Research Progress on the Application of Human Oral Microbiome in Forensic Individual Identification

doi:10.12116/j.issn.1004-5619.2021.510101

Abstract

Abstract:

The oral cavity is the second largest microbial bank in humans after the intestinal canal, colonizing a large number of microorganisms including viruses, bacteria, archaea, fungi and protozoa. The great number of microbial cells, good DNA stability, and individual has a unique microbial community, these characteristics make the human microbiome expected to become a new biomarker for forensic individual identification. This article describes the characteristics of human oral microorganisms and microbial molecular markers in detail, analyzes the potential application value of microorganisms in forensic individual identification, and reviews the research progress of human oral microorganisms in forensic individual identification.

Key words: forensic medicine, microbiology, oral cavity, biomarker, individual identification, review

CLC Number:

DF795.2

Shuang-shuang WANG, Feng SONG, Xiao-wen WEI, Hao-yu GU, Ke ZHANG, Yu-xiang ZHOU, Lan-rui JIANG, Hai-bo LUO. Research Progress on the Application of Human Oral Microbiome in Forensic Individual Identification[J]. Journal of Forensic Medicine, 2022, 38(4): 526-532.

References 57

1	SCHMEDES S E， SAJANTILA A， BUDOWLE B. Expansion of microbial forensics[J]. J Clin Microbiol，2016，54（8）：1964-1974. doi：10.1128/JCM.00046-16 .
2	TURNBAUGH P J， LEY R E， HAMADY M， et al. The human microbiome project[J]. Nature，2007，449（7164）：804-810. doi：10.1038/nature06244 .
3	HE J， LI Y， CAO Y， et al. The oral microbiome diversity and its relation to human diseases[J]. Folia Microbiol （Praha），2015，60（1）：69-80. doi：10 .
	1007/s12223 -014-0342-2.
4	DEWHIRST F E， CHEN T， IZARD J， et al. The human oral microbiome[J]. J Bacteriol，2010，192（19）：5002-5017. doi：10.1128/JB.00542-10 .
5	Human Microbiome Project Consortium. Structure， function and diversity of the healthy human microbiome[J]. Nature，2012，486（7402）：207-214. doi：10 .
	1038/nature 11234.
6	LEAKE S L， PAGNI M， FALQUET L， et al. The salivary microbiome for differentiating individuals： Proof of principle[J]. Microbes Infect，2016，18（6）：399-405. doi：10.1016/j.micinf.2016.03.011 .
7	D’ANGIOLELLA G， TOZZO P， GINO S， et al. Trick or treating in forensics -- The challenge of the saliva microbiome： A narrative review[J]. Microorganisms，2020，8（10）：1501. doi：10.3390/microorgani sms8101501 .
8	WADE W G. The oral microbiome in health and disease[J]. Pharmacol Res，2013，69（1）：137-143. doi：10.1016/j.phrs.2012.11.006 .
9	ZHANG Y， WANG X， LI H， et al. Human oral microbiota and its modulation for oral health[J]. Biomed Pharmacother，2018，99：883-893. doi：10.1016/
	j.biopha.2018.01.146.
10	Expanded Human Oral Microbiome Database （eHOMD） V 3 [DB/OL]. [2020-11-20]. .
11	AAS J A， PASTER B J， STOKES L N， et al. Defining the normal bacterial flora of the oral cavity[J]. J Clin Microbiol，2005，43（11）：5721-5732. doi：10 .
	1128/JCM.43.11.5721-5732.2005.
12	ZAURA E， KEIJSER B J F， HUSE S M， et al. Defining the healthy “core microbiome” of oral microbial communities[J]. BMC Microbiol，2009，9：259. doi：10.1186/1471-2180-9-259 .
13	FÁBIÁN T K， FEJÉRDY P， CSERMELY P. Salivary genomics， transcriptomics and proteomics： The emerging concept of the oral ecosystem and their use in the early diagnosis of cancer and other diseases[J]. Curr Genomics，2008，9（1）：11-21. doi：10.2174/138920208783884900 .
14	YANG L， LIU Y， WU H， et al. Current understanding of multi-species biofilms[J]. Int J Oral Sci，2011，3（2）：74-81. doi：10.4248/IJOS11027 .
15	FILOCHE S， WONG L， SISSONS C H. Oral biofilms： Emerging concepts in microbial ecology[J]. J Dent Res，2010，89（1）：8-18. doi：10.1177/0022034509351812 .
16	PORTER J R. Antony van Leeuwenhoek： Tercentenary of his discovery of bacteria[J]. Bacteriol Rev，1976，40（2）：260-269. doi：10.1128/br.40.2.260-269.1976 .
17	LAZAREVIC V， WHITESON K， HERNANDEZ D， et al. Study of inter- and intra-individual variations in the salivary microbiota[J]. BMC Genomics，2010，11：523. doi：10.1186/1471-2164-11-523 .
18	BIK E M， LONG C D， ARMITAGE G C， et al. Bacterial diversity in the oral cavity of 10 healthy individuals[J]. ISME J，2010，4（8）：962-974. doi：10.1038/ismej.2010.30 .
19	Benedetti B， Roberti P， Ciuffi M， et al. “From womb to tomb； we’re bound to others”： Microbiome in forensic science[J]. JPNIM，2019，8（2）：e080215. doi：10.7363/080215 .
20	NASIDZE I， LI J， QUINQUE D， et al. Global diversity in the human salivary microbiome[J]. Genome Res，2009，19（4）：636-643. doi：10.1101/gr.084616.108 .
21	CURTIS M A， ZENOBIA C， DARVEAU R P. The relationship of the oral microbiotia to periodontal health and disease[J]. Cell Host Microbe，2011，10（4）：302-306. doi：10.1016/j.chom.2011.09.008 .
22	SONG S J， LAUBER C， COSTELLO E K， et al. Cohabiting family members share microbiota with one another and with their dogs[J]. Elife，2013，2：e00458. doi：10.7554/elife.00458 .
23	MISIC A M， DAVIS M F， TYLDSLEY A S， et al. The shared microbiota of humans and companion animals as evaluated from Staphylococcus carriage sites[J]. Microbiome，2015，3：2. doi：10.1186/s40168-014-0052-7 .
24	PRUSSIN A J 2 ND， MARR L C. Sources of airborne microorganisms in the built environment[J]. Micro-biome，2015，3：78. doi：10.1186/s40168-015-0144-z .
25	MEADOW J F， ALTRICHTER A E， BATEMAN A C， et al. Humans differ in their personal microbial cloud[J]. PeerJ，2015，3：e1258. doi：10.7717/peerj.1258 .
26	KEMBEL S W， MEADOW J F， O’CONNOR T K， et al. Architectural design drives the biogeography of indoor bacterial communities[J]. PLoS One，2014，9（1）：e87093. doi：10.1371/journal.pone.0087093 .
27	MEADOW J F， ALTRICHTER A E， KEMBEL S W， et al. Bacterial communities on classroom surfaces vary with human contact[J]. Microbiome，2014，2（1）：7. doi：10.1186/2049-2618-2-7 .
28	LUONGO J C， BARBERÁN A， HACKER-CARY R， et al. Microbial analyses of airborne dust collected from dormitory rooms predict the sex of occupants[J]. Indoor Air，2017，27（2）：338-344. doi：10.1111/ina.12302 .
29	CHASE J， FOUQUIER J， ZARE M， et al. Geography and location are the primary drivers of office microbiome composition[J]. mSystems，2016，1（2）：e00022-e00016. doi：10.1128/mSystems.00022-16 .
30	周伟，张东升. 口腔微生物多样性研究进展[J].中国微生态学杂志，2015，27（6）：738-741. doi：10.13381/j.cnki.cjm.201506034 .
	ZHOU W， ZHANG D S. The microbial diversity of oral microorganisms： Research progress[J]. Zhongguo Weishengtaixue Zazhi，2015，27（6）：738-741.
31	AMES N J， RANUCCI A， MORIYAMA B， et al. The human microbiome and understanding the 16S rRNA gene in translational nursing science[J]. Nurs Res，2017，66（2）：184-197. doi：10.1097/NNR.0000000000000212 .
32	OGIER J C， PAGÈS S， GALAN M， et al. rpoB， a promising marker for analyzing the diversity of bacterial communities by amplicon sequencing[J]. BMC Microbiol，2019，19（1）：171. doi：10.1186/s12866-019-1546-z .
33	ADÉKAMBI T， DRANCOURT M， RAOULT D. The rpoB gene as a tool for clinical microbiologists[J]. Trends Microbiol，2009，17（1）：37-45. doi：10.1016/j.tim.2008.09.008 .
34	ADÉKAMBI T， SHINNICK T M， RAOULT D， et al. Complete rpoB gene sequencing as a suitable supplement to DNA-DNA hybridization for bacterial species and genus delineation[J]. Int J Syst Evol Microbiol，2008，58（Pt 8）：1807-1814. doi：10.1099/ijs.0.65440-0 .
35	DIAZ P I， HONG B Y， DUPUY A K， et al. Mining the oral mycobiome： Methods， components， and meaning[J]. Virulence，2017，8（3）：313-323. doi：10.1080/21505594.2016.1252015 .
36	IWEN P C， HINRICHS S H， RUPP M E. Utilization of the internal transcribed spacer regions as molecular targets to detect and identify human fungal pathogens[J]. Med Mycol，2002，40（1）：87-109. doi：10.1080/mmy.40.1.87.109 .
37	HAYASHI Y， SAITO T， OHSHIMA T， et al. Terminal RFLP analysis to determine the oral microbiota with hyposalivation[J]. Arch Microbiol，2014，196（7）：489-496. doi：10.1007/s00203-014-0987-x .
38	NISHI E， TASHIRO Y， SAKAI K. Discrimination among individuals using terminal restriction fragment length polymorphism profiling of bacteria derived from forensic evidence[J]. Int J Legal Med，2015，129（3）：425-433. doi：10.1007/s00414-014-1092-z .
39	TIAN Y， HE X， TORRALBA M， et al. Using DGGE profiling to develop a novel culture medium suitable for oral microbial communities[J]. Mol Oral Microbiol，2010，25（5）：357-367. doi：10.1111/j.2041-1014.2010.00585.x .
40	WANG K， MIAO T， LU W， et al. Analysis of oral microbial community and Th17-associated cytokines in saliva of patients with oral lichen planus[J]. Microbiol Immunol，2015，59（3）：105-113. doi：10.1111/
	1348-0421.12232.
41	HAO W， XU H， CHEN X， et al. Changes in dental plaque microbial richness and oral behavioral habits during caries development in young Chinese children[J]. Caries Res，2015，49（2）：116-123. doi：10 .
	1159/000366505.
42	HJELMSØ M H， HANSEN L H， BAELUM J， et al. High-resolution melt analysis for rapid comparison of bacterial community compositions[J]. Appl Environ Microbiol，2014，80（12）：3568-3575. doi：10.1128/ AEM.03923-13 .
43	CLARKE T H， GOMEZ A， SINGH H， et al. Integrating the microbiome as a resource in the forensics toolkit[J]. Forensic Sci Int Genet，2017，30：141-147. doi：10.1016/j.fsigen.2017.06.008 .
44	FAN X， ALEKSEYENKO A V， WU J， et al. Human oral microbiome and prospective risk for pancreatic cancer： A population-based nested case-control study[J]. Gut，2018，67（1）：120-127. doi：10.1136/gut jnl-2016-312580 .
45	CRIELAARD W， ZAURA E， SCHULLER A A， et al. Exploring the oral microbiota of children at various developmental stages of their dentition in the relation to their oral health[J]. BMC Med Genomics，2011，4：22. doi：10.1186/1755-8794-4-22 .
46	YANG F， ZENG X W， NING K， et al. Saliva microbiomes distinguish caries-active from healthy human populations[J]. ISME J，2012，6（1）：1-10. doi：10.1038/ismej.2011.71 .
47	HAO Y， TANG C， DU Q， et al. Comparative analysis of oral microbiome from Zang and Han populations living at different altitudes[J]. Arch Oral Biol，2021，121：104986. doi：10.1016/j.archoralbio.2020.104986 .
48	RASIAH I A， WONG L， ANDERSON S A， et al. Variation in bacterial DGGE patterns from human saliva： Over time， between individuals and in corresponding dental plaque microcosms[J]. Arch Oral Biol，2005，50（9）：779-787. doi：10.1016/j.archoralbio.2005.02.001 .
49	COSTELLO E K， LAUBER C L， HAMADY M， et al. Bacterial community variation in human body habitats across space and time[J]. Science，2009， 326（5960）：1694-1697. doi：10.1126/science.1177486 .
50	STAHRINGER S S， CLEMENTE J C， CORLEY R P， et al. Nurture trumps nature in a longitudinal survey of salivary bacterial communities in twins from early adolescence to early adulthood[J]. Genome Res，2012，22（11）：2146-2152. doi：10.1101/gr.140608.112 .
51	FREIRE M， MOUSTAFA A， HARKINS D M， et al. Longitudinal study of oral microbiome variation in twins[J]. Sci Rep，2020，10（1）：7954. doi：10.1038/s41598-020-64747-1 .
52	KENNEDY D M， STANTON J A， GARCÍA J A， et al. Microbial analysis of bite marks by sequence comparison of streptococcal DNA[J]. PLoS One，2012，7（12）：e51757. doi：10.1371/journal.pone.0051757 .
53	GROSS E L， LEYS E J， GASPAROVICH S R， et al. Bacterial 16S sequence analysis of severe caries in young permanent teeth[J]. J Clin Microbiol，2010，48（11）：4121-4128. doi：10.1128/jcm.01232-10 .
54	LEE W H， CHEN H M， YANG S F， et al. Bacterial alterations in salivary microbiota and their association in oral cancer[J]. Sci Rep，2017，7（1）：16540. doi：10.1038/s41598-017-16418-x .
55	ZHU X， WANG S， GU Y， et al. Possible variation of the human oral bacterial community after wearing removable partial dentures by DGGE[J]. World J Microbiol Biotechnol，2012，28（5）：2229-2236. doi：10.1007/s11274-012-1030-5 .
56	WU J， PETERS B A， DOMINIANNI C， et al. Cigarette smoking and the oral microbiome in a large study of American adults[J]. ISME J，2016，10（10）：2435-2446. doi：10.1038/ismej.2016.37 .
57	LAZAREVIC V， MANZANO S， GAÏA N， et al. Effects of amoxicillin treatment on the salivary microbiota in children with acute otitis media[J]. Clin Microbiol Infect，2013，19（8）：E335-E342. doi：10.1111/
	1469-0691.12213.

[1]	Wen LI, Hao-zhe LI, Chen CHEN, Wei-xiong CAI. Research Progress and Application Prospect of Facial Micro-Expression Analysis in Forensic Psychiatry [J]. Journal of Forensic Medicine, 2023, 39(5): 493-500.
[2]	Zhong-hua WANG, Shu-jin LI. Research Progress on Molecular Biology of Human Height Estimation [J]. Journal of Forensic Medicine, 2023, 39(5): 487-492.
[3]	Lu CHEN, Zhe ZHOU, Sheng-qi WANG. Process of Forensic Medicine in DNA Identification of Aged Human Remains [J]. Journal of Forensic Medicine, 2023, 39(5): 478-486.
[4]	Yong ZENG, Dong-hua ZOU, Ying FAN, Qing XU, Lu-yang TAO, Yi-jiu CHEN, Zheng-dong LI. Research Progress and Forensic Application of Human Vascular Finite Element Modeling and Biomechanics [J]. Journal of Forensic Medicine, 2023, 39(5): 471-477.
[5]	Hong-xia HAO, Jie-min CHEN, Rong-rong WANG, Xiao-ying YU, Meng WANG, Zhi-lu ZHOU, Yan-liang SHENG, Wen-tao XIA. The Value of VR-PVEP in Objective Evaluation of Monocular Refractive Visual Impairment [J]. Journal of Forensic Medicine, 2023, 39(4): 382-387.
[6]	Jie BAI, Jing SUN, Xiao-guang CHENG, Fan LIU, Hua LIU, Xu WANG. Construction and Application of Rib Fracture Diagnosis Model Based on YOLOv3 Algorithm [J]. Journal of Forensic Medicine, 2023, 39(4): 343-349.
[7]	Fei FAN, Juan WU, Zhen-hua DENG. Application Progress of Objective Audiological Detection Techniques in Forensic Clinical Medicine [J]. Journal of Forensic Medicine, 2023, 39(4): 360-366.
[8]	Jian XIANG, Xu WANG, Li-li YU, Kang-jia JIN, Ying-kai YANG. Objective Assessment of Visual Field Defects Caused by Optic Chiasm and Its Posterior Visual Pathway Injury [J]. Journal of Forensic Medicine, 2023, 39(4): 350-359.
[9]	Qing-qing XIANG, Li-fang CHEN, Qin SU, Yu-kun DU, Pei-yan LIANG, Xiao-dong KANG, He SHI, Qu-yi XU, Jian ZHAO, Chao LIU, Xiao-hui CHEN. Research Progress on Microbial Community Succession in the Postmortem Interval Estimation [J]. Journal of Forensic Medicine, 2023, 39(4): 399-405.
[10]	Zhang-ming GAO, Jing-yu SHI, Hao ZENG, Xue-jun ZHANG. Rapid Determination of Bucinnazine in Blood by UPLC-MS/MS [J]. Journal of Forensic Medicine, 2023, 39(4): 388-392.
[11]	Yu-qi CAO, Yan SHI, Ping XIANG, Yin-long GUO. Research Progress on Machine Learning Assisted Non-Targeted Screening Strategy for Identification of Fentanyl Analogs [J]. Journal of Forensic Medicine, 2023, 39(4): 406-416.
[12]	Xu WANG. Legal Theories， Disability Models and Principles of Disability Assessment [J]. Journal of Forensic Medicine, 2023, 39(4): 329-336.
[13]	Ran LI, Hong-yu SUN. Methods and Research Hotspots of Forensic Kinship Testing [J]. Journal of Forensic Medicine, 2023, 39(3): 231-239.
[14]	Xiao-yan MA, Hong-yu SUN, Qing LI. Research Progresses of Tri-Allelic Patterns in Autosomal STR in Forensic DNA Analysis [J]. Journal of Forensic Medicine, 2023, 39(3): 240-246.
[15]	Hao-yang WANG, Jian WU, Qian ZHANG, Xin-feng MIN, Xiu-yan LIU, Yin-long GUO. Structural Analysis and Characterization of 4-F-α-PVP Analog 4-F-3-Methyl-α- PVP Hydrochloride [J]. Journal of Forensic Medicine, 2023, 39(2): 144-150.