Horizontal gene transfer is the primary mechanism for the spread of antibiotic resistance in bacteria. How to detect when there is HGT between bacteria and their hosts?
Since the origin of the animal kingdom, marine animals have lived in association with viruses, prokaryotes and unicellular eukaryotes, often as symbionts. This long and continuous interaction has provided ample opportunity not only for the evolution of intimate interactions such as sharing of metabolic pathways, but also for horizontal gene transfer (HGT) of non-metazoan genes into metazoan genomes. The number of demonstrated cases of inter-kingdom HGT is currently small, such that it is not yet widely appreciated as a significant player in animal evolution. Sessile marine invertebrates that vertically inherit bacterial symbionts, that have no dedicated germ line, or that bud or excise pluripotent somatic cells during their life history may be particularly receptive to HGT from their symbionts. Closer scrutiny of the growing number of genomes being accrued for these animals may thus reveal HGT as a regular source of novel variation that can function to extend the host phenotype metabolically, morphologically, or even behaviorally. Taxonomic identification of symbionts will help to address the intriguing question of whether past HGT events may constrain contemporary symbioses.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4237138/
Ok this link will be very helpful for you:
http://www.cell.com/trends/parasitology/abstract/S1471-4922(13)00073-1
There is a lot of bioinformatic tools to predict HGT in available genomes. So if you want to analyze HGT in genomes of described simbiotic bacteria, you can use the NCBI available to predict it as a model. In a better case, you can use your own newly sequenced microbial genomes to do that.
The tools, can be classified in parametric and phylogenetic inference tools. The formers meassure genomic marks like GC content, genomic islands, etc. Some of these are included in the GIST tool, but i think that now could be new tools: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3302003/
As their name is, the phylogenetic tools use the protein sequence similarity between predicted CDS between distinct genomes and they calculate if there is closeness between orthologues from unrelated genomes. Between these, i can remember three tools:
HGTector: https://www.ncbi.nlm.nih.gov/pubmed/25159222
DarHorse: http://darkhorse.ucsd.edu/
HGTree: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702880/
There is a lot of software, but i wish that these could be usefull.
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