The fragmented distribution of speakers of the five major language families in Southeast Asia is the result of extensive human migrations. Hmong Mien, Austro-Asiatic and Austronesian are considered the older language families in the region 
, whereas the presence of the Sino-Tibetan and Tai-Kadai language families can be attributed to relatively recent population expansions. Most fragmented is the distribution of Hmong-Mien speakers living in numerous small enclaves surrounded by Sino-Tibetan and Tai-Kadai speakers in Southern China, Laos and Northern Vietnam because of an extreme expansion of the Chinese subfamily of Sino-Tibetan (mostly during the Zhou dynasty 1100 to 221 BC) which distributed Chinese languages continuously over a large region from North to South China, pushing speakers of other languages further south and west. The Austro-Asiatic language family (with the examples of Vietnamese from Vietnam and Khmer from Cambodia) was previously distributed from Vietnam in the east and South China in the north to the Malay Peninsula in the south and North India to the west 
before massive expansions of Indo-European speakers in India and Tibeto-Burman speakers (a subgroup of Sino-Tibetan different from Chinese) from South China into Myanmar restricted Austro-Asiatic languages to numerous enclaves in this area. A subsequent expansion of Tai-Kadai speakers during the early second millennium AD from their homeland in South China into Thailand and Laos replaced Austro-Asiatic speakers in large parts of Southeast Asia that previously belonged to the Khmer empire 
. Subsequently, Tai-Kadai is found from South China over Thailand to the Malay Peninsula and Myanmar.
In historic times, parts of Southeast Asia have repeatedly been ruled by colonial forces, but there has never been overall occupation 
. The Han Chinese invaded North Vietnam (Tonkin) in the 1st
century BC and stayed for nearly a millennium, after which Vietnamese dynasties from North Vietnam conquered central Vietnam (Annam) and South Vietnam (Cochin China). The French occupied the same area (Tonkin, Annam, Cochin China) during a far shorter period (1863–1953), and added present day Cambodia and Laos to their colonial French Indochina. Both of these colonial episodes excluded Siam (Thailand), the only country in Southeast Asia never colonized by a European power.
Archaeology suggests an ancient close connection between India and the Thailand/Cambodia region through settlement 
, accompanied by an increasing exposure to Indian culture from about 300 BC. Early states-like societies from Southeast Asia called by the Sanskrit term “mandala” had in common the adoption of Indian forms of religion (Hinduism), the Sanskrit language and aspects of government (Funan mandala from 100 to 550 AD, Chenla mandala from 550 to 802 AD and Angkorian mandala from 802 to 1431 AD) 
. However, the Indian influence in Southeast Asia was not supported by human mitochondrial DNA (mtDNA) data 
In previous studies, we have used housekeeping gene sequences of a bacterial parasite which infects the stomach of most humans, Helicobacter pylori
, to elucidate the patterns of human prehistory. H. pylori
accompanied modern humans during their migrations out of Africa ca. 60,000 years ago 
, and subsequent geographic separation plus founder effects have resulted in genetic populations of bacterial strains that are specific for large continental areas. In all, 7 bacterial genetic populations have been described 
: hpEurope (isolated from Europe, the Middle East, India and Iran), hpNEAfrica (isolated in Northeast Africa), hpAfrica1 (isolated from countries in Western Africa and South Africa), hpAfrica2 (so far only isolated from South Africa), hpAsia2 (isolated from Northern India and among isolates from Bangladesh, Thailand and Malaysia), hpSahul (from Australian Aboriginals and Papua New Guineans) and hpEastAsia with the subpopulations hspEAsia (from East Asians), hspMaori (from Taiwanese Aboriginals, Melanesians and Polynesians) and hspAmerind (Native Americans). All these modern populations derived from six ancestral populations that were designated ancestral Europe1 (AE1), ancestral Europe2 (AE2), ancestral EastAsia, ancestral Africa1, ancestral Africa2 
and ancestral Sahul 
The specific geographic distribution and ethnic association of the H. pylori
populations reflects numerous ancient and historic human migrations which established H. pylori
sequences as a useful genetic marker to unravel debated topics in human population history. For example, the genetic variation in H. pylori
has showed more discriminatory power in determining the ancient sources of human migrations in the Ladakh region of Northern India 
and in the Pacific (Austronesian expansion) 
than traditional human genetic markers such as the hypervariable region (HSV1) of mtDNA. Therefore, we analysed H. pylori
sequences from Cambodia which borders Thailand to its west and northwest, Vietnam to its east and southeast and Laos to its north, to gain additional insights into the human population history in continental Southeast Asia.