1
|
Sampling from four geographically divergent young female populations demonstrates forensic geolocation potential in microbiomes. Sci Rep 2022; 12:18547. [PMID: 36329122 PMCID: PMC9633824 DOI: 10.1038/s41598-022-21779-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 10/04/2022] [Indexed: 11/06/2022] Open
Abstract
Studies of human microbiomes using new sequencing techniques have increasingly demonstrated that their ecologies are partly determined by the lifestyle and habits of individuals. As such, significant forensic information could be obtained from high throughput sequencing of the human microbiome. This approach, combined with multiple analytical techniques demonstrates that bacterial DNA can be used to uniquely identify an individual and to provide information about their life and behavioral patterns. However, the transformation of these findings into actionable forensic information, including the geolocation of the samples, remains limited by incomplete understanding of the effects of confounding factors and the paucity of diverse sequences. We obtained 16S rRNA sequences of stool and oral microbiomes collected from 206 young and healthy females from four globally diverse populations, in addition to supporting metadata, including dietary and medical information. Analysis of these microbiomes revealed detectable geolocation signals between the populations, even for populations living within the same city. Accounting for other lifestyle variables, such as diet and smoking, lessened but does not remove the geolocation signal.
Collapse
|
2
|
Butler CA, Adams GG, Blum J, Byrne SJ, Carpenter L, Gussy MG, Calache H, Catmull DV, Reynolds EC, Dashper SG. Breastmilk influences development and composition of the oral microbiome. J Oral Microbiol 2022; 14:2096287. [PMID: 35832839 PMCID: PMC9272919 DOI: 10.1080/20002297.2022.2096287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Background Human microbiomes assemble in an ordered, reproducible manner yet there is limited information about early colonisation and development of bacterial communities that constitute the oral microbiome. Aim The aim of this study was to determine the effect of exposure to breastmilk on assembly of the infant oral microbiome during the first 20 months of life. Methods The oral microbiomes of 39 infants, 13 who were never breastfed and 26 who were breastfed for more than 10 months, from the longitudinal VicGeneration birth cohort study, were determined at four ages. In total, 519 bacterial taxa were identified and quantified in saliva by sequencing the V4 region of the bacterial 16S rRNA genes. Results There were significant differences in the development of the oral microbiomes of never breastfed and breastfed infants. Bacterial diversity was significantly higher in never breastfed infants at 2 months, due largely to an increased abundance of Veillonella and species from the Bacteroidetes phylum compared with breastfed infants. Conclusion These differences likely reflect breastmilk playing a prebiotic role in selection of early-colonising, health-associated oral bacteria, such as the Streptococcus mitis group. The microbiomes of both groups became more heterogenous following the introduction of solid foods.
Collapse
Affiliation(s)
- Catherine A. Butler
- Centre for Oral Health Research, Melbourne Dental School, University of Melbourne, Carlton, Vic, Australia
| | - Geoffrey G. Adams
- Centre for Oral Health Research, Melbourne Dental School, University of Melbourne, Carlton, Vic, Australia
| | - Jordan Blum
- Centre for Oral Health Research, Melbourne Dental School, University of Melbourne, Carlton, Vic, Australia
| | - Samantha J. Byrne
- Centre for Oral Health Research, Melbourne Dental School, University of Melbourne, Carlton, Vic, Australia
| | - Lauren Carpenter
- Child and Community Wellbeing Unit, Melbourne School of Population & Global Health, University of Melbourne, Carlton, Vic, Australia
| | - Mark G. Gussy
- Lincoln International Institute for Rural Health, College of Social Science, University of Lincoln, Lincoln, UK
| | - Hanny Calache
- School of Health and Social Development, Deakin University, Burwood, Vic, Australia
| | - Deanne V. Catmull
- Centre for Oral Health Research, Melbourne Dental School, University of Melbourne, Carlton, Vic, Australia
| | - Eric C. Reynolds
- Centre for Oral Health Research, Melbourne Dental School, University of Melbourne, Carlton, Vic, Australia
| | - Stuart G. Dashper
- Centre for Oral Health Research, Melbourne Dental School, University of Melbourne, Carlton, Vic, Australia
| |
Collapse
|
3
|
Cho HW, Eom YB. Forensic Analysis of Human Microbiome in Skin and Body Fluids Based on Geographic Location. Front Cell Infect Microbiol 2021; 11:695191. [PMID: 34458160 PMCID: PMC8388931 DOI: 10.3389/fcimb.2021.695191] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 07/26/2021] [Indexed: 01/16/2023] Open
Abstract
High-throughput DNA sequencing technologies have facilitated the in silico forensic analysis of human microbiome. Specific microbial species or communities obtained from the crime scene provide evidence of human contacts and their body fluids. The microbial community is influenced by geographic, ethnic, lifestyle, and environmental factors such as urbanization. An understanding of the effects of these external stressors on the human microbiome and determination of stable and changing elements are important in selecting appropriate targets for investigation. In this study, the Forensic Microbiome Database (FMD) (http://www.fmd.jcvi.org) containing the microbiome data of various locations in the human body in 35 countries was used. We focused on skin, saliva, vaginal fluid, and stool and found that the microbiome distribution differed according to the body part as well as the geographic location. In the case of skin samples, Staphylococcus species were higher than Corynebacterium species among Asians compared with Americans. Holdemanella and Fusobacterium were specific in the saliva of Koreans and Japanese populations. Lactobacillus was found in the vaginal fluids of individuals in all countries, whereas Serratia and Enterobacter were endemic to Bolivia and Congo, respectively. This study is the first attempt to collate and describe the observed variation in microbiomes from the forensic microbiome database. As additional microbiome databases are reported by studies worldwide, the diversity of the applications may exceed and expand beyond the initial identification of the host.
Collapse
Affiliation(s)
- Hye-Won Cho
- Department of Medical Sciences, Graduate School, Soonchunhyang University, Asan, South Korea
| | - Yong-Bin Eom
- Department of Medical Sciences, Graduate School, Soonchunhyang University, Asan, South Korea
- Department of Biomedical Laboratory Science, College of Medical Sciences, Soonchunhyang University, Asan, South Korea
| |
Collapse
|
4
|
Mashima I, Theodorea CF, Djais AA, Kunihiro T, Kawamura Y, Otomo M, Saitoh M, Tamai R, Kiyoura Y. Veillonella nakazawae sp. nov., an anaerobic Gram-negative coccus isolated from the oral cavity of Japanese children. Int J Syst Evol Microbiol 2020; 71. [PMID: 33263509 DOI: 10.1099/ijsem.0.004583] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two strains of previously unknown Gram-negative cocci, T1-7T and S6-16, were isolated from the oral cavity of healthy Japanese children. The two strains showed atypical phenotypic characteristics of members of the genus Veillonella, including catalase production. Sequencing of their 16S rRNA genes confirmed that they belong to genus Veillonella. Under anaerobic conditions, the two strains produced acetic acid and propionic acid as metabolic end-products in a trypticase-yeast extract-haemin medium containing 1 % (w/v) glucose, 1 % (w/v) fructose and 1 % (v/v) sodium lactate. Comparative analysis of the 16S rRNA, dnaK, rpoB and gltA gene sequences revealed that the two strains are phylogenetically homogeneous and comprise a distinct, novel lineage within the genus Veillonella. The sequences from the two strains shared the highest similarity, at 99.9, 95.8, 96.9 and 96.7 %, using the partial 16S rRNA, dnaK, rpoB and gltA gene sequences, respectively, with the type strains of the two most closely related species, Veillonella dispar ATCC 17748T and Veillonella infantium JCM 31738T. Furthermore, strain T1-7T shared the highest average nucleotide identity (ANI) value (94.06 %) with type strain of the most closely related species, V. infantium. At the same time, strain T1-7T showed the highest digital DNA-DNA hybridization (dDDH) value (55.5 %) with the type strain of V. infantium. The two strains reported in this study were distinguished from the previously reported species from the genus Veillonella based on catalase production, partial dnaK, rpoB and gltA sequences, average ANI and dDDH values. Based on these observations, the two strains represent a novel species, for which the name Veillonella nakazawae sp. nov. is proposed. The type strain is T1-7T (JCM 33966T=CCUG 74597T).
Collapse
Affiliation(s)
- Izumi Mashima
- Department of Microbiology, School of Pharmacy, Aichi-Gakuin University, 1-100 Kusumoto-cho, Chikusa-ku, Nagoya, Aichi 464-8650, Japan.,Department of Oral Medical Science, School of Dentistry, Ohu University, 31-1 Misumido, Tomita-machi, Koriyama, Fukushima 963-8611, Japan
| | - Citra F Theodorea
- Department of Oral Biology, Faculty of Dentistry, Universitas Indonesia, Salemba Raya No. 4, Jakarta Pusat 10430, Indonesia
| | - Ariadna A Djais
- Department of Oral Biology, Faculty of Dentistry, Universitas Indonesia, Salemba Raya No. 4, Jakarta Pusat 10430, Indonesia
| | - Tadao Kunihiro
- Techno Suruga Laboratory Co. Ltd., 330 Nagasaki, Shimizu-ku, Sizuoka 424-0065, Japan
| | - Yoshiaki Kawamura
- Department of Microbiology, School of Pharmacy, Aichi-Gakuin University, 1-100 Kusumoto-cho, Chikusa-ku, Nagoya, Aichi 464-8650, Japan
| | - Maiko Otomo
- Department of Pediatric Dentistry, School of Dentistry, Health Sciences University of Hokkaido, 1757 Kanazawa, Ishikari-Tobetsu, Hokkaido 061-0293, Japan
| | - Masato Saitoh
- Department of Pediatric Dentistry, School of Dentistry, Health Sciences University of Hokkaido, 1757 Kanazawa, Ishikari-Tobetsu, Hokkaido 061-0293, Japan
| | - Riyoko Tamai
- Department of Oral Medical Science, School of Dentistry, Ohu University, 31-1 Misumido, Tomita-machi, Koriyama, Fukushima 963-8611, Japan
| | - Yusuke Kiyoura
- Department of Oral Medical Science, School of Dentistry, Ohu University, 31-1 Misumido, Tomita-machi, Koriyama, Fukushima 963-8611, Japan
| |
Collapse
|