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Rojas-Velazquez D, Kidwai S, Kraneveld AD, Tonda A, Oberski D, Garssen J, Lopez-Rincon A. Methodology for biomarker discovery with reproducibility in microbiome data using machine learning. BMC Bioinformatics 2024; 25:26. [PMID: 38225565 PMCID: PMC10789030 DOI: 10.1186/s12859-024-05639-3] [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: 12/03/2023] [Accepted: 01/04/2024] [Indexed: 01/17/2024] Open
Abstract
BACKGROUND In recent years, human microbiome studies have received increasing attention as this field is considered a potential source for clinical applications. With the advancements in omics technologies and AI, research focused on the discovery for potential biomarkers in the human microbiome using machine learning tools has produced positive outcomes. Despite the promising results, several issues can still be found in these studies such as datasets with small number of samples, inconsistent results, lack of uniform processing and methodologies, and other additional factors lead to lack of reproducibility in biomedical research. In this work, we propose a methodology that combines the DADA2 pipeline for 16s rRNA sequences processing and the Recursive Ensemble Feature Selection (REFS) in multiple datasets to increase reproducibility and obtain robust and reliable results in biomedical research. RESULTS Three experiments were performed analyzing microbiome data from patients/cases in Inflammatory Bowel Disease (IBD), Autism Spectrum Disorder (ASD), and Type 2 Diabetes (T2D). In each experiment, we found a biomarker signature in one dataset and applied to 2 other as further validation. The effectiveness of the proposed methodology was compared with other feature selection methods such as K-Best with F-score and random selection as a base line. The Area Under the Curve (AUC) was employed as a measure of diagnostic accuracy and used as a metric for comparing the results of the proposed methodology with other feature selection methods. Additionally, we use the Matthews Correlation Coefficient (MCC) as a metric to evaluate the performance of the methodology as well as for comparison with other feature selection methods. CONCLUSIONS We developed a methodology for reproducible biomarker discovery for 16s rRNA microbiome sequence analysis, addressing the issues related with data dimensionality, inconsistent results and validation across independent datasets. The findings from the three experiments, across 9 different datasets, show that the proposed methodology achieved higher accuracy compared to other feature selection methods. This methodology is a first approach to increase reproducibility, to provide robust and reliable results.
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Affiliation(s)
- David Rojas-Velazquez
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, University of Utrecht, Utrecht, The Netherlands.
- Department of Data Science, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands.
| | - Sarah Kidwai
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, University of Utrecht, Utrecht, The Netherlands
| | - Aletta D Kraneveld
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, University of Utrecht, Utrecht, The Netherlands
- Department of Neuroscience, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Alberto Tonda
- UMR 518 MIA - PS, INRAE, Institut des Systèmes Complexes de Paris, Île - de - France (ISC-PIF) - UAR 3611 CNRS, Université Paris-Saclay, Paris, France
| | - Daniel Oberski
- Department of Data Science, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Johan Garssen
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, University of Utrecht, Utrecht, The Netherlands
- Global Centre of Excellence Immunology, Danone Nutricia Research, Utrecht, The Netherlands
| | - Alejandro Lopez-Rincon
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, University of Utrecht, Utrecht, The Netherlands
- Department of Data Science, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
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Faas MM, Liu Y, Wekema L, Weis GA, van Loo-Bouwman CA, Silva Lagos L. The Effect of Antibiotics Treatment on the Maternal Immune Response and Gut Microbiome in Pregnant and Non-Pregnant Mice. Nutrients 2023; 15:2723. [PMID: 37375627 DOI: 10.3390/nu15122723] [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: 04/14/2023] [Revised: 05/19/2023] [Accepted: 05/19/2023] [Indexed: 06/29/2023] Open
Abstract
The gut microbiota are involved in adaptations of the maternal immune response to pregnancy. We therefore hypothesized that inducing gut dysbiosis during pregnancy alters the maternal immune response. Thus, pregnant mice received antibiotics from day 9 to day 16 to disturb the maternal gut microbiome. Feces were collected before, during and after antibiotic treatment, and microbiota were measured using 16S RNA sequencing. Mice were sacrificed at day 18 of pregnancy and intestinal (Peyer's patches (PP) and mesenteric lymph nodes (MLN)) and peripheral immune responses (blood and spleen) were measured using flow cytometry. Antibiotic treatment decreased fetal and placental weight. The bacterial count and the Shannon index were significantly decreased (Friedman, followed by Dunn's test, p < 0.05) and the bacterial genera abundance was significantly changed (Permanova, p < 0.05) following antibiotics treatment as compared with before treatment. Splenic Th1 cells and activated blood monocytes were increased, while Th2, Th17 and FoxP3/RoRgT double-positive cells in the PP and MLNs were decreased in pregnant antibiotics-treated mice as compared with untreated pregnant mice. In addition, intestinal dendritic cell subsets were affected by antibiotics. Correlation of immune cells with bacterial genera showed various correlations between immune cells in the PP, MLN and peripheral circulation (blood and spleen). We conclude the disturbed gut microbiota after antibiotics treatment disturbed the maternal immune response. This disturbed maternal immune response may affect fetal and placental weight.
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Affiliation(s)
- Marijke M Faas
- Immunoendocrinology, Division of Medical Biology, Department of Pathology and Medical Biology, University Medical Center Groningen, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
- Department of Obstetrics and Gynaecology, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Yuanrui Liu
- Immunoendocrinology, Division of Medical Biology, Department of Pathology and Medical Biology, University Medical Center Groningen, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
| | - Lieske Wekema
- Immunoendocrinology, Division of Medical Biology, Department of Pathology and Medical Biology, University Medical Center Groningen, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
| | - Gisela A Weis
- Yili Innovation Center Europe, Bronland 12 E-1, 6708 WH Wageningen, The Netherlands
| | | | - Luis Silva Lagos
- Immunoendocrinology, Division of Medical Biology, Department of Pathology and Medical Biology, University Medical Center Groningen, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
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Ben-Azu B, del Re EC, VanderZwaag J, Carrier M, Keshavan M, Khakpour M, Tremblay MÈ. Emerging epigenetic dynamics in gut-microglia brain axis: experimental and clinical implications for accelerated brain aging in schizophrenia. Front Cell Neurosci 2023; 17:1139357. [PMID: 37256150 PMCID: PMC10225712 DOI: 10.3389/fncel.2023.1139357] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 04/27/2023] [Indexed: 06/01/2023] Open
Abstract
Brain aging, which involves a progressive loss of neuronal functions, has been reported to be premature in probands affected by schizophrenia (SCZ). Evidence shows that SCZ and accelerated aging are linked to changes in epigenetic clocks. Recent cross-sectional magnetic resonance imaging analyses have uncovered reduced brain reserves and connectivity in patients with SCZ compared to typically aging individuals. These data may indicate early abnormalities of neuronal function following cyto-architectural alterations in SCZ. The current mechanistic knowledge on brain aging, epigenetic changes, and their neuropsychiatric disease association remains incomplete. With this review, we explore and summarize evidence that the dynamics of gut-resident bacteria can modulate molecular brain function and contribute to age-related neurodegenerative disorders. It is known that environmental factors such as mode of birth, dietary habits, stress, pollution, and infections can modulate the microbiota system to regulate intrinsic neuronal activity and brain reserves through the vagus nerve and enteric nervous system. Microbiota-derived molecules can trigger continuous activation of the microglial sensome, groups of receptors and proteins that permit microglia to remodel the brain neurochemistry based on complex environmental activities. This remodeling causes aberrant brain plasticity as early as fetal developmental stages, and after the onset of first-episode psychosis. In the central nervous system, microglia, the resident immune surveillance cells, are involved in neurogenesis, phagocytosis of synapses and neurological dysfunction. Here, we review recent emerging experimental and clinical evidence regarding the gut-brain microglia axis involvement in SCZ pathology and etiology, the hypothesis of brain reserve and accelerated aging induced by dietary habits, stress, pollution, infections, and other factors. We also include in our review the possibilities and consequences of gut dysbiosis activities on microglial function and dysfunction, together with the effects of antipsychotics on the gut microbiome: therapeutic and adverse effects, role of fecal microbiota transplant and psychobiotics on microglial sensomes, brain reserves and SCZ-derived accelerated aging. We end the review with suggestions that may be applicable to the clinical setting. For example, we propose that psychobiotics might contribute to antipsychotic-induced therapeutic benefits or adverse effects, as well as reduce the aging process through the gut-brain microglia axis. Overall, we hope that this review will help increase the understanding of SCZ pathogenesis as related to chronobiology and the gut microbiome, as well as reveal new concepts that will serve as novel treatment targets for SCZ.
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Affiliation(s)
- Benneth Ben-Azu
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
- Department of Pharmacology, Faculty of Basic Medical Sciences, College of Health Sciences, Delta State University, Abraka, Nigeria
| | - Elisabetta C. del Re
- Department of Psychiatry, Harvard Medical School, Boston, MA, United States
- VA Boston Healthcare System, Brockton, MA, United States
- Beth Israel Deaconess Medical Center, Boston, MA, United States
| | - Jared VanderZwaag
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
| | - Micaël Carrier
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
| | - Matcheri Keshavan
- Department of Psychiatry, Harvard Medical School, Boston, MA, United States
- Beth Israel Deaconess Medical Center, Boston, MA, United States
| | | | - Marie-Ève Tremblay
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
- Axe Neurosciences, Centre de Recherche du CHU de Québec, Université Laval, Québec City, QC, Canada
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC, Canada
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada
- Department of Molecular Medicine, Université Laval, Québec City, QC, Canada
- Centre for Advanced Materials and Related Technology (CAMTEC), Institute on Aging and Lifelong Health (IALH), University of Victoria, Victoria, BC, Canada
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Galley JD, Mashburn-Warren L, Blalock LC, Lauber CL, Carroll JE, Ross KM, Hobel C, Coussons-Read M, Dunkel Schetter C, Gur TL. Maternal anxiety, depression and stress affects offspring gut microbiome diversity and bifidobacterial abundances. Brain Behav Immun 2023; 107:253-264. [PMID: 36240906 DOI: 10.1016/j.bbi.2022.10.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 09/22/2022] [Accepted: 10/09/2022] [Indexed: 11/06/2022] Open
Abstract
Uncovering mechanisms underlying fetal programming during pregnancy is of critical importance. Atypical neurodevelopment during the pre- and immediate postnatal period has been associated with long-term adverse health outcomes, including mood disorders and aberrant cognitive ability in offspring. Maternal factors that have been implicated in anomalous offspring development include maternal inflammation and tress, anxiety, and depression. One potential mechanism through which these factors perturb normal offspring postnatal development is through microbiome disruption. The mother is a primary source of early postnatal microbiome seeding for the offspring, and the transference of a healthy microbiome is key in normal neurodevelopment. Since psychological stress, mood disorders, and inflammation have all been implicated in altering maternal microbiome community structure, passing on aberrant microbial communities to the offspring that may then affect developmental outcomes. Therefore, we examined how maternal stress, anxiety and depression assessed with standardized instruments, and maternal inflammatory cytokine levels in the pre- and postnatal period are associated with the offspring microbiome within the first 13 months of life, utilizing full length 16S sequencing on infant stool samples, that allowed for species-level resolution. Results revealed that infants of mothers who reported higher anxiety and perceived stress had reduced alpha diversity. Additionally, the relative taxonomic quantitative abundances of Bifidobacterium dentium and other species that have been associated with either modulation of the gut-brain axis, or other beneficial health outcomes, were reduced in the offspring of mothers with higher anxiety, perceived stress, and depression. We also found associations between bifidobacteria and prenatal maternal pro-inflammatory cytokines IL-6, IL-8, and IL-10. In summary, specific microbial taxa involved in maintaining proper brain and immune function are lower in offspring born to mothers with anxiety, depression, or stress, providing strong evidence for a mechanism by which maternal factors may affect offspring health through microbiota dysregulation.
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Affiliation(s)
- Jeffrey D Galley
- Department of Psychiatry and Behavioral Health, The Ohio State University Wexner Medical Center, Columbus, OH, USA; Institute for Behavioral Medicine Research, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | | | - Lexie C Blalock
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Christian L Lauber
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA; Department of Pediatrics, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Judith E Carroll
- Cousins Center for Psychoneuroimmunology, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Kharah M Ross
- Center for Social Sciences, Athabasca University, Athabasca, Alberta, Canada
| | - Calvin Hobel
- Cedars-Sinai Medical Centre, Los Angeles, CA, USA
| | - Mary Coussons-Read
- Department of Psychology, The University of Colorado, Colorado Springs, CO, USA
| | | | - Tamar L Gur
- Department of Psychiatry and Behavioral Health, The Ohio State University Wexner Medical Center, Columbus, OH, USA; Institute for Behavioral Medicine Research, The Ohio State University Wexner Medical Center, Columbus, OH, USA; Department of Neuroscience, The Ohio State University, Columbus, OH, USA; Obstetrics and Gynecology, The Ohio State University Wexner Medical Center, Columbus, OH, USA.
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Doroftei B, Ilie OD, Diaconu R, Hutanu D, Stoian I, Ilea C. An Updated Narrative Mini-Review on the Microbiota Changes in Antenatal and Post-Partum Depression. Diagnostics (Basel) 2022; 12:diagnostics12071576. [PMID: 35885482 PMCID: PMC9315700 DOI: 10.3390/diagnostics12071576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/26/2022] [Accepted: 06/27/2022] [Indexed: 12/02/2022] Open
Abstract
Background: Antenatal depression (AND) and post-partum depression (PPD) are long-term debilitating psychiatric disorders that significantly influence the composition of the gut flora of mothers and infants that starts from the intrauterine life. Not only does bacterial ratio shift impact the immune system, but it also increases the risk of potentially life-threatening disorders. Material and Methods: Therefore, we conducted a narrative mini-review aiming to gather all evidence published between 2018–2022 regarding microflora changes in all three stages of pregnancy. Results: We initially identified 47 potentially eligible studies, from which only 7 strictly report translocations; 3 were conducted on rodent models and 4 on human patients. The remaining studies were divided based on their topic, precisely focused on how probiotics, breastfeeding, diet, antidepressants, exogenous stressors, and plant-derived compounds modulate in a bidirectional way upon behavior and microbiota. Almost imperatively, dysbacteriosis cause cognitive impairments, reflected by abnormal temperament and personality traits that last up until 2 years old. Thankfully, a distinct technique that involves fecal matter transfer between individuals has been perfected over the years and was successfully translated into clinical practice. It proved to be a reliable approach in diminishing functional non- and gastrointestinal deficiencies, but a clear link between depressive women’s gastrointestinal/vaginal microbiota and clinical outcomes following reproductive procedures is yet to be established. Another gut-dysbiosis-driving factor is antibiotics, known for their potential to trigger inflammation. Fortunately, the studies conducted on mice that lack microbiota offer, without a shadow of a doubt, insight. Conclusions: It can be concluded that the microbiota is a powerful organ, and its optimum functionality is crucial, likely being the missing puzzle piece in the etiopathogenesis of psychiatric disorders.
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Affiliation(s)
- Bogdan Doroftei
- Faculty of Medicine, University of Medicine and Pharmacy “Grigore T. Popa”, University Street, No. 16, 700115 Iasi, Romania; (B.D.); (I.S.); (C.I.)
- Clinical Hospital of Obstetrics and Gynecology “Cuza Voda”, Cuza Voda Street, No. 34, 700038 Iasi, Romania;
- Origyn Fertility Center, Palace Street, No. 3C, 700032 Iasi, Romania
| | - Ovidiu-Dumitru Ilie
- Department of Biology, Faculty of Biology, “Alexandru Ioan Cuza” University, Carol I Avenue, No. 20A, 700505 Iasi, Romania
- Correspondence:
| | - Roxana Diaconu
- Clinical Hospital of Obstetrics and Gynecology “Cuza Voda”, Cuza Voda Street, No. 34, 700038 Iasi, Romania;
- Origyn Fertility Center, Palace Street, No. 3C, 700032 Iasi, Romania
| | - Delia Hutanu
- Department of Biology, Faculty of Chemistry-Biology-Geography, West University of Timisoara, Vasile Pârvan Avenue, No. 4, 300115 Timisoara, Romania;
| | - Irina Stoian
- Faculty of Medicine, University of Medicine and Pharmacy “Grigore T. Popa”, University Street, No. 16, 700115 Iasi, Romania; (B.D.); (I.S.); (C.I.)
| | - Ciprian Ilea
- Faculty of Medicine, University of Medicine and Pharmacy “Grigore T. Popa”, University Street, No. 16, 700115 Iasi, Romania; (B.D.); (I.S.); (C.I.)
- Clinical Hospital of Obstetrics and Gynecology “Cuza Voda”, Cuza Voda Street, No. 34, 700038 Iasi, Romania;
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Antibiotic Treatment during Pregnancy Alters Offspring Gut Microbiota in a Sex-Dependent Manner. Biomedicines 2022; 10:biomedicines10051042. [PMID: 35625778 PMCID: PMC9138679 DOI: 10.3390/biomedicines10051042] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/18/2022] [Accepted: 04/21/2022] [Indexed: 02/06/2023] Open
Abstract
This study investigated the effect of antibiotics administered to pregnant dams on offspring gut microbiome composition and metabolic capabilities, and how these changes in the microbiota may influence their immune responses in both the periphery and the brain. We orally administered a broad-spectrum antibiotic (ABX) cocktail consisting of vancomycin 0.5 mg/mL, ampicillin 1 mg/mL, and neomycin 1 mg/mL to pregnant dams during late gestation through birth. Bacterial DNA was extracted from offspring fecal samples, and 16S ribosomal RNA gene was sequenced by Illumina, followed by analysis of gut microbiota composition and PICRUSt prediction. Serum and brain tissue cytokine levels were analyzed by Luminex. Our results indicate that the ABX-cocktail led to significant diversity and taxonomic changes to the offspring's gut microbiome. In addition, the predicted KEGG and MetaCyc pathways were significantly altered in the offspring. Finally, there were decreased innate inflammatory cytokines and chemokines and interleukin (IL)-17 seen in the brains of ABX-cocktail offspring in response to lipopolysaccharide (LPS) immune challenge. Our results suggest that maternal ABX can produce long-lasting effects on the gut microbiome and neuroimmune responses of offspring. These findings support the role of the early microbiome in the development of offspring gastrointestinal and immune systems.
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