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Characterization of the microbiota of head lice could improve our understanding of their public health\u00a0significance and potential role in pathogen transmission. Here, we characterize the\u00a0microbiota of\u00a0 head lice and investigate microbiota\u00a0differences among different clades of head lice.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      Head lice were collected from Hunan Province, China, and classified into clade A and clade B (CACB) using polymerase chain reaction (PCR)-based genotyping. The microbiota of pooled CACB of head lice samples\u00a0(\n                      <jats:italic>n<\/jats:italic>\n                      \u2009=\u200946) was investigated by metagenomic shotgun sequencing\u00a0and  comparatively analysed at the\u00a0phylum,\u00a0genus, and\u00a0species levels. In addition, the prevalence of potential pathogen DNA in head lice samples\u00a0(\n                      <jats:italic>n<\/jats:italic>\n                      \u2009=\u2009204) was assessed\u00a0using real-time PCR with stringent negative controls.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      We obtained non-redundant CACB microbial gene catalog comprising 79,232 genes, of which 4.70% (3,722\u00a0genes) were taxonomically assigned. The relative abundance of bacteria (2.52%) was higher than that of eukaryotes (2.04%), viruses (0.11%), and archaea (0.02%). Comparative analysis identified 655 and 750 unique genes in CACB, respectively. The dominant phyla in the CACB of head lice were Proteobacteria. At the genus level,\u00a0DNA sequences corresponding to\n                      <jats:italic>Anaplasma<\/jats:italic>\n                      (25.98%; 53\/204),\n                      <jats:italic>Mycobacterium<\/jats:italic>\n                      (24.02%; 49\/204),\n                      <jats:italic>Chlamydia<\/jats:italic>\n                      (23.53%; 48\/204),\n                      <jats:italic>Ehrlichia<\/jats:italic>\n                      (10.29%; 21\/204), and\n                      <jats:italic>Vibrio<\/jats:italic>\n                      (0.49%; 1\/204) were detected, suggesting the presence of bacterial\u00a0DNA\u00a0from these taxa.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>Our results provide a preliminary characterization of the annotated fraction of the CACB\u00a0microbiome in head lice. The high proportion of unannotated genes (&gt;95%)\u00a0underscores the limited representation of louse-associated microbial genomes in public databases and suggests \u00a0substantial, yet unexplored, microbial diversity. The detection of pathogen DNA does not confirm organism viability or vector competence,however it may\u00a0suggest prior\u00a0exposure, mechanical carriage, or residual DNA from\u00a0blood meals. These exploratory findings contribute new\u00a0insights into the microbiota associated with human lice.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s13071-026-07471-5","type":"journal-article","created":{"date-parts":[[2026,5,27]],"date-time":"2026-05-27T10:24:06Z","timestamp":1779877446000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Insights into the microbiota profile of Pediculus humanus capitis using metagenomic next-generation sequencing and molecular detection of unexpected pathogen DNA in Hunan Province, China"],"prefix":"10.1186","volume":"19","author":[{"given":"Yi-Tian","family":"Fu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuan-Ping","family":"Deng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"De-Yong","family":"Duan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yan-Yan","family":"Peng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yi-Liu","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ya","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zi-Kai","family":"Xu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hany M.","family":"Elsheikha","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guo-Hua","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,5,27]]},"reference":[{"key":"7471_CR1","doi-asserted-by":"publisher","DOI":"10.1186\/s40249-022-00986-w","volume":"11","author":"YT Fu","year":"2022","unstructured":"Fu YT, Yao C, Deng YP, Elsheikha HM, Shao R, Zhu XQ, et\u00a0al. 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Prior to the head lice examination, we prepared detailed study information sheets and informed consent forms, and briefed the school administration and teachers on the study\u2019s objectives and procedures. The teachers then distributed these materials and consent forms to the schoolchildren to be delivered to their parents\/caretakers. The information sheets provided by us detailed the purpose of the study, as well as the examination process, and emphasized the importance of head lice prevention and treatment. Parents\/caretakers reviewed the provided information and signed the consent forms if they agreed to their child\u2019s participation. The signed forms were collected by the teachers and handed over to us before any physical examination of the schoolchildren was conducted. Only children whose parents\/caretakers returned signed informed consent forms were included in the examination. Teachers served solely as intermediaries for document distribution and had no role in the decision-making process or data collection. The infested schoolchildren were treated and comforted by teachers and school psychologists, or treated by a physician, regardless of the severity of the head lice infestation. These ethical approval and informed consent procedures were strictly applied to all sampling cohorts and geographic locations involved in this study, including the cities of Yueyang, Loudi, and Changsha.","order":1,"name":"Ethics","label":"Ethical approval and consent to participate","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":2,"name":"Ethics","label":"Consent for publication","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare no competing interests.","order":3,"name":"Ethics","label":"Competing interests","group":{"name":"EthicsHeading","label":"Declarations"}}],"article-number":"298"}}