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Bloemendaal M, Vlaming P, de Boer A, Vermeulen-Kalk K, Bouman A, Kleefstra T, Arias Vasquez A. The role of the gut microbiota in patients with Kleefstra syndrome. Am J Med Genet B Neuropsychiatr Genet 2023; 192:124-138. [PMID: 36630271 DOI: 10.1002/ajmg.b.32926] [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: 01/31/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 01/12/2023]
Abstract
Kleefstra Syndrome (KS) is a rare monogenetic syndrome, caused by haploinsufficiency of the euchromatic histone methyl transferase 1 (EHMT1) gene, an important regulator of neurodevelopment. The clinical features of KS include intellectual disability, autistic behavior and gastrointestinal problems. The gut microbiota, an important modifier of the gut-brain-axis, may constitute an unexplored mechanism underlying clinical KS variation. We investigated the gut microbiota composition of 23 individuals with KS (patients) and 40 of their family members, to test whether (1) variation in the gut microbiota associates with KS diagnosis and (2) variation within the gut microbiota relates with KS syndrome symptoms. Both alpha and beta diversity of patients were different from their family members. Genus Coprococcus 3 was lower in abundance in patients compared to family members. Moreover, abundance of genus Merdibacter was lower in patients versus family members, but only in participants reporting intestinal complaints. Within the patient group, behavioral problems explained 7% of beta diversity variance. Also, within this group, we detected higher levels of Atopobiaceae - uncultured and Ruminococcaceae Subdoligranulum associated with higher symptom severity. These significant signatures in the gut microbiota composition in patients with KS suggest that microbiota differences are part of the KS phenotype.
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Affiliation(s)
- Mirjam Bloemendaal
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
- Department of Psychiatry, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Priscilla Vlaming
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Anneke de Boer
- Karakter Child and Adolescent Psychiatry University Centre, Nijmegen, The Netherlands
| | - Karlijn Vermeulen-Kalk
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
- Karakter Child and Adolescent Psychiatry University Centre, Nijmegen, The Netherlands
| | - Arianne Bouman
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Tjitske Kleefstra
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
- Department of Psychiatry, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
- Centre of Excellence for Neuropsychiatry, Vincent van Gogh Institute for Psychiatry, Venray, The Netherlands
| | - Alejandro Arias Vasquez
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
- Department of Psychiatry, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
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Li XM, Shi X, Yao Y, Shen YC, Wu XL, Cai T, Liang LX, Wang F. Effects of Stool Sample Preservation Methods on Gut Microbiota Biodiversity: New Original Data and Systematic Review with Meta-Analysis. Microbiol Spectr 2023; 11:e0429722. [PMID: 37093040 PMCID: PMC10269478 DOI: 10.1128/spectrum.04297-22] [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: 10/21/2022] [Accepted: 03/16/2023] [Indexed: 04/25/2023] Open
Abstract
Here, we aimed to compare the effects of different preservation methods on outcomes of fecal microbiota. We evaluated the effects of different preservation methods using stool sample preservation experiments for up to 1 year. The stool samples from feces of healthy volunteers were grouped based on whether absolute ethanol was added and whether they were hypothermically preserved. Besides, we performed a systematic review to combine current fecal microbiota preservation evidence. We found that Proteobacteria changed significantly and Veillonellaceae decreased significantly in the 12th month in the room temperature + absolute ethanol group. The four cryopreservation groups have more similarities with fresh sample in the 12 months; however, different cryopreservation methods have different effects on several phyla, families, and genera. A systematic review showed that the Shannon diversity and Simpson index of samples stored in RNAlater for 1 month were not statistically significant compared with those stored immediately at -80°C (P = 0.220 and P = 0.123, respectively). The -80°C refrigerator and liquid nitrogen cryopreservation with 10% glycerine can both maintain stable microbiota of stool samples for long-term preservation. The addition of absolute ethanol to cryopreserved samples had no significant difference in the effect of preserving fecal microbial characteristics. Our study provides empirical insights into preservation details for future studies of the long-term preservation of fecal microbiota. Systematic review and meta-analysis found that the gut microbiota structure, composition, and diversity of samples preserved by storage methods, such as preservation solution, are relatively stable, which were suitable for short-term storage at room temperature. IMPORTANCE The study of gut bacteria has become increasingly popular, and fecal sample preservation methods and times need to be standardized. Here, we detail a 12-month study of fecal sample preservation, and our study provides an empirical reference about experimental details for long-term high-quality storage of fecal samples in the field of gut microbiology research. The results showed that the combination of -80°C/liquid nitrogen deep cryopreservation and 10% glycerol was the most effective method for the preservation of stool samples, which is suitable for long-term storage for at least 12 months. The addition of anhydrous ethanol to the deep cryopreserved samples did not make a significant difference in the preservation of fecal microbiological characteristics. Combined with the results of systematic reviews and meta-analyses, we believe that, when researchers preserve fecal specimens, it is essential to select the proper preservation method and time period in accordance with the goal of the study.
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Affiliation(s)
- Xin-meng Li
- Department of Gastroenterology, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Non-resolving Inflammation and Cancer, Central South University, Changsha, Hunan, China
| | - Xiao Shi
- Department of Dermatology, Anhui Provincial Hospital, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, China
| | - Yao Yao
- Department of Gastroenterology, Zhangjiajie People’s Hospital, Zhangjiajie, Hunan, China
| | - Yi-cun Shen
- Department of Gastroenterology, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Non-resolving Inflammation and Cancer, Central South University, Changsha, Hunan, China
| | - Xiang-ling Wu
- Department of Gastroenterology, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Non-resolving Inflammation and Cancer, Central South University, Changsha, Hunan, China
| | - Ting Cai
- Department of Gastroenterology, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Non-resolving Inflammation and Cancer, Central South University, Changsha, Hunan, China
| | - Lun-xi Liang
- Department of Gastroenterology, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Non-resolving Inflammation and Cancer, Central South University, Changsha, Hunan, China
- Department of Gastroenterology, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, China
| | - Fen Wang
- Department of Gastroenterology, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Non-resolving Inflammation and Cancer, Central South University, Changsha, Hunan, China
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Combrink L, Humphreys IR, Washburn Q, Arnold HK, Stagaman K, Kasschau KD, Jolles AE, Beechler BR, Sharpton TJ. Best practice for wildlife gut microbiome research: A comprehensive review of methodology for 16S rRNA gene investigations. Front Microbiol 2023; 14:1092216. [PMID: 36910202 PMCID: PMC9992432 DOI: 10.3389/fmicb.2023.1092216] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 01/18/2023] [Indexed: 02/24/2023] Open
Abstract
Extensive research in well-studied animal models underscores the importance of commensal gastrointestinal (gut) microbes to animal physiology. Gut microbes have been shown to impact dietary digestion, mediate infection, and even modify behavior and cognition. Given the large physiological and pathophysiological contribution microbes provide their host, it is reasonable to assume that the vertebrate gut microbiome may also impact the fitness, health and ecology of wildlife. In accordance with this expectation, an increasing number of investigations have considered the role of the gut microbiome in wildlife ecology, health, and conservation. To help promote the development of this nascent field, we need to dissolve the technical barriers prohibitive to performing wildlife microbiome research. The present review discusses the 16S rRNA gene microbiome research landscape, clarifying best practices in microbiome data generation and analysis, with particular emphasis on unique situations that arise during wildlife investigations. Special consideration is given to topics relevant for microbiome wildlife research from sample collection to molecular techniques for data generation, to data analysis strategies. Our hope is that this article not only calls for greater integration of microbiome analyses into wildlife ecology and health studies but provides researchers with the technical framework needed to successfully conduct such investigations.
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Affiliation(s)
- Leigh Combrink
- Department of Microbiology, Oregon State University, Corvallis, OR, United States.,Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States.,School of Natural Resources and the Environment, University of Arizona, Tucson, AZ, United States
| | - Ian R Humphreys
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Quinn Washburn
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Holly K Arnold
- Department of Microbiology, Oregon State University, Corvallis, OR, United States.,Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States
| | - Keaton Stagaman
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Kristin D Kasschau
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Anna E Jolles
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States.,Department of Integrative Biology, Oregon State University, Corvallis, OR, United States
| | - Brianna R Beechler
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States
| | - Thomas J Sharpton
- Department of Microbiology, Oregon State University, Corvallis, OR, United States.,Department of Statistics, Oregon State University, Corvallis, OR, United States
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Su W, Du Y, Lian F, Wu H, Zhang X, Yang W, Duan Y, Pan Y, Liu W, Wu A, Zhao B, Wu C, Wu S. Standards for Collection, Preservation, and Transportation of Fecal Samples in TCM Clinical Trials. Front Cell Infect Microbiol 2022; 12:783682. [PMID: 35521221 PMCID: PMC9065286 DOI: 10.3389/fcimb.2022.783682] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 03/28/2022] [Indexed: 12/21/2022] Open
Abstract
Background Unlike chemical drugs with a single or a few kinds of active compounds, traditional Chinese medicines (TCMs)uses herbal formulas composed of numerous kinds of chemical constituents. Therefore, TCM clinical trials require unique and stricter standards for collecting, preserving, and transporting fecal samples than those used for chemical drugs. Unfortunately, there are no special standards for processing fecal samples in TCM clinical trials. Methods We invited interdisciplinary experts within TCM clinical trials and gut microbiome research to help formulate this standard. After more than a year’s in-depth discussion and amendments, we achieved a standard via expert interviews, literature research, questionnaire surveys, and public opinion solicitation. This standard has been reviewed and approved by the Standards Office of China of the Association of Chinese medicine. Results We established a sample information processing method prior to TCM clinical sample collection, which is adapted to the unique features of TCM. The method formulates detailed processing requirements for TCM information in addition to the factors that may disturb the gut microbiome. We also constructed a set of methods for collecting, preserving, and transporting fecal samples that meet the characteristics of TCM. These methods formulate detailed operating specifications on the collection approaches, storage conditions, transportation requirements, and management of fecal samples. Conclusions This standard guides the information processing prior to sample collection and the standard operating procedures for the collection, preservation, and transportation of fecal samples in TCM clinical trials, which also can be used as a reference by clinicians and researchers in modern medicines.
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Affiliation(s)
- Wenquan Su
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Yawei Du
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Fengmei Lian
- Department of Endocrinology, Guang’anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Hui Wu
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xinrong Zhang
- Fangshan Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Wenli Yang
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Yunfeng Duan
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yuanming Pan
- The 7th Medical Center, Chinese People’s Liberation Army General Hospital, Beijing, China
| | - Weijng Liu
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Aiming Wu
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Bowen Zhao
- Beijing QuantiHealth Technology Co, Ltd, Beijing, China
| | - Chongming Wu
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- *Correspondence: Shengxian Wu, ; Chongming Wu,
| | - Shengxian Wu
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
- *Correspondence: Shengxian Wu, ; Chongming Wu,
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Todberg T, Egeberg A, Zachariae C, Sørensen N, Pedersen O, Skov L. Patients with psoriasis have a dysbiotic taxonomic and functional gut microbiota. Br J Dermatol 2022; 187:89-98. [PMID: 35289939 DOI: 10.1111/bjd.21245] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 03/09/2022] [Accepted: 03/11/2022] [Indexed: 11/27/2022]
Abstract
BACKGROUND Accumulating evidence supports the findings of an altered gut microbiota in patients with autoimmune disease, however existing literature on the role of the gut microbiota in patients with psoriasis have demonstrated conflicting results and have mainly been based on 16s rRNA gene sequencing analysis OBJECTIVES: To examine whether the gut microbiota of patients with psoriasis was altered in composition and functional potentials compared with healthy controls and as a second approach compared with healthy cohabitant partners; further, to investigate relationships to disease severity and seasonal impact on the gut microbiota. METHODS In a case-control study, 126 faecal samples were collected from a sample of 53 systemically untreated patients with plaque psoriasis; 52 age, sex, and BMI matched healthy controls; and 21 cohabitant partners. A subpopulation of 18 patients with psoriasis and 19 healthy controls continued in a longitudinal study, where 4-6 faecal samples were collected over 9-12 months. The gut microbiota was characterized using shotgun metagenomic sequencing analysis. RESULTS A significantly lower richness (p=0.007) and difference in community composition (p=0.01) of metagenomic species (MGS) was seen in patients with psoriasis compared with healthy controls, and patients with psoriasis had a lower microbial diversity than their partners (p=0.04). Additionally, the functional richness was decreased in patients with psoriasis compared with healthy controls (p=0.01) and partners (p=0.05). Increased disease severity was correlated with alterations in taxonomy and function, with a slight tendency towards a lower richness of MGS, albeit not significant (p=0.08). The seasonal analysis showed no shifts in community composition in healthy controls or in patients with psoriasis. CONCLUSIONS The findings of a different gut microbiota in composition and functional potentials between patients with psoriasis and healthy controls support a linkage between the gut microbiota and psoriasis. These findings need to be validated in larger studies and a potential causal relation between the gut microbiota and psoriasis still needs to be shown.
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Affiliation(s)
- Tanja Todberg
- Department of Dermatology and Allergy, Herlev and Gentofte Hospital, University of Copenhagen, DK 2900, Hellerup, Denmark.,Copenhagen Research Group for Inflammatory Skin (CORGIS), Hellerup, Denmark
| | - Alexander Egeberg
- Department of Dermatology, Bispebjerg Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Claus Zachariae
- Department of Dermatology and Allergy, Herlev and Gentofte Hospital, University of Copenhagen, DK 2900, Hellerup, Denmark.,Copenhagen Research Group for Inflammatory Skin (CORGIS), Hellerup, Denmark
| | | | - Oluf Pedersen
- Novo Nordisk Foundation Centre for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lone Skov
- Department of Dermatology and Allergy, Herlev and Gentofte Hospital, University of Copenhagen, DK 2900, Hellerup, Denmark.,Copenhagen Research Group for Inflammatory Skin (CORGIS), Hellerup, Denmark
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Correction: Szopinska-Tokov et al. Investigating the Gut Microbiota Composition of Individuals with Attention-Deficit/Hyperactivity Disorder and Association with Symptoms. Microorganisms 2020, 8, 406. Microorganisms 2021; 9:microorganisms9071358. [PMID: 34201905 PMCID: PMC8306196 DOI: 10.3390/microorganisms9071358] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 05/26/2021] [Indexed: 12/12/2022] Open
Abstract
The authors wish to make the following correction to this paper [...].
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Bloemendaal M, Szopinska-Tokov J, Belzer C, Boverhoff D, Papalini S, Michels F, van Hemert S, Arias Vasquez A, Aarts E. Probiotics-induced changes in gut microbial composition and its effects on cognitive performance after stress: exploratory analyses. Transl Psychiatry 2021; 11:300. [PMID: 34016947 PMCID: PMC8137885 DOI: 10.1038/s41398-021-01404-9] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 03/24/2021] [Accepted: 04/21/2021] [Indexed: 02/04/2023] Open
Abstract
Stress negatively affects cognitive performance. Probiotics remediate somatic and behavioral stress responses, hypothetically by acting on the gut microbiota. Here, in exploratory analyses, we assessed gut microbial alterations after 28-days supplementation of multi-strain probiotics (EcologicBarrier consisting of Lactobacilli, Lactococci, and Bifidobacteria in healthy, female subjects (probiotics group n = 27, placebo group n = 29). In an identical pre-session and post-session, subjects performed a working memory task before and after an acute stress intervention. Global gut microbial beta diversity changed over time, but we were not able to detect differences between intervention groups. At the taxonomic level, Time by Intervention interactions were not significant after multiple comparison correction; the relative abundance of eight genera in the probiotics group was higher (uncorrected) relative to the placebo group: Butyricimonas, Parabacteroides, Alistipes, Christensenellaceae_R-7_group, Family_XIII_AD3011_group, Ruminococcaceae_UCG-003, Ruminococcaceae_UCG-005, and Ruminococcaceae_UCG-010. In a second analysis step, association analyses were done only within this selection of microbial genera, revealing the probiotics-induced change in genus Ruminococcaceae_UCG-003 was significantly associated with probiotics' effect on stress-induced working memory changes (rspearman(27) = 0.565; pFDR = 0.014) in the probiotics group only and independent of potential confounders (i.e., age, BMI, and baseline dietary fiber intake). That is subjects with a higher increase in Ruminococcaceae_UCG-003 abundance after probiotics were also more protected from negative effects of stress on working memory after probiotic supplementation. The bacterial taxa showing an increase in relative abundance in the probiotics group are plant fiber degrading bacteria and produce short-chain fatty acids that are known for their beneficial effect on gut and brain health, e.g., maintaining intestinal-barrier and blood-brain-barrier integrity. This study shows that gut microbial alterations, modulated through probiotics use, are related to improved cognitive performance in acute stress circumstances.
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Affiliation(s)
- Mirjam Bloemendaal
- Departments of Psychiatry and Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.
| | - Joanna Szopinska-Tokov
- Departments of Psychiatry and Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - David Boverhoff
- Donders Institute for Brain Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University, Nijmegen, the Netherlands
| | - Silvia Papalini
- Donders Institute for Brain Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University, Nijmegen, the Netherlands
- Laboratory for Biological Psychology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Franziska Michels
- Donders Institute for Brain Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University, Nijmegen, the Netherlands
| | | | - Alejandro Arias Vasquez
- Departments of Psychiatry and Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Esther Aarts
- Donders Institute for Brain Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University, Nijmegen, the Netherlands
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Kohn N, Szopinska-Tokov J, Llera Arenas A, Beckmann C, Arias-Vasquez A, Aarts E. Multivariate associative patterns between the gut microbiota and large-scale brain network connectivity. Gut Microbes 2021; 13:2006586. [PMID: 34856861 PMCID: PMC8726725 DOI: 10.1080/19490976.2021.2006586] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 10/21/2021] [Accepted: 11/02/2021] [Indexed: 02/04/2023] Open
Abstract
Research on the gut-brain axis has accelerated substantially over the course of the last years. Many reviews have outlined the important implications of understanding the relation of the gut microbiota with human brain function and behavior. One substantial drawback in integrating gut microbiome and brain data is the lack of integrative multivariate approaches that enable capturing variance in both modalities simultaneously. To address this issue, we applied a linked independent component analysis (LICA) to microbiota and brain connectivity data.We analyzed data from 58 healthy females (mean age = 21.5 years). Magnetic Resonance Imaging data were acquired using resting state functional imaging data. The assessment of gut microbial composition from feces was based on sequencing of the V4 16S rRNA gene region. We used the LICA model to simultaneously factorize the subjects' large-scale brain networks and microbiome relative abundance data into 10 independent components of spatial and abundance variation.LICA decomposition resulted in four components with non-marginal contribution of the microbiota data. The default mode network featured strongly in three components, whereas the two-lateralized fronto-parietal attention networks contributed to one component. The executive-control (with the default mode) network was associated to another component. We found that the abundance of Prevotella genus was associated with the strength of expression of all networks, whereas Bifidobacterium was associated with the default mode and frontoparietal-attention networks.We provide the first exploratory evidence for multivariate associative patterns between the gut microbiota and brain network connectivity in healthy humans considering the complexity of both systems.
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Affiliation(s)
- N. Kohn
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Centre, Nijmegen, The Netherlands
- Centre for Cognitive Neuroimaging, Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - J. Szopinska-Tokov
- Department of Psychiatry, Donders Institute for Brain, Nijmegen, The Netherlands
- Department of Human Genetics, Donders Institute for Brain, Nijmegen, The Netherlands
| | - A. Llera Arenas
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Centre, Nijmegen, The Netherlands
- Centre for Cognitive Neuroimaging, Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - C.F. Beckmann
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Centre, Nijmegen, The Netherlands
- Centre for Cognitive Neuroimaging, Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - A. Arias-Vasquez
- Department of Psychiatry, Donders Institute for Brain, Nijmegen, The Netherlands
- Department of Human Genetics, Donders Institute for Brain, Nijmegen, The Netherlands
| | - E Aarts
- Centre for Cognitive Neuroimaging, Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
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Aslam H, Marx W, Rocks T, Loughman A, Chandrasekaran V, Ruusunen A, Dawson SL, West M, Mullarkey E, Pasco JA, Jacka FN. The effects of dairy and dairy derivatives on the gut microbiota: a systematic literature review. Gut Microbes 2020; 12:1799533. [PMID: 32835617 PMCID: PMC7524346 DOI: 10.1080/19490976.2020.1799533] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The effects of dairy and dairy-derived products on the human gut microbiota remains understudied. A systematic literature search was conducted using Medline, CINAHL, Embase, Scopus, and PubMed databases with the aim of collating evidence on the intakes of all types of dairy and their effects on the gut microbiota in adults. Risk of bias was assessed using the Cochrane risk-of-bias tool.The search resulted in 6,592 studies, of which eight randomized controlled trials (RCTs) met pre-determined eligibility criteria for inclusion, consisting of a total of 468 participants. Seven studies assessed the effect of type of dairy (milk, yogurt, and kefir) and dairy derivatives (whey and casein) on the gut microbiota, and one study assessed the effect of the quantity of dairy (high dairy vs low dairy). Three studies showed that dairy types consumed (milk, yogurt, and kefir) increased the abundance of beneficial genera Lactobacillus and Bifidobacterium. One study showed that yogurt reduced the abundance of Bacteroides fragilis, a pathogenic strain. Whey and casein isolates and the quantity of dairy consumed did not prompt changes to the gut microbiota composition. All but one study reported no changes to bacterial diversity in response to dairy interventions and one study reported reduction in bacterial diversity in response to milk intake.In conclusion, the results of this review suggest that dairy products such as milk, yogurt, and kefir may modulate the gut microbiota composition in favor to the host. However, the broader health implications of these findings remain unclear and warrant further studies.
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Affiliation(s)
- Hajara Aslam
- IMPACT - The Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Barwon Health, Deakin University, Geelong, Victoria, Australia,CONTACT Hajara Aslam IMPACT – the Institute for Mental and Physical Health and Clinical Translation, Food & Mood Centre, School of Medicine, Barwon Health, Deakin University, Geelong, Victoria3220, Australia
| | - Wolfgang Marx
- IMPACT - The Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Barwon Health, Deakin University, Geelong, Victoria, Australia
| | - Tetyana Rocks
- IMPACT - The Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Barwon Health, Deakin University, Geelong, Victoria, Australia
| | - Amy Loughman
- IMPACT - The Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Barwon Health, Deakin University, Geelong, Victoria, Australia
| | - Vinoomika Chandrasekaran
- IMPACT - The Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Barwon Health, Deakin University, Geelong, Victoria, Australia
| | - Anu Ruusunen
- IMPACT - The Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Barwon Health, Deakin University, Geelong, Victoria, Australia,Department of Psychiatry, Kuopio University Hospital, Kuopio, Finland,Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Samantha L. Dawson
- IMPACT - The Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Barwon Health, Deakin University, Geelong, Victoria, Australia,Environmental & Genetic Epidemiology Research, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, Australia
| | - Madeline West
- IMPACT - The Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Barwon Health, Deakin University, Geelong, Victoria, Australia
| | - Eva Mullarkey
- Psychology Department, Wellesley College, Wellesley, MA, USA
| | - Julie A. Pasco
- IMPACT - The Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Barwon Health, Deakin University, Geelong, Victoria, Australia,Department of Medicine – Western Health, Melbourne Medical School, The University of Melbourne, St Albans, Victoria, Australia,Department of Epidemiology and Preventive Medicine, Monash University, Prahran, Victoria, Australia,Barwon Health, Geelong, Victoria, Australia
| | - Felice N. Jacka
- IMPACT - The Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Barwon Health, Deakin University, Geelong, Victoria, Australia,Department of Psychiatry, University of Melbourne, Victoria, Australia,Centre for Adolescent Health, Murdoch Children’s Research Institute, Victoria, Australia
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10
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Yang L, Hou K, Zhang B, Ouyang C, Lin A, Xu S, Ke D, Fang L, Chen Q, Wu J, Yan C, Lian Y, Jiang T, He J, Wang H, Fu Y, Xiao C, Chen Z. Preservation of the fecal samples at ambient temperature for microbiota analysis with a cost-effective and reliable stabilizer EffcGut. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 741:140423. [PMID: 32615432 DOI: 10.1016/j.scitotenv.2020.140423] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/31/2020] [Accepted: 06/20/2020] [Indexed: 02/05/2023]
Abstract
With the increasing researches on the role of gut microbiota in human health and disease, appropriate storage method of fecal samples at ambient temperature would conveniently guarantee the precise and reliable microbiota results. Nevertheless, less choice of stabilizer that is cost-efficient and feasible to be used in longer preservation period obstructed the large-scale metagenomics studies. Here, we evaluated the efficacy of a guanidine isothiocyanate-based reagent method EffcGut and compared it with the other already used storage method by means of 16S rRNA gene sequencing technology. We found that guanidine isothiocyanate-based reagent method at ambient temperature was not inferior to OMNIgene·GUT OM-200 and it could retain the similar bacterial community as that of -80 °C within 24 weeks. Furthermore, bacterial diversity and community structure difference were compared among different sample fraction (supernatant, suspension and precipitate) preserved in EffcGut and -80 °C. We found that supernatant under the preservation of EffcGut retained the similar community structure and composition as that of the low temperature preservation method.
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Affiliation(s)
- Luxi Yang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, School of Life Sciences, Xiamen University, Xiamen, China; Institute for Microbial Ecology, School of Medicine, Xiamen University, Xiamen, China
| | - Kaijian Hou
- Department of Endocrine and Metabolic Diseases, Longhu Hospital, the First Affiliated Hospital of Shantou University Medical College, China
| | - Bangzhou Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, School of Life Sciences, Xiamen University, Xiamen, China; Institute for Microbial Ecology, School of Medicine, Xiamen University, Xiamen, China
| | - Cong Ouyang
- Xiamen Treatgut Biotechnology Co., Ltd., Xiamen, China
| | - Aiqiang Lin
- Xiamen Treatgut Biotechnology Co., Ltd., Xiamen, China
| | - Shuangbin Xu
- Xiamen Treatgut Biotechnology Co., Ltd., Xiamen, China
| | - Dongxian Ke
- Xiamen Treatgut Biotechnology Co., Ltd., Xiamen, China
| | - Lujing Fang
- Xiamen Treatgut Biotechnology Co., Ltd., Xiamen, China
| | - Qiongyun Chen
- Institute for Microbial Ecology, School of Medicine, Xiamen University, Xiamen, China
| | - Jingtong Wu
- Institute for Microbial Ecology, School of Medicine, Xiamen University, Xiamen, China
| | - Changsheng Yan
- Institute for Microbial Ecology, School of Medicine, Xiamen University, Xiamen, China
| | - Yifan Lian
- Institute for Microbial Ecology, School of Medicine, Xiamen University, Xiamen, China
| | - Tao Jiang
- Xiamen Treatgut Biotechnology Co., Ltd., Xiamen, China
| | - Jianquan He
- Department of Rehabilitation, Zhongshan Hospital, Xiamen University, China
| | - Han Wang
- Xiamen Treatgut Biotechnology Co., Ltd., Xiamen, China
| | - Yousi Fu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, School of Life Sciences, Xiamen University, Xiamen, China
| | | | - Zhangran Chen
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, School of Life Sciences, Xiamen University, Xiamen, China; Institute for Microbial Ecology, School of Medicine, Xiamen University, Xiamen, China.
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11
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Manor O, Dai CL, Kornilov SA, Smith B, Price ND, Lovejoy JC, Gibbons SM, Magis AT. Health and disease markers correlate with gut microbiome composition across thousands of people. Nat Commun 2020; 11:5206. [PMID: 33060586 PMCID: PMC7562722 DOI: 10.1038/s41467-020-18871-1] [Citation(s) in RCA: 356] [Impact Index Per Article: 89.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 09/16/2020] [Indexed: 12/14/2022] Open
Abstract
Variation in the human gut microbiome can reflect host lifestyle and behaviors and influence disease biomarker levels in the blood. Understanding the relationships between gut microbes and host phenotypes are critical for understanding wellness and disease. Here, we examine associations between the gut microbiota and ~150 host phenotypic features across ~3,400 individuals. We identify major axes of taxonomic variance in the gut and a putative diversity maximum along the Firmicutes-to-Bacteroidetes axis. Our analyses reveal both known and unknown associations between microbiome composition and host clinical markers and lifestyle factors, including host-microbe associations that are composition-specific. These results suggest potential opportunities for targeted interventions that alter the composition of the microbiome to improve host health. By uncovering the interrelationships between host diet and lifestyle factors, clinical blood markers, and the human gut microbiome at the population-scale, our results serve as a roadmap for future studies on host-microbe interactions and interventions.
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Affiliation(s)
- Ohad Manor
- Century Therapeutics, Seattle, WA, 98102, USA.
| | | | | | - Brett Smith
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | - Nathan D Price
- Institute for Systems Biology, Seattle, WA, 98109, USA
- Department of Bioengineering, University of Washington, Seattle, WA, 98105, USA
| | | | - Sean M Gibbons
- Institute for Systems Biology, Seattle, WA, 98109, USA
- Department of Bioengineering, University of Washington, Seattle, WA, 98105, USA
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12
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Kurian SM, Gordon S, Barrick B, Dadlani MN, Fanelli B, Cornell JB, Head SR, Marsh CL, Case J. Feasibility and Comparison Study of Fecal Sample Collection Methods in Healthy Volunteers and Solid Organ Transplant Recipients Using 16S rRNA and Metagenomics Approaches. Biopreserv Biobank 2020; 18:425-440. [PMID: 32833508 DOI: 10.1089/bio.2020.0032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The human microbiome encompasses a variety of microorganisms that change dynamically and are in close contact with the body. The microbiome influences health and homeostasis, as well as the immune system, and any significant change in this equilibrium (dysbiosis) triggers both acute and chronic health conditions. Microbiome research has surged, in part, due to advanced sequencing technologies enabling rapid, accurate, and cost-effective identification of the microbiome. A major prerequisite for stool sample collection to study the gut microbiome in longitudinal prospective studies requires standardized protocols that can be easily replicated. However, there are still significant bottlenecks to stool specimen collection that contribute to low patient retention rates in microbiome studies. These barriers are further exacerbated in solid organ transplant recipients where diarrhea is estimated to occur in up to half the patient population. We sought to test two relatively easy sample collection methods (fecal swab and wipes) and compare them to the more cumbersome "gold" standard collection method (scoop) using two different sequencing technologies (16S ribosomal RNA sequencing and shotgun metagenomics). Our comparison of the collection methods shows that both the swabs and the wipes are comparable to the scoop method in terms of bacterial abundance and diversity. The swabs, however, were closer in representation to the scoop and were easier to collect and process compared to the wipes. Potential contamination of the swab and the wipe samples by abundant skin commensals was low in our analysis. Comparison of the two sequencing technologies showed that they were complementary, and that 16S sequencing provided enough coverage to detect and differentiate between bacterial species identified in the collected samples. Our pilot study demonstrates that alternative collection methods for stool sampling are a viable option in clinical applications, such as organ transplant studies. The use of these methods may result in better patient retention recruitment rates in serial microbiome studies.
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Affiliation(s)
- Sunil M Kurian
- Scripps Clinic Bio-Repository and Bio-Informatics Core, La Jolla, California, USA.,Scripps Center for Organ Transplantation, La Jolla, California, USA
| | - Skyler Gordon
- Genomics Core, Scripps Research, La Jolla, California, USA
| | - Bethany Barrick
- Scripps Clinic Bio-Repository and Bio-Informatics Core, La Jolla, California, USA.,Scripps Center for Organ Transplantation, La Jolla, California, USA
| | | | | | | | - Steven R Head
- Genomics Core, Scripps Research, La Jolla, California, USA
| | - Christopher L Marsh
- Scripps Clinic Bio-Repository and Bio-Informatics Core, La Jolla, California, USA.,Scripps Center for Organ Transplantation, La Jolla, California, USA
| | - Jamie Case
- Scripps Clinic Bio-Repository and Bio-Informatics Core, La Jolla, California, USA.,Scripps Center for Organ Transplantation, La Jolla, California, USA
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13
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Cunningham JL, Bramstång L, Singh A, Jayarathna S, Rasmusson AJ, Moazzami A, Müller B. Impact of time and temperature on gut microbiota and SCFA composition in stool samples. PLoS One 2020; 15:e0236944. [PMID: 32745090 PMCID: PMC7398539 DOI: 10.1371/journal.pone.0236944] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 07/16/2020] [Indexed: 01/08/2023] Open
Abstract
Gut dysbiosis has been implicated in the pathophysiology of a growing number of non-communicable diseases. High through-put sequencing technologies and short chain fatty acid (SCFA) profiling enables surveying of the composition and function of the gut microbiota and provide key insights into host-microbiome interactions. However, a methodological problem with analyzing stool samples is that samples are treated and stored differently prior to submission for analysis potentially influencing the composition of the microbiota and its metabolites. In the present study, we simulated the sample acquisition of a large-scale study, in which stool samples were stored for up to two days in the fridge or at room temperature before being handed over to the hospital. To assess the influence of time and temperature on the microbial community and on SCFA composition in a controlled experimental setting, the stool samples of 10 individuals were exposed to room and fridge temperatures for 24 and 48 hours, respectively, and analyzed using 16S rRNA gene amplicon sequencing, qPCR and nuclear magnetic resonance spectroscopy. To best of our knowledge, this is the first study to investigate the influence of storage time and temperature on the absolute abundance of methanogens, and of Lactobacillus reuteri. The results indicate that values obtained for methanogens, L. reuteri and total bacteria are still representative even after storage for up to 48 hours at RT (20°C) or 4°C. The overall microbial composition and structure appeared to be influenced more by laboratory errors introduced during sample processing than by the actual effects of temperature and time. Although microbial activity was demonstrated by elevated SCFA at both 4°C and RT, SCFAs ratios were more stable over the different conditions and may be considered as long as samples are come from similar storage conditions.
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Affiliation(s)
- Janet L. Cunningham
- Department of Neurosciences, Psychiatry, Uppsala University, Uppsala, Sweden
| | - Ludvig Bramstång
- Department of Neurosciences, Psychiatry, Uppsala University, Uppsala, Sweden
| | - Abhijeet Singh
- Department of Molecular Sciences, BioCentrum, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Shishanthi Jayarathna
- Department of Molecular Sciences, BioCentrum, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Annica J. Rasmusson
- Department of Neurosciences, Psychiatry, Uppsala University, Uppsala, Sweden
| | - Ali Moazzami
- Department of Molecular Sciences, BioCentrum, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Bettina Müller
- Department of Molecular Sciences, BioCentrum, Swedish University of Agricultural Sciences, Uppsala, Sweden
- * E-mail:
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14
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Szopinska-Tokov J, Dam S, Naaijen J, Konstanti P, Rommelse N, Belzer C, Buitelaar J, Franke B, Aarts E, Arias Vasquez A. Investigating the Gut Microbiota Composition of Individuals with Attention-Deficit/Hyperactivity Disorder and Association with Symptoms. Microorganisms 2020; 8:microorganisms8030406. [PMID: 32183143 PMCID: PMC7143990 DOI: 10.3390/microorganisms8030406] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 03/06/2020] [Accepted: 03/11/2020] [Indexed: 12/16/2022] Open
Abstract
Attention-deficit/hyperactivity disorder (ADHD) is a common neurodevelopmental disorder. Given the growing evidence of gut microbiota being involved in psychiatric (including neurodevelopmental) disorders, we aimed to identify differences in gut microbiota composition between participants with ADHD and controls and to investigate the role of the microbiota in inattention and hyperactivity/impulsivity. Fecal samples were collected from 107 participants (NADHD = 42; Ncontrols = 50; NsubthreholdADHD = 15; range age: 13-29 years). The relative quantification of bacterial taxa was done using 16S ribosomal RNA gene amplicon sequencing. Beta-diversity revealed significant differences in bacterial composition between participants with ADHD and healthy controls, which was also significant for inattention, but showing a trend in case of hyperactivity/impulsivity only. Ten genera showed nominal differences (p < 0.05) between both groups, of which seven genera were tested for their association with ADHD symptom scores (adjusting for age, sex, body mass index, time delay between feces collection and symptoms assessment, medication use, and family relatedness). Our results show that variation of a genus from the Ruminococcaceae family (Ruminococcaceae_UCG_004) is associated (after multiple testing correction) with inattention symptoms and support the potential role of gut microbiota in ADHD pathophysiology.
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Affiliation(s)
- Joanna Szopinska-Tokov
- Department of Psychiatry, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6525 GA Nijmegen, The Netherlands; (J.S.-T.); (N.R.); (B.F.)
| | - Sarita Dam
- Department of Cognitive Neuroscience, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6525 EN Nijmegen, The Netherlands; (S.D.); (J.N.); (J.B.)
| | - Jilly Naaijen
- Department of Cognitive Neuroscience, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6525 EN Nijmegen, The Netherlands; (S.D.); (J.N.); (J.B.)
| | - Prokopis Konstanti
- Laboratory of Microbiology, Wageningen University, 6708 WE Wageningen, The Netherlands; (P.K.); (C.B.)
| | - Nanda Rommelse
- Department of Psychiatry, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6525 GA Nijmegen, The Netherlands; (J.S.-T.); (N.R.); (B.F.)
- Karakter Child and Adolescent Psychiatry University Center, 6525 GC Nijmegen, The Netherlands
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University, 6708 WE Wageningen, The Netherlands; (P.K.); (C.B.)
| | - Jan Buitelaar
- Department of Cognitive Neuroscience, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6525 EN Nijmegen, The Netherlands; (S.D.); (J.N.); (J.B.)
- Karakter Child and Adolescent Psychiatry University Center, 6525 GC Nijmegen, The Netherlands
| | - Barbara Franke
- Department of Psychiatry, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6525 GA Nijmegen, The Netherlands; (J.S.-T.); (N.R.); (B.F.)
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6525 GA Nijmegen, The Netherlands
| | - Esther Aarts
- Centre for Cognitive Neuroimaging, Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6525 EN Nijmegen, The Netherlands;
| | - Alejandro Arias Vasquez
- Department of Psychiatry, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6525 GA Nijmegen, The Netherlands; (J.S.-T.); (N.R.); (B.F.)
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6525 GA Nijmegen, The Netherlands
- Correspondence: ; Tel.: +31-(0)-24-3613970
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15
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Watson EJ, Giles J, Scherer BL, Blatchford P. Human faecal collection methods demonstrate a bias in microbiome composition by cell wall structure. Sci Rep 2019; 9:16831. [PMID: 31727963 PMCID: PMC6856092 DOI: 10.1038/s41598-019-53183-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 10/24/2019] [Indexed: 12/14/2022] Open
Abstract
Clinical trial faecal collections present challenges through geographical spread and inexperienced participants. Collection techniques have been developed and tested to overcome these challenges, but previous studies investigating these techniques have demonstrated a highly variable capacity for sample preservation. Furthermore, these studies typically only examine either preservation of genetic content or metabolites, not both. This study investigated the Stool Nucleic Acid Collection and Preservation Tube (Norgen BioTek Corp) for the preservation of both microbial DNA and microbial organic acid metabolites in human faecal samples when compared to frozen samples. Twenty six healthy adult participants were instructed to collect a bowel movement, subsample into collection tubes and immediately transfer the remaining bulk to −20 °C storage. Resulting organic acid concentrations remained comparable across methods when the preservation tubes were used correctly. The 16S rRNA gene sequencing data revealed twenty significantly different bacterial genera between the two collection methods. Ten Gram-negative genera were more abundant in the collection tubes, and ten Gram-positive genera were more abundant in the fresh frozen samples. This study has illustrated that faecal collection methods bias the microbial community profile according to Gram status and this should be considered when designing studies that collect and store human faecal samples.
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Affiliation(s)
- Emma-Jane Watson
- CSIRO Health and Biosecurity, Gate 13 Kintore Avenue, Adelaide, South Australia, 5000, Australia
| | - Jennifer Giles
- CSIRO Health and Biosecurity, Gate 13 Kintore Avenue, Adelaide, South Australia, 5000, Australia
| | - Benjamin L Scherer
- CSIRO Health and Biosecurity, Gate 13 Kintore Avenue, Adelaide, South Australia, 5000, Australia
| | - Paul Blatchford
- CSIRO Health and Biosecurity, Gate 13 Kintore Avenue, Adelaide, South Australia, 5000, Australia. .,Zespri International Limited, 400 Maunganui Road, Mt Maunganui, 3149, New Zealand.
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16
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Ilett EE, Jørgensen M, Noguera-Julian M, Daugaard G, Murray DD, Helleberg M, Paredes R, Lundgren J, Sengeløv H, MacPherson C. Gut microbiome comparability of fresh-frozen versus stabilized-frozen samples from hospitalized patients using 16S rRNA gene and shotgun metagenomic sequencing. Sci Rep 2019; 9:13351. [PMID: 31527823 PMCID: PMC6746779 DOI: 10.1038/s41598-019-49956-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 09/04/2019] [Indexed: 02/06/2023] Open
Abstract
Collection of faecal samples for microbiome analysis in acutely sick patients is logistically difficult, particularly if immediate freezing is required (i.e. fresh-frozen, or FF sampling). Previous studies in healthy/non-hospitalized volunteers have shown that chemical stabilization (i.e. stabilized-frozen, or SF sampling) allows room-temperature storage with comparable results to FF samples. To test this in a hospital setting we compared FF and SF approaches across 17 patients undergoing haematopoietic stem cell transplantation (HSCT) using both 16S rRNA gene and shotgun metagenomic sequencing. A paired (same stool specimen) comparison of FF and SF samples was made, with an overall comparable level in relative taxonomic abundances between the two sampling techniques. Though shotgun metagenomic sequencing found significant differences for certain bacterial genera (P < 0.001), these were considered minor methodological effects. Within-sample diversity of either method was not significantly different (Shannon diversity P16SrRNA = 0.68 and Pshotgun = 0.89) and we could not reject the null hypothesis that between-sample variation in FF and SF were equivalent (P16SrRNA = 0.98 and Pshotgun = 1.0). This indicates that SF samples can be used to reliably study the microbiome in acutely sick patient populations, thus creating and enabling further outcomes-based metagenomic studies on similarly valuable cohorts.
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Affiliation(s)
- Emma E Ilett
- PERSIMUNE Centre of Excellence, Rigshospitalet, Blegdamsvej 9, DK-2100, Copenhagen Ø, Denmark.
| | - Mette Jørgensen
- PERSIMUNE Centre of Excellence, Rigshospitalet, Blegdamsvej 9, DK-2100, Copenhagen Ø, Denmark
| | - Marc Noguera-Julian
- Institut de Recerca de la SIDA - IrsiCaixa, Hospital Universitari Germans Trias i Pujol, Badalona, Catalonia, Spain
| | - Gedske Daugaard
- Department of Oncology, Rigshospitalet Blegdamsvej 9, DK-2100, Copenhagen Ø, Denmark
| | - Daniel D Murray
- PERSIMUNE Centre of Excellence, Rigshospitalet, Blegdamsvej 9, DK-2100, Copenhagen Ø, Denmark
| | - Marie Helleberg
- PERSIMUNE Centre of Excellence, Rigshospitalet, Blegdamsvej 9, DK-2100, Copenhagen Ø, Denmark
| | - Roger Paredes
- Institut de Recerca de la SIDA - IrsiCaixa, Hospital Universitari Germans Trias i Pujol, Badalona, Catalonia, Spain.,Infectious Diseases Service, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Jens Lundgren
- PERSIMUNE Centre of Excellence, Rigshospitalet, Blegdamsvej 9, DK-2100, Copenhagen Ø, Denmark
| | - Henrik Sengeløv
- Department of Haematology, Rigshospitalet, Blegdamsvej 9, DK-2100, Copenhagen Ø, Denmark
| | - Cameron MacPherson
- PERSIMUNE Centre of Excellence, Rigshospitalet, Blegdamsvej 9, DK-2100, Copenhagen Ø, Denmark
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