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Magnusson A, Jabbari Shiadeh SM, Ardalan M, Swolin-Eide D, Elfvin A. Gut microbiota differences in five-year-old children that were born preterm with a history of necrotizing enterocolitis: A pilot trial. iScience 2024; 27:110325. [PMID: 39055941 PMCID: PMC11269947 DOI: 10.1016/j.isci.2024.110325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 04/22/2024] [Accepted: 06/18/2024] [Indexed: 07/28/2024] Open
Abstract
The study explores the long-term effects of necrotizing enterocolitis (NEC) on gut microbiota in preterm infants by analyzing stool samples from 5-year-old children using shotgun metagenomic sequencing. It compares children with a history of NEC, treated surgically or medically, to preterm controls without NEC. Findings reveal persistent gut microbiota dysbiosis in NEC children, with reduced species diversity and evenness, especially in those treated surgically. The surgical NEC group had a lower Shannon index, indicating less microbial diversity. Significant differences in taxonomic profiles were observed, mainly influenced by surgical treatment. These results underscore the lasting impact of NEC and its treatment on gut microbiota, suggesting a need for strategies addressing long-term dysbiosis.
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Affiliation(s)
- Amanda Magnusson
- Department of Pediatrics, Institution of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Region Västra Götaland, Department of Pediatrics, The Queen Silvia Children’s Hospital, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Seyedeh Marziyeh Jabbari Shiadeh
- Department of Physiology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Medicine, Translational Neuropsychiatry Unit, Aarhus University, Aarhus, Denmark
| | - Maryam Ardalan
- Department of Physiology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Medicine, Translational Neuropsychiatry Unit, Aarhus University, Aarhus, Denmark
| | - Diana Swolin-Eide
- Department of Pediatrics, Institution of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Region Västra Götaland, Department of Pediatrics, The Queen Silvia Children’s Hospital, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Anders Elfvin
- Department of Pediatrics, Institution of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Region Västra Götaland, Department of Pediatrics, The Queen Silvia Children’s Hospital, Sahlgrenska University Hospital, Gothenburg, Sweden
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2
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Baraille M, Buttet M, Grimm P, Milojevic V, Julliand S, Julliand V. Changes of faecal bacterial communities and microbial fibrolytic activity in horses aged from 6 to 30 years old. PLoS One 2024; 19:e0303029. [PMID: 38829841 PMCID: PMC11146703 DOI: 10.1371/journal.pone.0303029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 04/17/2024] [Indexed: 06/05/2024] Open
Abstract
Horse owners and veterinarians report that from the age of 15, their horses can lose body condition and be more susceptible to diseases. Large intestinal microbiome changes may be involved. Indeed, microbiota is crucial for maintaining the condition and health of herbivores by converting fibres into nutrients. This study aimed to compare the faecal microbiome in horses aged from 6 to 30 years old (yo), living in the same environment and consuming the same diet, in order to assess whether the parameters changed linearly with age and whether there was a pivotal age category. Fifty horses were selected from the same environment and distributed across four age categories: 6-10 (n = 12), 11-15 (n = 11), 16-20 (n = 13), and 21-30 (n = 14) yo. All horses had no digestive problems, had teeth suitable for consuming their feed, and were up to date with their vaccination and deworming programmes. After three weeks of constant diet (ad libitum hay and 860 g of concentrate per day), one faecal sample per horse was collected on the same day. The bacterial communities' richness and intra-sample diversity were negatively correlated with age. There was a new distribution of non-beneficial and beneficial taxa, particularly in the 21-30 yo category. Although the faecal concentration of short-chain fatty acids remained stable, the acetate proportion was negatively correlated with age while it was the opposite for the proportions of butyrate, valerate, and iso-valerate. Additionally, the faecal pH was negatively correlated with age. Differences were more pronounced when comparing the 6-10 yo and 21-30 yo categories. The values of the parameters studied became more dispersed from the 16-20 yo category onwards, which appeared as a transitional moment, as it did not differ significantly from the younger and older categories for most of these parameters. Our data suggest that the microbiome changes with age. By highlighting the pivotal age of 16-20, this gives the opportunity to intervene before individuals reach extremes that could lead to pathological conditions.
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Affiliation(s)
- Marylou Baraille
- Institut Agro Dijon, Université de Bourgogne Franche–Comté, PAM UMR A 02.102, Dijon, France
- Lab To Field, Dijon, France
| | | | | | | | | | - Véronique Julliand
- Institut Agro Dijon, Université de Bourgogne Franche–Comté, PAM UMR A 02.102, Dijon, France
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3
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Chibuye M, Mende DR, Spijker R, Simuyandi M, Luchen CC, Bosomprah S, Chilengi R, Schultsz C, Harris VC. Systematic review of associations between gut microbiome composition and stunting in under-five children. NPJ Biofilms Microbiomes 2024; 10:46. [PMID: 38782939 PMCID: PMC11116508 DOI: 10.1038/s41522-024-00517-5] [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: 11/16/2023] [Accepted: 04/29/2024] [Indexed: 05/25/2024] Open
Abstract
Childhood stunting is associated with impaired cognitive development and increased risk of infections, morbidity, and mortality. The composition of the enteric microbiota may contribute to the pathogenesis of stunting. We systematically reviewed and synthesized data from studies using high-throughput genomic sequencing methods to characterize the gut microbiome in stunted versus non-stunted children under 5 years in LMICs. We included 14 studies from Asia, Africa, and South America. Most studies did not report any significant differences in the alpha diversity, while a significantly higher beta diversity was observed in stunted children in four out of seven studies that reported beta diversity. At the phylum level, inconsistent associations with stunting were observed for Bacillota, Pseudomonadota, and Bacteroidota phyla. No single genus was associated with stunted children across all 14 studies, and some associations were incongruent by specific genera. Nonetheless, stunting was associated with an abundance of pathobionts that could drive inflammation, such as Escherichia/Shigella and Campylobacter, and a reduction of butyrate producers, including Faecalibacterium, Megasphera, Blautia, and increased Ruminoccoccus. An abundance of taxa thought to originate in the oropharynx was also reported in duodenal and fecal samples of stunted children, while metabolic pathways, including purine and pyrimidine biosynthesis, vitamin B biosynthesis, and carbohydrate and amino acid degradation pathways, predicted linear growth. Current studies show that stunted children can have distinct microbial patterns compared to non-stunted children, which could contribute to the pathogenesis of stunting.
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Affiliation(s)
- Mwelwa Chibuye
- Department of Global Health, Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
- Research Division, Centre for Infectious Disease Research in Zambia, Lusaka, Zambia
- Amsterdam Institute of Infection and Immunity, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Daniel R Mende
- Amsterdam Institute of Infection and Immunity, Amsterdam University Medical Centers, Amsterdam, The Netherlands
- Department of Medical Microbiology and Infection Control, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Rene Spijker
- Department of Global Health, Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Michelo Simuyandi
- Research Division, Centre for Infectious Disease Research in Zambia, Lusaka, Zambia
| | - Chaluma C Luchen
- Department of Global Health, Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
- Research Division, Centre for Infectious Disease Research in Zambia, Lusaka, Zambia
| | - Samuel Bosomprah
- Research Division, Centre for Infectious Disease Research in Zambia, Lusaka, Zambia
- Department of Biostatistics, School of Public Health, University of Ghana, Legon, Accra, Ghana
| | - Roma Chilengi
- Research Division, Centre for Infectious Disease Research in Zambia, Lusaka, Zambia
- The Zambia National Public Health Institute (ZNPHI), Lusaka, Zambia
| | - Constance Schultsz
- Department of Global Health, Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute of Infection and Immunity, Amsterdam University Medical Centers, Amsterdam, The Netherlands
- Department of Medical Microbiology and Infection Control, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Vanessa C Harris
- Department of Global Health, Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands.
- Amsterdam Institute of Infection and Immunity, Amsterdam University Medical Centers, Amsterdam, The Netherlands.
- Division of Infectious Diseases, Department of Internal Medicine, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands.
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4
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Bali P, Lal P, Sivapuram MS, Kutikuppala LVS, Avti P, Chanana A, Kumar S, Anand A. Mind over Microbes: Investigating the Interplay between Lifestyle Factors, Gut Microbiota, and Brain Health. Neuroepidemiology 2024:1-23. [PMID: 38531341 DOI: 10.1159/000538416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 03/08/2024] [Indexed: 03/28/2024] Open
Abstract
BACKGROUND The gut microbiota (GM) of the human body comprises several species of microorganisms. This microorganism plays a significant role in the physiological and pathophysiological processes of various human diseases. METHODS The literature review includes studies that describe causative factors that influence GM. The GM is sensitive to various factors like circadian rhythms, environmental agents, physical activity, nutrition, and hygiene that together impact the functioning and composition of the gut microbiome. This affects the health of the host, including the psycho-neural aspects, due to the interconnectivity between the brain and the gut. Hence, this paper examines the relationship of GM with neurodegenerative disorders in the context of these aforesaid factors. CONCLUSION Future studies that identify the regulatory pathways associated with gut microbes can provide a causal link between brain degeneration and the gut at a molecular level. Together, this review could be helpful in designing preventive and treatment strategies aimed at GM, so that neurodegenerative diseases can be treated.
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Affiliation(s)
- Parul Bali
- Department of Biophysics, Postgraduate Institute of Medical Education and Research, Chandigarh, India
- Department of Neuroscience, University of Florida, Gainesville, Florida, USA
| | - Parth Lal
- Advance Pediatric Centre, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Madhava Sai Sivapuram
- Department of General Medicine, Dr. Pinnamaneni Siddhartha Institute of Medical Sciences and Research Foundation, Peda Avutapalli, India
| | | | - Pramod Avti
- Department of Biophysics, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | | | - Saurabh Kumar
- CCRYN-Collaborative Centre for Mind Body Intervention through Yoga, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Akshay Anand
- CCRYN-Collaborative Centre for Mind Body Intervention through Yoga, Postgraduate Institute of Medical Education and Research, Chandigarh, India
- Neuroscience Research Lab, Department of Neurology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
- Centre for Cognitive Science and Phenomenology, Panjab University, Chandigarh, India
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5
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Klimenko ES, Belkova NL, Rychkova LV, Darenskaya MA, Tugarinova OA, Semenova NV, Savinova YS, Bugun OV, Balzhirova DB, Kolesnikova LI. Alpha Diversity Indices as Indicators of the Variability of Gut Microbiota in Obese Adolescents of Different Ethnicities. Bull Exp Biol Med 2024; 176:591-594. [PMID: 38724810 DOI: 10.1007/s10517-024-06073-4] [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: 08/02/2023] [Indexed: 05/18/2024]
Abstract
We compared alpha diversity indices of the intestinal microbiota in adolescents with obesity and normal body weight, taking into account their ethnicity. Intestinal biocenosis was studied by metasequencing of amplicon libraries of V3-V4 fragments of the 16S rRNA gene. The alpha diversity of the microbiota was assessed using classical and alternative indices. Statistically significant differences in intestinal microbiota were observed between Russians with obesity and Buryats with normal body weight, as well as between Russians with obesity and Buryats with obesity when assessing the Shannon-Weaver, Chao1 indices, Faith phylogenetic diversity index, ACE, Fisher, Gini coefficient, Margalef, and Menkhinik indices. It was shown that alpha diversity indices can be used to assess significance of differences and variability of the intestinal microbiota in multifactorial diseases such as obesity in adolescents; however, the scope of application of the criteria should be considered.
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Affiliation(s)
- E S Klimenko
- Scientific Center for Family Health and Human Reproduction Problems, Irkutsk, Russia.
| | - N L Belkova
- Scientific Center for Family Health and Human Reproduction Problems, Irkutsk, Russia
| | - L V Rychkova
- Scientific Center for Family Health and Human Reproduction Problems, Irkutsk, Russia
| | - M A Darenskaya
- Scientific Center for Family Health and Human Reproduction Problems, Irkutsk, Russia
| | - O A Tugarinova
- Tarbagatai Central Region Clinic, Tarbagatai, Republic of Buryatiya, Russia
| | - N V Semenova
- Scientific Center for Family Health and Human Reproduction Problems, Irkutsk, Russia
| | - Yu S Savinova
- Scientific Center for Family Health and Human Reproduction Problems, Irkutsk, Russia
| | - O V Bugun
- Scientific Center for Family Health and Human Reproduction Problems, Irkutsk, Russia
| | - D B Balzhirova
- Scientific Center for Family Health and Human Reproduction Problems, Irkutsk, Russia
| | - L I Kolesnikova
- Scientific Center for Family Health and Human Reproduction Problems, Irkutsk, Russia
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6
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McVey Neufeld SF, Ahn M, Kunze WA, McVey Neufeld KA. Adolescence, the Microbiota-Gut-Brain Axis, and the Emergence of Psychiatric Disorders. Biol Psychiatry 2024; 95:310-318. [PMID: 37839790 DOI: 10.1016/j.biopsych.2023.10.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 09/06/2023] [Accepted: 10/07/2023] [Indexed: 10/17/2023]
Abstract
Second only to early life, adolescence is a period of dramatic change and growth. For the developing young adult, this occurs against a backdrop of distinct environmental challenges and stressors. A significant body of work has identified an important role for the microbiota-gut-brain (MGB) axis in the development and function of the brain. Given that the MGB axis is both highly plastic during the teenage years and vulnerable to environmental stressors, more attention needs to be drawn to its potential role in the emergence of psychiatric illnesses, many of which first manifest during adolescence. Here, we review the current literature surrounding the developing microbiome, enteric nervous system, vagus nerve, and brain during the adolescent period. We also examine preclinical and clinical research involving the MGB axis during this dynamic developmental window and argue that more research is needed to further understand the role of the MGB in the pathogenesis of brain disorders. Greater understanding of the adolescent MGB axis will open up the exciting potential for new microbial-based therapeutics for the treatment of these often-refractory psychiatric illnesses.
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Affiliation(s)
| | - Matthew Ahn
- McMaster Brain-Body Institute at St Joseph's Healthcare, McMaster University, Hamilton, Ontario, Canada
| | - Wolfgang A Kunze
- McMaster Brain-Body Institute at St Joseph's Healthcare, McMaster University, Hamilton, Ontario, Canada
| | - Karen-Anne McVey Neufeld
- McMaster Brain-Body Institute at St Joseph's Healthcare, McMaster University, Hamilton, Ontario, Canada.
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7
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Gopu V, Camacho FR, Toma R, Torres PJ, Cai Y, Krishnan S, Rajagopal S, Tily H, Vuyisich M, Banavar G. An accurate aging clock developed from large-scale gut microbiome and human gene expression data. iScience 2024; 27:108538. [PMID: 38230258 PMCID: PMC10790003 DOI: 10.1016/j.isci.2023.108538] [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: 09/25/2020] [Revised: 01/18/2021] [Accepted: 11/20/2023] [Indexed: 01/18/2024] Open
Abstract
Accurate measurement of the biological markers of the aging process could provide an "aging clock" measuring predicted longevity and enable the quantification of the effects of specific lifestyle choices on healthy aging. Using machine learning techniques, we demonstrate that chronological age can be predicted accurately from (1) the expression level of human genes in capillary blood and (2) the expression level of microbial genes in stool samples. The latter uses a very large metatranscriptomic dataset, stool samples from 90,303 individuals, which arguably results in a higher quality microbiome-aging model than prior work. Our analysis suggests associations between biological age and lifestyle/health factors, e.g., people on a paleo diet or with IBS tend to have higher model-predicted ages and people on a vegetarian diet tend to have lower model-predicted ages. We delineate the key pathways of systems-level biological decline based on the age-specific features of our model.
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Affiliation(s)
- Vishakh Gopu
- Viome Research Institute, Viome Life Sciences, Inc, Seattle, NY, USA
| | | | - Ryan Toma
- Viome Research Institute, Viome Life Sciences, Inc, Seattle, NY, USA
| | - Pedro J. Torres
- Viome Research Institute, Viome Life Sciences, Inc, Seattle, NY, USA
| | - Ying Cai
- Viome Research Institute, Viome Life Sciences, Inc, Seattle, NY, USA
| | - Subha Krishnan
- Viome Research Institute, Viome Life Sciences, Inc, Seattle, NY, USA
| | | | - Hal Tily
- Viome Research Institute, Viome Life Sciences, Inc, Seattle, NY, USA
| | - Momchilo Vuyisich
- Viome Research Institute, Viome Life Sciences, Inc, Seattle, NY, USA
| | - Guruduth Banavar
- Viome Research Institute, Viome Life Sciences, Inc, Seattle, NY, USA
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8
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Conrad MA, Bittinger K, Ren Y, Kachelries K, Vales J, Li H, Wu GD, Bushman FD, Devoto M, Baldassano RN, Kelsen JR. The intestinal microbiome of inflammatory bowel disease across the pediatric age range. Gut Microbes 2024; 16:2317932. [PMID: 38404111 PMCID: PMC10900269 DOI: 10.1080/19490976.2024.2317932] [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: 07/05/2023] [Accepted: 02/08/2024] [Indexed: 02/27/2024] Open
Abstract
Dysbiosis is associated with pediatric and adult-onset inflammatory bowel disease (IBD), but the role of dysbiosis and the microbiome in very early onset IBD (VEO-IBD) has not yet been described. Here, we aimed to demonstrate the impact of age and inflammation on microbial community structure using shotgun metagenomic sequencing in children with VEO-IBD, pediatric-onset IBD, and age-matched pediatric healthy controls (HC) observed longitudinally over the course of 8 weeks. We found disease-related differences in alpha and beta diversity between HC and children with IBD or VEO-IBD. Using a healthy microbial maturity index modeled from HC across the age range to characterize their gut microbiota, we found that children with pediatric-onset IBD and VEO-IBD had lower maturity than their age-matched HC groups, suggesting a disease effect on the microbial community. In addition, patients with pediatric IBD had significantly lower maturity than those with VEO-IBD, who had more heterogeneity at the youngest ages, highlighting differences in these two cohorts that were not captured in standard comparisons of alpha and beta diversity. These results demonstrate that young age and inflammation independently impact microbial community structure. However, the effect is not additive in the youngest patients, likely because of the heterogeneous and dynamic stool microbiome in this population.
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Affiliation(s)
- Máire A. Conrad
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yue Ren
- Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kelly Kachelries
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jennifer Vales
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Hongzhe Li
- Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Gary D. Wu
- Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Frederic D. Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Marcella Devoto
- Institute for Research in Genetics and Biomedicine, Consiglio Nazionale delle Ricerche, Monserrato, CA, Italy
- Department of Translational and Precision Medicine, Università Sapienza, Rome, Italy
| | - Robert N Baldassano
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Judith R. Kelsen
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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9
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Pacheco-Torres I, Hernández-Sánchez D, García-De la Peña C, Tarango-Arámbula LA, Crosby-Galván MM, Sánchez-Santillán P. Analysis of the Intestinal and Faecal Bacterial Microbiota of the Cervidae Family Using 16S Next-Generation Sequencing: A Review. Microorganisms 2023; 11:1860. [PMID: 37513032 PMCID: PMC10386072 DOI: 10.3390/microorganisms11071860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/01/2023] [Accepted: 07/15/2023] [Indexed: 07/30/2023] Open
Abstract
The Cervidae family has a wide distribution due to its adaptation to numerous ecological environments, which allows it to develop a diverse microbial community in its digestive tract. Recently, research has focused on the taxonomic composition and functionality of the intestinal and faecal microbiota of different cervid species worldwide, as well as their microbial diversity and variation under different associated factors such as age, sex, diet, distribution, and seasonal variation. In addition, there is special interest in knowing how cervids act as reservoirs of zoonotic pathogenic microorganisms, which represent a threat to public health. This review provides a synthesis of the growing field of microbiota determination in cervids worldwide, focusing on intestinal and faecal samples using 16S next-generation sequencing. It also documents factors influencing microbial diversity and composition, the microorganisms reported as pathogenic/zoonotic, and the perspectives regarding the conservation of these species. Knowing the interactions between bacteria and cervid health can drive management and conservation strategies for these species and help develop an understanding of their evolutionary history and the interaction with emerging disease-causing microorganisms.
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Affiliation(s)
| | | | | | | | | | - Paulino Sánchez-Santillán
- Faculty of Veterinary Medicine and Zootechnics No. 2, Autonomous University of Guerrero, Cuajinicuilapa 41940, Mexico
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10
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Wang R, Cai Y, Lu W, Zhang R, Shao R, Yau SY, Stubbs B, McIntyre RS, Su KP, Xu G, Qi L, So KF, Lin K. Exercise effect on the gut microbiota in young adolescents with subthreshold depression: A randomized psychoeducation-controlled Trial. Psychiatry Res 2023; 319:115005. [PMID: 36565548 DOI: 10.1016/j.psychres.2022.115005] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 11/28/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022]
Abstract
This 3-month randomized psychoeducation-controlled trial (RCT) of exercise was undertaken in young adolescents with subthreshold depression to examine the impact on gut microbiota. Participants (aged 12-14 years) were randomly assigned to an exercise or a psychoeducation-controlled group. The exercise intervention arm took moderate-intensity exercise, comprised of 30 min of running per day, 4 days a week for 3 months. Psychoeducation intervention consisted of 6 sessions of group activity including gaming, reading, and singing. The gut microbiota was assessed by metagenomic sequencing. After 3-month moderate-intensity exercise, the intervention group increased the relative abundance of Coprococcus, Blautia, Dorea, Tyzzerella at the genus level, as well as Tyzzerella nexilis, Ruminococcus obeum at species level when compared to the psychoeducation-controlled group. Moreover, EggNOG analyses showed that the defense and signal transduction mechanism were highly enriched after the active intervention, and changes were correlated with improvements in depressive symptoms measured by Chinese Patient Depression Questionnaire 9. The KEGG pathway of neurodegenerative diseases was depleted in the microbiome in young adolescents with subthreshold depression after exercise intervention. This 3-month RCT suggests that at both the genus and species levels, aerobic group exercise intervention improved in depressive symptoms and revealed changes in gut microbiota suggesting beneficial effects.
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Affiliation(s)
- Runhua Wang
- Department of Affective Disorders, The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yuanyuan Cai
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Weicong Lu
- Department of Affective Disorders, The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, China
| | - Ruoxi Zhang
- Department of Affective Disorders, The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, China
| | - Robin Shao
- Department of Affective Disorders, The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, China
| | - Suk-Yu Yau
- Department of Rehabilitation Sciences, The Hong Kong Polytechnic University, Hong Kong
| | - Brendon Stubbs
- Department of Psychological Medicine, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, United Kingdom
| | - Roger S McIntyre
- Mood Disorders Psychopharmacology Unit, University Health Network, Toronto, Canada
| | - Kuan-Pin Su
- Department of Psychiatry and MBI-Lab, China Medical University Hospital, Taichung, China
| | - Guiyun Xu
- Department of Affective Disorders, The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, China
| | - Liangwen Qi
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Kwok-Fai So
- Department of Affective Disorders, The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, China; Neuroscience and Neurorehabilitation Institute, University of Health and Rehabilitation Sciences, Qingdao, China; Ministry of Education Joint International Research Laboratory of CNS Regeneration, Jinan University, Guangzhou, China
| | - Kangguang Lin
- Department of Affective Disorders, The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, China; Neuroscience and Neurorehabilitation Institute, University of Health and Rehabilitation Sciences, Qingdao, China.
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11
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Gao L, Zhang Z, Xing Z, Li Q, Kong N, Wang L, Song L. The variation of intestinal autochthonous bacteria in cultured tiger pufferfish Takifugu rubripes. Front Cell Infect Microbiol 2022; 12:1062512. [PMID: 36583108 PMCID: PMC9792791 DOI: 10.3389/fcimb.2022.1062512] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 11/29/2022] [Indexed: 12/15/2022] Open
Abstract
Intestinal autochthonous bacteria play important roles in the maintenance of the physiological homeostasis of animals, especially contributing to the host immune system. In the present study, the variation of autochthonous bacterial community in the intestinal tract of 2-7 months-old tiger pufferfish Takifugu rubripes and bacterial communities in the seawater of recirculating aquaculture system (RAS) and the following offshore sea cage aquaculture system (OSCS) were analyzed during the aquaculture period from May to October 2021. Proteobacteria was found to be the most dominant phyla in both intestinal and seawater bacterial communities, which accounted for 68.82% and 65.65% of the total bacterial abundance, respectively. Arcobacter was the most core bacterial taxon in the intestinal bacterial community, with the most dominant abundance (42.89%) at the genus level and dominant positions in co-occurrence relationships with other bacterial taxa (node-betweenness value of 150). Enterococcaceae was specifically enriched in the intestinal bacterial community of pufferfishes from RAS, while Vibrionaceae was enriched in the intestinal bacterial community from OSCS. The F-values of beta diversity analysis between intestinal and seawater bacterial communities generally increased from May (6.69) to October (32.32), indicating the increasing differences between the intestinal and seawater bacterial communities along with the aquaculture process. Four bacterial taxa of Weissella sp., Akkermansia muciniphila, Dietzia sp. and Psychrobacter pacificensis had significant correlations with immune response parameters, and they were suggested to be the indicators for immune status and pathological process of pufferfish. The knowledge about the specific core bacteria, potentially pathogenic bacteria and the change of bacterial community in the intestinal tract of cultured pufferfish is of great scientific significance and will contribute to the understanding of intestinal bacterial homeostasis and biosecurity practice in pufferfish aquaculture.
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Affiliation(s)
- Lei Gao
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, China,Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, China,Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, China
| | - Ziyang Zhang
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, China,Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, China,Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, China
| | - Zhen Xing
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, China,Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, China,Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, China
| | - Qingsong Li
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, China,Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, China,Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, China
| | - Ning Kong
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, China,Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, China,Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, China
| | - Lingling Wang
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, China,Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, China,Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, China,Laboratory of Marine Fisheries Science and Food Production Process, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Linsheng Song
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, China,Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, China,Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, China,Laboratory of Marine Fisheries Science and Food Production Process, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China,*Correspondence: Linsheng Song,
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12
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Sgro M, Iacono G, Yamakawa GR, Kodila ZN, Marsland BJ, Mychasiuk R. Age matters: Microbiome depletion prior to repeat mild traumatic brain injury differentially alters microbial composition and function in adolescent and adult rats. PLoS One 2022; 17:e0278259. [PMID: 36449469 PMCID: PMC9710846 DOI: 10.1371/journal.pone.0278259] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 11/13/2022] [Indexed: 12/02/2022] Open
Abstract
Dysregulation of the gut microbiome has been shown to perpetuate neuroinflammation, alter intestinal permeability, and modify repetitive mild traumatic brain injury (RmTBI)-induced deficits. However, there have been no investigations regarding the comparative effects that the microbiome may have on RmTBI in adolescents and adults. Therefore, we examined the influence of microbiome depletion prior to RmTBI on microbial composition and metabolome, in adolescent and adult Sprague Dawley rats. Rats were randomly assigned to standard or antibiotic drinking water for 14 days, and to subsequent sham or RmTBIs. The gut microbiome composition and metabolome were analysed at baseline, 1 day after the first mTBI, and at euthanasia (11 days following the third mTBI). At euthanasia, intestinal samples were also collected to quantify tight junction protein (TJP1 and occludin) expression. Adolescents were significantly more susceptible to microbiome depletion via antibiotic administration which increased pro-inflammatory composition and metabolites. Furthermore, RmTBI induced a transient increase in 'beneficial bacteria' (Lachnospiraceae and Faecalibaculum) in only adolescents that may indicate compensatory action in response to the injury. Finally, microbiome depletion prior to RmTBI generated a microbiome composition and metabolome that exemplified a potentially chronic pathogenic and inflammatory state as demonstrated by increased Clostridium innocuum and Erysipelatoclostridium and reductions in Bacteroides and Clostridium Sensu Stricto. Results highlight that adolescents are more vulnerable to RmTBI compared to adults and dysbiosis prior to injury may exacerbate secondary inflammatory cascades.
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Affiliation(s)
- Marissa Sgro
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Giulia Iacono
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Glenn R. Yamakawa
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Zoe N. Kodila
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Benjamin J. Marsland
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Richelle Mychasiuk
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Victoria, Australia
- * E-mail:
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13
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Galena AE, Chai J, Zhang J, Bednarzyk M, Perez D, Ochrietor JD, Jahan-Mihan A, Arikawa AY. The effects of fermented vegetable consumption on the composition of the intestinal microbiota and levels of inflammatory markers in women: A pilot and feasibility study. PLoS One 2022; 17:e0275275. [PMID: 36201455 PMCID: PMC9536613 DOI: 10.1371/journal.pone.0275275] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 08/02/2022] [Indexed: 11/18/2022] Open
Abstract
The primary objective of this pilot study was to investigate the feasibility of regular consumption of fermented vegetables for six weeks on markers of inflammation and the composition of the gut microflora in women (clinical trials ID: NTC03407794). Thirty-one women were randomized into one of three groups: 100 g/day of fermented vegetables (group A), 100 g/day pickled vegetables (group B), or no vegetables (group C) for six weeks. Dietary intake was assessed by a food frequency questionnaire and blood and stool samples were provided before and after the intervention for measurement of C-reactive protein (CRP), tumor necrosis factor alpha (TNF-α), and lipopolysaccharide binding protein (LBP). Next-generation sequencing of the V4 region of the 16S rRNA gene was performed on the Illumina MiSeq platform. Participants' ages ranged between 18 and 69 years. Both groups A and B had a mean daily consumption of 91g of vegetables for 32 and 36 days, respectively. Serum CRP ranged between 0.9 and 265 ng/mL (SD = 92.4) at baseline, while TNF-α and LBP concentrations ranged between 0 and 9 pg/mL (SD = 2.3), and 7 and 29 μg/mL (SD = 4.4), respectively. There were no significant changes in levels of inflammatory markers among groups. At timepoint 2, group A showed an increase in Faecalibacterium prausnitzii (P = 0.022), a decrease in Ruminococcus torques (P<0.05), and a trend towards greater alpha diversity measured by the Shannon index (P = 0.074). The findings indicate that consumption of ~100 g/day of fermented vegetables for six weeks is feasible and may result in beneficial changes in the composition of the gut microbiota. Future trials should determine whether consumption of fermented vegetables is an effective strategy against gut dysbiosis.
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Affiliation(s)
- Amy E. Galena
- Department of Nutrition and Dietetics, University of North Florida, Jacksonville, FL, United States of America
| | - Jianmin Chai
- Division of Agriculture, Department of Animal Science, University of Arkansas, Fayetteville, AR, United States of America
| | - Jiangchao Zhang
- Division of Agriculture, Department of Animal Science, University of Arkansas, Fayetteville, AR, United States of America
| | - Michele Bednarzyk
- School of Nursing, University of North Florida, Jacksonville, FL, United States of America
| | - Doreen Perez
- School of Nursing, University of North Florida, Jacksonville, FL, United States of America
| | - Judith D. Ochrietor
- Department of Biology, University of North Florida, Jacksonville, FL, United States of America
| | - Alireza Jahan-Mihan
- Department of Nutrition and Dietetics, University of North Florida, Jacksonville, FL, United States of America
| | - Andrea Y. Arikawa
- Department of Nutrition and Dietetics, University of North Florida, Jacksonville, FL, United States of America
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14
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Sheu NW, Huang SH, Wu DC, Kao JY, Lin KD. Effects of Helicobacter pylori treatment on the incidences of autoimmune diseases and inflammatory bowel disease in patients with diabetes mellitus. PLoS One 2022; 17:e0265323. [PMID: 35604898 PMCID: PMC9126384 DOI: 10.1371/journal.pone.0265323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 02/21/2022] [Indexed: 11/29/2022] Open
Abstract
Background Helicobacter pylori infection is known to decrease the incidences of autoimmune diseases and inflammatory bowel disease(IBD). Our aim was investigating the effect of H. pylori treatment in diabetes mellitus(DM) patients. Methods Adults with newly-diagnosed H. pylori infection or peptic ulcer disease(PUD) within the general population and DM population were identified from the National Health Insurance Research Database of Taiwan from 2000–2010. 79,181 patients were assigned to the 3 groups: general population with PUD without H. pylori treatment(PUD-HPRx in general population), DM patients with PUD without H. pylori treatment(PUD-HPRx in DM), and DM patients with PUD who received H. pylori treatment(PUD+HPRx in DM). Results Higher incidences of autoimmune diseases and IBD were observed in the PUD+HPRx in DM group than in the PUD-HPRx in general population and PUD-HPRx in DM groups (autoimmune diseases = 5.14% vs 3.47% and 3.65%; IBD = 5.60% vs 3.17% and 3.25%; P<0.0001). A lower all-cause mortality was noted in the PUD+HPRx in DM group (HR: 0.937, P<0.001) than in the PUD-HPRx in DM group. Trends of a higher incidence of IBD and a lower mortality in younger patients in the PUD+HPRx in DM group compared with the PUD-HPRx in DM group were noted. Conclusions The results revealed that H. pylori treatment increased the incidences of autoimmune diseases and IBD and decreased the all-cause mortality in the DM group with PUD. The effect was more significant in younger patients. This finding assists in realizing the influence of H. pylori treatment in the DM population.
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Affiliation(s)
- Nai-Wei Sheu
- Department of Internal Medicine, Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Shu-Heng Huang
- Department of Internal Medicine, Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Deng-Chyang Wu
- Division of Gastroenterology, Department of Internal Medicine, Kaohsiung Medical University Hospital, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - John Y. Kao
- Division of Gastroenterology, Department of Internal Medicine, Michigan Medicine, University of Michigan, Ann Arbor, Michigan
| | - Kun-Der Lin
- Department of Internal Medicine, Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Kaohsiung Medical University Hospital, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- * E-mail:
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15
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Watkins CA, Gaines T, Strathdee F, Baily JL, Watson E, Hall AJ, Free A, Dagleish MP. A comparative study of the fecal microbiota of gray seal pups and yearlings ‐ a marine mammal sentinel species. Microbiologyopen 2022; 11:e1281. [PMID: 35765184 PMCID: PMC9126079 DOI: 10.1002/mbo3.1281] [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: 01/31/2022] [Revised: 03/17/2022] [Accepted: 03/17/2022] [Indexed: 12/12/2022] Open
Abstract
Gray seals (Halichoerus grypus) can act as sentinel species reflecting the condition of the environment they inhabit. Our previous research identified strains of pathogenic Campylobacter and Salmonella, originating from both human and agricultural animal hosts, on rectal swabs from live gray seal (H. grypus) pups and yearlings on the Isle of May, Scotland, UK. We examined rectal swabs from the same pup (n = 90) and yearling (n = 19) gray seals to gain further understanding into the effects of age‐related changes (pup vs. yearling) and three different natal terrestrial habitats on seal pup fecal microbiota. DNA was extracted from a subset of rectal swabs (pups n = 23, yearlings n = 9) using an optimized procedure, and the V4 region of the 16S ribosomal RNA gene was sequenced to identify each individual's microbiota. Diversity in pup samples was lower (3.92 ± 0.19) than yearlings (4.66 ± 0.39) although not significant at the p = 0.05 level (p = 0.062) but differences in the composition of the microbiota were (p < 0.001). Similarly, differences between the composition of the microbiota from pups from three different terrestrial habitats (Pilgrim's Haven [PH], Rona Rocks [RR], and Tarbet Slope [TS]) were highly significant (p < 0.001). Pairwise tests showed significant differences between all three habitats: PH versus TS (p = 0.019), PH versus RR (p = 0.042) and TS versus RR (p = 0.020). This preliminary study suggests a general trend, that seal microbiomes are modified by both age and, in pups, different terrestrial habitats. Furthermore, knowledge of the microbiota species present has the potential to be used in determining the environmental quality index.
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Affiliation(s)
- Craig A. Watkins
- Department of Vaccines and Diagnostics Moredun Research Institute Penicuik UK
| | - Taylor Gaines
- Department of Vaccines and Diagnostics Moredun Research Institute Penicuik UK
| | - Fiona Strathdee
- School of Biological Sciences University of Edinburgh Edinburgh UK
| | - Johanna L. Baily
- Department of Vaccines and Diagnostics Moredun Research Institute Penicuik UK
- Sea Mammal Research Unit, Scottish Oceans Institute University of St Andrews St Andrews UK
| | - Eleanor Watson
- Department of Vaccines and Diagnostics Moredun Research Institute Penicuik UK
| | - Ailsa J. Hall
- Sea Mammal Research Unit, Scottish Oceans Institute University of St Andrews St Andrews UK
| | - Andrew Free
- School of Biological Sciences University of Edinburgh Edinburgh UK
| | - Mark P. Dagleish
- Department of Vaccines and Diagnostics Moredun Research Institute Penicuik UK
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16
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Isolation and Characterization of Commensal Bifidobacteria Strains in Gut Microbiota of Neonates Born Preterm: A Prospective Longitudinal Study. Microorganisms 2022; 10:microorganisms10030654. [PMID: 35336229 PMCID: PMC8951322 DOI: 10.3390/microorganisms10030654] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 02/05/2023] Open
Abstract
Bifidobacterial population dynamics were investigated using a longitudinal analysis of dominant species isolated from feces of neonates born preterm (singletons (n = 10), pairs of twins (n = 11)) from birth up to 16 months of age. We performed quantification, isolation, and identification of the dominant bifidobacteria strains. The genetic relationship of the isolates was investigated via pulsed field gel electrophoresis (PFGE) genotyping, and PCR was used to screen the specific genetic marker tet genes. Additionally, all of the isolated strains were phenotypically characterized by their response to gastro-intestinal stresses and the MIC determination of tetracycline. In the same individual, our results showed a turnover of the bifidobacteria dominant population not only at species but also at strain levels. In addition, we found clonally related strains between twins. A minority of strains were tolerant to gastric (6%) and intestinal (16%) stresses. Thirteen percent of the strains were resistant to tetracycline. This work is original as it provides insights at the strain level of the early life in vivo dynamics of gut microbiota bifidobacteria in preterm neonates. It highlights the need to take into consideration the fluctuation of bifidobacteria populations that may occur for one individual.
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Toyofuku E, Takeshita K, Ohnishi H, Kiridoshi Y, Masuoka H, Kadowaki T, Nishikomori R, Nishimura K, Kobayashi C, Ebato T, Shigemura T, Inoue Y, Suda W, Hattori M, Morio T, Honda K, Kanegane H. Dysregulation of the Intestinal Microbiome in Patients With Haploinsufficiency of A20. Front Cell Infect Microbiol 2022; 11:787667. [PMID: 35155270 PMCID: PMC8834539 DOI: 10.3389/fcimb.2021.787667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 12/28/2021] [Indexed: 11/23/2022] Open
Abstract
Introduction Haploinsufficiency of A20 (HA20) is a form of inborn errors of immunity (IEI). IEIs are genetically occurring diseases, some of which cause intestinal dysbiosis. Due to the dysregulation of regulatory T cells (Tregs) observed in patients with HA20, gut dysbiosis was associated with Tregs in intestinal lamina propria. Methods Stool samples were obtained from 16 patients with HA20 and 15 of their family members. Infant samples and/or samples with recent antibiotics use were excluded; hence, 26 samples from 13 patients and 13 family members were analyzed. The 16S sequencing process was conducted to assess the microbial composition of samples. Combined with clinical information, the relationship between the microbiome and the disease activity was statistically analyzed. Results The composition of gut microbiota in patients with HA20 was disturbed compared with that in healthy family members. Age, disease severity, and use of immunosuppressants corresponded to dysbiosis. However, other explanatory factors, such as abdominal symptoms and probiotic treatment, were not associated. The overall composition at the phylum level was stable, but some genera were significantly increased or decreased. Furthermore, among the seven operational taxonomic units (OTUs) that increased, two OTUs, Streptococcus mutans and Lactobacillus salivarius, considerably increased in patients with autoantibodies than those without autoantibodies. Discussion Detailed interaction on intestinal epithelium remains unknown; the relationship between the disease and stool composition change helps us understand the mechanism of an immunological reaction to microorganisms.
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Affiliation(s)
- Etsushi Toyofuku
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
- Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kozue Takeshita
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
| | - Hidenori Ohnishi
- Department of Pediatrics, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Yuko Kiridoshi
- JSR-Keio University Medical and Chemical Innovation Center (JKiC), JSR Corporation, Tokyo, Japan
| | - Hiroaki Masuoka
- Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Tomonori Kadowaki
- Department of Pediatrics, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Ryuta Nishikomori
- Department of Pediatrics, Kyoto University Hospital, Kyoto, Japan
- Department of Pediatrics and Child Health, Kurume University School of Medicine, Kurume, Japan
| | - Kenichi Nishimura
- Department of Pediatrics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Chie Kobayashi
- Department of Child Health, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Takasuke Ebato
- Department of Pediatrics, Kitasato University Hospital, Sagamihara, Japan
| | - Tomonari Shigemura
- Department of Pediatrics, Shinshu University School of Medicine, Matsumoto, Japan
| | - Yuzaburo Inoue
- Department of Allergy and Rheumatology, Chiba Children's Hospital, Chiba, Japan
| | - Wataru Suda
- Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Masahira Hattori
- Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Tomohiro Morio
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Kenya Honda
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
| | - Hirokazu Kanegane
- Department of Child Health and Development, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
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Quantitative GC-TCD Measurements of Major Flatus Components: A Preliminary Analysis of the Diet Effect. SENSORS 2022; 22:s22030838. [PMID: 35161583 PMCID: PMC8840200 DOI: 10.3390/s22030838] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/14/2022] [Accepted: 01/21/2022] [Indexed: 02/01/2023]
Abstract
The impact of diet and digestive disorders in flatus composition remains largely unexplored. This is partially due to the lack of standardized sampling collection methods, and the easy atmospheric contamination. This paper describes a method to quantitatively determine the major gases in flatus and their application in a nutritional intervention. We describe how to direct sample flatus into Tedlar bags, and simultaneous analysis by gas chromatography–thermal conductivity detection (GC–TCD). Results are analyzed by univariate hypothesis testing and by multilevel principal component analysis. The reported methodology allows simultaneous determination of the five major gases with root mean measurement errors of 0.8% for oxygen (O2), 0.9% for nitrogen (N2), 0.14% for carbon dioxide (CO2), 0.11% for methane (CH4), and 0.26% for hydrogen (H2). The atmospheric contamination was limited to 0.86 (95% CI: [0.7–1.0])% for oxygen and 3.4 (95% CI: [1.4–5.3])% for nitrogen. As an illustration, the method has been successfully applied to measure the response to a nutritional intervention in a reduced crossover study in healthy subjects.
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The intestinal microbiota as a predictor for antidepressant treatment outcome in geriatric depression: a prospective pilot study. Int Psychogeriatr 2022; 34:33-45. [PMID: 33757609 DOI: 10.1017/s1041610221000120] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
OBJECTIVES (1) To investigate if gut microbiota can be a predictor of remission in geriatric depression and to identify features of the gut microbiota that is associated with remission. (2) To determine if changes in gut microbiota occur with remission in geriatric depression. DESIGN Secondary analysis of a parent randomized placebo-controlled trial (NCT02466958). SETTING Los Angeles, CA, USA (2016-2018). PARTICIPANTS Seventeen subjects with major depressive disorder, over 60 years of age, 41.2% female. INTERVENTION Levomilacipran (LVM) or placebo. MEASUREMENTS Remission was defined by Hamilton Depression Rating Scale score of 6 or less at 12 weeks. 16S-ribosomal RNA sequencing based fecal microbiota composition and diversity were measured at baseline and 12 weeks. Differences in fecal microbiota were evaluated between remitters and non-remitters as well as between baseline and post-treatment samples. LVM and placebo groups were combined in all the analyses. RESULTS Baseline microbiota showed no community level α-diversity or β-diversity differences between remitters and non-remitters. At the individual taxa level, a random forest classifier created with nine genera from the baseline microbiota was highly accurate in predicting remission (AUC = .857). Of these, baseline enrichment of Faecalibacterium, Agathobacter and Roseburia relative to a reference frame was associated with treatment outcome of remission. Differential abundance analysis revealed significant genus level changes from baseline to post-treatment in remitters, but not in non-remitters. CONCLUSIONS This is the first study demonstrating fecal microbiota as a potential predictor of treatment response in geriatric depression. Our findings need to be confirmed in larger prospective studies.
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HE Y, LUO Y, HUANG Q, ZHOU H, QIAN M, GUAN Z, LIU Q, ZHAO Q. Effect of Xiaoning liquid on gut microbiota in asthmatic mice by 16S rDNA high-throughput sequencing. FOOD SCIENCE AND TECHNOLOGY 2022. [DOI: 10.1590/fst.40721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Yuanyuan HE
- Hospital of Chengdu University of Traditional Chinese Medicine, P. R. China
| | - Yating LUO
- Xinjiang Yili Maternal and Child Health Care Hospital, China
| | - Qinwan HUANG
- Hospital of Chengdu University of Traditional Chinese Medicine, P. R. China
| | - Hongyun ZHOU
- Hospital of Chengdu University of Traditional Chinese Medicine, P. R. China
| | - Ming QIAN
- Xiangyang Hospital of Traditional Chinese Medicine, China
| | - Zhiwei GUAN
- Hospital of Chengdu University of Traditional Chinese Medicine, P. R. China
| | - Qianwei LIU
- Beijing University of Traditional Chinese Medicine, China
| | - Qiong ZHAO
- Hospital of Chengdu University of Traditional Chinese Medicine, P. R. China
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Wu L, Xie X, Liang T, Ma J, Yang L, Yang J, Li L, Xi Y, Li H, Zhang J, Chen X, Ding Y, Wu Q. Integrated Multi-Omics for Novel Aging Biomarkers and Antiaging Targets. Biomolecules 2021; 12:39. [PMID: 35053186 PMCID: PMC8773837 DOI: 10.3390/biom12010039] [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] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 12/17/2021] [Accepted: 12/19/2021] [Indexed: 12/12/2022] Open
Abstract
Aging is closely related to the occurrence of human diseases; however, its exact biological mechanism is unclear. Advancements in high-throughput technology provide new opportunities for omics research to understand the pathological process of various complex human diseases. However, single-omics technologies only provide limited insights into the biological mechanisms of diseases. DNA, RNA, protein, metabolites, and microorganisms usually play complementary roles and perform certain biological functions together. In this review, we summarize multi-omics methods based on the most relevant biomarkers in single-omics to better understand molecular functions and disease causes. The integration of multi-omics technologies can systematically reveal the interactions among aging molecules from a multidimensional perspective. Our review provides new insights regarding the discovery of aging biomarkers, mechanism of aging, and identification of novel antiaging targets. Overall, data from genomics, transcriptomics, proteomics, metabolomics, integromics, microbiomics, and systems biology contribute to the identification of new candidate biomarkers for aging and novel targets for antiaging interventions.
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Affiliation(s)
- Lei Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (L.W.); (X.X.); (T.L.); (L.Y.); (J.Y.); (L.L.); (Y.X.); (H.L.); (J.Z.)
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi’an 710021, China; (J.M.); (X.C.)
| | - Xinqiang Xie
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (L.W.); (X.X.); (T.L.); (L.Y.); (J.Y.); (L.L.); (Y.X.); (H.L.); (J.Z.)
| | - Tingting Liang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (L.W.); (X.X.); (T.L.); (L.Y.); (J.Y.); (L.L.); (Y.X.); (H.L.); (J.Z.)
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi’an 710021, China; (J.M.); (X.C.)
| | - Jun Ma
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi’an 710021, China; (J.M.); (X.C.)
| | - Lingshuang Yang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (L.W.); (X.X.); (T.L.); (L.Y.); (J.Y.); (L.L.); (Y.X.); (H.L.); (J.Z.)
| | - Juan Yang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (L.W.); (X.X.); (T.L.); (L.Y.); (J.Y.); (L.L.); (Y.X.); (H.L.); (J.Z.)
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi’an 710021, China; (J.M.); (X.C.)
| | - Longyan Li
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (L.W.); (X.X.); (T.L.); (L.Y.); (J.Y.); (L.L.); (Y.X.); (H.L.); (J.Z.)
| | - Yu Xi
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (L.W.); (X.X.); (T.L.); (L.Y.); (J.Y.); (L.L.); (Y.X.); (H.L.); (J.Z.)
| | - Haixin Li
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (L.W.); (X.X.); (T.L.); (L.Y.); (J.Y.); (L.L.); (Y.X.); (H.L.); (J.Z.)
| | - Jumei Zhang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (L.W.); (X.X.); (T.L.); (L.Y.); (J.Y.); (L.L.); (Y.X.); (H.L.); (J.Z.)
| | - Xuefeng Chen
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi’an 710021, China; (J.M.); (X.C.)
| | - Yu Ding
- Department of Food Science and Technology, Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China
| | - Qingping Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (L.W.); (X.X.); (T.L.); (L.Y.); (J.Y.); (L.L.); (Y.X.); (H.L.); (J.Z.)
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22
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Komanduri M, Savage K, Lea A, McPhee G, Nolidin K, Deleuil S, Stough C, Gondalia S. The Relationship between Gut Microbiome and Cognition in Older Australians. Nutrients 2021; 14:nu14010064. [PMID: 35010939 PMCID: PMC8746300 DOI: 10.3390/nu14010064] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/20/2021] [Accepted: 12/22/2021] [Indexed: 12/20/2022] Open
Abstract
Ageing is associated with changes in biological processes, including reductions in cognitive functions and gut microbiome diversity. However, not much is known about the relationship between cognition and the microbiome with increasing age. Therefore, we examined the relationship between the gut microbiome and cognition in 69 healthy participants aged 60–75 years. The gut microbiome was analysed with the 16S rRNA sequencing method. The cognitive assessment included the Cognitive Drug Research computerised assessment battery, which produced five cognitive factors corresponding to ‘Quality of Episodic Secondary Memory’, ‘Quality of Working Memory’, ‘Continuity of Attention, ‘Speed of Memory’ and ‘Power of Concentration’. Multiple linear regression showed that the bacterial family Carnobacteriaceae explained 9% of the variance in predicting Quality of Episodic Secondary Memory. Alcaligenaceae and Clostridiaceae explained 15% of the variance in predicting Quality of Working Memory; Bacteroidaceae, Barnesiellaceae, Rikenellaceae and Gemellaceae explained 11% of the variance in Power of Concentration. The present study provides specific evidence of a relationship between specific families of bacteria and different domains of cognition.
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Affiliation(s)
- Mrudhula Komanduri
- Centre for Human Psychopharmacology, Swinburne University of Technology, Hawthorn, VIC 3122, Australia; (K.S.); (A.L.); (G.M.); (K.N.); (S.D.); (C.S.); (S.G.)
- Correspondence:
| | - Karen Savage
- Centre for Human Psychopharmacology, Swinburne University of Technology, Hawthorn, VIC 3122, Australia; (K.S.); (A.L.); (G.M.); (K.N.); (S.D.); (C.S.); (S.G.)
| | - Ana Lea
- Centre for Human Psychopharmacology, Swinburne University of Technology, Hawthorn, VIC 3122, Australia; (K.S.); (A.L.); (G.M.); (K.N.); (S.D.); (C.S.); (S.G.)
| | - Grace McPhee
- Centre for Human Psychopharmacology, Swinburne University of Technology, Hawthorn, VIC 3122, Australia; (K.S.); (A.L.); (G.M.); (K.N.); (S.D.); (C.S.); (S.G.)
| | - Karen Nolidin
- Centre for Human Psychopharmacology, Swinburne University of Technology, Hawthorn, VIC 3122, Australia; (K.S.); (A.L.); (G.M.); (K.N.); (S.D.); (C.S.); (S.G.)
| | - Saurenne Deleuil
- Centre for Human Psychopharmacology, Swinburne University of Technology, Hawthorn, VIC 3122, Australia; (K.S.); (A.L.); (G.M.); (K.N.); (S.D.); (C.S.); (S.G.)
| | - Con Stough
- Centre for Human Psychopharmacology, Swinburne University of Technology, Hawthorn, VIC 3122, Australia; (K.S.); (A.L.); (G.M.); (K.N.); (S.D.); (C.S.); (S.G.)
| | - Shakuntla Gondalia
- Centre for Human Psychopharmacology, Swinburne University of Technology, Hawthorn, VIC 3122, Australia; (K.S.); (A.L.); (G.M.); (K.N.); (S.D.); (C.S.); (S.G.)
- Health and Biosecurity, Commonwealth Scientific and Industrial Research Organization, Adelaide, SA 5000, Australia
- Precision Health Future Science Platform, Commonwealth Scientific and Industrial Research Organisation, Adelaide, SA 5000, Australia
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23
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Mikrobiota jelitowa a leki. Interakcje wpływające na skuteczność i bezpieczeństwo farmakoterapii. POSTEP HIG MED DOSW 2021. [DOI: 10.2478/ahem-2021-0009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstrakt
Mikrobiota jelitowa stanowi nieodłączny element organizmu umożliwiający jego prawidłowe funkcjonowanie. Dzięki mikroorganizmom jelitowym możliwa jest stymulacja układu odpornościowego, synteza witamin czy poprawa wchłaniania składników odżywczych. Jednak jej aktywność może również niekorzystnie działać na organizm, m.in. z powodu przetwarzania treści jelitowej. Opisywana w artykule interakcja mikrobiota–lek uwzględnia pozytywny i negatywny wpływ mikroorganizmów jelitowych na farmakoterapię poprzez bezpośrednie i pośrednie oddziaływanie na lek w organizmie. Ze względu na to, że mikrobiom stanowi nieodłączny element organizmu, ingerencja nawet w jego niewielką część może doprowadzić do wystąpienia daleko idących, czasami niespodziewanych skutków. Stąd w celu poprawy skuteczności i bezpieczeństwa farmakoterapii konieczne jest wyjaśnienie mechanizmów oddziaływania mikrobioty na lek w organizmie.
W artykule podsumowano obecną wiedzę na temat biologicznej aktywności mikrobioty jelitowej, a zwłaszcza oddziaływań mikrobiota–leki determinujących skuteczność i bezpieczeństwo farmakoterapii. Wyszukiwanie przeprowadzono we wrześniu 2020 r. w bazach danych PubMed, Scopus, Web of Science, Cochrane Library i powszechnie dostępnej literaturze z użyciem terminów: „mikrobiota jelitowa”, „mikrobiom”, „metabolizm leku”, „interakcje mikrobiota–lek”. W artykule omówiono interakcje między mikrobiotą a lekami m.in. z grupy antybiotyków, inhibitorów pompy protonowej, sulfonamidów, pochodnych kwasu 5-aminosalicylowego, niesteroidowych leków przeciwzapalnych, przeciwnowotworowych, statyn czy metforminą.
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24
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Sgro M, Kodila ZN, Brady RD, Reichelt AC, Mychaisuk R, Yamakawa GR. Synchronizing Our Clocks as We Age: The Influence of the Brain-Gut-Immune Axis on the Sleep-Wake Cycle Across the Lifespan. Sleep 2021; 45:6425072. [PMID: 34757429 DOI: 10.1093/sleep/zsab268] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/11/2021] [Indexed: 11/12/2022] Open
Abstract
The microbes that colonize the small and large intestines, known as the gut microbiome, play an integral role in optimal brain development and function. The gut microbiome is a vital component of the bi-directional communication pathway between the brain, immune system, and gut, also known as the brain-gut-immune axis. To date there has been minimal investigation into the implications of improper development of the gut microbiome and the brain-gut-immune axis on the sleep-wake cycle, particularly during sensitive periods of physical and neurological development, such as childhood, adolescence, and senescence. Therefore, this review will explore the current literature surrounding the overlapping developmental periods of the gut microbiome, brain, and immune system from birth through to senescence, while highlighting how the brain-gut-immune axis affects maturation and organisation of the sleep-wake cycle. We also examine how dysfunction to either the microbiome or the sleep-wake cycle negatively affects the bidirectional relationship between the brain and gut, and subsequently the overall health and functionality of this complex system. Additionally, this review integrates therapeutic studies to demonstrate when dietary manipulations, such as supplementation with probiotics and prebiotics, can modulate the gut microbiome to enhance health of the brain-gut-immune axis and optimize our sleep-wake cycle.
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Affiliation(s)
- Marissa Sgro
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Zoe N Kodila
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Rhys D Brady
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Amy C Reichelt
- Department of Medical Sciences, Adelaide Medical School, The University of Adelaide, Adelaide, Australia
| | - Richelle Mychaisuk
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Glenn R Yamakawa
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, VIC, Australia
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25
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Influence of Human Age on the Prebiotic Effect of Pectin-Derived Oligosaccharides Obtained from Apple Pomace. FERMENTATION-BASEL 2021. [DOI: 10.3390/fermentation7040224] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The aim of this study was to evaluate the prebiotic effect of pectin-derived oligosaccharides (POS) obtained from apple pomace on the growth and metabolism of microbiota from the human gastrointestinal tract as a function of the age of the host. The counts of major bacterial groups Bifidobacterium sp., lactobacilli, Clostridium sp., Bacteroides sp., Enterococcus sp. and Enterobacteria were assessed during long-term in vitro fermentation of mixed cultures in a prebiotic medium. Comparative assessment of bacterial diversity in the human fecal microbiota was performed relative to the age of the host, from childhood to old age, through younger years and middle age. The age group of the host was found to be an important factor that determined the prebiotic effect of POS, which was related to both the qualitative and quantitative composition of fecal microbiota and its metabolism. In contrast to the microbiota of elderly subjects, the child-derived intestinal microbiota underwent significantly different alterations in terms of the proportion and composition of lactic acid bacteria, leading to a more favorable pattern of short-chain fatty acids (SCFA) and lactic acid levels.
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26
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Xiao Y, Yang C, Yu L, Tian F, Wu Y, Zhao J, Zhang H, Yang R, Chen W, Hill C, Cui Y, Zhai Q. Human gut-derived B. longum subsp. longum strains protect against aging in a D-galactose-induced aging mouse model. MICROBIOME 2021; 9:180. [PMID: 34470652 PMCID: PMC8411540 DOI: 10.1186/s40168-021-01108-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/02/2021] [Indexed: 05/02/2023]
Abstract
BACKGROUND Probiotics have been used to regulate the gut microbiota and physiology in various contexts, but their precise mechanisms of action remain unclear. RESULTS By population genomic analysis of 418 Bifidobacterium longum strains, including 143 newly sequenced in this study, three geographically distinct gene pools/populations, BLAsia1, BLAsia2, and BLothers, were identified. Genes involved in cell wall biosynthesis, particularly peptidoglycan biosynthesis, varied considerably among the core genomes of the different populations, but accessory genes that contributed to the carbohydrate metabolism were significantly distinct. Although active transmission was observed inter-host, inter-country, inter-city, intra-community, and intra-family, a single B. longum clone seemed to reside within each individual. A significant negative association was observed between host age and relative abundance of B. longum, while there was a strong positive association between host age and strain genotype [e.g., single nucleotide polymorphisms in the arginine biosynthesis pathway]. Further animal experiments performed with the B. longum isolates via using a D-galactose-induced aging mouse model supported these associations, in which B. longum strains with different genotypes in arginine biosynthesis pathway showed divergent abilities on protecting against host aging possibly via their different abilities to modify the metabolism of gut microbes. CONCLUSIONS This is the first known example of research on the evolutionary history and transmission of this probiotic species. Our results propose a new mechanistic insight for promoting host longevity via the informed use of specific probiotics or molecules. Video abstract.
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Affiliation(s)
- Yue Xiao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122 People’s Republic of China
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071 China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122 Jiangsu China
- International Joint Research Laboratory for Probiotics At Jiangnan University, Wuxi, 214122 Jiangsu China
| | - Chao Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071 China
| | - Leilei Yu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122 People’s Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122 Jiangsu China
| | - Fengwei Tian
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122 People’s Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122 Jiangsu China
| | - Yarong Wu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071 China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122 People’s Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122 Jiangsu China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122 People’s Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122 Jiangsu China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122 Jiangsu China
- (Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou, 225004 China
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071 China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122 People’s Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122 Jiangsu China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122 Jiangsu China
- Beijing Innovation Centre of Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing, 100048 People’s Republic of China
| | - Colin Hill
- School of Microbiology & APC Microbiome Institute, University College Cork, Cork, T12 YN60 Ireland
| | - Yujun Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071 China
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122 People’s Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122 Jiangsu China
- International Joint Research Laboratory for Probiotics At Jiangnan University, Wuxi, 214122 Jiangsu China
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27
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Landay A, Bartley JM, Banerjee D, Hargis G, Haynes L, Keshavarzian A, Kuo CL, Kwon OS, Li S, Li S, Oh J, Ozbolat IT, Ucar D, Xu M, Yao X, Unutmaz D, Kuchel GA. Network Topology of Biological Aging and Geroscience-Guided Approaches to COVID-19. FRONTIERS IN AGING 2021; 2:695218. [PMID: 35128530 PMCID: PMC8813169 DOI: 10.3389/fragi.2021.695218] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 06/22/2021] [Indexed: 01/08/2023]
Abstract
Aging has emerged as the greatest and most prevalent risk factor for the development of severe COVID-19 infection and death following exposure to the SARS-CoV-2 virus. The presence of multiple co-existing chronic diseases and conditions of aging further enhances this risk. Biological aging not only enhances the risk of chronic diseases, but the presence of such conditions further accelerates varied biological processes or "hallmarks" implicated in aging. Given growing evidence that it is possible to slow the rate of many biological aging processes using pharmacological compounds has led to the proposal that such geroscience-guided interventions may help enhance immune resilience and improve outcomes in the face of SARS-CoV-2 infection. Our review of the literature indicates that most, if not all, hallmarks of aging may contribute to the enhanced COVID-19 vulnerability seen in frail older adults. Moreover, varied biological mechanisms implicated in aging do not function in isolation from each other, and exhibit intricate effects on each other. With all of these considerations in mind, we highlight limitations of current strategies mostly focused on individual single mechanisms, and we propose an approach which is far more multidisciplinary and systems-based emphasizing network topology of biological aging and geroscience-guided approaches to COVID-19.
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Affiliation(s)
- Alan Landay
- Department of Medicine, Rush School of Medicine, Chicago, IL, United States
| | - Jenna M. Bartley
- UConn Center on Aging, University of Connecticut School of Medicine, Farmington, CT, United States
- Department of Immunology, University of Connecticut School of Medicine, Farmington, CT, United States
| | - Dishary Banerjee
- Engineering Science and Mechanics Department, The Huck Institutes of the Life Sciences, Penn State University, University Park, PA, United States
| | - Geneva Hargis
- UConn Center on Aging, University of Connecticut School of Medicine, Farmington, CT, United States
| | - Laura Haynes
- UConn Center on Aging, University of Connecticut School of Medicine, Farmington, CT, United States
- Department of Immunology, University of Connecticut School of Medicine, Farmington, CT, United States
| | - Ali Keshavarzian
- Division of Digestive Diseases, Departments of Medicine, Pharmacology, Molecular Biophysics and Physiology, Rush University Medical Center, Chicago, IL, United States
| | - Chia-Ling Kuo
- UConn Center on Aging, University of Connecticut School of Medicine, Farmington, CT, United States
- Connecticut Convergence Institute for Translation in Regenerative Engineering, Storrs, CT, United States
| | - Oh Sung Kwon
- UConn Center on Aging, University of Connecticut School of Medicine, Farmington, CT, United States
- Department of Kinesiology, University of Connecticut, Storrs, CT, United States
| | - Sheng Li
- Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT, United States
| | - Shuzhao Li
- Department of Immunology, University of Connecticut School of Medicine, Farmington, CT, United States
- Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
| | - Julia Oh
- Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT, United States
| | - Ibrahim Tarik Ozbolat
- Engineering Science and Mechanics Department, The Huck Institutes of the Life Sciences, Penn State University, University Park, PA, United States
- Biomedical Engineering Department, Neurosurgery Department, Materials Research Institute, Penn State University, University Park, PA, United States
| | - Duygu Ucar
- Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT, United States
| | - Ming Xu
- UConn Center on Aging, University of Connecticut School of Medicine, Farmington, CT, United States
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT, United States
| | - Xudong Yao
- Department of Chemistry, University of Connecticut, Storrs, CT, United States
| | - Derya Unutmaz
- Department of Immunology, University of Connecticut School of Medicine, Farmington, CT, United States
- Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
| | - George A. Kuchel
- UConn Center on Aging, University of Connecticut School of Medicine, Farmington, CT, United States
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28
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Li H, Du X, Yan L, Tang Z, Zhang L, Zheng Q, Zeng X, Chen G, Yue H, Fu X. Low Abundance of Lactococcus lactis in Human Colorectal Cancer Is Associated with Decreased Natural Killer Cells. Nutr Cancer 2021; 74:938-946. [PMID: 34192986 DOI: 10.1080/01635581.2021.1944649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
A limited number of studies have demonstrated the role of Lactococcus lactis (L. lactis) in human colorectal cancers (CRCs). The association of L. lactis abundance with the density of natural killer (NK) cells has not been investigated before. In this study, the L. lactis abundance in 60 CRC specimens, 20 adenoma (AD) specimens, and 29 normal colorectal tissues (NCs) specimens was investigated using the fluorescence in situ hybridization of 16S ribosomal RNA. The density of NK cells was detected using immunofluorescence in 28 CRC specimens, 12 AD specimens, and 22 NC specimens. The presence of L. lactis in NCs (48.28%) was detected significantly higher than that in the AD (20.00%, P = .044) and CRC (23.33%, P = .018) specimens. The abundance of L. lactis in NCs (32.73 ± 7.24) was also found to be significantly higher than that in AD (8.91 ± 5.89, P = .029) and CRC (5.63 ± 1.67, P = .003) specimens. In addition, the density of NKp30+ NK cells in NCs (51.14 ± 4.84) was significantly higher than that in the AD (6.10 ± 1.31) and CRC (1.72 ± 0.40) specimens (P < .001). Moreover, a positive association of L. lactis abundance with NKp30+ NK cells density in the colorectal samples (P < .001) was observed. The low abundance of L. lactis in the CRC tissues was associated with the decreased NK cells, which suggested that this might contribute to the progression of CRC by decreasing the number of NK cells.Supplemental data for this article is available online at https://doi.org/10.1080/01635581.2021.1944649.
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Affiliation(s)
- Huan Li
- Department of Gastroenterology, The Central Hospital of Guangyuan City, Sichuan, China
| | - Xinhao Du
- Department of Digestive Endoscopy, The Affiliated Hospital of North Sichuan Medical College, Sichuan, China
| | - Li Yan
- Department of Digestive Endoscopy, The Affiliated Hospital of North Sichuan Medical College, Sichuan, China
| | - Zhenzhen Tang
- Department of Digestive Endoscopy, The Affiliated Hospital of North Sichuan Medical College, Sichuan, China
| | - Ling Zhang
- Department of Digestive Endoscopy, The Affiliated Hospital of North Sichuan Medical College, Sichuan, China
| | - Qiao Zheng
- Department of Digestive Endoscopy, The Affiliated Hospital of North Sichuan Medical College, Sichuan, China
| | - Xianghao Zeng
- Department of Digestive Endoscopy, The Affiliated Hospital of North Sichuan Medical College, Sichuan, China
| | - Guimei Chen
- Department of Digestive Endoscopy, The Affiliated Hospital of North Sichuan Medical College, Sichuan, China
| | - Huawen Yue
- Department of Digestive Endoscopy, The Affiliated Hospital of North Sichuan Medical College, Sichuan, China
| | - Xiangsheng Fu
- Department of Gastroenterology, The First Affiliated Hospital of Chengdu Medical College, Sichuan, China
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29
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Xu X, Zhang Z. Sex- and age-specific variation of gut microbiota in Brandt's voles. PeerJ 2021; 9:e11434. [PMID: 34164232 PMCID: PMC8194415 DOI: 10.7717/peerj.11434] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 04/20/2021] [Indexed: 12/14/2022] Open
Abstract
Background Gut microbiota plays a key role in the survival and reproduction of wild animals which rely on microbiota to break down plant compounds for nutrients. As compared to laboratory animals, wild animals face much more threat of environmental changes (e.g. food shortages and risk of infection). Therefore, studying the gut microbiota of wild animals can help us better understand the mechanisms animals use to adapt to their environment. Methods We collected the feces of Brandt’s voles in the grassland, of three age groups (juvenile, adult and old), in both sexes. We studied the gut microbiota by 16S rRNA sequencing. Results The main members of gut microbiota in Brandt’s voles were Firmicutes, Bacteroidetes and Proteobacteria. As voles get older, the proportion of Firmicutes increased gradually, and the proportion of Bacteroides decreased gradually. The diversity of the microbiota of juveniles is lower, seems like there is still a lot of space for colonization, and there are large variations in the composition of the microbiome between individuals. In adulthood, the gut microbiota tends to be stable, and the diversity is highest. In adult, the abundances of Christensenellaceae and Peptococcus of female were significantly higher than male voles. Conclusions The gut microbiota of Brandt’s vole was influenced by sex and age, probably due to growth needs and hormone levels. Gut microbiota of wild animals were much influenced by their life-history reflected by their age and sex. Future studies will be directed to identify functions of these “wild microbiota” in regulating physiological or behavioral processes of wild animals in different life stage or sexes.
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Affiliation(s)
- Xiaoming Xu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, Beijing, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, Beijing, China
| | - Zhibin Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, Beijing, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, Beijing, China
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Abstract
Animals live in symbiosis with numerous microbe species. While some can protect hosts from infection and benefit host health, components of the microbiota or changes to the microbial landscape have the potential to facilitate infections and worsen disease severity. Pathogens and pathobionts can exploit microbiota metabolites, or can take advantage of a depletion in host defences and changing conditions within a host, to cause opportunistic infection. The microbiota might also favour a more virulent evolutionary trajectory for invading pathogens. In this review, we consider the ways in which a host microbiota contributes to infectious disease throughout the host's life and potentially across evolutionary time. We further discuss the implications of these negative outcomes for microbiota manipulation and engineering in disease management.
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Affiliation(s)
- Emily J. Stevens
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Kieran A. Bates
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Kayla C. King
- Department of Zoology, University of Oxford, Oxford, United Kingdom
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Narasimhan H, Ren CC, Deshpande S, Sylvia KE. Young at Gut-Turning Back the Clock with the Gut Microbiome. Microorganisms 2021; 9:microorganisms9030555. [PMID: 33800340 PMCID: PMC8001982 DOI: 10.3390/microorganisms9030555] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/01/2021] [Accepted: 03/02/2021] [Indexed: 12/17/2022] Open
Abstract
Over the past century, we have witnessed an increase in life-expectancy due to public health measures; however, we have also seen an increase in susceptibility to chronic disease and frailty. Microbiome dysfunction may be linked to many of the conditions that increase in prevalence with age, including type 2 diabetes, cardiovascular disease, Alzheimer's disease, and cancer, suggesting the need for further research on these connections. Moreover, because both non-modifiable (e.g., age, sex, genetics) and environmental (e.g., diet, infection) factors can influence the microbiome, there are vast opportunities for the use of interventions related to the microbiome to promote lifespan and healthspan in aging populations. To understand the mechanisms mediating many of the interventions discussed in this review, we also provide an overview of the gut microbiome's relationships with the immune system, aging, and the brain. Importantly, we explore how inflammageing (low-grade chronic inflammation that often develops with age), systemic inflammation, and senescent cells may arise from and relate to the gut microbiome. Furthermore, we explore in detail the complex gut-brain axis and the evidence surrounding how gut dysbiosis may be implicated in several age-associated neurodegenerative diseases. We also examine current research on potential interventions for healthspan and lifespan as they relate to the changes taking place in the microbiome during aging; and we begin to explore how the reduction in senescent cells and senescence-associated secretory phenotype (SASP) interplay with the microbiome during the aging process and highlight avenues for further research in this area.
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Affiliation(s)
| | - Clarissa C. Ren
- Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA;
| | | | - Kristyn E. Sylvia
- The Society for Cardiovascular Angiography and Interventions, Washington, DC 20036, USA
- Correspondence: ; Tel.: +1-774-226-6214
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Touchefeu Y, Duchalais E, Bruley des Varannes S, Alameddine J, Mirallie E, Matysiak-Budnik T, Le Bastard Q, Javaudin F, Rimbert M, Jotereau F, Montassier E. Concomitant decrease of double-positive lymphocyte population CD4CD8αα and Faecalibacterium prausnitzii in patients with colorectal cancer. Eur J Gastroenterol Hepatol 2021; 32:149-156. [PMID: 32675782 DOI: 10.1097/meg.0000000000001842] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
INTRODUCTION AND AIMS Changes in the composition of the gut microbiota in patients with colorectal cancer (CRC) compatible with a contribution of the gut microbiota in carcinogenesis have been reported. In particular, a decrease Faecalibacterium prausnitzii has been identified. A CD4CD8αα, double-positive lymphocyte population (DP8α) has recently been demonstrated in the human colon and blood with regulatory functions and specificity for F. prausnitzii. Here, we aimed to detect dysbiosis in the fecal microbiome of patients with CRC by metagenomic analysis, and to look for changes in the levels of DP8α circulating T cells specific for F. prausnitzii in these patients. PATIENTS AND METHODS Patients with CRC and control subjects were prospectively included. None had received antibiotics in the previous month or any anti-tumor treatment. A stool sample was collected for each participant, and analyzed by shotgun sequencing. The DP8α T cell population was identified and quantified on fresh whole blood by flow cytometry with anti-CD45, anti-CD3, anti-CD4 and anti-CD8α co-labeling. RESULTS Twenty-one patients with CRC and 20 controls subjects were included. We found that mean relative abundance of five species was significantly decreased in CRC patients compared with controls, including F. prausnitzii, Barnesiella intestinihominis, Alistipes finegoldii, Bacteroides eggerthii and Eubacterium siraeum. We also found that the DP8α T cell population was significantly decreased in the blood of CRC patients compared with controls. CONCLUSION In our work, we showed that a reduced abundance of F. prausnitzii in CRC patients was associated to a significant decrease in the circulating DP8α Treg population, suggesting a potential involvement of reduced activity of DP8α T cells in colonic carcinogenesis. These findings open new diagnostic and therapeutic strategies for CRC.
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Affiliation(s)
- Yann Touchefeu
- Institut des Maladies de l'Appareil Digestif, CHU Nantes
- INSERM U1235
| | - Emilie Duchalais
- Institut des Maladies de l'Appareil Digestif, CHU Nantes
- INSERM U1235
| | | | | | - Eric Mirallie
- Institut des Maladies de l'Appareil Digestif, CHU Nantes
| | | | - Quentin Le Bastard
- Université de Nantes, Microbiotas Hosts Antibiotics and bacterial Resistances (MiHAR)
- Department of Emergency Medicine, CHU Nantes
| | - François Javaudin
- Université de Nantes, Microbiotas Hosts Antibiotics and bacterial Resistances (MiHAR)
- Department of Emergency Medicine, CHU Nantes
| | - Marie Rimbert
- Laboratoire d'immunologie, CIMNA, CHU de Nantes
- Centre de Recherche en Transplantation et Immunologie (CRTI), UMR 1064, INSERM
| | | | - Emmanuel Montassier
- Université de Nantes, Microbiotas Hosts Antibiotics and bacterial Resistances (MiHAR)
- Department of Emergency Medicine, CHU Nantes
- EA3826 Thérapeutiques Anti-Infectieuses, Institut de Recherche en Santé 2 Nantes Biotech, Medical University of Nantes
- Surgical Intensive Care Unit, Hotel Dieu, CHU Nantes, Nantes, France
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Ronan V, Yeasin R, Claud EC. Childhood Development and the Microbiome-The Intestinal Microbiota in Maintenance of Health and Development of Disease During Childhood Development. Gastroenterology 2021; 160:495-506. [PMID: 33307032 PMCID: PMC8714606 DOI: 10.1053/j.gastro.2020.08.065] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/25/2020] [Accepted: 08/29/2020] [Indexed: 12/11/2022]
Abstract
The composition of the intestinal microbiome affects health from the prenatal period throughout childhood, and many diseases have been associated with dysbiosis. The gut microbiome is constantly changing, from birth throughout adulthood, and several variables affect its development and content. Features of the intestinal microbiota can affect development of the brain, immune system, and lungs, as well as body growth. We review the development of the gut microbiome, proponents of dysbiosis, and interactions of the microbiota with other organs. The gut microbiome should be thought of as an organ system that has important effects on childhood development. Dysbiosis has been associated with diseases in children and adults, including autism, attention deficit hyperactivity disorder, asthma, and allergies.
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Affiliation(s)
- Victoria Ronan
- Department of Pediatrics, The University of Chicago, Chicago, IL
| | - Rummanu Yeasin
- Department of Pediatrics, The University of Chicago, Chicago, IL,Windsor University School of Medicine
| | - Erika C. Claud
- Department of Pediatrics, The University of Chicago, Chicago, IL,Corresponding Author: Erika C. Claud, MD, Department of Pediatrics, The University of Chicago, 5841 S. Maryland Ave, MC6060, Chicago, IL 60137, Phone 773-702-6210, Fax: 773-702-0764,
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Rohana H, Azrad M, Nitzan O, Adler A, Binyamin D, Koren O, Peretz A. Characterization of Clostridioides difficile Strains, the Disease Severity, and the Microbial Changes They Induce. J Clin Med 2020; 9:jcm9124099. [PMID: 33353133 PMCID: PMC7766075 DOI: 10.3390/jcm9124099] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 12/13/2020] [Accepted: 12/14/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Clostridioides difficile infection (CDI) is a major nosocomial disease. The characteristics of different strains, the disease severity they cause, their susceptibility to antibiotics, and the changes they inflict on gut microbiome, have not been comprehensively studied in Israel. METHODS A severity score was calculated for 70 patients. Stool samples were tested for toxins presence using a special kit. Bacteria were isolated, identified by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) and antibiotic susceptibility tests were performed for several antibiotics. Strains were classified by Multi-locus sequence typing (MLST), and changes in gut microbiome were tested. RESULTS ST04 (22.5%) and ST37 (12.7%) were the most frequent strains. Clade (phylogenetic lineage) 1 was the most (81.4%) prevalent. We found significant associations between ST and age (p = 0.024) and between ST and moxifloxacin susceptibility (p = 0.001). At the clade level, we found significant associations with binary toxin gene occurrence (p = 0.002), and with susceptibility to both metronidazole and vancomycin (p = 0.024, 0.035, respectively). Differences in intestine microbiome were affected by age, clades' distribution and STs. CONCLUSIONS By defining the characteristics of the different strains and clades, clinicians can choose medical interventions based on the predicted response or disease severity associated with each strain, enabling new advances in the field of personalized medicine.
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Affiliation(s)
- Hanan Rohana
- The Azrieli Faculty of Medicine, Bar Ilan University, Safed 1311502, Israel; (H.R.); (O.N.); (D.B.); (O.K.)
| | - Maya Azrad
- Baruch Padeh Medical Center, Clinical Microbiology Laboratory, Poriya, Tiberias 1528001, Israel;
| | - Orna Nitzan
- The Azrieli Faculty of Medicine, Bar Ilan University, Safed 1311502, Israel; (H.R.); (O.N.); (D.B.); (O.K.)
- Baruch Padeh Medical Center, Unit of Infectious Diseases, Poriya, Tiberias 1528001, Israel
| | - Amos Adler
- Tel Aviv Sourasky Medical Centre, Microbiology Laboratory, Tel Aviv 6423906, Israel;
- The Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Dana Binyamin
- The Azrieli Faculty of Medicine, Bar Ilan University, Safed 1311502, Israel; (H.R.); (O.N.); (D.B.); (O.K.)
| | - Omry Koren
- The Azrieli Faculty of Medicine, Bar Ilan University, Safed 1311502, Israel; (H.R.); (O.N.); (D.B.); (O.K.)
| | - Avi Peretz
- The Azrieli Faculty of Medicine, Bar Ilan University, Safed 1311502, Israel; (H.R.); (O.N.); (D.B.); (O.K.)
- Baruch Padeh Medical Center, Clinical Microbiology Laboratory, Poriya, Tiberias 1528001, Israel;
- Correspondence: ; Tel.: +972-4-665-2322
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Badal VD, Vaccariello ED, Murray ER, Yu KE, Knight R, Jeste DV, Nguyen TT. The Gut Microbiome, Aging, and Longevity: A Systematic Review. Nutrients 2020; 12:E3759. [PMID: 33297486 PMCID: PMC7762384 DOI: 10.3390/nu12123759] [Citation(s) in RCA: 203] [Impact Index Per Article: 50.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/03/2020] [Accepted: 12/03/2020] [Indexed: 12/12/2022] Open
Abstract
Aging is determined by complex interactions among genetic and environmental factors. Increasing evidence suggests that the gut microbiome lies at the core of many age-associated changes, including immune system dysregulation and susceptibility to diseases. The gut microbiota undergoes extensive changes across the lifespan, and age-related processes may influence the gut microbiota and its related metabolic alterations. The aim of this systematic review was to summarize the current literature on aging-associated alterations in diversity, composition, and functional features of the gut microbiota. We identified 27 empirical human studies of normal and successful aging suitable for inclusion. Alpha diversity of microbial taxa, functional pathways, and metabolites was higher in older adults, particularly among the oldest-old adults, compared to younger individuals. Beta diversity distances significantly differed across various developmental stages and were different even between oldest-old and younger-old adults. Differences in taxonomic composition and functional potential varied across studies, but Akkermansia was most consistently reported to be relatively more abundant with aging, whereas Faecalibacterium, Bacteroidaceae, and Lachnospiraceae were relatively reduced. Older adults have reduced pathways related to carbohydrate metabolism and amino acid synthesis; however, oldest-old adults exhibited functional differences that distinguished their microbiota from that of young-old adults, such as greater potential for short-chain fatty acid production and increased butyrate derivatives. Although a definitive interpretation is limited by the cross-sectional design of published reports, we integrated findings of microbial composition and downstream functional pathways and metabolites, offering possible explanations regarding age-related processes.
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Affiliation(s)
- Varsha D. Badal
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA; (V.D.B.); (E.D.V.); (E.R.M.); (K.E.Y.); (D.V.J.)
- Sam and Rose Stein Institute for Research on Aging, University of California San Diego, La Jolla, CA 92093, USA
| | - Eleonora D. Vaccariello
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA; (V.D.B.); (E.D.V.); (E.R.M.); (K.E.Y.); (D.V.J.)
| | - Emily R. Murray
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA; (V.D.B.); (E.D.V.); (E.R.M.); (K.E.Y.); (D.V.J.)
| | - Kasey E. Yu
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA; (V.D.B.); (E.D.V.); (E.R.M.); (K.E.Y.); (D.V.J.)
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA;
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, USA
| | - Dilip V. Jeste
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA; (V.D.B.); (E.D.V.); (E.R.M.); (K.E.Y.); (D.V.J.)
- Sam and Rose Stein Institute for Research on Aging, University of California San Diego, La Jolla, CA 92093, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, USA
- Department of Neurosciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Tanya T. Nguyen
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA; (V.D.B.); (E.D.V.); (E.R.M.); (K.E.Y.); (D.V.J.)
- Sam and Rose Stein Institute for Research on Aging, University of California San Diego, La Jolla, CA 92093, USA
- VA San Diego Healthcare System, La Jolla, CA 92161, USA
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Lach G, Fülling C, Bastiaanssen TFS, Fouhy F, Donovan ANO, Ventura-Silva AP, Stanton C, Dinan TG, Cryan JF. Enduring neurobehavioral effects induced by microbiota depletion during the adolescent period. Transl Psychiatry 2020; 10:382. [PMID: 33159036 PMCID: PMC7648059 DOI: 10.1038/s41398-020-01073-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/15/2020] [Accepted: 10/05/2020] [Indexed: 12/20/2022] Open
Abstract
The gut microbiota is an essential regulator of many aspects of host physiology. Disruption of gut microbial communities affects gut-brain communication which ultimately can manifest as changes in brain function and behaviour. Transient changes in gut microbial composition can be induced by various intrinsic and extrinsic factors, however, it is possible that enduring shifts in the microbiota composition can be achieved by perturbation at a timepoint when the gut microbiota has not fully matured or is generally unstable, such as during early life or ageing. In this study, we investigated the effects of 3-week microbiota depletion with antibiotic treatment during the adolescent period and in adulthood. Following a washout period to restore the gut microbiota, behavioural and molecular hallmarks of gut-brain communication were investigated. Our data revealed that transient microbiota depletion had long-lasting effects on microbiota composition and increased anxiety-like behaviour in mice exposed to antibiotic treatment during adolescence but not in adulthood. Similarly, gene expression in the amygdala was more severely affected in mice treated during adolescence. Taken together these data highlight the vulnerability of the gut microbiota during the critical adolescent period and the long-lasting impact manipulations of the microbiota can have on gene expression and behaviour in adulthood.
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Affiliation(s)
- Gilliard Lach
- grid.7872.a0000000123318773APC Microbiome Ireland, University College Cork, Cork, Ireland ,grid.4305.20000 0004 1936 7988Present Address: University of Edinburgh, Edinburgh, Scotland UK
| | - Christine Fülling
- grid.7872.a0000000123318773APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Thomaz F. S. Bastiaanssen
- grid.7872.a0000000123318773APC Microbiome Ireland, University College Cork, Cork, Ireland ,grid.7872.a0000000123318773Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| | - Fiona Fouhy
- grid.7872.a0000000123318773APC Microbiome Ireland, University College Cork, Cork, Ireland ,grid.6435.40000 0001 1512 9569Teagasc Food Research Centre, Food Biosciences Department, Moorepark, Fermoy, Ireland
| | - Aoife N. O’ Donovan
- grid.7872.a0000000123318773APC Microbiome Ireland, University College Cork, Cork, Ireland ,grid.6435.40000 0001 1512 9569Teagasc Food Research Centre, Food Biosciences Department, Moorepark, Fermoy, Ireland ,grid.7872.a0000000123318773School of Microbiology, University College Cork, Cork, Ireland
| | | | - Catherine Stanton
- grid.7872.a0000000123318773APC Microbiome Ireland, University College Cork, Cork, Ireland ,grid.6435.40000 0001 1512 9569Teagasc Food Research Centre, Food Biosciences Department, Moorepark, Fermoy, Ireland
| | - Timothy G. Dinan
- grid.7872.a0000000123318773APC Microbiome Ireland, University College Cork, Cork, Ireland ,grid.7872.a0000000123318773Department of Psychiatry and Neurobehavioural Sciences, University College Cork, Cork, Ireland
| | - John F. Cryan
- grid.7872.a0000000123318773APC Microbiome Ireland, University College Cork, Cork, Ireland ,grid.7872.a0000000123318773Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
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Yuan X, Chen R, Zhang Y, Lin X, Yang X. Gut microbiota: effect of pubertal status. BMC Microbiol 2020; 20:334. [PMID: 33143658 PMCID: PMC7640488 DOI: 10.1186/s12866-020-02021-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 10/26/2020] [Indexed: 12/13/2022] Open
Abstract
Background The make-up of gut microbiota at different puberty stages has not been reported. This cross-sectional study analyzed the bio-diversity of gut microbiota at different puberty stages. Result The subjects (aged 5–15 years) were divided into non-pubertal (n = 42, male%: 66.7%) or pubertal groups (n = 47, male%:44.68); in both groups, Firmicutes, Bacteroidetes and Proteobacteria were the dominant phylum. There was no difference of alpha- and beta-diversity among disparate puberty stages. Non-pubertal subjects had members of the order Clostridiales, family Clostridiaceae, genus Coprobacillus which were significantly more prevalent than puberty subjects. Also, the pubertal subjects had members of class Betaproteobacteria, order Burkholderiales which were significantly more prevalent than the non-pubertal subjects. Their relative abundance was independent of BMI-Z. In the pubertal subjects, the abundance of genus Adlercreutzia, Ruminococcus, Dorea, Clostridium and Parabacteroides was associated with the level of testosterone. Conclusions This is the first report of the diversity of gut microbiota at different puberty stages. The various species of gut microbiota changed gradually associated with puberty stages. Differences in gut microflora at different pubertal status may be related to androgen levels. Supplementary Information Supplementary information accompanies this paper at 10.1186/s12866-020-02021-0.
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Affiliation(s)
- Xin Yuan
- Department of Endocrinology, Genetics and Metabolism, Fuzhou Children's Hospital of Fujian Medical University, NO.145, 817 Middle Road, Fuzhou, 350005, China
| | - Ruimin Chen
- Department of Endocrinology, Genetics and Metabolism, Fuzhou Children's Hospital of Fujian Medical University, NO.145, 817 Middle Road, Fuzhou, 350005, China.
| | - Ying Zhang
- Department of Endocrinology, Genetics and Metabolism, Fuzhou Children's Hospital of Fujian Medical University, NO.145, 817 Middle Road, Fuzhou, 350005, China
| | - Xiangquan Lin
- Department of Endocrinology, Genetics and Metabolism, Fuzhou Children's Hospital of Fujian Medical University, NO.145, 817 Middle Road, Fuzhou, 350005, China
| | - Xiaohong Yang
- Department of Endocrinology, Genetics and Metabolism, Fuzhou Children's Hospital of Fujian Medical University, NO.145, 817 Middle Road, Fuzhou, 350005, China
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Is inflammageing influenced by the microbiota in the aged gut? A systematic review. Exp Gerontol 2020; 141:111079. [DOI: 10.1016/j.exger.2020.111079] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 08/02/2020] [Accepted: 08/28/2020] [Indexed: 12/21/2022]
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Intestinal stem cells heterogeneity and clonal dominance during aging: two faces of the same coin? Mech Ageing Dev 2020; 189:111247. [PMID: 32505859 DOI: 10.1016/j.mad.2020.111247] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 04/03/2020] [Accepted: 04/05/2020] [Indexed: 11/20/2022]
Abstract
Intestinal epithelium undergoes dysfunctions and diseases over time with an exponential increase in the elderly population. Recent studies reported that the intestinal stem cells (ISCs) show a functional decline during aging and a lack of an appropriate cell identity control. Increase of cell-to-cell heterogeneity is a hallmark of aging tissues and organs, however there is little experimental evidence with regard to the cell heterogeneity of the ISCs. On the other hand, the ISCs continuously experience a niche clonality process that diminishes the initial cell heterogeneity over time. In this review, we discuss the latest findings on these topics focusing on the potential mechanisms driving intestinal stem cell heterogeneity and clonality during aging.
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Translational Potential of Metabolomics on Animal Models of Inflammatory Bowel Disease-A Systematic Critical Review. Int J Mol Sci 2020; 21:ijms21113856. [PMID: 32485793 PMCID: PMC7312423 DOI: 10.3390/ijms21113856] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 05/24/2020] [Accepted: 05/26/2020] [Indexed: 12/16/2022] Open
Abstract
In the development of inflammatory bowel disease (IBD), the gut microbiota has been established as a key factor. Recently, metabolomics has become important for understanding the functional relevance of gut microbial changes in disease. Animal models for IBD enable the study of factors involved in disease development. However, results from animal studies may not represent the human situation. The aim of this study was to investigate whether results from metabolomics studies on animal models for IBD were similar to those from studies on IBD patients. Medline and Embase were searched for relevant studies up to May 2017. The Covidence systematic review software was used for study screening, and quality assessment was conducted for all included studies. Data showed a convergence of ~17% for metabolites differentiated between IBD and controls in human and animal studies with amino acids being the most differentiated metabolite subclass. The acute dextran sodium sulfate model appeared as a good model for analysis of systemic metabolites in IBD, but analytical platform, age, and biological sample type did not show clear correlations with any significant metabolites. In conclusion, this systematic review highlights the variation in metabolomics results, and emphasizes the importance of expanding the applied detection methods to ensure greater coverage and convergence between the various different patient phenotypes and animal models of inflammatory bowel disease.
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Comparison Between the Gut Microbiota in Different Gastrointestinal Segments of Large-Tailed Han and Small-Tailed Han Sheep Breeds with High-Throughput Sequencing. Indian J Microbiol 2020; 60:436-450. [PMID: 33087993 DOI: 10.1007/s12088-020-00885-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 05/11/2020] [Indexed: 12/27/2022] Open
Abstract
Commensal microorganisms are essential to the normal development and function of many aspects of animal biology. However, the dynamic shift patterns of the microbiota of different gut segments in sheep and the correlation between fat type large-tailed phenotype and microbiota remain poorly unknown. This study therefore sought to assess the composition and distribution of the intestinal microbiome, and compared the difference of gut microbiota from different gastrointestinal segments within breeds and same intestinal sections between breeds. For these analyses, 16S rRNA V4 regions from 4 gut sections prepared from each of six individuals (3 from each breed) were sequenced to detect the microbiome composition in these samples. These analyses revealed the presence of 51,173 operational taxonomic units distributed across 24 phyla and 420 genera in these samples, with Firmicutes and Bacteroidetes being the most prevalent phyla of microbes present in these samples. Moreover, the bacterial composition showed distinct microbial communities in different gastrointestinal segments within breed, but showed similar and relative fixed bacterial abundance in the same intestinal segments from individuals of different breeds. We also found that only a few bacterial species (Lachnospiraceae, Akkermansia) were needed to distinguish between Small-tailed Han sheep (STH) and Large-tailed Han sheep (LTH) and their metabolic process maybe influence the fat type large-tailed phenotype formation in sheep. The functional profile analysis revealed that the environment information processing, genetic information processing, and metabolic pathways were enriched in all samples. The main functional roles of the gut microbiota were amino acid metabolism, replication and repair, carbohydrate metabolism, and membrane transport. Finally, our findings suggested that distinguished gut species between STH and LTH have relative fixed and the potential correlation is existing between the intestinal microorganisms and the large-tailed phenotype trait formation of sheep, which may offer clues for further investigation to detect the roles of intestinal microbiota in the metabolism and fat deposition in the tail of sheep.
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Wang LJ, Yang CY, Chou WJ, Lee MJ, Chou MC, Kuo HC, Yeh YM, Lee SY, Huang LH, Li SC. Gut microbiota and dietary patterns in children with attention-deficit/hyperactivity disorder. Eur Child Adolesc Psychiatry 2020; 29:287-297. [PMID: 31119393 DOI: 10.1007/s00787-019-01352-2] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 05/13/2019] [Indexed: 12/26/2022]
Abstract
Attention-deficit/hyperactivity disorder (ADHD) is a common neurodevelopmental disorder, but the underlying pathophysiological mechanisms of ADHD remain unclear. Gut microbiota has been recognized to influence brain function and behaviors. Therefore, this study aimed to determine whether imbalanced gut microbiomes identified by a 16S rRNA sequencing approach are involved in the pathophysiology of ADHD. We recruited a total of 30 children with ADHD (mean age: 8.4 years) and a total of 30 healthy controls (mean age: 9.3 years) for this study. The dietary patterns of all participants were assessed with the food frequency questionnaire. The microbiota of fecal samples were investigated using 16S rRNA V3V4 amplicon sequencing, followed by bioinformatics and statistical analyses. We found that the gut microbiota communities in ADHD patients showed a significantly higher Shannon index and Chao index than the control subjects. Furthermore, the linear discriminant analysis effect size (LEfSe) analysis was used to identify differentially enriched bacteria between ADHD patients and healthy controls. The relative abundance of Bacteroides coprocola (B. coprocola) was decreased, while the relative abundance of Bacteroides uniformis (B. uniformis), Bacteroides ovatus (B. ovatus), and Sutterella stercoricanis (S. stercoricanis) were increased in the ADHD group. Of all participants, S. stercoricanis demonstrated a significant association with the intake of dairy, nuts/seeds/legumes, ferritin and magnesium. B. ovatus and S. stercoricanis were positively correlated to ADHD symptoms. In conclusion, we suggest that the gut microbiome community is associated with dietary patterns, and linked to the susceptibility to ADHD.
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Affiliation(s)
- Liang-Jen Wang
- Department of Child and Adolescent Psychiatry, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Department of Chinese Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chia-Yu Yang
- Department of Microbiology and Immunology/Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Division of Colon and Rectal Surgery, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Wen-Jiun Chou
- Department of Child and Adolescent Psychiatry, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Min-Jing Lee
- Department of Child and Adolescent Psychiatry, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Miao-Chun Chou
- Department of Child and Adolescent Psychiatry, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Ho-Chang Kuo
- Department of Pediatrics, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Kawasaki Disease Center, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Yuan-Ming Yeh
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Genomic Medicine Research Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Sheng-Yu Lee
- Department of Psychiatry, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan.,Department of Psychiatry, College of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Lien-Hung Huang
- Genomics and Proteomics Core Laboratory, Department of Medical Research, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, No.123, Ta-Pei Road, Kaohsiung City, Taiwan
| | - Sung-Chou Li
- Genomics and Proteomics Core Laboratory, Department of Medical Research, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, No.123, Ta-Pei Road, Kaohsiung City, Taiwan.
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Xing PY, Pettersson S, Kundu P. Microbial Metabolites and Intestinal Stem Cells Tune Intestinal Homeostasis. Proteomics 2020; 20:e1800419. [PMID: 31994831 DOI: 10.1002/pmic.201800419] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 01/07/2020] [Indexed: 12/13/2022]
Abstract
Microorganisms that colonize the gastrointestinal tract, collectively known as the gut microbiota, are known to produce small molecules and metabolites that significantly contribute to host intestinal development, functions, and homeostasis. Emerging insights from microbiome research reveal that gut microbiota-derived signals and molecules influence another key player maintaining intestinal homeostasis-the intestinal stem cell niche, which regulates epithelial self-renewal. In this review, the literature on gut microbiota-host crosstalk is surveyed, highlighting the effects of gut microbial metabolites on intestinal stem cells. The production of various classes of metabolites, their actions on intestinal stem cells are discussed and, finally, how the production and function of metabolites are modulated by aging and dietary intake is commented upon.
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Affiliation(s)
- Peter Yuli Xing
- Singapore Centre for Environmental Life Sciences Engineering, 60 Nanyang Drive, Singapore, 637551, Singapore.,Interdisciplinary Graduate School, Nanyang Technological University, 50 Nanyang Avenue, South Spine, Level B3, Block S2-B3a, Singapore, 639798, Singapore
| | - Sven Pettersson
- Singapore Centre for Environmental Life Sciences Engineering, 60 Nanyang Drive, Singapore, 637551, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore, 308232, Singapore.,Department of Neurobiology, Care Sciences and Society, Karolinska Institute, SE, 17 177, Stockholm, Sweden
| | - Parag Kundu
- Singapore Centre for Environmental Life Sciences Engineering, 60 Nanyang Drive, Singapore, 637551, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore, 308232, Singapore.,The Center for Microbes, Development and Health, Laboratory for Microbiota-Host Interactions, Institute Pasteur of Shanghai, Chinese Academy of Sciences, 320 Yueyang Road, Life Science Research Building, Shanghai, 200031, China
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Tarasiuk A, Fichna J. Gut microbiota: what is its place in pharmacology? Expert Rev Clin Pharmacol 2019; 12:921-930. [DOI: 10.1080/17512433.2019.1670058] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Aleksandra Tarasiuk
- Department of Biochemistry, Faculty of Medicine, Medical University of Lodz, Lodz, Poland
| | - Jakub Fichna
- Department of Biochemistry, Faculty of Medicine, Medical University of Lodz, Lodz, Poland
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Role of Personalized Nutrition in Chronic-Degenerative Diseases. Nutrients 2019; 11:nu11081707. [PMID: 31344895 PMCID: PMC6723746 DOI: 10.3390/nu11081707] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 07/15/2019] [Accepted: 07/20/2019] [Indexed: 02/07/2023] Open
Abstract
Human nutrition is a branch of medicine based on foods biochemical interactions with the human body. The phenotypic transition from health to disease status can be attributed to changes in genes and/or protein expression. For this reason, a new discipline has been developed called “-omic science”. In this review, we analyzed the role of “-omics sciences” (nutrigenetics, nutrigenomics, proteomics and metabolomics) in the health status and as possible therapeutic tool in chronic degenerative diseases. In particular, we focused on the role of nutrigenetics and the relationship between eating habits, changes in the DNA sequence and the onset of nutrition-related diseases. Moreover, we examined nutrigenomics and the effect of nutrients on gene expression. We perused the role of proteomics and metabolomics in personalized nutrition. In this scenario, we analyzed also how dysbiosis of gut microbiota can influence the onset and progression of chronic degenerative diseases. Moreover, nutrients influencing and regulating gene activity, both directly and indirectly, paves the way for personalized nutrition that plays a key role in the prevention and treatment of chronic degenerative diseases.
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de la Cuesta-Zuluaga J, Kelley ST, Chen Y, Escobar JS, Mueller NT, Ley RE, McDonald D, Huang S, Swafford AD, Knight R, Thackray VG. Age- and Sex-Dependent Patterns of Gut Microbial Diversity in Human Adults. mSystems 2019; 4:e00261-19. [PMID: 31098397 PMCID: PMC6517691 DOI: 10.1128/msystems.00261-19] [Citation(s) in RCA: 182] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 04/30/2019] [Indexed: 11/22/2022] Open
Abstract
Gut microbial diversity changes throughout the human life span and is known to be associated with host sex. We investigated the association of age, sex, and gut bacterial alpha diversity in three large cohorts of adults from four geographical regions: subjects from the United States and United Kingdom in the American Gut Project (AGP) citizen-science initiative and two independent cohorts of Colombians and Chinese. In three of the four cohorts, we observed a strong positive association between age and alpha diversity in young adults that plateaued after age 40 years. We also found sex-dependent differences that were more pronounced in younger adults than in middle-aged adults, with women having higher alpha diversity than men. In contrast to the other three cohorts, no association of alpha diversity with age or sex was observed in the Chinese cohort. The association of alpha diversity with age and sex remained after adjusting for cardiometabolic parameters in the Colombian cohort and antibiotic usage in the AGP cohort. We further attempted to predict the microbiota age in individuals using a machine-learning approach for the men and women in each cohort. Consistent with our alpha-diversity-based findings, U.S. and U.K. women had a significantly higher predicted microbiota age than men, with a reduced difference being seen above age 40 years. This difference was not observed in the Colombian cohort and was observed only in middle-aged Chinese adults. Together, our results provide new insights into the influence of age and sex on the biodiversity of the human gut microbiota during adulthood while highlighting similarities and differences across diverse cohorts. IMPORTANCE Microorganisms in the human gut play a role in health and disease, and in adults higher gut biodiversity has been linked to better health. Since gut microorganisms may be pivotal in the development of microbial therapies, understanding the factors that shape gut biodiversity is of utmost interest. We performed large-scale analyses of the relationship of age and sex to gut bacterial diversity in adult cohorts from four geographic regions: the United States, the United Kingdom, Colombia, and China. In the U.S., U.K., and Colombian cohorts, bacterial biodiversity correlated positively with age in young adults but plateaued at about age 40 years, with no positive association being found in middle-aged adults. Young, but not middle-aged, adult women had higher gut bacterial diversity than men, a pattern confirmed via supervised machine learning. Interestingly, in the Chinese cohort, minimal associations were observed between gut biodiversity and age or sex. Our results highlight the patterns of adult gut biodiversity and provide a framework for future research.
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Affiliation(s)
| | - Scott T. Kelley
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Yingfeng Chen
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Juan S. Escobar
- Vidarium—Nutrition, Health and Wellness Research Center, Grupo Empresarial Nutresa, Medellin, Colombia
| | - Noel T. Mueller
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Welch Center for Epidemiology, Prevention and Clinical Research, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Ruth E. Ley
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Daniel McDonald
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
| | - Shi Huang
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
| | - Austin D. Swafford
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, California, USA
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, California, USA
- Department of Computer Science, University of California, San Diego, La Jolla, California, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Varykina G. Thackray
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, California, USA
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Gadecka A, Bielak-Zmijewska A. Slowing Down Ageing: The Role of Nutrients and Microbiota in Modulation of the Epigenome. Nutrients 2019; 11:nu11061251. [PMID: 31159371 PMCID: PMC6628342 DOI: 10.3390/nu11061251] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 05/27/2019] [Accepted: 05/28/2019] [Indexed: 12/13/2022] Open
Abstract
The human population is getting ageing. Both ageing and age-related diseases are correlated with an increased number of senescent cells in the organism. Senescent cells do not divide but are metabolically active and influence their environment by secreting many proteins due to a phenomenon known as senescence associated secretory phenotype (SASP). Senescent cells differ from young cells by several features. They possess more damaged DNA, more impaired mitochondria and an increased level of free radicals that cause the oxidation of macromolecules. However, not only biochemical and structural changes are related to senescence. Senescent cells have an altered chromatin structure, and in consequence, altered gene expression. With age, the level of heterochromatin decreases, and less condensed chromatin is more prone to DNA damage. On the one hand, some gene promoters are easily available for the transcriptional machinery; on the other hand, some genes are more protected (locally increased level of heterochromatin). The structure of chromatin is precisely regulated by the epigenetic modification of DNA and posttranslational modification of histones. The methylation of DNA inhibits transcription, histone methylation mostly leads to a more condensed chromatin structure (with some exceptions) and acetylation plays an opposing role. The modification of both DNA and histones is regulated by factors present in the diet. This means that compounds contained in daily food can alter gene expression and protect cells from senescence, and therefore protect the organism from ageing. An opinion prevailed for some time that compounds from the diet do not act through direct regulation of the processes in the organism but through modification of the physiology of the microbiome. In this review we try to explain the role of some food compounds, which by acting on the epigenetic level might protect the organism from age-related diseases and slow down ageing. We also try to shed some light on the role of microbiome in this process.
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Affiliation(s)
- Agnieszka Gadecka
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur St., 02-093 Warsaw, Poland.
| | - Anna Bielak-Zmijewska
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur St., 02-093 Warsaw, Poland.
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Smith LK, Wissel EF. Microbes and the Mind: How Bacteria Shape Affect, Neurological Processes, Cognition, Social Relationships, Development, and Pathology. PERSPECTIVES ON PSYCHOLOGICAL SCIENCE 2019; 14:397-418. [DOI: 10.1177/1745691618809379] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Recent data suggest that the human body is not so exclusively human after all. Specifically, humans share their bodies with approximately 10 trillion microorganisms, collectively known as the microbiome. Chief among these microbes are bacteria, and there is a growing consensus that they are critical to virtually all facets of normative functioning. This article reviews the ways in which bacteria shape affect, neurological processes, cognition, social relationships, development, and psychological pathology. To date, the vast majority of research on interactions between microbes and humans has been conducted by scientists outside the field of psychology, despite the fact that psychological scientists are experts in many of the topics being explored. This review aims to orient psychological scientists to the most relevant research and perspectives regarding the microbiome so that we might contribute to the now widespread, interdisciplinary effort to understand the relationship between microbes and the mind.
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Affiliation(s)
- Leigh K. Smith
- Department of Psychology, University of California, Davis
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Rahayu ES, Utami T, Mariyatun M, Hasan PN, Kamil RZ, Setyawan RH, Pamungkaningtyas FH, Harahap IA, Wiryohanjoyo DV, Pramesi PC, Cahyanto MN, Sujaya IN, Juffrie M. Gut microbiota profile in healthy Indonesians. World J Gastroenterol 2019; 25:1478-1491. [PMID: 30948911 PMCID: PMC6441913 DOI: 10.3748/wjg.v25.i12.1478] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 01/11/2019] [Accepted: 01/26/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Recently, gut microbiota has been associated with various diseases other than intestinal disease. Thus, there has been rapid growth in the study of gut microbiota. Considering the numerous factors influencing gut microbiota such as age, diet, etc., area-based research is required. Indonesia has numerous different tribes and each of these tribes have different lifestyles. Hence, it is expected that each tribe has a specific gut microbiota. A deeper insight into the composition of gut microbiota can be used to determine the condition of gut microbiota in Indonesians and to consider which treatment may be suitable and effective to improve health status.
AIM To investigate the gut microbiota of Indonesian subjects represented by Javanese and Balinese tribes by analyzing fecal samples.
METHODS Fecal samples were collected from a total of 80 individuals with 20 in each of the young groups ranging from 25-45 years and the elderly group aged 70 years or more from two different regions, Yogyakarta and Bali. Fecal sample collection was performed at the end of the assessment period (day 14 ± 1 d) during which time the subjects were not allowed to consume probiotic or antibiotic products. The quantification of various Clostridium subgroups, Lactobacillus subgroups, Enterococcus, Streptococcus, Staphylococcus, Bacteroides fragilis group and Prevotella, Bifidobacterium and Atopobium cluster, Enterobacteriaceae and Pseudomonas was performed using the Yakult intestinal flora-scan (YIF-SCAN).
RESULTS The bacterial population in younger subjects’ feces was higher than that in the elderly population, with a total of approximately 10.0 – 10.6 log10 bacterial cells/g feces. The most abundant bacteria in all groups were Clostridium, followed by Prevotella, Atopobium, Bifidobacterium and Bacteroides. In the elderly, an increase in Enterobacteriaceae, Coliform and Escherichia coli was found. In terms of bacterial counts in Yogyakarta, total bacteria, Clostridium coccoides (C. coccoides) group, Bifidobacterium, Prevotella, Lactobacillus plantarum subgroup, and Streptococcus were significantly higher (P < 0.05) in younger than elderly subjects, while the Lactobacillus gasseri subgroup, Lactobacillus casei subgroup, and Lactobacillus reuteri subgroup counts were significantly lower (P < 0.05) in younger subjects. In Balinese subjects, total bacteria, C. coccoides group, Clostridium leptum subgroup, Bacteroides fragilis group, and Prevotella were significantly higher (P < 0.05) in younger compared to elderly individuals, while the Lactobacillus ruminis subgroup, and Enterobacteriaceae were significantly lower (P < 0.05) in younger subjects. The results also revealed that, besides the C. coccoides group and Clostridium leptum group being the most abundant gut microbiota in both Yogyakarta and Balinese people, the latter was indicated by a higher Clostridium perfringens count, which was almost 10 times that of Yogyakarta subjects. This may be a response to different lifestyles in the different tribes; however, this phenomenon requires further extensive study.
CONCLUSION Bacterial populations were higher in younger than in elderly subjects. Most abundant bacterial groups were Clostridium, Prevotella, Atopobium, Bifidobacterium, and Bacteroides. The level of Clostridium perfringens in Yogyakarta subjects was lower than that in Balinese subjects.
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Affiliation(s)
- Endang Sutriswati Rahayu
- Department of Food and Agricultural Technology, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | - Tyas Utami
- Department of Food and Agricultural Technology, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | - Mariyatun Mariyatun
- Department of Food and Agricultural Technology, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | - Pratama Nur Hasan
- Department of Food and Agricultural Technology, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | - Rafli Zulfa Kamil
- Department of Food and Agricultural Technology, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | - Ryan Haryo Setyawan
- Department of Food and Agricultural Technology, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | | | - Iskandar Azmy Harahap
- Department of Food and Agricultural Technology, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | - Devin Varian Wiryohanjoyo
- Department of Food and Agricultural Technology, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | - Putrika Citta Pramesi
- Department of Food and Agricultural Technology, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | - Muhammad Nur Cahyanto
- Department of Food and Agricultural Technology, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | - I Nengah Sujaya
- Department of Public Health, Udayana University, Denpasar 80234, Indonesia
| | - Mohammad Juffrie
- Department of Public Health, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
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Uebelhack R, Bongartz U, Seibt S, Bothe G, Chong PW, De Costa P, Wszelaki N. Double-Blind, Randomized, Three-Armed, Placebo-Controlled, Clinical Investigation to Evaluate the Benefit and Tolerability of Two Dosages of IQP-AE-103 in Reducing Body Weight in Overweight and Moderately Obese Subjects. J Obes 2019; 2019:3412952. [PMID: 30863632 PMCID: PMC6377993 DOI: 10.1155/2019/3412952] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 12/13/2018] [Accepted: 12/19/2018] [Indexed: 12/03/2022] Open
Abstract
Objective This study was performed to determine the efficacy and tolerability/safety of IQP-AE-103 on body weight reduction in overweight to moderately obese adults. Methods A double-blind, randomized, placebo-controlled trial involved one hundred and eight subjects (BMI between 25 and 35 kg/m2) that were randomly assigned to either the low-dose or the high-dose IQP-AE-103 group, or the placebo group. Following a 2-week run-in period, subjects received two capsules of investigational product after three daily main meals for 12 weeks. Subjects were instructed to maintain a nutritionally balanced hypocaloric diet according to the individual's energy requirement. Body weight, body fat, and waist and hip circumference were measured at baseline, and after 2, 4, 8, and 12 weeks. Subjects also rated their feelings of hunger and fullness using visual analogue scales, and food craving on a 5-point scale at the same time intervals. Blood samplings for safety laboratory parameters were taken before and at the end of the study. Results After 12 weeks of intake, the high-dose IQP-AE-103 group had a significantly greater weight loss compared with the placebo (5.03 ± 2.50 kg vs. 0.98 ± 2.06 kg, respectively; p < 0.001) and the low-dose group (3.01 ± 2.19 kg; p=0.001). The high-dose group experienced a decrease in body fat of 3.15 ± 2.41 kg compared with a decrease of 0.23 ± 2.74 kg for the placebo group (p < 0.001). High-dose IQP-AE-103 also decreased the feeling of hunger in 66% subjects. A beneficial effect of IQP-AE-103 on the lipid metabolism was also demonstrated in the subgroup of subjects with baseline total cholesterol levels above 6.2 mmol/L. No side effects related to the intake of IQP-AE-103 were reported. Conclusions These findings indicate that IQP-AE-103 could be an effective and safe weight loss intervention. This trial is registered with NCT03058367.
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Affiliation(s)
- Ralf Uebelhack
- analyze & realize GmbH, Weißenseer Weg 111, 10369 Berlin, Germany
| | - Udo Bongartz
- analyze & realize GmbH, Weißenseer Weg 111, 10369 Berlin, Germany
| | | | - Gordana Bothe
- analyze & realize GmbH, Waldseeweg 6, 13467 Berlin, Germany
| | - Pee Win Chong
- Zaluvida Corporate Sdn Bhd, E-16 Plaza Mont Kiara, 2 Jalan Kiara, 50480 Kuala Lumpur, Malaysia
| | - Patricia De Costa
- InQpharm Group Sdn Bhd, E-16 Plaza Mont Kiara, 2 Jalan Kiara, 50480 Kuala Lumpur, Malaysia
| | - Natalia Wszelaki
- Zaluvida Corporate Sdn Bhd, E-16 Plaza Mont Kiara, 2 Jalan Kiara, 50480 Kuala Lumpur, Malaysia
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