horizontal transfers because they result in the death of the bacterial hosts . on the contrary another factor that might affect the efficiency with which phages and plasmids can shuttle tes between bacteria is the breadth of mge host range . while a substantial number of broad host - range plasmids and phages have been characterized , the majority of plasmids and phages are believed to have a relatively narrow host range and to be capable of transferring genetic material only between closely related species of the same genus . this trend is indeed consistent with the observation that horizontal transfer of both is and non - is dna is more frequent between closely related bacteria than between distantly related bacterial lineages . overall , the available data on mge host range do not seem to indicate any dramatic difference between typical phage and plasmid host ranges . however , studies of mge host ranges remain relatively scarce and are often plagued with various pitfalls and limitations . a method was recently developed to predict plasmid host range based on genomic signatures expected to be shared ( or not ) between plasmids and bacterial chromosomes , depending on plasmid host range breadth . this method , which exclusively relies on sequence data , was first validated on various plasmids belonging to six well - studied incompatibility groups ( inc.f , inc.h , inc.i , inc.n , inc.p and inc.w ) and was then applied to other less studied plasmids ( inc.q , inc.u , proma , inc.a / c and inc.p-9 ) for which host range was mostly inferred to be wide . given the rate at which new mges and bacterial genomes are currently added to public databases , it will certainly help to better delineate the host range of numerous mges . it is however important to keep in mind that simple entry of a te - carrying mge into a new bacterial cell is potentially sufficient for te horizontal transfer to happen . in other words , mges can facilitate te horizontal transfer even in the absence of successful phage replication or plasmid maintenance . therefore , the host range relevant to a particular mge ( i.e. , the number of bacterial species in which a phage can successfully replicate or in which a plasmid can be maintained ) might be narrower than the host range truly relevant to te horizontal transfer . our comparison of is abundance in phages and plasmids has provided the first formal test of the relative contributions of phages and plasmids to is horizontal transfer between bacterial cells , suggesting that plasmids are better vectors of is horizontal transfer than phages . this result seems to also hold for other tes , such as transposons and group ii introns . in fact , the better capacity of plasmids to shuttle tes compared with phages is probably not due to an intrinsic property of tes , as a recent study showed that this trend seems to apply to all types of dna sequences . we have summarized a number of potential underlying causes for the differential implication of phages and plasmids in the horizontal transfer of tes . while strength and efficiency of selection are clearly major players in this game , a number of other parameters ( e.g. , low - frequency insertions in phages and mge host range ) may have a non - trivial impact as well . however , the actual magnitude of the different factors currently remains difficult to evaluate with accuracy . there is no doubt that the ever - increasing amount of genomic data being made available will soon allow for refined estimates of these parameters .