1
|
Wang M, Fontaine S, Jiang H, Li G. ADAPT: Analysis of Microbiome Differential Abundance by Pooling Tobit Models. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.14.594186. [PMID: 38798558 PMCID: PMC11118451 DOI: 10.1101/2024.05.14.594186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Microbiome differential abundance analysis remains a challenging problem despite multiple methods proposed in the literature. The excessive zeros and compositionality of metagenomics data are two main challenges for differential abundance analysis. We propose a novel method called "analysis of differential abundance by pooling Tobit models" (ADAPT) to overcome these two challenges. ADAPT uniquely treats zero counts as left-censored observations to facilitate computation and enhance interpretation. ADAPT also encompasses a theoretically justified way of selecting non-differentially abundant microbiome taxa as a reference for hypothesis testing. We generate synthetic data using independent simulation frameworks to show that ADAPT has more consistent false discovery rate control and higher statistical power than competitors. We use ADAPT to analyze 16S rRNA sequencing of saliva samples and shotgun metagenomics sequencing of plaque samples collected from infants in the COHRA2 study. The results provide novel insights into the association between the oral microbiome and early childhood dental caries.
Collapse
Affiliation(s)
- Mukai Wang
- Department of Biostatistics, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Simon Fontaine
- Department of Statistics, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Hui Jiang
- Department of Biostatistics, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Gen Li
- Department of Biostatistics, University of Michigan, Ann Arbor, 48109, MI, USA
| |
Collapse
|
2
|
Shao Q, Feng D, Yu Z, Chen D, Ji Y, Ye Q, Cheng D. The role of microbial interactions in dental caries: Dental plaque microbiota analysis. Microb Pathog 2023; 185:106390. [PMID: 37858633 DOI: 10.1016/j.micpath.2023.106390] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 09/10/2023] [Accepted: 10/10/2023] [Indexed: 10/21/2023]
Abstract
OBJECTIVES Dental caries is a result of the ecological dysfunction of the polymicrobial community on the tooth surface, which evolves through microbial interactions. In this study, we conducted a thorough analysis of the dental plaque microbiome to comprehend its multi-microbial aetiology. MATERIALS AND METHOD In this study, plaque was collected from healthy tooth surfaces, shallow carious teeth and deep carious teeth, and bacterial composition and abundance were assessed using 16S rRNA high-throughput sequencing. Random forest and LEfSe were used to profile various microorganisms at each stage. Additionally, we developed a molecular ecological network (MEN) based on random matrix theory (RMT) to examine microbial interactions for the first time. RESULTS Our results reveal that Scardovia wiggsiae, Streptococcus mutans, and Propionibacterium acidifaciens may be associated with initial caries, and Propionibacterium acidifaciens differentiates between shallow and deep caries. As caries progressed, the alpha diversity index declined, indicating a decrease in microbial variety. The network topological indices such as centralization betweenness revealed that the caries network had become more complex, involving more microbial interactions. The shallow network revealed a high negative correlation ratio across nodes, indicating that microbes competed heavily. In contrast, the positive correlation ratio of deep network nodes was high, and microorganisms transitioned from a competitive to a synergistic state. CONCLUSIONS This study suggests that microbial diversity and interactions are critical to caries progression and that future caries research should give greater consideration to the role of microbial interaction factors in caries progression.
Collapse
Affiliation(s)
- Qingyi Shao
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Zhejiang, China
| | - Danfeng Feng
- Department of Stomatology, Tongde Hospital of Zhejiang Province, Zhejiang, China
| | - Zhendi Yu
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Zhejiang, China
| | - Danlei Chen
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Zhejiang, China
| | - Youqi Ji
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Zhejiang, China
| | - Qing Ye
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, National Children's Regional Medical Center, Zhejiang, China.
| | - Dongqing Cheng
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Zhejiang, China.
| |
Collapse
|
3
|
Gao S, Wang J. Maternal and infant microbiome: next-generation indicators and targets for intergenerational health and nutrition care. Protein Cell 2023; 14:807-823. [PMID: 37184065 PMCID: PMC10636639 DOI: 10.1093/procel/pwad029] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 05/04/2023] [Indexed: 05/16/2023] Open
Abstract
Microbes are commonly sensitive to shifts in the physiological and pathological state of their hosts, including mothers and babies. From this perspective, the microbiome may be a good indicator for diseases during pregnancy and has the potential to be used for perinatal health monitoring. This is embodied in the application of microbiome from multi body sites for auxiliary diagnosis, early prediction, prolonged monitoring, and retrospective diagnosis of pregnancy and infant complications, as well as nutrition management and health products developments of mothers and babies. Here we summarized the progress in these areas and explained that the microbiome of different body sites is sensitive to different diseases and their microbial biomarkers may overlap between each other, thus we need to make a diagnosis prudently for those diseases. Based on the microbiome variances and additional anthropometric and physical data, individualized responses of mothers and neonates to meals and probiotics/prebiotics were predictable, which is of importance for precise nutrition and probiotics/prebiotics managements and developments. Although a great deal of encouraging performance was manifested in previous studies, the efficacy could be further improved by combining multi-aspect data such as multi-omics and time series analysis in the future. This review reconceptualizes maternal and infant health from a microbiome perspective, and the knowledge in it may inspire the development of new options for the prevention and treatment of adverse pregnancy outcomes and bring a leap forward in perinatal health care.
Collapse
Affiliation(s)
- Shengtao Gao
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Jinfeng Wang
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| |
Collapse
|
4
|
Arishi RA, Lai CT, Geddes DT, Stinson LF. Impact of breastfeeding and other early-life factors on the development of the oral microbiome. Front Microbiol 2023; 14:1236601. [PMID: 37744908 PMCID: PMC10513450 DOI: 10.3389/fmicb.2023.1236601] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 08/25/2023] [Indexed: 09/26/2023] Open
Abstract
The oral cavity is home to the second most diverse microbiome in the human body. This community contributes to both oral and systemic health. Acquisition and development of the oral microbiome is a dynamic process that occurs over early life; however, data regarding longitudinal assembly of the infant oral microbiome is scarce. While numerous factors have been associated with the composition of the infant oral microbiome, early feeding practices (breastfeeding and the introduction of solids) appear to be the strongest determinants of the infant oral microbiome. In the present review, we draw together data on the maternal, infant, and environmental factors linked to the composition of the infant oral microbiome, with a focus on early nutrition. Given evidence that breastfeeding powerfully shapes the infant oral microbiome, the review explores potential mechanisms through which human milk components, including microbes, metabolites, oligosaccharides, and antimicrobial proteins, may interact with and shape the infant oral microbiome. Infancy is a unique period for the oral microbiome. By enhancing our understanding of oral microbiome assembly in early life, we may better support both oral and systemic health throughout the lifespan.
Collapse
Affiliation(s)
- Roaa A. Arishi
- School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia
- Ministry of Health, Riyadh, Saudi Arabia
| | - Ching T. Lai
- School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia
| | - Donna T. Geddes
- School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia
| | - Lisa F. Stinson
- School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia
| |
Collapse
|
5
|
Blostein F, Zou T, Bhaumik D, Salzman E, Bakulski K, Shaffer J, Marazita M, Foxman B. Bacterial Community Modifies Host Genetics Effect on Early Childhood Caries. J Dent Res 2023; 102:1098-1105. [PMID: 37395259 PMCID: PMC10552462 DOI: 10.1177/00220345231175356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2023] Open
Abstract
By age 5, approximately one-fifth of children have early childhood caries (ECC). Both the oral microbiome and host genetics are thought to influence susceptibility. Whether the oral microbiome modifies genetic susceptibility to ECC has not been tested. We test whether the salivary bacteriome modifies the association of a polygenic score (PGS, a score derived from genomic data that summarizes genetic susceptibility to disease) for primary tooth decay on ECC in the Center for Oral Health Research in Appalachia 2 longitudinal birth cohort. Children were genotyped using the Illumina Multi-Ethnic Genotyping Array and underwent annual dental examinations. We constructed a PGS for primary tooth decay using weights from an independent, genome-wide association meta-analysis. Using Poisson regression, we tested for associations between the PGS (high versus low) and ECC incidence, adjusting for demographic characteristics (n = 783). An incidence-density sampled subset of the cohort (n = 138) had salivary bacteriome data at 24 mo of age. We tested for effect modification of the PGS on ECC case status by salivary bacterial community state type (CST). By 60 mo, 20.69% of children had ECC. High PGS was not associated with an increased rate of ECC (incidence rate ratio, 1.09; 95% confidence interval [CI], 0.83-1.42). However, having a cariogenic salivary bacterial CST at 24 mo was associated with ECC (odds ratio [OR], 7.48; 95% CI, 3.06-18.26), which was robust to PGS adjustment. An interaction existed between the salivary bacterial CST and the PGS on the multiplicative scale (P = 0.04). The PGS was associated with ECC (OR, 4.83; 95% CI, 1.29-18.17) only among individuals with a noncariogenic salivary bacterial CST (n = 70). Genetic causes of caries may be harder to detect when not accounting for cariogenic oral microbiomes. As certain salivary bacterial CSTs increased ECC risk across genetic risk strata, preventing colonization of cariogenic microbiomes would be universally beneficial.
Collapse
Affiliation(s)
- F. Blostein
- Department of Epidemiology, University of Michigan School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - T. Zou
- Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - D. Bhaumik
- Department of Epidemiology, University of Michigan School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - E. Salzman
- Department of Epidemiology, University of Michigan School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - K.M. Bakulski
- Department of Epidemiology, University of Michigan School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - J.R. Shaffer
- Department of Oral and Craniofacial Sciences, Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - M.L. Marazita
- Department of Oral and Craniofacial Sciences, Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
- Clinical and Translational Sciences Institute, and Department of Psychiatry, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - B. Foxman
- Department of Epidemiology, University of Michigan School of Public Health, University of Michigan, Ann Arbor, MI, USA
| |
Collapse
|
6
|
Blostein F, Zou T, Bhaumik D, Salzman E, Bakulski KM, Shaffer JR, Marazita ML, Foxman B. Bacterial community modifies host genetics effect on early childhood caries. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.01.11.23284235. [PMID: 37090669 PMCID: PMC10120800 DOI: 10.1101/2023.01.11.23284235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Background By age five approximately one-fifth of children have early childhood caries (ECC). Both the oral microbiome and host genetics are thought to influence susceptibility. Whether the oral microbiome modifies genetic susceptibility to ECC has not been tested. We test whether the salivary bacteriome modifies the association of a polygenic score (PGS, a score derived from genomic data that summarizes genetic susceptibility to disease) for primary tooth decay on ECC in the Center for Oral Health Research in Appalachia 2 longitudinal birth cohort. Methods Children were genotyped using the Illumina Multi-Ethnic Genotyping Array and underwent annual dental examinations. We constructed a PGS for primary tooth decay using weights from an independent, genome-wide association meta-analysis. Using Poisson regression, we tested for associations between the PGS (high versus low) and ECC incidence, adjusting for demographic characteristics (n=783). An incidence-density sampled subset of the cohort (n=138) had salivary bacteriome data at 24- months of age. We tested for effect modification of the PGS on ECC case status by salivary bacterial community state type (CST). Results By 60-months, 20.69% of children had ECC. High PGS was not associated with an increased rate of ECC (incidence-rate ratio:1.09 (95% confidence interval (CI): 0.83, 1.42)). However, having a cariogenic salivary bacterial CST at 24-months was associated with ECC (odds ratio (OR): 7.48 (95%CI: 3.06, 18.26)), which was robust to PGS adjustment. An interaction existed between the salivary bacterial CST and the PGS on the multiplicative scale (P= 0.04). The PGS was associated with ECC (OR: 4.83 (95% CI: 1.29, 18.17)) only among individuals with a noncariogenic salivary bacterial CST (n=70). Conclusions Genetic causes of caries may be harder to detect when not accounting for cariogenic oral microbiomes. As certain salivary bacterial CSTs increased ECC-risk across genetic-risk strata, preventing colonization of cariogenic microbiomes would be universally beneficial.
Collapse
Affiliation(s)
- Freida Blostein
- Department of Epidemiology, University of Michigan School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Tianyu Zou
- Department of Oral and Craniofacial Sciences, Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Deesha Bhaumik
- Department of Epidemiology, University of Michigan School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Elizabeth Salzman
- Department of Epidemiology, University of Michigan School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Kelly M Bakulski
- Department of Epidemiology, University of Michigan School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - John R Shaffer
- Department of Oral and Craniofacial Sciences, Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Mary L Marazita
- Department of Oral and Craniofacial Sciences, Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Clinical and Translational Sciences Institute, and Department of Psychiatry, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Betsy Foxman
- Department of Epidemiology, University of Michigan School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| |
Collapse
|