What is the difference between insertion sequences and transposons

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Sign In. Advanced Search. Search Menu. Article Navigation. Close mobile search navigation Article Navigation. Volume Article Contents Abstract. The IS families. IS derivatives. Characteristics of family life. Bacterial insertion sequences: their genomic impact and diversity. Patricia Siguier , Patricia Siguier. Oxford Academic. Edith Gourbeyre. Mick Chandler. Editor: Alain Filloux. Revision received:. Select Format Select format. Permissions Icon Permissions. Abstract Insertion sequences ISs , arguably the smallest and most numerous autonomous transposable elements TEs , are important players in shaping their host genomes.

Figure 1. Open in new tab Download slide. Table 1 General characteristics of IS families. Open in new tab. Figure 2.

Figure 3. Figure 4. Figure 5. Figure 6. Characterization of a small mobilizable transposon, MTnSag1, in Streptococcus agalactiae. Google Scholar Crossref. Search ADS. Effect of temperature and light on growth of and photosynthesis by Synechococcus isolates typical of those predominating in the octopus spring microbial mat community of Yellowstone National Park.

Atomic structure of the RuvC resolvase: a Holliday junction-specific endonuclease from E. Functional characterization of IS, an IS4 family element involved in mobilization and expression of beta-lactam resistance genes.

New superfamilies of eukaryotic DNA transposons and their internal divisions. Transcriptional slippage in bacteria: distribution in sequenced genomes and utilization in IS element gene expression. Transposase and cointegrase: specialized transposition proteins of the bacterial insertion sequence IS21 and related elements. ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria. Lateral gene transfer between obligate intracellular bacteria: evidence from the Rickettsia massiliae genome.

Google Scholar PubMed. A chimeric ribozyme in Clostridium difficile combines features of group I introns and insertion elements. Atypical association of DDE transposition with conjugation specifies a new family of mobile elements.

Shuffling of Sulfolobus genomes by autonomous and non-autonomous mobile elements. Transposon-like Correia elements: structure, distribution and genetic exchange between pathogenic Neisseria sp.

Short- and long-term evolutionary dynamics of bacterial insertion sequences: insights from Wolbachia endosymbionts. IS is active for transposition into the chromosome of Escherichia coli K and inserts specifically into palindromic units of bacterial interspersed mosaic elements.

Birth of a chimeric primate gene by capture of the transposase gene from a mobile element. A family of small repeated elements with some transposon-like properties in the genome of Neisseria gonorrhoeae.

De Palmenaer. Translational control of transposition activity of the bacterial insertion sequence IS1. Transcription attenuation associated with bacterial repetitive extragenic BIME elements.

Functional similarities between retroviruses and the IS3 family of bacterial insertion sequences? Miniature inverted repeat transposable elements and their relationship to established DNA transposons.

I am what I eat and I eat what I am: acquisition of bacterial genes by giant viruses. Sequence analysis of the inversion region containing the pilin genes of Moraxella bovis. Distribution of IS91 family insertion sequences in bacterial genomes: evolutionary implications.

Massive presence of insertion sequences in the genome of SOPE, the primary endosymbiont of the rice weevil Sitophilus oryzae. Horizontal transfer and evolution of prokaryote transposable elements in eukaryotes. DNA polymerase I and a protein complex bind specifically to E. The movement of Tn3-like elements: transposition and cointegrate resolution. Modular evolution of TnGBSs, a new family of integrative and conjugative elements associating insertion sequence transposition, plasmid replication, and conjugation for their spreading.

The diversity of prokaryotic DDE transposases of the mutator superfamily, insertion specificity, and association with conjugation machineries. In vitro reconstitution of a single-stranded transposition mechanism of IS Resetting the site: redirecting integration of an insertion sequence in a predictable way.

ISA from Bacillus thuringiensis is functional in Escherichia coli : transposition and insertion specificity. Structural and functional characterization of IS and ISfamily elements. Multiple oligomerisation domains in the IS transposase: a leucine zipper motif is essential for activity. IS transposition is regulated by protein-protein interactions via a leucine zipper motif. Clostridium difficile IStron CdISt1: discovery of a variant encoding two complete transposase-like proteins.

Reconstitution of a functional IS single-strand transpososome: role of non-canonical base pairing. Integrating prokaryotes and eukaryotes: DNA transposases in light of structure. Phage infection of the obligate intracellular bacterium, Chlamydia psittaci strain guinea pig inclusion conjunctivitis. Conserved sequence motifs in the initiator proteins for rolling circle DNA replication encoded by diverse replicons from eubacteria, eucaryotes and archaebacteria.

Characterization and distribution of IS in the radioresistant bacterium Deinococcus radiodurans. Enhanced expression of the multidrug efflux pumps AcrAB and AcrEF associated with insertion element transposition in Escherichia coli mutants Selected with a fluoroquinolone. Novel sequence organization and insertion specificity of IS and IS chimaeric transposable elements of Helicobacter pylori.

Functional organization and insertion specificity of IS, a chimeric element of Helicobacter pylori. Transposable element ISHp of Helicobacter pylori : nonrandom geographic distribution, functional organization, and insertion specificity. Metaproteomics reveals abundant transposase expression in mutualistic endosymbionts.

Suppression of hypersensitivity of Escherichia coli acrB mutant to organic solvents by integrational activation of the acrEF operon with the IS1 or IS2 element. Plasmid reference center registry of transposon Tn allocations through July A novel type of transposon generated by insertion element IS present in a pSC derivative.

IS91 transposase is related to the rolling-circle-type replication proteins of the pUB family of plasmids. The processing of repetitive extragenic palindromes: the structure of a repetitive extragenic palindrome bound to its associated nuclease.

Transpositional recombination: mechanistic insights from studies of mu and other elements. Class 2 TEs are characterized by the presence of terminal inverted repeats , about 9 to 40 base pairs long, on both of their ends Figure 3.

As the name suggests and as Figure 3 shows, terminal inverted repeats are inverted complements of each other; for instance, the complement of ACGCTA the inverted repeat on the right side of the TE in the figure is TGCGAT which is the reverse order of the terminal inverted repeat on the left side of the TE in the figure.

One of the roles of terminal inverted repeats is to be recognized by transposase. Figure 3: The structure of a DNA transposon. DNA transposons, also known as class 2 transposable elements, are flanked at both ends by terminal inverted repeats. The inverted repeats are complements of each other the repeat at one end is a mirror image of, and composed of complementary nucleotides to, the repeat at the opposing end.

Genetics: A Conceptual Approach , 2nd ed. In addition, all TEs in both class 1 and class 2 contain flanking direct repeats Figure 3. Flanking direct repeats are not actually part of the transposable element ; rather, they play a role in insertion of the TE.

Moreover, after a TE is excised, these repeats are left behind as "footprints. L1 elements average about 6 kilobases in length. In contrast, Alu elements average only a few hundred nucleotides, thus making them a short interspersed transposable element, or SINE. Alu is particularly prolific, having originated in primates and expanding in a relatively short time to about 1 million copies per cell in humans. The fact that roughly half of the human genome is made up of TEs, with a significant portion of them being L1 and Alu retrotransposons, raises an important question: What do all these jumping genes do, besides jump?

Much of what a transposon does depends on where it lands. Landing inside a gene can result in a mutation , as was discovered when insertions of L1 into the factor VIII gene caused hemophilia Kazazian et al. Similarly, a few years later, researchers found L1 in the APC genes in colon cancer cells but not in the APC genes in healthy cells in the same individuals. This confirms that L1 transposes in somatic cells in mammals, and that this element might play a causal role in disease development Miki et al.

Another example of transposon silencing involves plants in the genus Arabidopsis. Researchers who study these plants have found they contain more than 20 different mutator transposon sequences a type of transposon identified in maize.

In wild-type plants, these sequences are methylated , or silenced. However, in plants that are defective for one of the enzymes responsible for methylation, these transposons are transcribed. Moreover, several different mutant phenotypes have been explored in the methylation-deficient plants, and these phenotypes have been linked to transposon insertions Miura et al.

Based on studies such as these, scientists know that some TEs are epigenetically silenced; in recent years, however, researchers have begun to wonder whether certain TEs might themselves have a role in epigenetic silencing.

It has taken decades for scientists to collect enough evidence to consider that maybe McClintock's speculation had a kernel of truth to it. RNAi is a naturally occurring mechanism that eukaryotes often use to regulate gene expression. Yang and Kazazian demonstrated that this results in homologous sequences that can hybridize, thereby forming a double-stranded RNA molecule that can serve as a substrate for RNAi.

Furthermore, when the investigators inhibited endogenous siRNA silencing mechanisms, they saw an increase in L1 transcripts, suggesting that transcription from L1 is indeed inhibited by siRNA.

The fact that transposable elements do not always excise perfectly and can take genomic sequences along for the ride has also resulted in a phenomenon scientists call exon shuffling. Exon shuffling results in the juxtaposition of two previously unrelated exons, usually by transposition, thereby potentially creating novel gene products Moran et al.

The ability of transposons to increase genetic diversity, together with the ability of the genome to inhibit most TE activity, results in a balance that makes transposable elements an important part of evolution and gene regulation in all organisms that carry these sequences.

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Nature , — link to article. Koga, A. Vertebrate DNA transposon as a natural mutator: The medaka fish Tol2 element contributes to genetic variation without recognizable traces. Molecular Biology and Evolution 23 , — doi McLean, P. McClintock, B. Mutable loci in maize. Carnegie Institution of Washington Yearbook 50 , — link to article. Miki, Y. Disruption of the APC gene by a retrotransposal insertion of L1 sequence in colon cancer. Cancer Research 52 , — Miura, A. Mobilization of transposons by a mutation abolishing full DNA methylation in Arabidopsis.

Moran, J. Exon shuffling by L1 retrotransposition. SanMiguel, P. Nested retrotransposons in the intergenic regions of the maize genome. Slotkin, R.

Transposable elements and the epigenetic regulation of the genome. Nature Reviews Genetics 8 , — link to article. Yang, N. L1 retrotransposition is suppressed by endogenously encoded small interfering RNAs in human cultured cells. Nature Structural and Molecular Biology 13 , — link to article. It is also plausible that ISs that had mobilized ARGs in the past are still maintained and continue to accumulate ARGs under conditions of antibiotic selection pressure.

This would result in coselection for IS-bearing bacteria, thereby providing opportunities for them to form associations with yet other ARGs. Nevertheless, other factors, such as a higher tendency for self-replication or a lower cost of transposition for the host, could help specific ISs to outcompete others and enhance associations with ARGs. The lower left corner of Fig. These ISs have fewer significant associations with ARGs, probably due to their low abundance in the genomic database, which could result in lower statistical power in permutation tests.

The possibility cannot be excluded that there might be bacteria where such ISs are significantly associated with more ARGs, but if so, those genomes remain to be sequenced. Interestingly, there were also more-abundant ISs that showed few significant associations with ARGs, suggesting that they may have other primary roles or taxonomic preferences. This includes some members of the IS family that are known to modulate virulence in Gram-positive bacteria 24 , members of the IS L3 family e.

The latter is exclusive to the Mycobacterium tuberculosis complex and has even been used as a strain-specific marker for typing in epidemiological studies of tuberculosis Transposition of IS is controlled by the host due to its possible deleterious effect With very slow transposition events, it has a limited chance to be associated with various ARGs. The ISs with the most significant associations displayed a similar level of diversity in terms of the antibiotic classes to which the associated ARGs provide resistance Fig.

This suggests that there is no or limited differential preference between ISs and antibiotic classes. This was as expected, in contrast to ISs with few associations, which showed a much larger range of variability of associated ARGs Fig. We cannot, however, rule out the possibility that the members of the latter group might have associations with integrons and plasmids in bacterial genomes that have yet to be sequenced.

Integrons offer rapid bacterial adaptation in response to antibiotic stress by capturing and expressing ARGs in the form of gene cassettes.

By accessing versatile resistance gene cassettes, ISs involved in the mobilization of integrons would thus have a higher chance of being coselected and maintained on bacterial genomes under selection pressure from antibiotics. The variability of all the ORFs in relation to the variability of the identified ARGs within tentative composite transposons was therefore analyzed Fig.

Tentative composite transposons with higher ARG richness bigger marker size had, in general, lower Jaccard indices. This shows that the dynamic transposition of ISs is connected to high ARG richness such that different instances of the tentative composite transposons should mobilize different genes, including ARGs, in order to be possibly coselected and maintained with ARGs in the genomes of various bacterial hosts. This is further illustrated in Fig.

There were, however, some tentative composite transposons belonging to the Tn 3 family e. Since some of the members of the Tn 3 family are unit transposons 13 , they could mobilize genetic materials and enhance their associations with ARGs without being dependent on another IS.

Transposition of the second IS within the unit transposons might have been happened once and have been maintained since then. Thus, despite the high level of ARG richness between the two ISs, the variability of the surrounded context is low.

The variability seen between two unit transposons e. However, the Jaccard index could rather represent the variable genetic context captured by each of the transposases in these groups alone. Nevertheless, analyses of variability within composite transposons along with other pieces of information about ISs could help identify dynamic ISs with strong associations with ARGs.

The colors represent different IS domains, and the sizes of the markers are scaled to reflect the ARG richness within tentative composite transposons. Next, we investigated the abundance of ISs and ARGs in a large collection of metagenomes representing human and animal microbiomes as well as the external environment Fig. The IS richness data, calculated from the unique number of identified IS names, are presented in Fig.

The metagenomes from external environments e. However, some of the IS domains with lower IS richness e. This highlights their possible associations with specific bacteria common in these environments or a selection under the given environmental conditions. From the analysis of the bacterial genomes, we also found that these ISs were common in Staphylococcus aureus , which is a commensal that is highly abundant in the human microbiome, especially on the skin.

A similar pattern could be found in the vaginal metagenomes, where high abundances of ISs within the IS i. These ISs are often encountered in Lactobacillus , which is common in the vaginal microflora.

Moreover, association of Tn 3 e. From the genomic analyses, we found that these ISs have strong associations with ARGs and, possibly through these associations, the genetic contexts containing both ISs and ARGs were selected by the high levels of antibiotics found in those environments Moreover, the distributions of ISs were compared between environments Fig.

This analysis showed that some environments were rather similar to each other in terms of IS composition. For instance, the human gut- and animal-associated metagenomes were highly similar, especially those associated with the oral and gut microbiomes. Insertion sequences and ARGs in metagenomic data sets. The main diagonal shows the within-environment similarities. To further investigate the variability between individual metagenomic data sets, we performed a multidimensional scaling MDS analysis based on the IS abundance Fig.

This showed that most of the human- and animal-associated metagenomes e. Furthermore, the animal and human gut metagenomes showed a lower level of within-environment variability than the metagenomes from external environments, such as the marine, soil, and sediment metagenomes, which were more diverse.

This is also aligned with the values shown on the main diagonal of Fig. This demonstrates that the specific associations observed in the bacterial genome data are also present in bacterial communities. Tracing the associations of ISs with ARGs, identified from analyzing bacterial genome data, in metagenomes.

A Wilcoxon test confirms a highly significant difference between them absence of a difference is indicated by a horizontal dashed red line. The sizes of the markers are scaled according to the ARG richness from genome data. Bottom panel Stack bar chart showing the distribution of ISs across different environments. The average of relative abundances of ISs across metagenomes in each environment was used. Insertion sequences with a wide range of correlational spectra are abundant in different environments Fig.

In presumably somewhat less human-impacted environments such as marine environments and soil, ISs with weaker correlations with ARGs are abundant, whereas those with stronger correlations are found mostly in human-, animal-, and wastewater-impacted environments. Genomic analyses could provide taxonomical clues on distribution of ISs in different environments.

For instance, strong associations of IS Atsp1 average correlation, 0. There are ISs with a high average correlation with ARGs in metagenome data, even though no significant associations have been found in the genome data.

Metagenomic data sets represent complex microbial communities, allowing ISs that are located on the same bacterial genomes or in the concomitant hosts to follow the same pattern. For instance, IS Ec23 average correlation, 0. Moreover, IS Lpl1 average correlation, 0. A metagenomic data set from gut- or wastewater-impacted environments probably contains both IS Lpl1 and ARG-associated ISs, causing increased correlation. Nevertheless, we must also consider that metagenomic samples might contain novel associations of ISs with ARGs, or even different bacterial hosts containing new associations that have not been identified through the whole-genome sequencing approach.

Considering the genomic and metagenomic analyses of ISs, we would prioritize exploring the content around the groups of ISs listed in Table 1. Exploring the content around specific ISs could hence be critical for identifying many as-yet-unrecognized ARGs.

ISs associated with a high diversity of ARGs group 1 or with a generally variable context group 2. Table 1 lists some ISs that constitute parts of highly variable tentative composite transposons, which thereby have the potential to also carry novel resistance determinants.

Similarly, IS psa2 in fish pathogens or IS in members of oral, vaginal, and gut microbiota could impose such risks as well. With a well-designed strategy, the contexts of ISs already associated with a high diversity of known ARGs may be explored further to find novel putative ARGs.

Knowledge of such associations can be used to guide the analysis of whole-genome sequencing data to find ORFs around ISs of interests with regard to candidate genes that could confer resistance to antibiotics. Moreover, targeted amplicon sequencing may be employed to extract genetic context within composite transposons of interest from complex bacterial communities.

In such a culture-independent approach, the recovered genetic material could be amplified by specific primers that could target pairs of ISs, which could then be sequenced, preferably with long-sequencing technologies e.

Functional metagenomic techniques used on amplified composite transposons may also be applied to increase the chances of finding completely novel classes of ARGs. ISs with strong associations with ARGs were identified, and tentative composite transposons with the potential of mobilizing novel putative ARGs into human pathogens were suggested.

This could involve functional or sequence-based screening of ORFs around specific genes, and particularly around those located within certain composite transposons.

This report also provides a general framework to explore other mobile genetic elements such as ISCR and unit transposons as well as unknown insertion sequences to facilitate discovery of mobile novel ARGs. ARGs from the ResFinder database downloaded 15 April 30 were used as it contains only mobile genes. Genes were first translated using Prodigal v2. The genomes were annotated as follows.

Prodigal v2. Moreover, we included all the transposases from the Tn 3 family in our analyses, even though some of its members function as unit transposons.

The genomes containing matching ORFs were analyzed with the pipeline described above. Throughout the text, we use the following insertion sequence nomenclature.

We refer to IS names as ISs for simplicity, except in cases in which we explicitly mention the variant, family, or domain to refer to individual ORFs, the assigned family, or the set of ISs with the same DDE domains, respectively.

For a given distance, the relative frequencies of gene functions around each ARG or IS variant were calculated by dividing the number of occurrences by the total number of matches of the ARG or IS variants among the analyzed genomes. Insertion sequences from the same IS domain with an ORF-distance of less than 30 were considered tentative composite transposons.

Acknowledging the difficulty of accurately identifying functional composite transposons, we hypothesized that it is more likely that IS pairs with the same protein domain could detect the necessary motifs required for transposition and thus function as composite transposons. Moreover, the lengths of operational composite transposons can differ between IS families and might span more than 30 ORFs. However, the longer the distance used to define tentative composite transposons, the larger the probability of encountering IS copies that were not functionally interacting with each other.

With this approach, we could evaluate tentative composite transposons in the sequenced genome data, their various genetic contexts, associations with ARGs, and occurrences in human pathogens. The similarity of the gene contents between two tentative composite transposons was calculated using the pairwise Jaccard index. The Jaccard index of two instances of a composite transposon is defined as the ratio of the number of common genes to the total number of unique genes surrounded by ISs.

The mean overall pairwise Jaccard indices were then reported as variability metrics for each composite transposase. To measure the statistical significance of the associations of ISs and ARGs, permutation tests were employed as follows. All ORFs within the respective genomes e. This was repeated 10, times, resulting in an empirical null distribution.

A normal distribution was fitted to the distribution using the SciPy package [ 41 ] , and the significance, in the form of a one-sided P value, was reported, after calculating the probability for a more extreme observation. In total, 1, metagenomic data sets produced by a similar platform, i.

We selected metagenomes from various environments representing different geographical and environmental conditions from the MGnify 42 and MG-RAST 43 databases. The metagenomes were assigned to groups based on their source as follows. Human microbiomes were divided into gut, vaginal, skin, oral, and airway groups. Animal-associated metagenomes were mostly comprised of animal feces collected from pigs and poultry.

Reads that mapped to several reference proteins were counted multiple times. The relative abundances of IS names, families, and domains were calculated on the basis of the average relative abundances of the corresponding IS variants.

IS richness and between-sample similarity values were calculated based on downsampled data sets where one million reads were randomly selected without replacement.

The pairwise similarities of metagenomes within and between environments were calculated, and then the average was reported.