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Alquria TA, Acharya A, Tordik P, Griffin I, Martinho FC. Impact of root canal disinfection on the bacteriome present in primary endodontic infection: A next generation sequencing study. Int Endod J 2024; 57:1124-1135. [PMID: 38700876 DOI: 10.1111/iej.14074] [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] [Received: 02/22/2024] [Revised: 04/05/2024] [Accepted: 04/08/2024] [Indexed: 07/03/2024]
Abstract
AIM To investigate the bacteriome present in teeth with primary endodontic infection (PEI) and apical periodontitis (AP) and to determine quantitatively and qualitatively the impact of chemomechanical preparation (CMP) using 2.5% sodium hypochlorite NAOCl on the bacteriome found in PEI with AP using the Illumina MiSeq platform. METHODOLOGY Thirty-six paired samples from 18 patients were successfully sequenced and analysed. Samples were collected at two sampling times: before (s1) and after (s2) CMP using 2.5% NaOCl. The DNA was extracted from s1 and s2 samples and quantified using quantitative PCR (qPCR). All 36 samples were sequenced using the Illumina MiSeq platform. Raw V3-V4 amplicon sequencing data were processed with the DADA2 pipeline to generate amplicon sequence variants (ASVs). Alpha diversity metrics representing abundance (Chao1) and diversity and evenness (Shannon, Simpson) were computed. The paired-sample Wilcoxon's test was used to compare alpha diversity metrics and qPCR counts between s1 and s2. The PERMANOVA method (with 999 permutations) was applied to compare community composition between sample types (s1 versus s2) and between patient IDs. ALDEx2 (ANOVA-like differential expression tool for high-throughput sequencing data) to investigate differentially abundant taxa between s1 and s2. A paired-sample Wilcoxon's test was used to compare alpha diversity metrics and qPCR counts between s1 and s2. RESULTS The qPCR counts were significantly higher in s1 compared to s2 (p = .0007). The Chao1 index indicated no difference in alpha diversity (p < .7019); whereas Shannon (p = .0056) and Simpson (p = .02685) indexes showed higher values in s2. The PERMANOVA test using Adonis2 showed a significant effect of sample time on community composition (R2 = .0630, p = .012). Patient ID also showed a significant effect on community composition (R2 = .6961, p = .001). At the genus level, Dialister, Mogibacterium, Prevotella, and Olsenella were differentially enriched at s1, while Actinomyces, Stenotrophomonas_unclassified, Enterococcus_unclassified, and Actinomyces_unclassified were differentially enriched in s2. CONCLUSION The bacteriome present in teeth with PEI with AP is complex and diverse. CMP using 2.5% NaOCl showed a high quantitatively and qualitatively disinfectant impact on the bacteriome present in PEI with AP.
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Affiliation(s)
- Theeb Abdullah Alquria
- Department of Advanced Oral Sciences and Therapeutics, School of Dentistry, University of Maryland, Baltimore, Maryland, USA
| | - Aneesha Acharya
- Department of Periodontics and Oral Implantology, Dr D.Y. Patil Dental College and Hospital, Dr D Y Patil Vidyapeeth, Pune, India
- Periodontology and Implant Dentistry, Faculty of Dentistry, The University of Hong Kong, Hong Kong, Hong Kong SAR
| | - Patricia Tordik
- Department of Advanced Oral Sciences and Therapeutics, School of Dentistry, University of Maryland, Baltimore, Maryland, USA
| | - Ina Griffin
- Department of Advanced Oral Sciences and Therapeutics, School of Dentistry, University of Maryland, Baltimore, Maryland, USA
| | - Frederico C Martinho
- Department of Advanced Oral Sciences and Therapeutics, School of Dentistry, University of Maryland, Baltimore, Maryland, USA
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He M, Zhao N, Satten GA. MIDASim: a fast and simple simulator for realistic microbiome data. MICROBIOME 2024; 12:135. [PMID: 39039570 PMCID: PMC11264979 DOI: 10.1186/s40168-024-01822-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 04/22/2024] [Indexed: 07/24/2024]
Abstract
BACKGROUND Advances in sequencing technology has led to the discovery of associations between the human microbiota and many diseases, conditions, and traits. With the increasing availability of microbiome data, many statistical methods have been developed for studying these associations. The growing number of newly developed methods highlights the need for simple, rapid, and reliable methods to simulate realistic microbiome data, which is essential for validating and evaluating the performance of these methods. However, generating realistic microbiome data is challenging due to the complex nature of microbiome data, which feature correlation between taxa, sparsity, overdispersion, and compositionality. Current methods for simulating microbiome data are deficient in their ability to capture these important features of microbiome data, or can require exorbitant computational time. METHODS We develop MIDASim (MIcrobiome DAta Simulator), a fast and simple approach for simulating realistic microbiome data that reproduces the distributional and correlation structure of a template microbiome dataset. MIDASim is a two-step approach. The first step generates correlated binary indicators that represent the presence-absence status of all taxa, and the second step generates relative abundances and counts for the taxa that are considered to be present in step 1, utilizing a Gaussian copula to account for the taxon-taxon correlations. In the second step, MIDASim can operate in both a nonparametric and parametric mode. In the nonparametric mode, the Gaussian copula uses the empirical distribution of relative abundances for the marginal distributions. In the parametric mode, a generalized gamma distribution is used in place of the empirical distribution. RESULTS We demonstrate improved performance of MIDASim relative to other existing methods using gut and vaginal data. MIDASim showed superior performance by PERMANOVA and in terms of alpha diversity and beta dispersion in either parametric or nonparametric mode. We also show how MIDASim in parametric mode can be used to assess the performance of methods for finding differentially abundant taxa in a compositional model. CONCLUSIONS MIDASim is easy to implement, flexible and suitable for most microbiome data simulation situations. MIDASim has three major advantages. First, MIDASim performs better in reproducing the distributional features of real data compared to other methods, at both the presence-absence level and the relative-abundance level. MIDASim-simulated data are more similar to the template data than competing methods, as quantified using a variety of measures. Second, MIDASim makes few distributional assumptions for the relative abundances, and thus can easily accommodate complex distributional features in real data. Third, MIDASim is computationally efficient and can be used to simulate large microbiome datasets. Video Abstract.
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Affiliation(s)
- Mengyu He
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA, 30329, USA
| | - Ni Zhao
- Department of Biostatistics, Johns Hopkins University, Baltimore, MD, 21205, USA.
| | - Glen A Satten
- Department of Gynecology and Obstetrics, Emory University, Atlanta, GA, 30329, USA
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Tilves C, Mueller NT, Zmuda JM, Kuipers AL, Methé B, Li K, Carr JJ, Terry JG, Wheeler V, Nair S, Miljkovic I. Associations of Fecal Microbiota with Ectopic Fat in African Caribbean Men. Microorganisms 2024; 12:812. [PMID: 38674756 PMCID: PMC11052294 DOI: 10.3390/microorganisms12040812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 04/10/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
OBJECTIVE The gut microbiome has been associated with visceral fat (VAT) in European and Asian populations; however, associations with VAT and with ectopic fats among African-ancestry individuals are not known. Our objective was to investigate cross-sectional associations of fecal microbiota diversity and composition with VAT and ectopic fat, as well as body mass index (BMI), among middle-aged and older African Caribbean men. METHODS We included in our analysis n = 193 men (mean age = 62.2 ± 7.6 years; mean BMI = 28.3 ± 4.9 kg/m2) from the Tobago Health Study. We assessed fecal microbiota using V4 16s rRNA gene sequencing. We evaluated multivariable-adjusted associations of microbiota features (alpha diversity, beta diversity, microbiota differential abundance) with BMI and with computed tomography-measured VAT and ectopic fats (pericardial and intermuscular fat; muscle and liver attenuation). RESULTS Lower alpha diversity was associated with higher VAT and BMI, and somewhat with higher pericardial and liver fat. VAT, BMI, and pericardial fat each explained similar levels of variance in beta diversity. Gram-negative Prevotellaceae and Negativicutes microbiota showed positive associations, while gram-positive Ruminococcaceae microbiota showed inverse associations, with ectopic fats. CONCLUSIONS Fecal microbiota features associated with measures of general adiposity also extend to metabolically pernicious VAT and ectopic fat accumulation in older African-ancestry men.
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Affiliation(s)
- Curtis Tilves
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO 80045, USA;
- LEAD Center, Colorado School of Public Health, Aurora, CO 80045, USA
| | - Noel T. Mueller
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO 80045, USA;
- LEAD Center, Colorado School of Public Health, Aurora, CO 80045, USA
- Department of Pediatrics, Colorado School of Medicine, Aurora, CO 80045, USA
| | - Joseph M. Zmuda
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, PA 15261, USA; (J.M.Z.); (A.L.K.); (I.M.)
| | - Allison L. Kuipers
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, PA 15261, USA; (J.M.Z.); (A.L.K.); (I.M.)
| | - Barbara Methé
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA 15213, USA; (B.M.); (K.L.)
| | - Kelvin Li
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA 15213, USA; (B.M.); (K.L.)
| | - John Jeffrey Carr
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA; (J.J.C.); (J.G.T.); (S.N.)
| | - James G. Terry
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA; (J.J.C.); (J.G.T.); (S.N.)
| | - Victor Wheeler
- Tobago Health Studies Office, TTMF Jerningham Court, James Park Upper Scarborough, Scarborough, Trinidad and Tobago;
| | - Sangeeta Nair
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA; (J.J.C.); (J.G.T.); (S.N.)
| | - Iva Miljkovic
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, PA 15261, USA; (J.M.Z.); (A.L.K.); (I.M.)
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Zong Y, Zhao H, Wang T. mbDecoda: a debiased approach to compositional data analysis for microbiome surveys. Brief Bioinform 2024; 25:bbae205. [PMID: 38701410 PMCID: PMC11066923 DOI: 10.1093/bib/bbae205] [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] [Received: 12/18/2023] [Revised: 04/05/2024] [Accepted: 04/15/2024] [Indexed: 05/05/2024] Open
Abstract
Potentially pathogenic or probiotic microbes can be identified by comparing their abundance levels between healthy and diseased populations, or more broadly, by linking microbiome composition with clinical phenotypes or environmental factors. However, in microbiome studies, feature tables provide relative rather than absolute abundance of each feature in each sample, as the microbial loads of the samples and the ratios of sequencing depth to microbial load are both unknown and subject to considerable variation. Moreover, microbiome abundance data are count-valued, often over-dispersed and contain a substantial proportion of zeros. To carry out differential abundance analysis while addressing these challenges, we introduce mbDecoda, a model-based approach for debiased analysis of sparse compositions of microbiomes. mbDecoda employs a zero-inflated negative binomial model, linking mean abundance to the variable of interest through a log link function, and it accommodates the adjustment for confounding factors. To efficiently obtain maximum likelihood estimates of model parameters, an Expectation Maximization algorithm is developed. A minimum coverage interval approach is then proposed to rectify compositional bias, enabling accurate and reliable absolute abundance analysis. Through extensive simulation studies and analysis of real-world microbiome datasets, we demonstrate that mbDecoda compares favorably with state-of-the-art methods in terms of effectiveness, robustness and reproducibility.
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Affiliation(s)
- Yuxuan Zong
- Department of Bioinformatics and Biostatistics, Shanghai Jiao Tong University, Shanghai, China
- SJTU-Yale Joint Center of Biostatistics and Data Science, Shanghai Jiao Tong University, Shanghai, China
| | - Hongyu Zhao
- SJTU-Yale Joint Center of Biostatistics and Data Science, Shanghai Jiao Tong University, Shanghai, China
- Department of Biostatistics, Yale University, New Haven, CT
| | - Tao Wang
- Department of Bioinformatics and Biostatistics, Shanghai Jiao Tong University, Shanghai, China
- SJTU-Yale Joint Center of Biostatistics and Data Science, Shanghai Jiao Tong University, Shanghai, China
- Department of Statistics, Shanghai Jiao Tong University, Shanghai, China
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Shen X, Tilves C, Kim H, Tanaka T, Spira AP, Chia CW, Talegawkar SA, Ferrucci L, Mueller NT. Plant-based diets and the gut microbiome: findings from the Baltimore Longitudinal Study of Aging. Am J Clin Nutr 2024; 119:628-638. [PMID: 38218318 PMCID: PMC10972708 DOI: 10.1016/j.ajcnut.2024.01.006] [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] [Received: 10/13/2023] [Revised: 01/04/2024] [Accepted: 01/08/2024] [Indexed: 01/15/2024] Open
Abstract
BACKGROUND Mounting evidence indicates that although some plant-based diets are healthful, others are not. Changes in the gut microbiome and microbiome-dependent metabolites, such as trimethylamine N-oxide (TMAO), may explain differential health effects of plant-based diets. However, human data are sparse on whether qualitatively distinct types of plant-based diets differentially affect gut microbiome diversity, composition, particularly at the species level, and/or metabolites. OBJECTIVES We aimed to examine cross-sectional associations of different plant-based indices with adult gut microbiome diversity, composition, and the metabolite TMAO. METHODS We studied 705 adults in the Baltimore Longitudinal Study of Aging with data for diet, fecal microbiome (shotgun metagenomic sequencing), and key covariates. We derived healthful plant-based diet index (hPDI) and unhealthful plant-based diet index (uPDI) using data from food frequency questionnaires. We examined plant-based diet indices with microbiome α-diversity (richness and evenness measures), β-diversity (Bray-Curtis and UniFrac measures), composition (species level), and plasma TMAO. We used regression models to determine associations before and after adjustment for age, sex, education, physical activity, smoking status, body mass index, and total energy intake. RESULTS The analytic sample (mean age, 71.0 years, SD = 12.8 years) comprised 55.6% female and 67.5% non-Hispanic White participants. hPDI was positively and uPDI negatively associated with microbiome α-diversity, driven by microbial evenness (Pielou P < 0.05). hPDI was also positively associated with relative abundance of 3 polysaccharide-degrading bacterial species (Faecalibacterium prausnitzii, Eubacterium eligens, and Bacteroides thetaiotaomicron) and inversely associated with 6 species (Blautia hydrogenotrophica, Doreasp CAG 317, Eisenbergiella massiliensis, Sellimonas intestinalis, Blautia wexlerae, and Alistipes shahii). Furthermore, hPDI was inversely associated with TMAO. Associations did not differ by age, sex, or race. CONCLUSIONS Greater adherence to a healthful plant-based diet is associated with microbiome features that have been linked to positive health; adherence to an unhealthful plant-based diet has opposing or null associations with these features.
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Affiliation(s)
- Xinyi Shen
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, United States; Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins University, Baltimore, MD, United States; Tufts University School of Medicine, Tufts University, Boston, MA, United States
| | - Curtis Tilves
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, United States; Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins University, Baltimore, MD, United States; Lifecourse Epidemiology of Adiposity and Diabetes (LEAD) Center, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Hyunju Kim
- Department of Epidemiology, University of Washington School of Public Health, Seattle, WA, United States
| | - Toshiko Tanaka
- Intramural Research Program, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Adam P Spira
- Department of Mental Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, United States; Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, United States; Center on Aging and Health, Johns Hopkins University, Baltimore, MD, United States
| | - Chee W Chia
- Intramural Research Program, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Sameera A Talegawkar
- Departments of Exercise and Nutrition Sciences and Epidemiology, Milken Institute School of Public Health at the George Washington University, Washington, DC, United States
| | - Luigi Ferrucci
- Intramural Research Program, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Noel T Mueller
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, United States; Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins University, Baltimore, MD, United States; Lifecourse Epidemiology of Adiposity and Diabetes (LEAD) Center, University of Colorado Anschutz Medical Campus, Aurora, CO, United States; Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, United States.
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Rogers MB, Harner A, Buhay M, Firek B, Methé B, Morris A, Palmer OMP, Promes SB, Sherwin RL, Southerland L, Vieira AR, Yende S, Morowitz MJ, Huang DT. The salivary microbiota of patients with acute lower respiratory tract infection-A multicenter cohort study. PLoS One 2024; 19:e0290062. [PMID: 38206940 PMCID: PMC10783762 DOI: 10.1371/journal.pone.0290062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 08/01/2023] [Indexed: 01/13/2024] Open
Abstract
The human microbiome contributes to health and disease, but the oral microbiota is understudied relative to the gut microbiota. The salivary microbiota is easily accessible, underexplored, and may provide insight into response to infections. We sought to determine the composition, association with clinical features, and heterogeneity of the salivary microbiota in patients with acute lower respiratory tract infection (LRTI). We conducted a multicenter prospective cohort study of 147 adults with acute LRTI presenting to the emergency department of seven hospitals in three states (Pennsylvania, Michigan, and Ohio) between May 2017 and November 2018. Salivary samples were collected in the emergency department, at days 2-5 if hospitalized, and at day 30, as well as fecal samples if patients were willing. We compared salivary microbiota profiles from patients to those of healthy adult volunteers by sequencing and analyzing bacterial 16-rRNA. Compared to healthy volunteers, the salivary microbiota of patients with LRTI was highly distinct and strongly enriched with intestinal anaerobes such as Bacteroidaceae, Ruminococcaceae, and Lachnospiraceae (e.g., mean 10% relative abundance of Bacteroides vs < 1% in healthy volunteers). Within the LRTI population, COPD exacerbation was associated with altered salivary microbiota composition compared to other LRTI conditions. The largest determinant of microbiota variation within the LRTI population was geography (city in which the hospital was located).
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Affiliation(s)
- Matthew B. Rogers
- University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Ashley Harner
- University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Megan Buhay
- University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Brian Firek
- University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Barbara Methé
- University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Alison Morris
- University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | | | - Susan B. Promes
- Pennsylvania State University, State College, Pennsylvania, United States of America
| | | | - Lauren Southerland
- The Ohio State University Wexner Medical Center, Columbus, Ohio, United States of America
| | - Alexandre R. Vieira
- University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Sachin Yende
- University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Michael J. Morowitz
- University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - David T. Huang
- University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
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Lin H, Peddada SD. Multigroup analysis of compositions of microbiomes with covariate adjustments and repeated measures. Nat Methods 2024; 21:83-91. [PMID: 38158428 PMCID: PMC10776411 DOI: 10.1038/s41592-023-02092-7] [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] [Received: 04/04/2023] [Accepted: 10/17/2023] [Indexed: 01/03/2024]
Abstract
Microbiome differential abundance analysis methods for two groups are well-established in the literature. However, many microbiome studies involve more than two groups, sometimes even ordered groups such as stages of a disease, and require different types of comparison. Standard pairwise comparisons are inefficient in terms of power and false discovery rates. In this Article, we propose a general framework, ANCOM-BC2, for performing a wide range of multigroup analyses with covariate adjustments and repeated measures. We illustrate our methodology through two real datasets. The first example explores the effects of aridity on the soil microbiome, and the second example investigates the effects of surgical interventions on the microbiome of patients with inflammatory bowel disease.
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Affiliation(s)
- Huang Lin
- Biostatistics and Computational Biology Branch, NIEHS, NIH, Research Triangle Park, NC, USA
- Department of Epidemiology and Biostatistics, University of Maryland, College Park, MD, USA
| | - Shyamal Das Peddada
- Biostatistics and Computational Biology Branch, NIEHS, NIH, Research Triangle Park, NC, USA.
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Tilves C, Zhao HJ, Differding MK, Zhang M, Liu T, Hoyo C, Østbye T, Benjamin-Neelon SE, Mueller NT. Associations of Plastic Bottle Exposure with Infant Growth, Fecal Microbiota, and Short-Chain Fatty Acids. Microorganisms 2023; 11:2924. [PMID: 38138068 PMCID: PMC10745781 DOI: 10.3390/microorganisms11122924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/23/2023] [Accepted: 11/30/2023] [Indexed: 12/24/2023] Open
Abstract
BACKGROUND/OBJECTIVES Murine models show that plastics, via their chemical constituents (e.g., phthalates), influence microbiota, metabolism, and growth. However, research on plastics in humans is lacking. Here, we examine how the frequency of plastic bottle exposure is associated with fecal microbiota, short-chain fatty acids (SCFAs), and anthropometry in the first year of life. SUBJECTS/METHODS In 442 infants from the prospective Nurture birth cohort, we examined the association of frequency of plastic bottle feeding at 3 months with anthropometric outcomes (skinfolds, length-for-age, and weight-for-length) at 12 months of age and growth trajectories between 3 and 12 months. Furthermore, in a subset of infants (n = 70) that contributed fecal samples at 3 months and 12 months of age, we examined plastic bottle frequency in relation to fecal microbiota composition and diversity (measured by 16S rRNA gene sequencing of V4 region), and fecal SCFA concentrations (quantified using gas chromatography mass spectrometry). RESULTS At 3 months, 67.6% of infants were plastic bottle fed at every feeding, 15.4% were exclusively breast milk fed, and 48.9% were exclusively formula fed. After adjustment for potential confounders, infants who were plastic bottle fed less than every feeding compared to those who were plastic bottle fed at every feeding at 3 months did not show differences in anthropometry over the first 12 months of life, save for lower length-for-age z-score at 12 months (adjusted β = -0.45, 95% CI: -0.76, -0.13). Infants who were plastic bottle fed less than every feeding versus every feeding had lower fecal microbiota alpha diversity at 3 months (mean difference for Shannon index: -0.59, 95% CI: -0.99, -0.20) and lower isovaleric acid concentration at 3 months (mean difference: -2.12 μmol/g, 95% CI: -3.64, -0.60), but these results were attenuated following adjustment for infant diet. Plastic bottle frequency was not strongly associated with microbiota diversity or SCFAs at 12 months after multivariable adjustment. Frequency of plastic bottle use was associated with differential abundance of some bacterial taxa, however, significance was not consistent between statistical approaches. CONCLUSIONS Plastic bottle frequency at 3 months was not strongly associated with measures of adiposity or growth (save for length-for-age) over the first year of life, and while plastic bottle use was associated with some features of fecal microbiota and SCFAs in the first year, these findings were attenuated in multivariable models with infant diet. Future research is needed to assess health effects of exposure to other plastic-based products and objective measures of microplastics and plastic constituents like phthalates.
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Affiliation(s)
- Curtis Tilves
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA; (C.T.); (H.J.Z.); (M.K.D.); (M.Z.); (T.L.)
- Lifecourse Epidemiology of Adiposity and Diabetes (LEAD) Center, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Heather Jianbo Zhao
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA; (C.T.); (H.J.Z.); (M.K.D.); (M.Z.); (T.L.)
- Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5T 3M7, Canada
| | - Moira K. Differding
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA; (C.T.); (H.J.Z.); (M.K.D.); (M.Z.); (T.L.)
| | - Mingyu Zhang
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA; (C.T.); (H.J.Z.); (M.K.D.); (M.Z.); (T.L.)
- Department of Population Medicine, Harvard Pilgrim Health Care Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Tiange Liu
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA; (C.T.); (H.J.Z.); (M.K.D.); (M.Z.); (T.L.)
| | - Cathrine Hoyo
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA;
| | - Truls Østbye
- Department of Family Medicine and Community Health, Duke University, Durham, NC 27708, USA;
| | - Sara E. Benjamin-Neelon
- Department of Health, Behavior and Society, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA;
| | - Noel T. Mueller
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA; (C.T.); (H.J.Z.); (M.K.D.); (M.Z.); (T.L.)
- Lifecourse Epidemiology of Adiposity and Diabetes (LEAD) Center, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Department of Pediatrics Section of Nutrition, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
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Hu YJ, Satten GA. Compositional analysis of microbiome data using the linear decomposition model (LDM). Bioinformatics 2023; 39:btad668. [PMID: 37930883 PMCID: PMC10639033 DOI: 10.1093/bioinformatics/btad668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 09/13/2023] [Accepted: 10/31/2023] [Indexed: 11/08/2023] Open
Abstract
SUMMARY There are compelling reasons to test compositional hypotheses about microbiome data. We present here linear decomposition model-centered log ratio (LDM-clr), an extension of our LDM approach to allow fitting linear models to centered-log-ratio-transformed taxa count data. As LDM-clr is implemented within the existing LDM program, this extension enjoys all the features supported by LDM, including a compositional analysis of differential abundance at both the taxon and community levels, while allowing for a wide range of covariates and study designs for either association or mediation analysis. AVAILABILITY AND IMPLEMENTATION LDM-clr has been added to the R package LDM, which is available on GitHub at https://github.com/yijuanhu/LDM.
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Affiliation(s)
- Yi-Juan Hu
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA 30322, United States
| | - Glen A Satten
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, GA 30322, United States
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Yue Y, Read TD, Fedirko V, Satten GA, Hu YJ. Integrative analysis of microbial 16S gene and shotgun metagenomic sequencing data improves statistical efficiency. RESEARCH SQUARE 2023:rs.3.rs-3376801. [PMID: 37886529 PMCID: PMC10602108 DOI: 10.21203/rs.3.rs-3376801/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Background The most widely used technologies for profiling microbial communities are 16S marker-gene sequencing and shotgun metagenomic sequencing. Interestingly, many microbiome studies have performed both sequencing experiments on the same cohort of samples. The two sequencing datasets often reveal consistent patterns of microbial signatures, highlighting the potential for an integrative analysis to improve power of testing these signatures. However, differential experimental biases, partially overlapping samples, and differential library sizes pose tremendous challenges when combining the two datasets. Currently, researchers either discard one dataset entirely or use different datasets for different objectives. Methods In this article, we introduce the first method of this kind, named Com-2seq, that combines the two sequencing datasets for testing differential abundance at the genus and community levels while overcoming these difficulties. The new method is based on our LOCOM model (Hu et al., 2022), which employs logistic regression for testing taxon differential abundance while remaining robust to experimental bias. To benchmark the performance of Com-2seq, we introduce two ad hoc approaches: applying LOCOM to pooled taxa count data and combining LOCOM p-values from analyzing each dataset separately. Results Our simulation studies indicate that Com-2seq substantially improves statistical efficiency over analysis of either dataset alone and works better than the two ad hoc approaches. An application of Com-2seq to two real microbiome studies uncovered scientifically plausible findings that would have been missed by analyzing individual datasets. Conclusions Com-2seq performs integrative analysis of 16S and metagenomic sequencing data, which improves statistical efficiency and has the potential to accelerate the search of microbial communities and taxa that are involved in human health and diseases.
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Affiliation(s)
- Ye Yue
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA, 30322, USA
| | - Timothy D. Read
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Veronika Fedirko
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Department of Epidemiology, Emory University, Atlanta, GA, 30322, USA
| | - Glen A. Satten
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Yi-Juan Hu
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA, 30322, USA
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Hu Y, Satten GA, Hu YJ. Impact of Experimental Bias on Compositional Analysis of Microbiome Data. Genes (Basel) 2023; 14:1777. [PMID: 37761917 PMCID: PMC10530728 DOI: 10.3390/genes14091777] [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] [Received: 08/04/2023] [Revised: 09/05/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Microbiome data are subject to experimental bias that is caused by DNA extraction and PCR amplification, among other sources, but this important feature is often ignored when developing statistical methods for analyzing microbiome data. McLaren, Willis, and Callahan (2019) proposed a model for how such biases affect the observed taxonomic profiles; this model assumes the main effects of bias without taxon-taxon interactions. Our newly developed method for testing the differential abundance of taxa, LOCOM, is the first method to account for experimental bias and is robust to the main effect biases. However, there is also evidence for taxon-taxon interactions. In this report, we formulated a model for interaction biases and used simulations based on this model to evaluate the impact of interaction biases on the performance of LOCOM as well as other available compositional analysis methods. Our simulation results indicate that LOCOM remained robust to a reasonable range of interaction biases. The other methods tend to have an inflated FDR even when there were only main effect biases. LOCOM maintained the highest sensitivity even when the other methods could not control the FDR. We thus conclude that LOCOM outperforms the other methods for compositional analysis of microbiome data considered here.
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Affiliation(s)
- Yingtian Hu
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA 30322, USA;
| | - Glen A. Satten
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, GA 30322, USA;
| | - Yi-Juan Hu
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA 30322, USA;
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Yue Y, Read TD, Fedirko V, Satten GA, Hu YJ. Integrative analysis of microbial 16S gene and shotgun metagenomic sequencing data improves statistical efficiency. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.27.546795. [PMID: 37425938 PMCID: PMC10327031 DOI: 10.1101/2023.06.27.546795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
The most widely used technologies for profiling microbial communities are 16S marker-gene sequencing and shotgun metagenomic sequencing. Interestingly, many microbiome studies have performed both sequencing experiments on the same cohort of samples. The two sequencing datasets often reveal consistent patterns of microbial signatures, highlighting the potential for an integrative analysis to improve power of testing these signatures. However, differential experimental biases, partially overlapping samples, and differential library sizes pose tremendous challenges when combining the two datasets. Currently, researchers either discard one dataset entirely or use different datasets for different objectives. In this article, we introduce the first method of this kind, named Com-2seq, that combines the two sequencing datasets for the objective of testing differential abundance at the genus and community levels while overcoming these difficulties. We demonstrate that Com-2seq substantially improves statistical efficiency over analysis of either dataset alone and works better than two ad hoc approaches.
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13
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Hu YJ, Satten GA. Compositional analysis of microbiome data using the linear decomposition model (LDM). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.26.542540. [PMID: 37398068 PMCID: PMC10312423 DOI: 10.1101/2023.05.26.542540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Summary There are compelling reasons to test compositional hypotheses about microbiome data. We present here LDM-clr, an extension of our linear decomposition model (LDM) approach to allow fitting linear models to centered-log-ratio-transformed taxa count data. As LDM-clr is implemented within the existing LDM program, it enjoys all the features supported by LDM, including a compositional analysis of differential abundance at both the taxon and community levels, while allowing for a wide range of covariates and study designs for either association or mediation analysis. Availability and Implementation LDM-clr has been added to the R package LDM, which is available on GitHub at https://github.com/yijuanhu/LDM . Contact yijuan.hu@emory.edu. Supplementary information Supplementary data are available at Bioinformatics online.
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Calle ML, Pujolassos M, Susin A. coda4microbiome: compositional data analysis for microbiome cross-sectional and longitudinal studies. BMC Bioinformatics 2023; 24:82. [PMID: 36879227 PMCID: PMC9990256 DOI: 10.1186/s12859-023-05205-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 02/22/2023] [Indexed: 03/08/2023] Open
Abstract
BACKGROUND One of the main challenges of microbiome analysis is its compositional nature that if ignored can lead to spurious results. Addressing the compositional structure of microbiome data is particularly critical in longitudinal studies where abundances measured at different times can correspond to different sub-compositions. RESULTS We developed coda4microbiome, a new R package for analyzing microbiome data within the Compositional Data Analysis (CoDA) framework in both, cross-sectional and longitudinal studies. The aim of coda4microbiome is prediction, more specifically, the method is designed to identify a model (microbial signature) containing the minimum number of features with the maximum predictive power. The algorithm relies on the analysis of log-ratios between pairs of components and variable selection is addressed through penalized regression on the "all-pairs log-ratio model", the model containing all possible pairwise log-ratios. For longitudinal data, the algorithm infers dynamic microbial signatures by performing penalized regression over the summary of the log-ratio trajectories (the area under these trajectories). In both, cross-sectional and longitudinal studies, the inferred microbial signature is expressed as the (weighted) balance between two groups of taxa, those that contribute positively to the microbial signature and those that contribute negatively. The package provides several graphical representations that facilitate the interpretation of the analysis and the identified microbial signatures. We illustrate the new method with data from a Crohn's disease study (cross-sectional data) and on the developing microbiome of infants (longitudinal data). CONCLUSIONS coda4microbiome is a new algorithm for identification of microbial signatures in both, cross-sectional and longitudinal studies. The algorithm is implemented as an R package that is available at CRAN ( https://cran.r-project.org/web/packages/coda4microbiome/ ) and is accompanied with a vignette with a detailed description of the functions. The website of the project contains several tutorials: https://malucalle.github.io/coda4microbiome/.
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Affiliation(s)
- M. Luz Calle
- Biosciences Department, Faculty of Sciences, Technology and Engineering, University of Vic - Central University of Catalonia, Carrer de La Laura, 13, 08500 Vic, Spain
| | - Meritxell Pujolassos
- Biosciences Department, Faculty of Sciences, Technology and Engineering, University of Vic - Central University of Catalonia, Carrer de La Laura, 13, 08500 Vic, Spain
| | - Antoni Susin
- Mathematical Department, UPC-Barcelona Tech, Barcelona, Spain
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Hu Y, Satten GA, Hu YJ. Impact of experimental bias on compositional analysis of microbiome data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.08.527766. [PMID: 36798370 PMCID: PMC9934628 DOI: 10.1101/2023.02.08.527766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Microbiome data are subject to experimental bias that is caused by DNA extraction, PCR amplification among other sources, but this important feature is often ignored when developing statistical methods for analyzing microbiome data. McLaren, Willis and Callahan (2019) proposed a model for how such bias affects the observed taxonomic profiles, which assumes main effects of bias without taxon-taxon interactions. Our newly developed method, LOCOM (logistic regression for compositional analysis) for testing differential abundance of taxa, is the first method that accounted for experimental bias and is robust to the main effect biases. However, there is also evidence for taxon-taxon interactions. In this report, we formulated a model for interaction biases and used simulations based on this model to evaluate the impact of interaction biases on the performance of LOCOM as well as other available compositional analysis methods. Our simulation results indicated that LOCOM remained robust to a reasonable range of interaction biases. The other methods tended to have inflated FDR even when there were only main effect biases. LOCOM maintained the highest sensitivity even when the other methods cannot control the FDR. We thus conclude that LOCOM outperforms the other methods for compositional analysis of microbiome data considered here.
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Zhao HJ, Tilves C, Differding M, Zhang M, Liu T, Benjamin-Neelon S, Hoyo C, Ostbye T, Mueller N. Associations of Plastic Bottle Exposure with Infant Fecal Microbiota, Short-Chain Fatty Acids, and Growth. RESEARCH SQUARE 2023:rs.3.rs-2454597. [PMID: 36712078 PMCID: PMC9882695 DOI: 10.21203/rs.3.rs-2454597/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Background Plastic exposures have been shown to impact the microbiome, metabolism and growth of animals. However, no human studies have examined how plastic exposures are associated with fecal microbiota, microbial metabolites, or growth. Here we examine the association of plastic bottle feeding with infant fecal microbiota, microbial short-chain fatty acid (SCFA) metabolites, and anthropometry in the first year of life. Methods 462 infants from the prospective Nurture Birth Cohort were included to examine frequency of plastic bottle feeding (every feeding vs. less than every feeding) at 3 months with anthropometric outcomes (skinfolds, length-for-age, and weight-for-length) at 1 year. A subset of 64 and 67 infants were included in analyses examining the fecal microbiota and fecal SCFAs, respectively. Microbial taxa were measured by 16S rRNA gene sequencing of the V4 region and SCFA concentrations were quantified using gas chromatography at 3 and 12 months of age. Results After adjustment for potential confounders, less frequent plastic bottle use was associated with lower fecal microbiota alpha Shannon diversity at 3 months (mean difference for plastic bottle used less than every feeding vs. every feeding = -0.53, 95% CI: -0.90, -0.17, p < 0.01) and lower propionic acid concentration at 3 months (mean log + 1 difference for plastic bottle used every feeding vs. less than every feeding = -0.53, 95% CI: -1.00, -0.06, p = 0.03). Furthermore, compared to infants who used plastic bottle at every feeding, infants who were plastic bottle-fed less frequently (1 -3 times/day) at 3 months had significantly lower length-for-age z-scores at 12 months (mean difference= -0.40, 95% CI: -0.72, -0.07, p = 0.016). Conclusion Plastic bottle exposure may impact early infant gut microbiota and microbial SCFAs, which may in turn affect growth.
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Affiliation(s)
| | - Curtis Tilves
- Johns Hopkins University Bloomberg School of Public Health
| | | | | | - Tiange Liu
- Johns Hopkins Bloomberg School of Public Health
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