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To gain better insights into the general composition of the microbiome on a global scale, the characterization of microbiomes from a broad range of populations, including non-industrialized societies, is needed. Here, we used the portion of non-human reads obtained through an expanded exome capture sequencing approach to characterize the saliva microbiomes of 52 individuals from eight ethnolinguistically diverse southern African populations from Angola (Kuvale, Kwepe, Himba, Tjimba, Kwisi, Twa, !Xun) and Zimbabwe (Tshwa), including foragers, food-producers, and peripatetic groups (low-status communities who provide services to their dominant neighbors).<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Our results indicate that neither host genetics nor livelihood seem to influence the oral microbiome profile, with<jats:italic>Neisseria<\/jats:italic>,<jats:italic>Streptococcus<\/jats:italic>,<jats:italic>Prevotella<\/jats:italic>,<jats:italic>Rothia<\/jats:italic>, and<jats:italic>Porphyromonas<\/jats:italic>being the five most frequent genera in southern African groups, in line with what has been shown for other human populations. However, we found that some Tshwa and Twa individuals display an enrichment of pathogenic genera from the<jats:italic>Enterobacteriaceae<\/jats:italic>family (i.e.<jats:italic>Enterobacter<\/jats:italic>,<jats:italic>Citrobacter<\/jats:italic>,<jats:italic>Salmonella<\/jats:italic>) of the<jats:italic>Proteobacteria<\/jats:italic>phylum, probably reflecting deficient sanitation and poor health conditions associated with social marginalization.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>Taken together, our results suggest that socio-economic status, rather than ethnolinguistic affiliation or subsistence mode, is a key factor in shaping the salivary microbial profiles of human populations in southern Africa.<\/jats:p><\/jats:sec>","DOI":"10.1186\/s12866-023-02970-2","type":"journal-article","created":{"date-parts":[[2023,8,18]],"date-time":"2023-08-18T11:02:19Z","timestamp":1692356539000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe"],"prefix":"10.1186","volume":"23","author":[{"given":"V\u00edtor","family":"Ara\u00fajo","sequence":"first","affiliation":[]},{"given":"Anne-Maria","family":"Fehn","sequence":"additional","affiliation":[]},{"given":"Admire","family":"Phiri","sequence":"additional","affiliation":[]},{"given":"Jeffrey","family":"Wills","sequence":"additional","affiliation":[]},{"given":"Jorge","family":"Rocha","sequence":"additional","affiliation":[]},{"given":"Magdalena","family":"Gay\u00e0-Vidal","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2023,8,18]]},"reference":[{"issue":"7402","key":"2970_CR1","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1038\/nature11234","volume":"486","author":"HMP Consortium","year":"2012","unstructured":"Consortium HMP. 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The saliva samples and personal data were collected with the written informed consent of all participants and the permission of local authorities, the Provincial Governments of Namibe and Kunene (Angola), and the Ministry of the Local Governance (Zimbabwe). Ethical approval for this study was obtained from CIBIO\/InBIO-University of Porto, ISCED, the University of Zimbabwe, and the Tsoro-o-tso San Development Trust boards.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors report there are no competing interests or conflicts of interest to declare.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}},{"value":"Supplementary Material for this article can be found online in the supporting information tab for this article.","order":5,"name":"Ethics","group":{"name":"EthicsHeading","label":"Supplementary Information"}}],"article-number":"226"}}