The saliva microbiome of Pan and Homo.

Background: It is increasingly recognized that the bacteria that live in and on the human body (the microbiome) can play an important role in health and disease. The composition of the microbiome is potentially influenced by both internal factors (such as phylogeny and host physiology) and external factors (such as diet and local environment), and interspecific comparisons can aid in understanding the importance of these factors.

Results: To gain insights into the relative importance of these factors on saliva microbiome diversity, we here analyze the saliva microbiomes of chimpanzees (Pan troglodytes) and bonobos (Pan paniscus) from two sanctuaries in Africa, and from human workers at each sanctuary.

High diversity of the saliva microbiome in Batwa Pygmies.

We describe the saliva microbiome diversity in Batwa Pygmies, a former hunter-gatherer group from Uganda, using next-generation sequencing of partial 16S rRNA sequences. Microbial community diversity in the Batwa is significantly higher than in agricultural groups from Sierra Leone and the Democratic Republic of Congo. We found 40 microbial genera in the Batwa, which have previously not been described in the human oral cavity.

High-throughput sequencing of complete human mtDNA genomes from the Caucasus and West Asia: high diversity and demographic inferences.

To investigate the demographic history of human populations from the Caucasus and surrounding regions, we used high-throughput sequencing to generate 147 complete mtDNA genome sequences from random samples of individuals from three groups from the Caucasus (Armenians, Azeri and Georgians), and one group each from Iran and Turkey. Overall diversity is very high, with 144 different sequences that fall into 97 different haplogroups found among the 147 individuals. Bayesian skyline plots (BSPs) of population size change through time show a population expansion around 40-50 kya, followed by a constant population size, and then another expansion around 15-18 kya for the groups from the Caucasus and Iran.

A Y-STR database of Iranian and Azerbaijanian minority populations.

Seventeen Y-chromosomal short tandem repeats (Y-STR) DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385a, DYS385b, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635 and GATA H4 were studied in five minor linguistic groups from Iran (Arabs, Gilaki, Mazandarani, Bakhtiari and Southern Talysh) and one from Azerbaijan (Northern Talysh) with the goal of constructing of a representative Y-STR database for this region in Southwest Asia. Analysis of Molecular Variance (AMOVA) reveals non-significant or low genetic distances between the Iranian Gilaki, Mazandarani, Bakhtiari and non-Iranian Turkish, Azerbaijanian, Armenian and Kurd populations, but larger genetic distances to both Talysh populations, the Iranian Arabs, Georgian and Kazakh populations.

Comparative analysis of human saliva microbiome diversity by barcoded pyrosequencing and cloning approaches.

Metagenomic studies traditionally rely on cloning polymerase chain reaction (PCR) products and sequencing multiple clones. However, this approach is tedious and expensive, thereby limiting the range and scale of questions that can be addressed. Recent developments in DNA sequencing technologies enable a dramatic increase in throughput via parallel in-depth analysis of many samples with limited sample processing and lower costs.

Global diversity in the human salivary microbiome.

The human salivary microbiome may play a role in diseases of the oral cavity and interact with microbiomes from other parts of the human body (in particular, the intestinal tract), but little is known about normal variation in the salivary microbiome. We analyzed 14,115 partial ( approximately 500 bp) 16S ribosomal RNA (rRNA) sequences from saliva samples from 120 healthy individuals (10 individuals from each of 12 worldwide locations). These sequences could be assigned to 101 known bacterial genera, of which 39 were not previously reported from the human oral cavity; phylogenetic analysis suggests that an additional 64 unknown genera are present.

mtDNA and Y-chromosome variation in the Talysh of Iran and Azerbaijan.

The Northern Talysh from Azerbaijan and the Southern Talysh from Iran self-identify as one ethnic group and speak a Northwestern Iranian language. However, the Northern and Southern Talysh dialects are so different that they may actually be separate languages. Does this linguistic differentiation reflect internal change due to isolation, or could contact-induced change have played a role? We analyzed mtDNA HVI sequences, 11 Y-chromosome bi-allelic markers, and 9 Y-STR loci in Northern and Southern Talysh and compared them with their neighboring groups.

Genomic complexity of the Y-STR DYS19: inversions, deletions and founder lineages carrying duplications.

The Y-STR DYS19 is firmly established in the repertoire of Y-chromosomal markers used in forensic analysis yet is poorly understood at the molecular level, lying in a complex genomic environment and exhibiting null alleles, as well as duplications and occasional triplications in population samples. Here, we analyse three null alleles and 51 duplications and show that DYS19 can also be involved in inversion events, so that even its location within the short arm of the Y chromosome is uncertain. Deletion mapping in the three chromosomes carrying null alleles shows that their deletions are less than approximately 300 kb in size.

Dynamic nature of the proximal AZFc region of the human Y chromosome: multiple independent deletion and duplication events revealed by microsatellite analysis.

The human Y chromosome shows frequent structural variants, some of which are selectively neutral, while others cause impaired fertility due to the loss of spermatogenic genes. The large-scale use of multiple Y-chromosomal microsatellites in forensic and population genetic studies can reveal such variants, through the absence or duplication of specific markers in haplotypes. We describe Y chromosomes in apparently normal males carrying null and duplicated alleles at the microsatellite DYS448, which lies in the proximal part of the azoospermia factor c (AZFc) region, important in spermatogenesis, and made up of "ampliconic" repeats that act as substrates for nonallelic homologous recombination (NAHR).

Boundaries and clines in the West Eurasian Y-chromosome landscape: insights from the European part of Russia.

Previous studies of Y chromosome variation have revealed that western Europe, the Volga-Ural region, and the Caucasus differ dramatically with respect to Y-SNP haplogroup composition. The European part of Russia is situated in between these three regions; to determine if these differences reflect clines or boundaries in the Y-chromosome landscape, we analyzed 12 Y-SNPs in 545 males from 12 populations from the European part of Russia. The majority of Russian Y chromosomes (from 74% to 94%) belong to three Y chromosomal lineages [I-M170, R1a1-M17, and N3-TAT] that are also frequent in the rest of east Europe, north Europe, and/or in the Volga-Ural region.

Analysis of Y chromosome STR haplotypes in the European part of Russia reveals high diversities but non-significant genetic distances between populations.

A total of 17 Y-specific STR loci were studied in 12 districts of the European part of Russia aiming to ascertain the amount of substructure required for the construction of a representative regional database. All groups exhibited high haplotype diversities but low inter-population variance as measured by an analysis of molecular variance. However, when Western Russia is taken as a whole, the genetic distances to the neighbouring populations were significant.

Y-chromosomal STR haplotypes in Kalmyk population samples.

Seventeen Y-chromosomal short tandem repeats (STRs), DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, GATA-H4, DYS448, DYS456, DYS458, DYS635 were typed in DNA samples from the Kalmyk population (n=99). The population is characterized by a high proportion of duplicated DYS19 alleles and deletions of the locus DYS448 on the background of the Central Asian haplogroup C*. AMOVA analysis reveals a close vicinity to Mongolian and Kazakh populations and large genetic distance to geographical neighbours from Russia, Ukraine and the Caucasus.

The Gagauz, a linguistic enclave, are not a genetic isolate.

The Gagauz are a Turkic-speaking group that migrated from Turkey to their present location in the southern part of the Republic of Moldova about 150 years ago. Surrounded by Indo-European-speaking populations, they thus form a linguistic enclave, which raises the following question: to what extent have they remained in genetic isolation from their geographic neighbours? Analyses of mtDNA and Y chromosome variation indicate that despite their linguistic differences, the Gagauz have admixed extensively with neighbouring groups. Our data suggest that there has been more mtDNA than Y chromosome admixture, in keeping with the patrilocal nature of these groups.

Evaluation of saliva as a source of human DNA for population and association studies.

A simple noninvasive procedure for saliva sample collection and DNA extraction was developed. On average, the amount of human DNA (as measured by a TaqMan-based assay) was about 11.4 microg/mL saliva, which is more than can be obtained from other noninvasive samples such as cheek swabs.

Concomitant replacement of language and mtDNA in South Caspian populations of Iran.

The Gilaki and Mazandarani occupy the South Caspian region of Iran and speak languages belonging to the North-Western branch of Iranian languages . It has been suggested that their ancestors came from the Caucasus region, perhaps displacing an earlier group in the South Caspian . Linguistic evidence supports this scenario, in that the Gilaki and Mazandarani languages (but not other Iranian languages) share certain typological features with Caucasian languages .

Genetic evidence for the Mongolian ancestry of Kalmyks.

The Kalmyks are an ethnic group along the lower Volga River in Russia who are thought to have migrated there from Mongolia about 300 years ago. To investigate their origins, we studied mtDNA and Y-chromosome variation in 99 Kalmyks. Both mtDNA HV1 sequences and Y-chromosome SNP haplogroups indicate a close relationship of Kalmyks with Mongolians.

MtDNA and Y-chromosome variation in Kurdish groups.

In order to investigate the origins and relationships of Kurdish-speaking groups, mtDNA HV1 sequences, eleven Y chromosome bi-allelic markers, and 9 Y-STR loci were analyzed among three Kurdish groups: Zazaki and Kurmanji speakers from Turkey, and Kurmanji speakers from Georgia. When compared with published data from other Kurdish groups and from European, Caucasian, and West and Central Asian groups, Kurdish groups are most similar genetically to other West Asian groups, and most distant from Central Asian groups, for both mtDNA and the Y-chromosome. However, Kurdish groups show a closer relationship with European groups than with Caucasian groups based on mtDNA, but the opposite based on the Y-chromosome, indicating some differences in their maternal and paternal histories.

Haplotypes from the Caucasus, Turkey and Iran for nine Y-STR loci.

Nine Y chromosome short tandem repeat (STR) loci (DYS385a, DYS385b, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393 and DYS19 (DYS394)) were typed in 669 individuals belonging to 16 populations from the Caucasus, Turkey and Iran.

Testing hypotheses of language replacement in the Caucasus: evidence from the Y-chromosome.

A previous analysis of mtDNA variation in the Caucasus found that Indo-European-speaking Armenians and Turkic-speaking Azerbaijanians were more closely related genetically to other Caucasus populations (who speak Caucasian languages) than to other Indo-European or Turkic groups, respectively. Armenian and Azerbaijanian therefore represent language replacements, possibly via elite dominance involving primarily male migrants, in which case genetic relationships of Armenians and Azerbaijanians based on the Y-chromosome should more closely reflect their linguistic relationships. We therefore analyzed 11 bi-allelic Y-chromosome markers in 389 males from eight populations, representing all major linguistic groups in the Caucasus.