title: Phylogenetic and functional gene structure shifts of the oral microbiomes in periodontitis patients.
abstract: Determining the composition and function of subgingival dental plaque is crucial to understanding human periodontal health and disease, but it is challenging because of the complexity of the interactions between human microbiomes and human body. Here, we examined the phylogenetic and functional gene differences between periodontal and healthy individuals using MiSeq sequencing of 16S rRNA gene amplicons and a specific functional gene array (a combination of GeoChip 4.0 for biogeochemical processes and HuMiChip 1.0 for human microbiomes). Our analyses indicated that the phylogenetic and functional gene structure of the oral microbiomes were distinctly different between periodontal and healthy groups. Also, 16S rRNA gene sequencing analysis indicated that 39 genera were significantly different between healthy and periodontitis groups, and Fusobacterium, Porphyromonas, Treponema, Filifactor, Eubacterium, Tannerella, Hallella, Parvimonas, Peptostreptococcus and Catonella showed higher relative abundances in the periodontitis group. In addition, functional gene array data showed that a lower gene number but higher signal intensity of major genes existed in periodontitis, and a variety of genes involved in virulence factors, amino acid metabolism and glycosaminoglycan and pyrimidine degradation were enriched in periodontitis, suggesting their potential importance in periodontal pathogenesis. However, the genes involved in amino acid synthesis and pyrimidine synthesis exhibited a significantly lower relative abundance compared with healthy group. Overall, this study provides new insights into our understanding of phylogenetic and functional gene structure of subgingival microbial communities of periodontal patients and their importance in pathogenesis of periodontitis.
authors.affiliation: State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Li
authors.affiliation: State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.
authors.forename: Jinzhi
authors.initials: J
authors.lastname: He
authors.affiliation: Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.
authors.forename: Zhili
authors.initials: Z
authors.lastname: He
authors.affiliation: State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.
authors.forename: Yuan
authors.initials: Y
authors.lastname: Zhou
authors.affiliation: Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.
authors.forename: Mengting
authors.initials: M
authors.lastname: Yuan
authors.affiliation: State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.
authors.forename: Xin
authors.initials: X
authors.lastname: Xu
authors.affiliation: State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.
authors.forename: Feifei
authors.initials: F
authors.lastname: Sun
authors.affiliation: State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.
authors.forename: Chengcheng
authors.initials: C
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.
authors.forename: Jiyao
authors.initials: J
authors.lastname: Li
authors.affiliation: State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.
authors.forename: Wenbo
authors.initials: W
authors.lastname: Xie
authors.affiliation: Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.
authors.forename: Ye
authors.initials: Y
authors.lastname: Deng
authors.affiliation: Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.
authors.forename: Yujia
authors.initials: Y
authors.lastname: Qin
authors.affiliation: Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.
authors.forename: Joy D
authors.initials: JD
authors.lastname: VanNostrand
authors.affiliation: State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.
authors.forename: Liying
authors.initials: L
authors.lastname: Xiao
authors.affiliation: Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.
authors.forename: Liyou
authors.initials: L
authors.lastname: Wu
authors.affiliation: Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.
authors.forename: Jizhong
authors.initials: J
authors.lastname: Zhou
authors.affiliation: 1] State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China [2] UCLA School of Dentistry, Los Angeles, CA, USA.
authors.forename: Wenyuan
authors.initials: W
authors.lastname: Shi
authors.affiliation: State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.
authors.forename: Xuedong
authors.initials: X
authors.lastname: Zhou
mesh_terms: D000328:Adult; D000596:Amino Acids / Q000096:biosynthesis / Q000378:metabolism; D001419:Bacteria / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism; D050260:Carbohydrate Metabolism / Q000235:genetics; D003773:Dental Plaque / Q000382:microbiology; D005260:Female; D005798:Genes, Bacterial; D006025:Glycosaminoglycans / Q000235:genetics; D006801:Humans; D008297:Male; D064307:Microbiota; D010518:Periodontitis / Q000382:microbiology*; D010802:Phylogeny; D011743:Pyrimidines / Q000096:biosynthesis / Q000378:metabolism; D037521:Virulence Factors / Q000235:genetics
chemical_list: D000596:Amino Acids; D006025:Glycosaminoglycans; D011743:Pyrimidines; D037521:Virulence Factors