About half the human population carries a Gram-negative bacteria called Helicobacter pylori (hp for short) in their stomachs. It is a microaerophilic bacterium belonging to the Epsilonproteobacteria which was discovered in 1984, and has lived inside of our ancestors for many tens of thousands of years.
It can cause several illnesses: peptic and duodenal ulcers, chronic gastritis and even cancer. Fortunately these diseases only occur in a minority of those infected with the bacteria. Most of us don't even notice we carry it, and will not notice any problems.
The interesting part is that it is transmitted mainly within families and, is a clear indicator of lineage and origin of those families. There are however instances of horizontal transmission (attributed to sharing drinking water in rural South America), but inter ethnic exchange is rare and may take centuries (as indicated by the hp Europe strain found among black South Africans). 
The bacteria is commonly transmitted person-to-person by saliva, and in developing countries, by fecal contamination of food or water.
Genetics and Helicobacter pylori
The original stock of hp evolved with their human hosts and diverged into several major hp populations, spreading across the globe with our migrating ancestors (hpAfrica1, hpEurope, hspEAsia, and hspAmerind,named after their geographical locations).
As can be expected, and following the logic that America was the last corner of the world to be inhabited, the literature stresses the "similarities between the hspAmerind and hspEAsia populations suggest[ing] that the first colonizers of the New World brought H. pylori with them..." from Eastern Asia, horizontal transmission is highlighted by an "apparent dominance by the hpEurope population at least in Latin America" .
The former may not be so true, but the latter definitvely is: the European hp strains were evidently transmitted due to admixture between natives and the large migration of Europeans to Latin America.
Regarding the "similarity" between East Asian and Amerindian hp, check this:
Some strains differ in their proteins which affect their hosts in differwnt ways. The most studiwd ones are CagA and VacA:/p
"However, the single-gene trees for cagA and vacA show strong divergence [between Amerindian hp] from both hspEAsia and hpEurope counterparts. The exaggerated evolution of these genes that has occurred over the ~15,000 years since the arrival of Amerindian ancestors to the Americas makes them less suitable for deducing evolutionary relationships but highlights the need to assess the physiological activities of the Amerindian alleles...
... phylogenetic analysis of the host-interactive genes vacA and cagA shows substantial divergence of Amerindian from Old World forms and indicates new genotypes (e.g., VacA m3) involving these loci."
There seems to be some contradiction here. On one hand we are told that Amerindian and East Asian hp are "close" to each other, but then we are told that they is a "Strong divergence" between some of their proteins.
A large difference between strains (i.e. accumulation of mutations) is always taken as an indication of a long period of time separating them. Giving them time to evolve separately (However the paper says that it is an "exaggerated evolution", below we see why.)
In this case, since the authors have adopted the orthodox time frame used in this paper (which is repeated in most papers, of 15 ky for the peopling of America as mentioned above), they cannot assume an ancient split as an explanation. With no other alternative, the authors imagine some host-parasite interaction that favored the "exaggerated evolution" of these unique hp strains!:
"This difference suggests that there has been a greater impact of host interaction on the hspAmerind lineage than on other H. pylori lineages.[...] suggest[ing] that parallel, yet to be identified host polymorphism skewing relevant to both CagA and VacA interactions exists in Amerindians." 
A more reasonable explanation
Why not just assume that the H. pylori among Amerindians is really old, ancient, that its differences that set it apart from the H. pylori of Europeans, Africans and East Asians, is due to the long span of time since they hp lineages split.
I could even suggest that the Amerindian strains are unique because they derived from an ancestral strain received from Neanderthals (horizontal transmission - well humans had sex with them, it is likely that some hp got exchanged via mother-child or even through saliva in mate-mate interactions).
The following image shows the CagA phylogenetic tree (Adapted from Fig. 7 in ). Notice how Amerindians stand midway between Eurasians on the top and Euro - Africans on the bottom. They are clearly not a branch on the Eurasian side. They are a separate lineage, maybe the ancestral one:
Of course, since orthodoxy upholds the Out Of Africa theory and a 30-15 kya peopling of America, papers are written to conform to (and to confirm) orthodoxy.
See another post (July 4, 2014) on the H. pylori and Homo erectus
 Wirth, T., Meyer, A and Achtman, M., (2005). Deciphering host migrations and origins by means of their microbe. Molecular Ecology 14, 3289–3306 doi: 10.1111/j.1365-294X.2005.02687.x
 Mane, S. P., (2010). Host-Interactive Genes in Amerindian Helicobacter pylori Diverge from Their Old World Homologs and Mediate Inflammatory Responses?. doi: 10.1128/JB.00063-10 J. Bacteriol. June 2010 vol. 192 no. 12 3078-3092
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