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Zakis DR, Brandt BW, van der Waal SV, Keijser BJF, Crielaard W, van der Plas DW, Volgenant CM, Zaura E. The effect of different sweeteners on the oral microbiome: a randomized clinical exploratory pilot study. J Oral Microbiol 2024; 16:2369350. [PMID: 38919384 PMCID: PMC11198155 DOI: 10.1080/20002297.2024.2369350] [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: 02/01/2024] [Accepted: 06/07/2024] [Indexed: 06/27/2024] Open
Abstract
Introduction The aim of the study was to evaluate the modulating effects of five commonly used sweetener (glucose, inulin, isomaltulose, tagatose, trehalose) containing mouth rinses on the oral microbiome. Methods A single-centre, double-blind, parallel randomized clinical trial was performed with healthy, 18-55-year-old volunteers (N = 65), who rinsed thrice-daily for two weeks with a 10% solution of one of the allocated sweeteners. Microbiota composition of supragingival dental plaque and the tongue dorsum coating was analysed by 16S RNA gene amplicon sequencing of the V4 hypervariable region (Illumina MiSeq). As secondary outcomes, dental plaque red fluorescence and salivary pH were measured. Results Dental plaque microbiota changed significantly for two groups: inulin (F = 2.0239, p = 0.0006 PERMANOVA, Aitchison distance) and isomaltulose (F = 0.67, p = 0.0305). For the tongue microbiota, significant changes were observed for isomaltulose (F = 0.8382, p = 0.0452) and trehalose (F = 1.0119, p = 0.0098). In plaque, 13 species changed significantly for the inulin group, while for tongue coating, three species changed for the trehalose group (ALDEx2, p < 0.1). No significant changes were observed for the secondary outcomes. Conclusion The effects on the oral microbiota were sweetener dependant with the most pronounced effect on plaque microbiota. Inulin exhibited the strongest microbial modulating potential of the sweeteners tested. Further full-scale clinical studies are required.
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Affiliation(s)
- Davis R. Zakis
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam, Vrije Universiteit Amsterdam and University of Amsterdam, Amsterdam, The Netherlands
- Department of Cariology, Academic Centre for Dentistry Amsterdam, Vrije Universiteit Amsterdam and University of Amsterdam, Amsterdam, The Netherlands
| | - Bernd W. Brandt
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam, Vrije Universiteit Amsterdam and University of Amsterdam, Amsterdam, The Netherlands
| | - Suzette V. van der Waal
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam, Vrije Universiteit Amsterdam and University of Amsterdam, Amsterdam, The Netherlands
| | - Bart J. F. Keijser
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam, Vrije Universiteit Amsterdam and University of Amsterdam, Amsterdam, The Netherlands
- Research Group Microbiology and Systems Biology, TNO, Leiden, The Netherlands
| | - Wim Crielaard
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam, Vrije Universiteit Amsterdam and University of Amsterdam, Amsterdam, The Netherlands
| | - Derek W.K. van der Plas
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam, Vrije Universiteit Amsterdam and University of Amsterdam, Amsterdam, The Netherlands
| | - Catherine M.C. Volgenant
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam, Vrije Universiteit Amsterdam and University of Amsterdam, Amsterdam, The Netherlands
- Department of Cariology, Academic Centre for Dentistry Amsterdam, Vrije Universiteit Amsterdam and University of Amsterdam, Amsterdam, The Netherlands
| | - Egija Zaura
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam, Vrije Universiteit Amsterdam and University of Amsterdam, Amsterdam, The Netherlands
- Department of Cariology, Academic Centre for Dentistry Amsterdam, Vrije Universiteit Amsterdam and University of Amsterdam, Amsterdam, The Netherlands
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Hagen M, Dass R, Westhues C, Blom J, Schultheiss SJ, Patz S. Interpretable machine learning decodes soil microbiome's response to drought stress. ENVIRONMENTAL MICROBIOME 2024; 19:35. [PMID: 38812054 PMCID: PMC11138018 DOI: 10.1186/s40793-024-00578-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 05/10/2024] [Indexed: 05/31/2024]
Abstract
BACKGROUND Extreme weather events induced by climate change, particularly droughts, have detrimental consequences for crop yields and food security. Concurrently, these conditions provoke substantial changes in the soil bacterial microbiota and affect plant health. Early recognition of soil affected by drought enables farmers to implement appropriate agricultural management practices. In this context, interpretable machine learning holds immense potential for drought stress classification of soil based on marker taxa. RESULTS This study demonstrates that the 16S rRNA-based metagenomic approach of Differential Abundance Analysis methods and machine learning-based Shapley Additive Explanation values provide similar information. They exhibit their potential as complementary approaches for identifying marker taxa and investigating their enrichment or depletion under drought stress in grass lineages. Additionally, the Random Forest Classifier trained on a diverse range of relative abundance data from the soil bacterial micobiome of various plant species achieves a high accuracy of 92.3 % at the genus rank for drought stress prediction. It demonstrates its generalization capacity for the lineages tested. CONCLUSIONS In the detection of drought stress in soil bacterial microbiota, this study emphasizes the potential of an optimized and generalized location-based ML classifier. By identifying marker taxa, this approach holds promising implications for microbe-assisted plant breeding programs and contributes to the development of sustainable agriculture practices. These findings are crucial for preserving global food security in the face of climate change.
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Affiliation(s)
- Michelle Hagen
- Computomics GmbH, Eisenbahnstraße 1, 72072, Tübingen, Baden-Württemberg, Germany
| | - Rupashree Dass
- Computomics GmbH, Eisenbahnstraße 1, 72072, Tübingen, Baden-Württemberg, Germany
| | - Cathy Westhues
- Computomics GmbH, Eisenbahnstraße 1, 72072, Tübingen, Baden-Württemberg, Germany
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus Liebig University Gießen, Heinrich-Buff-Ring 58, 35390, Gießen, Hesse, Germany
| | | | - Sascha Patz
- Computomics GmbH, Eisenbahnstraße 1, 72072, Tübingen, Baden-Württemberg, Germany.
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Zhang K, Paul K, Jacobs JP, Cockburn MG, Bronstein JM, Del Rosario I, Ritz B. Ambient long-term exposure to organophosphorus pesticides and the human gut microbiome: an observational study. Environ Health 2024; 23:41. [PMID: 38627687 PMCID: PMC11020204 DOI: 10.1186/s12940-024-01078-y] [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: 01/16/2024] [Accepted: 04/02/2024] [Indexed: 04/19/2024]
Abstract
BACKGROUND Organophosphorus pesticides (OP) have been associated with various human health conditions. Animal experiments and in-vitro models suggested that OP may also affect the gut microbiota. We examined associations between ambient chronic exposure to OP and gut microbial changes in humans. METHODS We recruited 190 participants from a community-based epidemiologic study of Parkinson's disease living in a region known for heavy agricultural pesticide use in California. Of these, 61% of participants had Parkinson's disease and their mean age was 72 years. Microbiome and predicted metagenome data were generated by 16S rRNA gene sequencing of fecal samples. Ambient long-term OP exposures were assessed using pesticide application records combined with residential addresses in a geographic information system. We examined gut microbiome differences due to OP exposures, specifically differences in microbial diversity based on the Shannon index and Bray-Curtis dissimilarities, and differential taxa abundance and predicted Metacyc pathway expression relying on regression models and adjusting for potential confounders. RESULTS OP exposure was not associated with alpha or beta diversity of the gut microbiome. However, the predicted metagenome was sparser and less evenly expressed among those highly exposed to OP (p = 0.04). Additionally, we found that the abundance of two bacterial families, 22 genera, and the predicted expression of 34 Metacyc pathways were associated with long-term OP exposure. These pathways included perturbed processes related to cellular respiration, increased biosynthesis and degradation of compounds related to bacterial wall structure, increased biosynthesis of RNA/DNA precursors, and decreased synthesis of Vitamin B1 and B6. CONCLUSION In support of previous animal studies and in-vitro findings, our results suggest that ambient chronic OP pesticide exposure alters gut microbiome composition and its predicted metabolism in humans.
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Affiliation(s)
- Keren Zhang
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA, USA
| | - Kimberly Paul
- Department of Neurology, UCLA David Geffen School of Medicine, Los Angeles, CA, USA
| | - Jonathan P Jacobs
- The Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Division of Gastroenterology, Hepatology and Parenteral Nutrition, VA Greater Los Angeles Healthcare System, Los Angeles, CA, USA
| | - Myles G Cockburn
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jeff M Bronstein
- Department of Neurology, UCLA David Geffen School of Medicine, Los Angeles, CA, USA
| | - Irish Del Rosario
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA, USA
| | - Beate Ritz
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA, USA.
- Department of Environmental Health Sciences, UCLA Fielding School of Public Health, Los Angeles, CA, USA.
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Fall C, Romero-Camacho MP, Olguín MT, Rosas-Echeverría K, Esparza-Soto M, Salinas-Tapia H, Lucero-Chávez M, Alcaraz-Ibarra S. Aerobic digestibility of waste aerobic granular sludge (AGS) assessed by respirometry, physical-chemical analyses, modeling and 16S rRNA gene sequencing. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 356:120639. [PMID: 38520857 DOI: 10.1016/j.jenvman.2024.120639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 02/20/2024] [Accepted: 03/10/2024] [Indexed: 03/25/2024]
Abstract
Research has evolved on aerobic granular sludge (AGS) process, but still there are very few studies on the treatment of excess AGS sludge, with almost none considering its aerobic digestion. Here therefore, the aerobic digestibility of typical AGS sludge was assessed. Granules were produced from acetate-based synthetic wastewater (WW) and were subjected to aerobic digestion for 64 d. The stabilization process was monitored over time through physical-chemical parameters, oxygen uptake rates (OUR) and 16S rRNA gene sequencing. The microbial analyses revealed that the cultivated granules were dominated by slow-growing bacteria, mainly ordinary heterotrophic organisms with potential for polyhydroxyalkanoates (PHA) aerobic storage (PHA-OHOs), polyphosphate and glycogen accumulating organisms (PAOs and GAOs), fermentative anaerobes and nitrifiers (AOB and NOB). Differential abundance analysis of the bacterial data (before versus after digestion) discriminated between the most vulnerable microbiome genera and those most resistant to aerobic digestion. Furthermore, modeling of the stabilization process determined that the endogenous decay rate constant (bH) for the heterotrophs present in the granules was notably low; bH = 0.05 d-1 (average), four times less than for common activated sludge (AS), which is rated at 0.2 d-1. For first time, the research reveals another important feature of AGS sludge, i.e. the slow-decaying character of its bacteria (along with their known slow-growing character). This results in slower stabilization, need of bigger digesters and reconsideration of the specific OUR limits in biosolids regulations (SOUR limit of 1.5 mg/gTSS.h), for waste AGS compared to conventional waste AS. The study suggests that aerobic digestion of waste AGS (fully-granulated) could differ from that of conventional AS. Future work is needed on aerobic digestibility of real AGS sludges from municipal and industrial WWs, compared to synthetic WWs.
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Affiliation(s)
- C Fall
- Universidad Autónoma del Estado de México (UAEM), Instituto Interamericano de Ciencias y Tecnología del Agua (IITCA), Carr. Toluca-Ixtlahuaca, km. 14.5, C.P. 50120, San Cayetano, Toluca, Mexico.
| | - M P Romero-Camacho
- Universidad Autónoma del Estado de México (UAEM), Instituto Interamericano de Ciencias y Tecnología del Agua (IITCA), Carr. Toluca-Ixtlahuaca, km. 14.5, C.P. 50120, San Cayetano, Toluca, Mexico
| | - M T Olguín
- Instituto Nacional de Investigaciones Nucleares (ININ), México. La Marquesa, Ocoyoacac, Mexico
| | - K Rosas-Echeverría
- Universidad Autónoma del Estado de México (UAEM), Instituto Interamericano de Ciencias y Tecnología del Agua (IITCA), Carr. Toluca-Ixtlahuaca, km. 14.5, C.P. 50120, San Cayetano, Toluca, Mexico
| | - M Esparza-Soto
- Universidad Autónoma del Estado de México (UAEM), Instituto Interamericano de Ciencias y Tecnología del Agua (IITCA), Carr. Toluca-Ixtlahuaca, km. 14.5, C.P. 50120, San Cayetano, Toluca, Mexico
| | - H Salinas-Tapia
- Universidad Autónoma del Estado de México (UAEM), Instituto Interamericano de Ciencias y Tecnología del Agua (IITCA), Carr. Toluca-Ixtlahuaca, km. 14.5, C.P. 50120, San Cayetano, Toluca, Mexico
| | - M Lucero-Chávez
- Universidad Autónoma del Estado de México (UAEM), Instituto Interamericano de Ciencias y Tecnología del Agua (IITCA), Carr. Toluca-Ixtlahuaca, km. 14.5, C.P. 50120, San Cayetano, Toluca, Mexico
| | - S Alcaraz-Ibarra
- Universidad Autónoma del Estado de México (UAEM), Instituto Interamericano de Ciencias y Tecnología del Agua (IITCA), Carr. Toluca-Ixtlahuaca, km. 14.5, C.P. 50120, San Cayetano, Toluca, Mexico
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Maki KA, Crayton CB, Butera G, Wallen GR. Examining the relationship between the oral microbiome, alcohol intake and alcohol-comorbid neuropsychological disorders: protocol for a scoping review. BMJ Open 2024; 14:e079823. [PMID: 38514150 PMCID: PMC10961520 DOI: 10.1136/bmjopen-2023-079823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 02/22/2024] [Indexed: 03/23/2024] Open
Abstract
INTRODUCTION Heavy alcohol use and alcohol use disorder (AUD) continues to rise as a public health problem and increases the risk for disease. Elevated rates of anxiety, depression, sleep disruption and stress are associated with alcohol use. Symptoms may progress to diagnosed neurophysiological conditions and increase risk for relapse if abstinence is attempted. Research on mechanisms connecting the gastrointestinal microbiome to neuropsychological disorders through the gut-brain axis is well-established. Less is known how the oral microbiome and oral microbial-associated biomarkers may signal to the brain. Therefore, a synthesis of research studying relationships between alcohol intake, alcohol-associated neurophysiological symptoms and the oral microbiome is needed to understand the state of the current science. In this paper, we outline our protocol to collect, evaluate and synthesise research focused on associations between alcohol intake and AUD-related neuropsychological disorders with the oral microbiome. METHODS AND ANALYSIS The search strategy was developed and will be executed in collaboration with a medical research librarian. Studies will be screened by two independent investigators according to the aim of the scoping review, along with the outlined exclusion and inclusion criteria. After screening, data will be extracted and synthesised from the included papers according to predefined demographic, clinical and microbiome methodology metrics. ETHICS AND DISSEMINATION A scoping review of primary sources is needed to synthesise the data on relationships between alcohol use, neuropsychological conditions associated with AUD and the oral microbiome. The proposed scoping review is based on the data from publicly available databases and does not require ethical approval. We expect the results of this synthesis will identify gaps in the growing literature and highlight potential mechanisms linking the oral-brain axis to addiction and other associated neuropsychological conditions. The study findings and results will be disseminated through journals and conferences related to psychology, neuroscience, dentistry and the microbiome.
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Affiliation(s)
- Katherine A Maki
- Clinical Center, Translational Biobehavioral and Health Disparities Branch, National Institutes of Health, Bethesda, Maryland, USA
| | - Chelsea B Crayton
- Clinical Center, Translational Biobehavioral and Health Disparities Branch, National Institutes of Health, Bethesda, Maryland, USA
| | - Gisela Butera
- Division of Library Services, National Institutes of Health, Bethesda, Maryland, USA
| | - Gwenyth R Wallen
- Clinical Center, Translational Biobehavioral and Health Disparities Branch, National Institutes of Health, Bethesda, Maryland, USA
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Hui TKL, Lo ICN, Wong KKW, Tsang CTT, Tsang LM. Metagenomic analysis of gut microbiome illuminates the mechanisms and evolution of lignocellulose degradation in mangrove herbivorous crabs. BMC Microbiol 2024; 24:57. [PMID: 38350856 PMCID: PMC10863281 DOI: 10.1186/s12866-024-03209-4] [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: 10/07/2023] [Accepted: 01/28/2024] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND Sesarmid crabs dominate mangrove habitats as the major primary consumers, which facilitates the trophic link and nutrient recycling in the ecosystem. Therefore, the adaptations and mechanisms of sesarmid crabs to herbivory are not only crucial to terrestrialization and its evolutionary success, but also to the healthy functioning of mangrove ecosystems. Although endogenous cellulase expressions were reported in crabs, it remains unknown if endogenous enzymes alone can complete the whole lignocellulolytic pathway, or if they also depend on the contribution from the intestinal microbiome. We attempt to investigate the role of gut symbiotic microbes of mangrove-feeding sesarmid crabs in plant digestion using a comparative metagenomic approach. RESULTS Metagenomics analyses on 43 crab gut samples from 23 species of mangrove crabs with different dietary preferences revealed a wide coverage of 127 CAZy families and nine KOs targeting lignocellulose and their derivatives in all species analyzed, including predominantly carnivorous species, suggesting the crab gut microbiomes have lignocellulolytic capacity regardless of dietary preference. Microbial cellulase, hemicellulase and pectinase genes in herbivorous and detritivorous crabs were differentially more abundant when compared to omnivorous and carnivorous crabs, indicating the importance of gut symbionts in lignocellulose degradation and the enrichment of lignocellulolytic microbes in response to diet with higher lignocellulose content. Herbivorous and detritivorous crabs showed highly similar CAZyme composition despite dissimilarities in taxonomic profiles observed in both groups, suggesting a stronger selection force on gut microbiota by functional capacity than by taxonomy. The gut microbiota in herbivorous sesarmid crabs were also enriched with nitrogen reduction and fixation genes, implying possible roles of gut microbiota in supplementing nitrogen that is deficient in plant diet. CONCLUSIONS Endosymbiotic microbes play an important role in lignocellulose degradation in most crab species. Their abundance is strongly correlated with dietary preference, and they are highly enriched in herbivorous sesarmids, thus enhancing their capacity in digesting mangrove leaves. Dietary preference is a stronger driver in determining the microbial CAZyme composition and taxonomic profile in the crab microbiome, resulting in functional redundancy of endosymbiotic microbes. Our results showed that crabs implement a mixed mode of digestion utilizing both endogenous and microbial enzymes in lignocellulose degradation, as observed in most of the more advanced herbivorous invertebrates.
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Affiliation(s)
- Tom Kwok Lun Hui
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Irene Ching Nam Lo
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Karen Ka Wing Wong
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Chandler Tsz To Tsang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Ling Ming Tsang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
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Luo K, Wang Z, Peters BA, Hanna DB, Wang T, Sollecito CC, Grassi E, Wiek F, St Peter L, Usyk M, Post WS, Landay AL, Hodis HN, Weber KM, French A, Golub ET, Lazar J, Gustafson D, Sharma A, Anastos K, Clish CB, Knight R, Kaplan RC, Burk RD, Qi Q. Tryptophan metabolism, gut microbiota, and carotid artery plaque in women with and without HIV infection. AIDS 2024; 38:223-233. [PMID: 37199567 PMCID: PMC10640661 DOI: 10.1097/qad.0000000000003596] [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: 05/19/2023]
Abstract
OBJECTIVE The perturbation of tryptophan (TRP) metabolism has been linked with HIV infection and cardiovascular disease (CVD), but the interrelationship among TRP metabolites, gut microbiota, and atherosclerosis remain unclear in the context of HIV infection. METHODS We included 361 women (241 HIV+, 120 HIV-) with carotid artery plaque assessments from the Women's Interagency HIV Study, measured 10 plasma TRP metabolites and profiled fecal gut microbiome. TRP metabolite-related gut bacteria were selected through the Analysis of Compositions of Microbiomes with Bias Correction method. Associations of TRP metabolites and related microbial features with plaque were examined using multivariable logistic regression. RESULTS Although plasma kynurenic acid (KYNA) [odds ratio (OR) = 1.93, 95% confidence interval (CI): 1.12-3.32 per one SD increase; P = 0.02) and KYNA/TRP [OR = 1.83 (95% CI 1.08-3.09), P = 0.02] were positively associated with plaque, indole-3-propionate (IPA) [OR = 0.62 (95% CI 0.40-0.98), P = 0.03] and IPA/KYNA [OR = 0.51 (95% CI 0.33-0.80), P < 0.01] were inversely associated with plaque. Five gut bacterial genera and many affiliated species were positively associated with IPA (FDR-q < 0.25), including Roseburia spp ., Eubacterium spp., Lachnospira spp., and Coprobacter spp.; but no bacterial genera were found to be associated with KYNA. Furthermore, an IPA-associated-bacteria score was inversely associated with plaque [OR = 0.47 (95% CI 0.28-0.79), P < 0.01]. But no significant effect modification by HIV serostatus was observed in these associations. CONCLUSION In a cohort of women living with and without HIV infection, plasma IPA levels and related gut bacteria were inversely associated with carotid artery plaque, suggesting a potential beneficial role of IPA and its gut bacterial producers in atherosclerosis and CVD.
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Affiliation(s)
- Kai Luo
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Zheng Wang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Brandilyn A Peters
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, USA
| | - David B Hanna
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Tao Wang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Christopher C Sollecito
- Department of Microbiology & Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Evan Grassi
- Department of Microbiology & Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Fanua Wiek
- Department of Microbiology & Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Lauren St Peter
- Department of Microbiology & Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Mykhaylo Usyk
- Department of Microbiology & Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Wendy S Post
- Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Alan L Landay
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Howard N Hodis
- Atherosclerosis Research Unit, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - Audrey French
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Elizabeth T Golub
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Jason Lazar
- Department of Medicine, State University of New York Downstate Medical Center, Brooklyn, New York, USA
| | - Deborah Gustafson
- Department of Neurology, State University of New York-Downstate Medical Center, Brooklyn, New York, USA
| | - Anjali Sharma
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Kathryn Anastos
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Obstetrics & Gynecology and Women’s Health, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Clary B Clish
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rob Knight
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Robert C Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Robert D Burk
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Microbiology & Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Obstetrics & Gynecology and Women’s Health, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Qibin Qi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
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Eckermann HA, Meijer J, Cooijmans K, Lahti L, de Weerth C. Daily skin-to-skin contact alters microbiota development in healthy full-term infants. Gut Microbes 2024; 16:2295403. [PMID: 38197254 DOI: 10.1080/19490976.2023.2295403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 12/12/2023] [Indexed: 01/11/2024] Open
Abstract
The gut microbiota is vital for human body development and function. Its development in early life is influenced by various environmental factors. In this randomized controlled trial, the gut microbiota was obtained as a secondary outcome measure in a study on the effects of one hour of daily skin-to-skin contact (SSC) for five weeks in healthy full-term infants. Specifically, we studied the effects on alpha/beta diversity, volatility, microbiota maturation, and bacterial and gut-brain-axis-related functional abundances in microbiota assessed thrice in the first year. Pregnant Dutch women (n = 116) were randomly assigned to the SSC or care-as-usual groups. The SSC group participants engaged in one hour of daily SSC from birth to five weeks of age. Stool samples were collected at two, five, and 52 weeks and the V4 region was sequenced. We observed significant differences in the microbiota composition, bacterial abundances, and predicted functional pathways between the groups. The SSC group exhibited lower microbiota volatility during early infancy. Microbiota maturation was slower in the SSC group during the first year and our results suggested that breastfeeding duration may have partially mediated this relation. Our findings provide evidence that postpartum SSC may influence microbiota development. Replication is necessary to validate and generalize these results. Future studies should include direct stress measurements and extend microbiota sampling beyond the first year to investigate stress as a mechanism and research SSC's impact on long-term microbiota maturation trajectories.
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Affiliation(s)
- Henrik Andreas Eckermann
- Donders Institute for Brain, Cognition and Behaviour, Department of Cognitive Neuroscience, Radboud university medical center, Nijmegen, The Netherlands
| | - Jennifer Meijer
- Donders Institute for Brain, Cognition and Behaviour, Department of Cognitive Neuroscience, Radboud university medical center, Nijmegen, The Netherlands
| | - Kelly Cooijmans
- Donders Institute for Brain, Cognition and Behaviour, Department of Cognitive Neuroscience, Radboud university medical center, Nijmegen, The Netherlands
- Behavioural Science Institute, Radboud University, Nijmegen, The Netherlands
| | - Leo Lahti
- Department of Computing, University of Turku, Turku, Finland
| | - Carolina de Weerth
- Donders Institute for Brain, Cognition and Behaviour, Department of Cognitive Neuroscience, Radboud university medical center, Nijmegen, The Netherlands
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Desorcy-Scherer K, Fricke HP, Hernandez LL. Selective serotonin reuptake inhibitors during pregnancy and lactation: A scoping review of effects on the maternal and infant gut microbiome. Dev Psychobiol 2024; 66:e22441. [PMID: 38131241 PMCID: PMC11017378 DOI: 10.1002/dev.22441] [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: 07/13/2023] [Revised: 10/30/2023] [Accepted: 11/06/2023] [Indexed: 12/23/2023]
Abstract
Perinatal mood disorders are a tremendous burden to childbearing families and treatment with selective serotonin reuptake inhibitor (SSRI) antidepressants is increasingly common. Exposure to SSRIs may affect serotonin signaling and ultimately, microbes that live in the gut. Health of the gut microbiome during pregnancy, lactation, and early infancy is critical, yet there is limited evidence to describe the relationship between SSRI exposure and gut microbiome status in this population. The purpose of this Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA)-compliant scoping review is to assess evidence and describe key concepts regarding whether SSRI exposure affects the maternal and infant gut microbiome. Sources were collected from PubMed, Web of Science, and Scopus databases, and an additional gray literature search was performed. Our search criteria returned only three sources, two rodent models and one human subjects research study. Results suggest that fluoxetine (SSRI) exposure may affect maternal gut microbiome dynamics during pregnancy and lactation. There were no available sources to describe the relationship between perinatal SSRI exposure and the infant gut microbiome. There is a significant gap in the literature regarding whether SSRI antidepressants affect the maternal and infant gut microbiome. Future studies are required to better understand how SSRI antidepressant exposure affects perinatal health.
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Affiliation(s)
| | - Hannah P. Fricke
- Department of Animal and Dairy Sciences, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Laura L. Hernandez
- Department of Animal and Dairy Sciences, University of Wisconsin–Madison, Madison, Wisconsin, USA
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10
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Seppi M, Pasqualini J, Facchin S, Savarino EV, Suweis S. Emergent Functional Organization of Gut Microbiomes in Health and Diseases. Biomolecules 2023; 14:5. [PMID: 38275746 PMCID: PMC10813293 DOI: 10.3390/biom14010005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 12/13/2023] [Accepted: 12/14/2023] [Indexed: 01/27/2024] Open
Abstract
Continuous and significant progress in sequencing technologies and bioinformatics pipelines has revolutionized our comprehension of microbial communities, especially for human microbiomes. However, most studies have focused on studying the taxonomic composition of the microbiomes and we are still not able to characterize dysbiosis and unveil the underlying ecological consequences. This study explores the emergent organization of functional abundances and correlations of gut microbiomes in health and disease. Leveraging metagenomic sequences, taxonomic and functional tables are constructed, enabling comparative analysis. First, we show that emergent taxonomic and functional patterns are not useful to characterize dysbiosis. Then, through differential abundance analyses applied to functions, we reveal distinct functional compositions in healthy versus unhealthy microbiomes. In addition, we inquire into the functional correlation structure, revealing significant differences between the healthy and unhealthy groups, which may significantly contribute to understanding dysbiosis. Our study demonstrates that scrutinizing the functional organization in the microbiome provides novel insights into the underlying state of the microbiome. The shared data structure underlying the functional and taxonomic compositions allows for a comprehensive macroecological examination. Our findings not only shed light on dysbiosis, but also underscore the importance of studying functional interrelationships for a nuanced understanding of the dynamics of the microbial community. This research proposes a novel approach, bridging the gap between microbial ecology and functional analyses, promising a deeper understanding of the intricate world of the gut microbiota and its implications for human health.
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Affiliation(s)
- Marcello Seppi
- Laboratory of Interdisciplinary Physics (LIPh), Physics and Astronomy Department, University of Padua, Via Marzolo 8, 35131 Padua, Italy; (M.S.); (J.P.)
| | - Jacopo Pasqualini
- Laboratory of Interdisciplinary Physics (LIPh), Physics and Astronomy Department, University of Padua, Via Marzolo 8, 35131 Padua, Italy; (M.S.); (J.P.)
| | - Sonia Facchin
- Department of Surgery, Oncology and Gastroenterology (DiSCOG), University of Padua, Via Giustiniani 2, 35121 Padua, Italy; (S.F.); (E.V.S.)
| | - Edoardo Vincenzo Savarino
- Department of Surgery, Oncology and Gastroenterology (DiSCOG), University of Padua, Via Giustiniani 2, 35121 Padua, Italy; (S.F.); (E.V.S.)
| | - Samir Suweis
- Laboratory of Interdisciplinary Physics (LIPh), Physics and Astronomy Department, University of Padua, Via Marzolo 8, 35131 Padua, Italy; (M.S.); (J.P.)
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11
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Bellato M, Cappellato M, Longhin F, Del Vecchio C, Brancaccio G, Cattelan AM, Brun P, Salaris C, Castagliuolo I, Di Camillo B. Uncover a microbiota signature of upper respiratory tract in patients with SARS-CoV-2 + . Sci Rep 2023; 13:16867. [PMID: 37803040 PMCID: PMC10558486 DOI: 10.1038/s41598-023-43040-x] [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: 06/01/2023] [Accepted: 09/18/2023] [Indexed: 10/08/2023] Open
Abstract
The outbreak of Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, forced us to face a pandemic with unprecedented social, economic, and public health consequences. Several nations have launched campaigns to immunize millions of people using various vaccines to prevent infections. Meanwhile, therapeutic approaches and discoveries continuously arise; however, identifying infected patients that are going to experience the more severe outcomes of COVID-19 is still a major need, to focus therapeutic efforts, reducing hospitalization and mitigating drug adverse effects. Microbial communities colonizing the respiratory tract exert significant effects on host immune responses, influencing the susceptibility to infectious agents. Through 16S rDNAseq we characterized the upper airways' microbiota of 192 subjects with nasopharyngeal swab positive for SARS-CoV-2. Patients were divided into groups based on the presence of symptoms, pneumonia severity, and need for oxygen therapy or intubation. Indeed, unlike most of the literature, our study focuses on identifying microbial signatures predictive of disease progression rather than on the probability of infection itself, for which a consensus is lacking. Diversity, differential abundance, and network analysis at different taxonomic levels were synergistically adopted, in a robust bioinformatic pipeline, highlighting novel possible taxa correlated with patients' disease progression to intubation.
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Affiliation(s)
- Massimo Bellato
- Department of Information Engineering, University of Padova, 35131, Padova, Italy
| | - Marco Cappellato
- Department of Information Engineering, University of Padova, 35131, Padova, Italy
| | - Francesca Longhin
- Department of Information Engineering, University of Padova, 35131, Padova, Italy
| | - Claudia Del Vecchio
- Department of Molecular Medicine, University of Padova, 35121, Padova, Italy
| | - Giuseppina Brancaccio
- Department of Molecular Medicine, University of Padova, 35121, Padova, Italy
- Infectious Diseases Unit, University Hospital Padova, 35128, Padova, Italy
| | - Anna Maria Cattelan
- Department of Molecular Medicine, University of Padova, 35121, Padova, Italy
- Infectious Diseases Unit, University Hospital Padova, 35128, Padova, Italy
| | - Paola Brun
- Department of Molecular Medicine, University of Padova, 35121, Padova, Italy
| | - Claudio Salaris
- Department of Molecular Medicine, University of Padova, 35121, Padova, Italy
| | - Ignazio Castagliuolo
- Department of Molecular Medicine, University of Padova, 35121, Padova, Italy
- Microbiology and Virology Unit, University Hospital Padova, 35121, Padova, Italy
| | - Barbara Di Camillo
- Department of Information Engineering, University of Padova, 35131, Padova, Italy.
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020, Legnaro (PD), Italy.
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12
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Salloum PM, Jorge F, Poulin R. Different trematode parasites in the same snail host: Species-specific or shared microbiota? Mol Ecol 2023; 32:5414-5428. [PMID: 37615348 DOI: 10.1111/mec.17111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 08/07/2023] [Accepted: 08/10/2023] [Indexed: 08/25/2023]
Abstract
The concept that microbes associated with macroorganisms evolve as a unit has swept evolutionary ecology. However, this idea is controversial due to factors such as imperfect vertical transmission of microbial lineages and high microbiome variability among conspecific individuals of the same population. Here, we tested several predictions regarding the microbiota of four trematodes (Galactosomum otepotiense, Philophthalmus attenuatus, Acanthoparyphium sp. and Maritrema novaezealandense) that parasitize the same snail host population. We predicted that each parasite species would harbour a distinct microbiota, with microbial composition similarity decreasing with increasing phylogenetic distance among parasite species. We also predicted that trematode species co-infecting the same individual host would influence each other's microbiota. We detected significant differences in alpha and beta diversity, as well as differential abundance, in the microbiota of the four trematode species. We found no evidence that phylogenetically closely related trematodes had more similar microbiota. We also uncovered indicator bacterial taxa that were significantly associated with each trematode species. Trematode species sharing the same snail host showed evidence of mostly one-sided bacterial exchanges, with the microbial community of one species approaching that of the other. We hypothesize that natural selection acting on specific microbial lineages may be important to maintain differences in horizontally acquired microbes, with vertical transmission also playing a role. In particular, one trematode species had a more consistent and diverse bacteriota than the others, potentially a result of stronger stabilizing pressures. We conclude that species-specific processes shape microbial community assembly in different trematodes exploiting the same host population.
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Affiliation(s)
| | - Fátima Jorge
- Otago Micro and Nano Imaging, Electron Microscopy Unit, University of Otago, Dunedin, New Zealand
| | - Robert Poulin
- Department of Zoology, University of Otago, Dunedin, New Zealand
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13
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Regueira-Iglesias A, Balsa-Castro C, Blanco-Pintos T, Tomás I. Critical review of 16S rRNA gene sequencing workflow in microbiome studies: From primer selection to advanced data analysis. Mol Oral Microbiol 2023; 38:347-399. [PMID: 37804481 DOI: 10.1111/omi.12434] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 09/01/2023] [Accepted: 09/14/2023] [Indexed: 10/09/2023]
Abstract
The multi-batch reanalysis approach of jointly reevaluating gene/genome sequences from different works has gained particular relevance in the literature in recent years. The large amount of 16S ribosomal ribonucleic acid (rRNA) gene sequence data stored in public repositories and information in taxonomic databases of the same gene far exceeds that related to complete genomes. This review is intended to guide researchers new to studying microbiota, particularly the oral microbiota, using 16S rRNA gene sequencing and those who want to expand and update their knowledge to optimise their decision-making and improve their research results. First, we describe the advantages and disadvantages of using the 16S rRNA gene as a phylogenetic marker and the latest findings on the impact of primer pair selection on diversity and taxonomic assignment outcomes in oral microbiome studies. Strategies for primer selection based on these results are introduced. Second, we identified the key factors to consider in selecting the sequencing technology and platform. The process and particularities of the main steps for processing 16S rRNA gene-derived data are described in detail to enable researchers to choose the most appropriate bioinformatics pipeline and analysis methods based on the available evidence. We then produce an overview of the different types of advanced analyses, both the most widely used in the literature and the most recent approaches. Several indices, metrics and software for studying microbial communities are included, highlighting their advantages and disadvantages. Considering the principles of clinical metagenomics, we conclude that future research should focus on rigorous analytical approaches, such as developing predictive models to identify microbiome-based biomarkers to classify health and disease states. Finally, we address the batch effect concept and the microbiome-specific methods for accounting for or correcting them.
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Affiliation(s)
- Alba Regueira-Iglesias
- Oral Sciences Research Group, Special Needs Unit, Department of Surgery and Medical-Surgical Specialties, School of Medicine and Dentistry, Universidade de Santiago de Compostela, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, A Coruña, Spain
| | - Carlos Balsa-Castro
- Oral Sciences Research Group, Special Needs Unit, Department of Surgery and Medical-Surgical Specialties, School of Medicine and Dentistry, Universidade de Santiago de Compostela, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, A Coruña, Spain
| | - Triana Blanco-Pintos
- Oral Sciences Research Group, Special Needs Unit, Department of Surgery and Medical-Surgical Specialties, School of Medicine and Dentistry, Universidade de Santiago de Compostela, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, A Coruña, Spain
| | - Inmaculada Tomás
- Oral Sciences Research Group, Special Needs Unit, Department of Surgery and Medical-Surgical Specialties, School of Medicine and Dentistry, Universidade de Santiago de Compostela, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, A Coruña, Spain
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14
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Cho H, Qu Y, Liu C, Tang B, Lyu R, Lin BM, Roach J, Azcarate-Peril MA, Aguiar Ribeiro A, Love MI, Divaris K, Wu D. Comprehensive evaluation of methods for differential expression analysis of metatranscriptomics data. Brief Bioinform 2023; 24:bbad279. [PMID: 37738402 PMCID: PMC10516371 DOI: 10.1093/bib/bbad279] [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: 03/07/2023] [Revised: 06/23/2023] [Accepted: 07/18/2023] [Indexed: 09/24/2023] Open
Abstract
Understanding the function of the human microbiome is important but the development of statistical methods specifically for the microbial gene expression (i.e. metatranscriptomics) is in its infancy. Many currently employed differential expression analysis methods have been designed for different data types and have not been evaluated in metatranscriptomics settings. To address this gap, we undertook a comprehensive evaluation and benchmarking of 10 differential analysis methods for metatranscriptomics data. We used a combination of real and simulated data to evaluate performance (i.e. type I error, false discovery rate and sensitivity) of the following methods: log-normal (LN), logistic-beta (LB), MAST, DESeq2, metagenomeSeq, ANCOM-BC, LEfSe, ALDEx2, Kruskal-Wallis and two-part Kruskal-Wallis. The simulation was informed by supragingival biofilm microbiome data from 300 preschool-age children enrolled in a study of childhood dental disease (early childhood caries, ECC), whereas validations were sought in two additional datasets from the ECC study and an inflammatory bowel disease study. The LB test showed the highest sensitivity in both small and large samples and reasonably controlled type I error. Contrarily, MAST was hampered by inflated type I error. Upon application of the LN and LB tests in the ECC study, we found that genes C8PHV7 and C8PEV7, harbored by the lactate-producing Campylobacter gracilis, had the strongest association with childhood dental disease. This comprehensive model evaluation offers practical guidance for selection of appropriate methods for rigorous analyses of differential expression in metatranscriptomics. Selection of an optimal method increases the possibility of detecting true signals while minimizing the chance of claiming false ones.
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Affiliation(s)
- Hunyong Cho
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, United States
| | - Yixiang Qu
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, United States
| | - Chuwen Liu
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, United States
| | - Boyang Tang
- Department of Statistics, University of Connecticut, Storrs, CT, United States
| | - Ruiqi Lyu
- School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States
| | - Bridget M Lin
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, United States
| | - Jeffrey Roach
- Research Computing, University of North Carolina, Chapel Hill, NC, United States
| | - M Andrea Azcarate-Peril
- Department of Medicine and Nutrition, University of North Carolina, Chapel Hill, NC, United States
| | - Apoena Aguiar Ribeiro
- Division of Diagnostic Sciences, University of North Carolina, Chapel Hill, NC, United States
| | - Michael I Love
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, United States
- Department of Genetics, University of North Carolina, Chapel Hill, NC, United States
| | - Kimon Divaris
- Division of Pediatric and Public Health, University of North Carolina, Chapel Hill, NC, United States
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, United States
| | - Di Wu
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, United States
- Division of Oral and Craniofacial Health Sciences, Adam School of Dentistry, University of North Carolina, Chapel Hill, NC, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, United States
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15
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Wang L, Trasanidis N, Wu T, Dong G, Hu M, Bauer DE, Pinello L. Dictys: dynamic gene regulatory network dissects developmental continuum with single-cell multiomics. Nat Methods 2023; 20:1368-1378. [PMID: 37537351 DOI: 10.1038/s41592-023-01971-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 07/05/2023] [Indexed: 08/05/2023]
Abstract
Gene regulatory networks (GRNs) are key determinants of cell function and identity and are dynamically rewired during development and disease. Despite decades of advancement, challenges remain in GRN inference, including dynamic rewiring, causal inference, feedback loop modeling and context specificity. To address these challenges, we develop Dictys, a dynamic GRN inference and analysis method that leverages multiomic single-cell assays of chromatin accessibility and gene expression, context-specific transcription factor footprinting, stochastic process network and efficient probabilistic modeling of single-cell RNA-sequencing read counts. Dictys improves GRN reconstruction accuracy and reproducibility and enables the inference and comparative analysis of context-specific and dynamic GRNs across developmental contexts. Dictys' network analyses recover unique insights in human blood and mouse skin development with cell-type-specific and dynamic GRNs. Its dynamic network visualizations enable time-resolved discovery and investigation of developmental driver transcription factors and their regulated targets. Dictys is available as a free, open-source and user-friendly Python package.
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Affiliation(s)
- Lingfei Wang
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital Research Institute, Department of Pathology, Harvard Medical School, Boston, MA, USA
- Gene Regulation Observatory, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nikolaos Trasanidis
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital Research Institute, Department of Pathology, Harvard Medical School, Boston, MA, USA
- Hugh and Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, UK
| | - Ting Wu
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Guanlan Dong
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital Research Institute, Department of Pathology, Harvard Medical School, Boston, MA, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Department of Pediatrics, Harvard Medical School, Bioinformatics and Integrative Genomics PhD Program, Harvard Medical School, Boston, MA, USA
| | - Michael Hu
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital Research Institute, Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Daniel E Bauer
- Gene Regulation Observatory, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Luca Pinello
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital Research Institute, Department of Pathology, Harvard Medical School, Boston, MA, USA.
- Gene Regulation Observatory, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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16
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Ojala T, Häkkinen AE, Kankuri E, Kankainen M. Current concepts, advances, and challenges in deciphering the human microbiota with metatranscriptomics. Trends Genet 2023; 39:686-702. [PMID: 37365103 DOI: 10.1016/j.tig.2023.05.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 05/24/2023] [Accepted: 05/25/2023] [Indexed: 06/28/2023]
Abstract
Metatranscriptomics refers to the analysis of the collective microbial transcriptome of a sample. Its increased utilization for the characterization of human-associated microbial communities has enabled the discovery of many disease-state related microbial activities. Here, we review the principles of metatranscriptomics-based analysis of human-associated microbial samples. We describe strengths and weaknesses of popular sample preparation, sequencing, and bioinformatics approaches and summarize strategies for their use. We then discuss how human-associated microbial communities have recently been examined and how their characterization may change. We conclude that metatranscriptomics insights into human microbiotas under health and disease have not only expanded our knowledge on human health, but also opened avenues for rational antimicrobial drug use and disease management.
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Affiliation(s)
- Teija Ojala
- Department of Pharmacology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | | | - Esko Kankuri
- Department of Pharmacology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Matti Kankainen
- Hematology Research Unit, University of Helsinki, Helsinki, Finland; Laboratory of Genetics, HUS Diagnostic Center, Hospital District of Helsinki and Uusimaa (HUS), Helsinki, Finland.
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17
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López-García E, Benítez-Cabello A, Arenas-de Larriva AP, Gutierrez-Mariscal FM, Pérez-Martínez P, Yubero-Serrano EM, Arroyo-López FN, Garrido-Fernández A. Application of Compositional Data Analysis to Study the Relationship between Bacterial Diversity in Human Faeces and Sex, Age, and Weight. Biomedicines 2023; 11:2134. [PMID: 37626632 PMCID: PMC10452682 DOI: 10.3390/biomedicines11082134] [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: 06/30/2023] [Revised: 07/20/2023] [Accepted: 07/26/2023] [Indexed: 08/27/2023] Open
Abstract
This work uses Compositional Data Analysis (CoDA) to examine the typical human faecal bacterial diversity in 39 healthy volunteers from the Andalusian region (Spain). Stool samples were subjected to high-throughput sequencing of the V3 and V4 regions of the 16S ribosomal RNA gene using Illumina MiSeq. The numbers of sequences per sample and their genus-level assignment were carried out using the Phyloseq R package. The alpha diversity indices of the faecal bacterial population were not influenced by the volunteer's sex (male or female), age (19-46 years), and weight (48.6-99.0 kg). To study the relationship between these variables and the faecal bacterial population, the ALDEx2 and coda4microbiome CoDA packages were used. Applying ALDEx2, a trend suggesting a connection between sex and the genera Senegalimassilia and Negatibacillus (slightly more abundant in females) and Desulfovibrio (more abundant in males) was found. Moreover, age was tentatively associated with Streptococcus, Tizzerella, and Ruminococaceae_UCG-003, while weight was linked to Senegalimassilia. The exploratory tool of the coda4microbiome package revealed numerous bacterial log-ratios strongly related to sex and, to a lesser extent, age and weight. Moreover, the cross-sectional analysis identified bacterial signature balances able to assign sex to samples regardless of controlling for volunteers' age or weight. Desulfovibrio, Faecalitalea, and Romboutsia were relevant in the numerator, while Coprococcus, Streptococcus, and Negatibacillus were prominent in the denominator; the greater presence of these could characterise the female sex. Predictions for age included Caproiciproducens, Coprobacter, and Ruminoclostridium in the numerator and Odoribacter, Ezakiella, and Tyzzerella in the denominator. The predictions depend on the relationship between both groups, but the abundance of the first group and scarcity of the second could be related to older individuals. However, the association of the faecal bacterial population with weight did not yield a satisfactory model, indicating scarce influence. These results demonstrate the usefulness of the CoDA methodology for studying metagenomics data and, specifically, human microbiota.
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Affiliation(s)
- Elio López-García
- Food Biotechnology Department, Instituto de la Grasa (CSIC), Carretera Utrera km 1, Campus Universitario Pablo de Olavide, Building 46, 41013 Seville, Spain; (E.L.-G.); (F.N.A.-L.); (A.G.-F.)
| | - Antonio Benítez-Cabello
- Food Biotechnology Department, Instituto de la Grasa (CSIC), Carretera Utrera km 1, Campus Universitario Pablo de Olavide, Building 46, 41013 Seville, Spain; (E.L.-G.); (F.N.A.-L.); (A.G.-F.)
| | - Antonio Pablo Arenas-de Larriva
- Unidad de Gestión Clínica Medicina Interna, Lipids and Atherosclerosis Unit, Maimonides Institute for Biomedical Research in Córdoba, Reina Sofia University Hospital, University of Córdoba, 14004 Córdoba, Spain; (A.P.A.-d.L.); (F.M.G.-M.); (P.P.-M.); (E.M.Y.-S.)
| | - Francisco Miguel Gutierrez-Mariscal
- Unidad de Gestión Clínica Medicina Interna, Lipids and Atherosclerosis Unit, Maimonides Institute for Biomedical Research in Córdoba, Reina Sofia University Hospital, University of Córdoba, 14004 Córdoba, Spain; (A.P.A.-d.L.); (F.M.G.-M.); (P.P.-M.); (E.M.Y.-S.)
- CIBER Physiopathology of Obesity and Nutrition (CIBEROBN), Institute of Health Carlos III, 28029 Madrid, Spain
| | - Pablo Pérez-Martínez
- Unidad de Gestión Clínica Medicina Interna, Lipids and Atherosclerosis Unit, Maimonides Institute for Biomedical Research in Córdoba, Reina Sofia University Hospital, University of Córdoba, 14004 Córdoba, Spain; (A.P.A.-d.L.); (F.M.G.-M.); (P.P.-M.); (E.M.Y.-S.)
- CIBER Physiopathology of Obesity and Nutrition (CIBEROBN), Institute of Health Carlos III, 28029 Madrid, Spain
| | - Elena María Yubero-Serrano
- Unidad de Gestión Clínica Medicina Interna, Lipids and Atherosclerosis Unit, Maimonides Institute for Biomedical Research in Córdoba, Reina Sofia University Hospital, University of Córdoba, 14004 Córdoba, Spain; (A.P.A.-d.L.); (F.M.G.-M.); (P.P.-M.); (E.M.Y.-S.)
- CIBER Physiopathology of Obesity and Nutrition (CIBEROBN), Institute of Health Carlos III, 28029 Madrid, Spain
| | - Francisco Noé Arroyo-López
- Food Biotechnology Department, Instituto de la Grasa (CSIC), Carretera Utrera km 1, Campus Universitario Pablo de Olavide, Building 46, 41013 Seville, Spain; (E.L.-G.); (F.N.A.-L.); (A.G.-F.)
| | - Antonio Garrido-Fernández
- Food Biotechnology Department, Instituto de la Grasa (CSIC), Carretera Utrera km 1, Campus Universitario Pablo de Olavide, Building 46, 41013 Seville, Spain; (E.L.-G.); (F.N.A.-L.); (A.G.-F.)
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18
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Hughes RL, Frankenfeld CL, Gohl DM, Huttenhower C, Jackson SA, Vandeputte D, Vogtmann E, Comstock SS, Kable ME. Methods in Nutrition & Gut Microbiome Research: An American Society for Nutrition Satellite Session [13 October 2022]. Nutrients 2023; 15:nu15112451. [PMID: 37299414 DOI: 10.3390/nu15112451] [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: 04/11/2023] [Revised: 05/14/2023] [Accepted: 05/19/2023] [Indexed: 06/12/2023] Open
Abstract
The microbial cells colonizing the human body form an ecosystem that is integral to the regulation and maintenance of human health. Elucidation of specific associations between the human microbiome and health outcomes is facilitating the development of microbiome-targeted recommendations and treatments (e.g., fecal microbiota transplant; pre-, pro-, and post-biotics) to help prevent and treat disease. However, the potential of such recommendations and treatments to improve human health has yet to be fully realized. Technological advances have led to the development and proliferation of a wide range of tools and methods to collect, store, sequence, and analyze microbiome samples. However, differences in methodology at each step in these analytic processes can lead to variability in results due to the unique biases and limitations of each component. This technical variability hampers the detection and validation of associations with small to medium effect sizes. Therefore, the American Society for Nutrition (ASN) Nutritional Microbiology Group Engaging Members (GEM), sponsored by the Institute for the Advancement of Food and Nutrition Sciences (IAFNS), hosted a satellite session on methods in nutrition and gut microbiome research to review currently available methods for microbiome research, best practices, as well as tools and standards to aid in comparability of methods and results. This manuscript summarizes the topics and research discussed at the session. Consideration of the guidelines and principles reviewed in this session will increase the accuracy, precision, and comparability of microbiome research and ultimately the understanding of the associations between the human microbiome and health.
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Affiliation(s)
| | | | - Daryl M Gohl
- University of Minnesota Genomics Center, Minneapolis, MN 55455, USA
- Department of Genetics, Cell Biology, and Developmental Biology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Curtis Huttenhower
- Department of Biostatistics and Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Scott A Jackson
- Complex Microbial Systems Group, Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Doris Vandeputte
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14850, USA
| | - Emily Vogtmann
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sarah S Comstock
- Department of Food Science and Human Nutrition, Michigan State University, East Lansing, MI 48824, USA
| | - Mary E Kable
- USDA-ARS Western Human Nutrition Research Center, University of California-Davis, Davis, CA 95616, USA
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Sorbie A, Delgado Jiménez R, Weiler M, Benakis C. Protocol for microbiota analysis of a murine stroke model. STAR Protoc 2023; 4:101969. [PMID: 36625216 PMCID: PMC9843484 DOI: 10.1016/j.xpro.2022.101969] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 10/26/2022] [Accepted: 12/09/2022] [Indexed: 01/11/2023] Open
Abstract
Investigations on the microbiota in neurological diseases such as stroke are increasingly common; however, stroke researchers may have limited experience with designing such studies. Here, we describe a protocol to conduct a stroke microbiota study in mice, from experimental stroke surgery and sample collection to data analysis. We provide details on sample processing and sequencing and provide a reproducible data analysis pipeline. In doing so, we hope to enable researchers to conduct robust studies and facilitate identification of stroke-associated microbial signatures. For complete details on the use and execution of this protocol, please refer to Sorbie et al. (2022).1.
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Affiliation(s)
- Adam Sorbie
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany.
| | - Rosa Delgado Jiménez
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
| | - Monica Weiler
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
| | - Corinne Benakis
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
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Rud I, Almli VL, Berget I, Tzimorotas D, Varela P. Taste perception and oral microbiota: recent advances and future perspectives. Curr Opin Food Sci 2023. [DOI: 10.1016/j.cofs.2023.101030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2023]
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