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Climent-Pérez P, Martínez-González AE, Andreo-Martínez P. Contributions of Artificial Intelligence to Analysis of Gut Microbiota in Autism Spectrum Disorder: A Systematic Review. CHILDREN (BASEL, SWITZERLAND) 2024; 11:931. [PMID: 39201866 PMCID: PMC11352523 DOI: 10.3390/children11080931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 07/26/2024] [Accepted: 07/27/2024] [Indexed: 09/03/2024]
Abstract
BACKGROUND Autism spectrum disorder (ASD) is a highly heterogeneous neurodevelopmental disorder whose etiology is not known today, but everything indicates that it is multifactorial. For example, genetic and epigenetic factors seem to be involved in the etiology of ASD. In recent years, there has been an increase in studies on the implications of gut microbiota (GM) on the behavior of children with ASD given that dysbiosis in GM may trigger the onset, development and progression of ASD through the microbiota-gut-brain axis. At the same time, significant progress has occurred in the development of artificial intelligence (AI). METHODS The aim of the present study was to perform a systematic review of articles using AI to analyze GM in individuals with ASD. In line with the PRISMA model, 12 articles using AI to analyze GM in ASD were selected. RESULTS Outcomes reveal that the majority of relevant studies on this topic have been conducted in China (33.3%) and Italy (25%), followed by the Netherlands (16.6%), Mexico (16.6%) and South Korea (8.3%). CONCLUSIONS The bacteria Bifidobacterium is the most relevant biomarker with regard to ASD. Although AI provides a very promising approach to data analysis, caution is needed to avoid the over-interpretation of preliminary findings. A first step must be taken to analyze GM in a representative general population and ASD samples in order to obtain a GM standard according to age, sex and country. Thus, more work is required to bridge the gap between AI in mental health research and clinical care in ASD.
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Affiliation(s)
- Pau Climent-Pérez
- Department of Computing Technology, University of Alicante, 03690 San Vicente del Raspeig, Alicante, Spain;
| | | | - Pedro Andreo-Martínez
- Department of Agricultural Chemistry, Faculty of Chemistry, Regional Campus of International Excellence “Campus Mare Nostrum”, University of Murcia, Campus of Espinardo, 30100 Murcia, Spain;
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Yang C, Xiao H, Zhu H, Du Y, Wang L. Revealing the gut microbiome mystery: A meta-analysis revealing differences between individuals with autism spectrum disorder and neurotypical children. Biosci Trends 2024; 18:233-249. [PMID: 38897955 DOI: 10.5582/bst.2024.01123] [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] [Indexed: 06/21/2024]
Abstract
The brain-gut axis intricately links gut microbiota (GM) dysbiosis to the development or worsening of autism spectrum disorder (ASD). However, the precise GM composition in ASD and the effectiveness of probiotics are unclear. To address this, we performed a thorough meta-analysis of 28 studies spanning PubMed, PsycINFO, Web of Science, Scopus, and MEDLINE, involving 1,256 children with ASD and 1042 neurotypical children, up to February 2024. Using Revman 5.3, we analyzed the relative abundance of 8 phyla and 64 genera. While individuals with ASD did not exhibit significant differences in included phyla, they exhibited elevated levels of Parabacteroides, Anaerostipes, Faecalibacterium, Clostridium, Dorea, Phascolarctobacterium, Lachnoclostridium, Catenibacterium, and Collinsella along with reduced percentages of Barnesiella, Odoribacter, Paraprevotella, Blautia, Turicibacter, Lachnospira, Pseudomonas, Parasutterella, Haemophilus, and Bifidobacterium. Notably, discrepancies in Faecalibacterium, Clostridium, Dorea, Phascolarctobacterium, Catenibacterium, Odoribacter, and Bifidobacterium persisted even upon systematic exclusion of individual studies. Consequently, the GM of individuals with ASD demonstrates an imbalance, with potential increases or decreases in both beneficial and harmful bacteria. Therefore, personalized probiotic interventions tailored to ASD specifics are imperative, rather than a one-size-fits-all approach.
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Affiliation(s)
- Changjiang Yang
- Faculty of Education, East China Normal University, Shanghai, China
| | - Hongli Xiao
- Faculty of Education, East China Normal University, Shanghai, China
| | - Han Zhu
- Faculty of Education, East China Normal University, Shanghai, China
| | - Yijie Du
- Qingpu Traditional Chinese Medicine Hospital, Shanghai, China
| | - Ling Wang
- Laboratory for Reproductive Immunology, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
- The Academy of Integrative Medicine, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Female Reproductive Endocrine-related Diseases, Shanghai, China
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Borrego-Ruiz A, Borrego JJ. Neurodevelopmental Disorders Associated with Gut Microbiome Dysbiosis in Children. CHILDREN (BASEL, SWITZERLAND) 2024; 11:796. [PMID: 39062245 PMCID: PMC11275248 DOI: 10.3390/children11070796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 06/20/2024] [Accepted: 06/25/2024] [Indexed: 07/28/2024]
Abstract
The formation of the human gut microbiome initiates in utero, and its maturation is established during the first 2-3 years of life. Numerous factors alter the composition of the gut microbiome and its functions, including mode of delivery, early onset of breastfeeding, exposure to antibiotics and chemicals, and maternal stress, among others. The gut microbiome-brain axis refers to the interconnection of biological networks that allow bidirectional communication between the gut microbiome and the brain, involving the nervous, endocrine, and immune systems. Evidence suggests that the gut microbiome and its metabolic byproducts are actively implicated in the regulation of the early brain development. Any disturbance during this stage may adversely affect brain functions, resulting in a variety of neurodevelopmental disorders (NDDs). In the present study, we reviewed recent evidence regarding the impact of the gut microbiome on early brain development, alongside its correlation with significant NDDs, such as autism spectrum disorder, attention-deficit/hyperactivity disorder, Tourette syndrome, cerebral palsy, fetal alcohol spectrum disorders, and genetic NDDs (Rett, Down, Angelman, and Turner syndromes). Understanding changes in the gut microbiome in NDDs may provide new chances for their treatment in the future.
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Affiliation(s)
- Alejandro Borrego-Ruiz
- Departamento de Psicología Social y de las Organizaciones, Universidad Nacional de Educación a Distancia (UNED), 28040 Madrid, Spain;
| | - Juan J. Borrego
- Departamento de Microbiología, Universidad de Málaga, 29071 Málaga, Spain
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA, Plataforma BIONAND, 29010 Málaga, Spain
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Korteniemi J, Karlsson L, Aatsinki A. Systematic Review: Autism Spectrum Disorder and the Gut Microbiota. FOCUS (AMERICAN PSYCHIATRIC PUBLISHING) 2024; 22:242-251. [PMID: 38680985 PMCID: PMC11046714 DOI: 10.1176/appi.focus.24022008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
Objective Autism spectrum disorders (ASD) are a varying group of disorders characterized by deficiency in social interaction and restrictive patterns of behavior and interests. While there are several studies focusing on the neuro-psychiatric pathogenesis of ASD, its etiology remains unclear. The role of gut-brain-axis in ASD has been studied increasingly and a correlation between symptoms and the composition of gut microbiota has been documented in various works. Despite this, the significance of individual microbes and their function is still widely unknown. This work aims to elucidate the current knowledge of the interrelations between ASD and the gut microbiota in children based on scientific evidence. Methods This is a systematic review done by a literature search focusing on the main findings concerning the gut microbiota composition, interventions targeting the gut microbiota, and possible mechanisms explaining the results in children aged between 2 and 18 years of age. Results Most studies in this review found significant differences between microbial communities, while there was notable variation in results regarding diversity indices or taxonomic level abundance. The most consistent results regarding taxa differences in ASD children's gut microbiota were higher levels of Proteobacteria, Actinobacteria and Sutterella compared to controls. Conclusion These results show that the gut microbiota of children with ASD is altered compared to one of neurotypically developed children. More research is needed to discover whether some of these features could be used as potential biomarkers for ASD and how the gut microbiota could be targeted in therapeutical interventions.Appeared originally in Acta Psychiatr Scand 2023;148:242-254.
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Affiliation(s)
- Jenni Korteniemi
- FinnBrain Birth Cohort Study, Turku Brain and Mind Center, Department of Clinical Medicine, Psychiatry, University of Turku, Turku, Finland (Korteniemi, Karlsson, Aatsinki); Centre for Population Health Research, Turku University Hospital, University of Turku, Turku, Finland (Karlsson, Aatsinki); Department of Clinical Medicine, Paediatrics and Adolescent Medicine, Turku University Hospital, University of Turku, Turku, Finland (Karlsson)
| | - Linnea Karlsson
- FinnBrain Birth Cohort Study, Turku Brain and Mind Center, Department of Clinical Medicine, Psychiatry, University of Turku, Turku, Finland (Korteniemi, Karlsson, Aatsinki); Centre for Population Health Research, Turku University Hospital, University of Turku, Turku, Finland (Karlsson, Aatsinki); Department of Clinical Medicine, Paediatrics and Adolescent Medicine, Turku University Hospital, University of Turku, Turku, Finland (Karlsson)
| | - Anna Aatsinki
- FinnBrain Birth Cohort Study, Turku Brain and Mind Center, Department of Clinical Medicine, Psychiatry, University of Turku, Turku, Finland (Korteniemi, Karlsson, Aatsinki); Centre for Population Health Research, Turku University Hospital, University of Turku, Turku, Finland (Karlsson, Aatsinki); Department of Clinical Medicine, Paediatrics and Adolescent Medicine, Turku University Hospital, University of Turku, Turku, Finland (Karlsson)
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5
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Hung LY, Margolis KG. Autism spectrum disorders and the gastrointestinal tract: insights into mechanisms and clinical relevance. Nat Rev Gastroenterol Hepatol 2024; 21:142-163. [PMID: 38114585 DOI: 10.1038/s41575-023-00857-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/11/2023] [Indexed: 12/21/2023]
Abstract
Autism spectrum disorders (ASDs) are recognized as central neurodevelopmental disorders diagnosed by impairments in social interactions, communication and repetitive behaviours. The recognition of ASD as a central nervous system (CNS)-mediated neurobehavioural disorder has led most of the research in ASD to be focused on the CNS. However, gastrointestinal function is also likely to be affected owing to the neural mechanistic nature of ASD and the nervous system in the gastrointestinal tract (enteric nervous system). Thus, it is unsurprising that gastrointestinal disorders, particularly constipation, diarrhoea and abdominal pain, are highly comorbid in individuals with ASD. Gastrointestinal problems have also been repeatedly associated with increased severity of the core symptoms diagnostic of ASD and other centrally mediated comorbid conditions, including psychiatric issues, irritability, rigid-compulsive behaviours and aggression. Despite the high prevalence of gastrointestinal dysfunction in ASD and its associated behavioural comorbidities, the specific links between these two conditions have not been clearly delineated, and current data linking ASD to gastrointestinal dysfunction have not been extensively reviewed. This Review outlines the established and emerging clinical and preclinical evidence that emphasizes the gut as a novel mechanistic and potential therapeutic target for individuals with ASD.
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Affiliation(s)
- Lin Y Hung
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, NY, USA
| | - Kara Gross Margolis
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, NY, USA.
- Department of Cell Biology, NYU Grossman School of Medicine and Langone Medical Center, New York, NY, USA.
- Department of Pediatrics, NYU Grossman School of Medicine and Langone Medical Center, New York, NY, USA.
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Korteniemi J, Karlsson L, Aatsinki A. Systematic review: Autism spectrum disorder and the gut microbiota. Acta Psychiatr Scand 2023; 148:242-254. [PMID: 37395517 DOI: 10.1111/acps.13587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 05/02/2023] [Accepted: 06/10/2023] [Indexed: 07/04/2023]
Abstract
OBJECTIVE Autism spectrum disorders (ASD) are a varying group of disorders characterized by deficiency in social interaction and restrictive patterns of behavior and interests. While there are several studies focusing on the neuropsychiatric pathogenesis of ASD, its etiology remains unclear. The role of gut-brain-axis in ASD has been studied increasingly and a correlation between symptoms and the composition of gut microbiota has been documented in various works. Despite this, the significance of individual microbes and their function is still widely unknown. This work aims to elucidate the current knowledge of the interrelations between ASD and the gut microbiota in children based on scientific evidence. METHODS This is a systematic review done by a literature search focusing on the main findings concerning the gut microbiota composition, interventions targeting the gut microbiota, and possible mechanisms explaining the results in children aged between 2 and 18 years of age. RESULTS Most studies in this review found significant differences between microbial communities, while there was notable variation in results regarding diversity indices or taxonomic level abundance. The most consistent results regarding taxa differences in ASD children's gut microbiota were higher levels of Proteobacteria, Actinobacteria and Sutterella compared to controls. CONCLUSION These results show that the gut microbiota of children with ASD is altered compared to one of neurotypically developed children. More research is needed to discover whether some of these features could be used as potential biomarkers for ASD and how the gut microbiota could be targeted in therapeutical interventions.
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Affiliation(s)
- Jenni Korteniemi
- FinnBrain Birth Cohort Study, Turku Brain and Mind Center, Department of Clinical Medicine, Psychiatry, University of Turku, Turku, Finland
| | - Linnea Karlsson
- FinnBrain Birth Cohort Study, Turku Brain and Mind Center, Department of Clinical Medicine, Psychiatry, University of Turku, Turku, Finland
- Centre for Population Health Research, Turku University Hospital, University of Turku, Turku, Finland
- Department of Clinical Medicine, Paediatrics and Adolescent Medicine, Turku University Hospital, University of Turku, Turku, Finland
| | - Anna Aatsinki
- FinnBrain Birth Cohort Study, Turku Brain and Mind Center, Department of Clinical Medicine, Psychiatry, University of Turku, Turku, Finland
- Centre for Population Health Research, Turku University Hospital, University of Turku, Turku, Finland
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7
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Herrera-Mejía J, Campos-Vega R, Wall-Medrano A, Jiménez-Vega F. A Two-Step Single Plex PCR Method for Evaluating Key Colonic Microbiota Markers in Young Mexicans with Autism Spectrum Disorders: Protocol and Pilot Epidemiological Application. Diagnostics (Basel) 2023; 13:2387. [PMID: 37510132 PMCID: PMC10377852 DOI: 10.3390/diagnostics13142387] [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: 05/26/2023] [Revised: 07/09/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Many neurological disorders have a distinctive colonic microbiome (CM) signature. Particularly, children with autism spectrum disorders (ASD) exhibit a very dissimilar CM when compared to neurotypical (NT) ones, mostly at the species level. Thus far, knowledge on this matter comes from high-throughput (yet very expensive and time-consuming) analytical platforms, such as massive high-throughput sequencing of bacterial 16S rRNA. Here, pure (260/280 nm, ~1.85) stool DNA samples (200 ng.µL-1) from 48 participants [39 ASD, 9 NT; 3-13 y] were used to amplify four candidate differential CM markers [Bacteroides fragilis (BF), Faecalibacterium prausnitzii (FP), Desulfovibrio vulgaris (DV), Akkermansia muciniphila (AM)], using micro-organism-specific oligonucleotide primers [265 bp (BF), 198 bp (FP), 196 bp (DV), 327 bp (AM)] and a standardized two-step [low (step 1: °Tm-5 °C) to high (stage 2: °Tm-0 °C) astringent annealing] PCR protocol (2S-PCR). The method was sensitive enough to differentiate all CM biomarkers in the studied stool donors [↑ abundance: NT (BF, FP, AM), ASD (DV)], and phylogenetic analysis confirmed the primers' specificity.
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Affiliation(s)
- Julián Herrera-Mejía
- Instituto de Ciencias Biomédicas, Universidad Autónoma de Ciudad Juárez, Anillo Envolvente del PRONAF y Estocolmo s/n, Ciudad Juárez 32310, Chihuahua, Mexico
| | - Rocío Campos-Vega
- Programa de Posgrado en Alimentos del Centro de la República (PROPAC), Research and Graduate Studies in Food Science, School of Chemistry, Universidad Autónoma de Querétaro, Santiago de Querétaro 76010, Querétaro, Mexico
| | - Abraham Wall-Medrano
- Instituto de Ciencias Biomédicas, Universidad Autónoma de Ciudad Juárez, Anillo Envolvente del PRONAF y Estocolmo s/n, Ciudad Juárez 32310, Chihuahua, Mexico
| | - Florinda Jiménez-Vega
- Instituto de Ciencias Biomédicas, Universidad Autónoma de Ciudad Juárez, Anillo Envolvente del PRONAF y Estocolmo s/n, Ciudad Juárez 32310, Chihuahua, Mexico
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8
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Levkova M, Chervenkov T, Pancheva R. Genus-Level Analysis of Gut Microbiota in Children with Autism Spectrum Disorder: A Mini Review. CHILDREN (BASEL, SWITZERLAND) 2023; 10:1103. [PMID: 37508600 PMCID: PMC10377934 DOI: 10.3390/children10071103] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 06/20/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023]
Abstract
Autism is a global health problem, probably due to a combination of genetic and environmental factors. There is emerging data that the gut microbiome of autistic children differs from the one of typically developing children and it is important to know which bacterial genera may be related to autism. We searched different databases using specific keywords and inclusion criteria and identified the top ten bacterial genera from the selected articles that were significantly different between the studied patients and control subjects studied. A total of 34 studies that met the inclusion criteria were identified. The genera Bacteroides, Bifidobacterium, Clostridium, Coprococcus, Faecalibacterium, Lachnospira, Prevotella, Ruminococcus, Streptococcus, and Blautia exhibited the most substantial data indicating that their fluctuations in the gastrointestinal tract could be linked to the etiology of autism. It is probable that autism symptoms are influenced by both increased levels of harmful bacteria and decreased levels of beneficial bacteria. Interestingly, these genera demonstrated varying patterns of increased or decreased levels across different articles. To validate and eliminate the sources of this fluctuation, further research is needed. Consequently, future investigations on the causes of autism should prioritize the examination of the bacterial genera discussed in this publication.
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Affiliation(s)
- Mariya Levkova
- Department of Medical Genetics, Medical University Varna, Marin Drinov Str 55, 9000 Varna, Bulgaria
- Laboratory of Medical Genetics, St. Marina Hospital, Hristo Smirnenski Blv 1, 9000 Varna, Bulgaria
| | - Trifon Chervenkov
- Laboratory of Medical Genetics, St. Marina Hospital, Hristo Smirnenski Blv 1, 9000 Varna, Bulgaria
- Laboratory of Clinical Immunology, St. Marina Hospital, Hristo Smirnenski Blv 1, 9000 Varna, Bulgaria
| | - Rouzha Pancheva
- Department of Hygiene and Epidemiology, Medical University Varna, Marin Drinov Str 55, 9000 Varna, Bulgaria
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Qiu Z, Luo D, Yin H, Chen Y, Zhou Z, Zhang J, Zhang L, Xia J, Xie J, Sun Q, Xu W. Lactiplantibacillus plantarum N-1 improves autism-like behavior and gut microbiota in mouse. Front Microbiol 2023; 14:1134517. [PMID: 37007488 PMCID: PMC10060657 DOI: 10.3389/fmicb.2023.1134517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 02/21/2023] [Indexed: 03/18/2023] Open
Abstract
IntroductionThe gut-brain axis has been widely recognized in autism spectrum disorder (ASD), and probiotics are considered to potentially benefit the rescuing of autism-like behaviors. As a probiotic strain, Lactiplantibacillus plantarumN-1(LPN-1) was utilized to investigate its effects on gut microbiota and autism-like behaviors in ASD mice constructed by maternal immune activation (MIA).MethodsAdult offspring of MIA mice were given LPN-1 at the dosage of 2 × 109 CFU/g for 4 weeks before subject to the behavior and gut microbiota evaluation.ResultsThe behavioral tests showed that LPN-1 intervention was able to rescue autism-like behaviors in mice, including anxiety and depression. In which the LPN-1 treatment group increased the time spent interacting with strangers in the three-chamber test, their activity time and distance in the central area increased in the open field test, and their immobility time decreased when hanging their tails. Moreover, the supplementation of LPN-1 reversed the intestinal flora structure of ASD mice by enhancing the relative abundance of the pivotal microorganisms of Allobaculum and Oscillospira, while reducing those harmful ones like Sutterella at the genus level.DiscussionThese results suggested that LPN-1 supplementation may improve autism-like behaviors, possibly via regulating the gut microbiota.
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Affiliation(s)
- Zhongqing Qiu
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Chengdu Third People’s Hospital, Chengdu, China
| | - Dongmei Luo
- Key Laboratory of Bio-resources and Eco-Environment, The Ministry of the Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Heng Yin
- Chengdu Third People’s Hospital, Chengdu, China
| | - Yajun Chen
- Chengdu Third People’s Hospital, Chengdu, China
| | - Zhiwei Zhou
- Key Laboratory of Bio-resources and Eco-Environment, The Ministry of the Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Jing Zhang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
- Reproductive Endocrinology and Regulation Laboratory West China Second University Hospital, Sichuan University, Chengdu, China
| | - Linzhu Zhang
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Chengdu Third People’s Hospital, Chengdu, China
| | - Jinrong Xia
- Chengdu Third People’s Hospital, Chengdu, China
| | - Jiang Xie
- Chengdu Third People’s Hospital, Chengdu, China
- *Correspondence: Jiang Xie,
| | - Qun Sun
- Key Laboratory of Bio-resources and Eco-Environment, The Ministry of the Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Qun Sun,
| | - Wenming Xu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
- Reproductive Endocrinology and Regulation Laboratory West China Second University Hospital, Sichuan University, Chengdu, China
- Wenming Xu,
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Borsom EM, Conn K, Keefe CR, Herman C, Orsini GM, Hirsch AH, Palma Avila M, Testo G, Jaramillo SA, Bolyen E, Lee K, Caporaso JG, Cope EK. Predicting Neurodegenerative Disease Using Prepathology Gut Microbiota Composition: a Longitudinal Study in Mice Modeling Alzheimer's Disease Pathologies. Microbiol Spectr 2023; 11:e0345822. [PMID: 36877047 PMCID: PMC10101110 DOI: 10.1128/spectrum.03458-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 01/12/2023] [Indexed: 03/07/2023] Open
Abstract
The gut microbiota-brain axis is suspected to contribute to the development of Alzheimer's disease (AD), a neurodegenerative disease characterized by amyloid-β plaque deposition, neurofibrillary tangles, and neuroinflammation. To evaluate the role of the gut microbiota-brain axis in AD, we characterized the gut microbiota of female 3xTg-AD mice modeling amyloidosis and tauopathy and wild-type (WT) genetic controls. Fecal samples were collected fortnightly from 4 to 52 weeks, and the V4 region of the 16S rRNA gene was amplified and sequenced on an Illumina MiSeq. RNA was extracted from the colon and hippocampus, converted to cDNA, and used to measure immune gene expression using reverse transcriptase quantitative PCR (RT-qPCR). Diversity metrics were calculated using QIIME2, and a random forest classifier was applied to predict bacterial features that are important in predicting mouse genotype. Gene expression of glial fibrillary acidic protein (GFAP; indicating astrocytosis) was elevated in the colon at 24 weeks. Markers of Th1 inflammation (il6) and microgliosis (mrc1) were elevated in the hippocampus. Gut microbiota were compositionally distinct early in life between 3xTg-AD mice and WT mice (permutational multivariate analysis of variance [PERMANOVA], 8 weeks, P = 0.001, 24 weeks, P = 0.039, and 52 weeks, P = 0.058). Mouse genotypes were correctly predicted 90 to 100% of the time using fecal microbiome composition. Finally, we show that the relative abundance of Bacteroides species increased over time in 3xTg-AD mice. Taken together, we demonstrate that changes in bacterial gut microbiota composition at prepathology time points are predictive of the development of AD pathologies. IMPORTANCE Recent studies have demonstrated alterations in the gut microbiota composition in mice modeling Alzheimer's disease (AD) pathologies; however, these studies have only included up to 4 time points. Our study is the first of its kind to characterize the gut microbiota of a transgenic AD mouse model, fortnightly, from 4 weeks of age to 52 weeks of age, to quantify the temporal dynamics in the microbial composition that correlate with the development of disease pathologies and host immune gene expression. In this study, we observed temporal changes in the relative abundances of specific microbial taxa, including the genus Bacteroides, that may play a central role in disease progression and the severity of pathologies. The ability to use features of the microbiota to discriminate between mice modeling AD and wild-type mice at prepathology time points indicates a potential role of the gut microbiota as a risk or protective factor in AD.
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Affiliation(s)
- Emily M. Borsom
- Center for Applied Microbiome Sciences, the Pathogen and Microbiome Institute, Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Kathryn Conn
- Center for Applied Microbiome Sciences, the Pathogen and Microbiome Institute, Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Christopher R. Keefe
- Center for Applied Microbiome Sciences, the Pathogen and Microbiome Institute, Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Chloe Herman
- Center for Applied Microbiome Sciences, the Pathogen and Microbiome Institute, Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Gabrielle M. Orsini
- Center for Applied Microbiome Sciences, the Pathogen and Microbiome Institute, Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Allyson H. Hirsch
- Center for Applied Microbiome Sciences, the Pathogen and Microbiome Institute, Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Melanie Palma Avila
- Center for Applied Microbiome Sciences, the Pathogen and Microbiome Institute, Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - George Testo
- Center for Applied Microbiome Sciences, the Pathogen and Microbiome Institute, Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Sierra A. Jaramillo
- Center for Applied Microbiome Sciences, the Pathogen and Microbiome Institute, Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Evan Bolyen
- Center for Applied Microbiome Sciences, the Pathogen and Microbiome Institute, Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Keehoon Lee
- Center for Applied Microbiome Sciences, the Pathogen and Microbiome Institute, Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - J. Gregory Caporaso
- Center for Applied Microbiome Sciences, the Pathogen and Microbiome Institute, Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Emily K. Cope
- Center for Applied Microbiome Sciences, the Pathogen and Microbiome Institute, Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
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11
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Galley JD, Mashburn-Warren L, Blalock LC, Lauber CL, Carroll JE, Ross KM, Hobel C, Coussons-Read M, Dunkel Schetter C, Gur TL. Maternal anxiety, depression and stress affects offspring gut microbiome diversity and bifidobacterial abundances. Brain Behav Immun 2023; 107:253-264. [PMID: 36240906 DOI: 10.1016/j.bbi.2022.10.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 09/22/2022] [Accepted: 10/09/2022] [Indexed: 11/06/2022] Open
Abstract
Uncovering mechanisms underlying fetal programming during pregnancy is of critical importance. Atypical neurodevelopment during the pre- and immediate postnatal period has been associated with long-term adverse health outcomes, including mood disorders and aberrant cognitive ability in offspring. Maternal factors that have been implicated in anomalous offspring development include maternal inflammation and tress, anxiety, and depression. One potential mechanism through which these factors perturb normal offspring postnatal development is through microbiome disruption. The mother is a primary source of early postnatal microbiome seeding for the offspring, and the transference of a healthy microbiome is key in normal neurodevelopment. Since psychological stress, mood disorders, and inflammation have all been implicated in altering maternal microbiome community structure, passing on aberrant microbial communities to the offspring that may then affect developmental outcomes. Therefore, we examined how maternal stress, anxiety and depression assessed with standardized instruments, and maternal inflammatory cytokine levels in the pre- and postnatal period are associated with the offspring microbiome within the first 13 months of life, utilizing full length 16S sequencing on infant stool samples, that allowed for species-level resolution. Results revealed that infants of mothers who reported higher anxiety and perceived stress had reduced alpha diversity. Additionally, the relative taxonomic quantitative abundances of Bifidobacterium dentium and other species that have been associated with either modulation of the gut-brain axis, or other beneficial health outcomes, were reduced in the offspring of mothers with higher anxiety, perceived stress, and depression. We also found associations between bifidobacteria and prenatal maternal pro-inflammatory cytokines IL-6, IL-8, and IL-10. In summary, specific microbial taxa involved in maintaining proper brain and immune function are lower in offspring born to mothers with anxiety, depression, or stress, providing strong evidence for a mechanism by which maternal factors may affect offspring health through microbiota dysregulation.
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Affiliation(s)
- Jeffrey D Galley
- Department of Psychiatry and Behavioral Health, The Ohio State University Wexner Medical Center, Columbus, OH, USA; Institute for Behavioral Medicine Research, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | | | - Lexie C Blalock
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Christian L Lauber
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA; Department of Pediatrics, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Judith E Carroll
- Cousins Center for Psychoneuroimmunology, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Kharah M Ross
- Center for Social Sciences, Athabasca University, Athabasca, Alberta, Canada
| | - Calvin Hobel
- Cedars-Sinai Medical Centre, Los Angeles, CA, USA
| | - Mary Coussons-Read
- Department of Psychology, The University of Colorado, Colorado Springs, CO, USA
| | | | - Tamar L Gur
- Department of Psychiatry and Behavioral Health, The Ohio State University Wexner Medical Center, Columbus, OH, USA; Institute for Behavioral Medicine Research, The Ohio State University Wexner Medical Center, Columbus, OH, USA; Department of Neuroscience, The Ohio State University, Columbus, OH, USA; Obstetrics and Gynecology, The Ohio State University Wexner Medical Center, Columbus, OH, USA.
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12
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Soltysova M, Tomova A, Ostatnikova D. Gut Microbiota Profiles in Children and Adolescents with Psychiatric Disorders. Microorganisms 2022; 10:2009. [PMID: 36296284 PMCID: PMC9608804 DOI: 10.3390/microorganisms10102009] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/28/2022] [Accepted: 09/30/2022] [Indexed: 11/16/2022] Open
Abstract
The aim of our work is to summarize the current state of knowledge on gut microbiota differences in children and adolescents with psychiatric disorders. To find the relevant articles, the PubMed, Web of Science, and Google Scholar databases were searched. Articles in English presenting original data and comparing the composition of gut microbiota in child psychiatric patients with gut microbiota in healthy children and adolescents were selected. Finally, we identified 55 articles eligible for our purpose. The majority of patients with autism spectrum disorders (ASD) were investigated. A smaller number of studies evaluating the gut microbiota in children and adolescents with attention-deficit/hyperactivity disorder (ADHD), Rett syndrome, anorexia nervosa, depressive disorder (DD), and tic disorders were found. The main findings of this research are discussed in our review, focusing on the age-related gut microbiota specificity for psychiatric disorders and the differences between individual diagnosis. To conclude, the gut microbiota in children and adolescents with psychiatric disorders is evidently different from that in controls. The most pronounced differences are seen in children with ASD, less in ADHD. Moreover, the changes are not identical to those in adult psychiatric patients, as Ruminococcus, Turicibacter, and Bilophila were increased in adults, and decreased in children with ASD, and Parabacteroides and Alistipes were more frequently represented in adults, but less frequently represented in children with depression. The available data suggest some genera have a different abundance in individual psychiatric disorders (e.g., Bilophila, Bifidobacterium, Clostridium, Coprococcus, Faecalibacterium, and Ruminococcus), suggesting their importance for the gut-brain axis. Other bacterial genera might be more important for the pathophysiology of specific disorder in children and adolescents, as Akkermansia and Desulfovibrio for ASD, or Romboutsia for DD. Based on the research findings, we assume that gut microbiota corrections have the potential to improve clinical symptoms in psychiatric patients.
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Affiliation(s)
- Marcela Soltysova
- Academic Research Center for Autism, Institute of Physiology, Faculty of Medicine in Bratislava, Comenius University, 813 72 Bratislava, Slovakia
- Child Psychiatry Outpatient Care Unit, Zvolen Hospital, 960 01 Zvolen, Slovakia
| | - Aleksandra Tomova
- Child Psychiatry Outpatient Care Unit, Zvolen Hospital, 960 01 Zvolen, Slovakia
| | - Daniela Ostatnikova
- Child Psychiatry Outpatient Care Unit, Zvolen Hospital, 960 01 Zvolen, Slovakia
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13
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Ling Z, Cheng Y, Chen F, Yan X, Liu X, Shao L, Jin G, Zhou D, Jiang G, Li H, Zhao L, Song Q. Changes in fecal microbiota composition and the cytokine expression profile in school-aged children with depression: A case-control study. Front Immunol 2022; 13:964910. [PMID: 36059521 PMCID: PMC9437487 DOI: 10.3389/fimmu.2022.964910] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
Depression in childhood negatively affects the growth and development, school performance, and peer or family relationships of affected children, and may even lead to suicide. Despite this, its etiology and pathophysiology remain largely unknown. Increasing evidence supports that gut microbiota plays a vital role in the development of childhood depression. However, little is known about the underlying mechanisms, as most clinical studies investigating the link between gut microbiota and depression have been undertaken in adult cohorts. In present study, a total of 140 school-aged children (6–12 years) were enrolled, including 92 with depression (male/female: 42/50) and 48 healthy controls (male/female: 22/26) from Lishui, Zhejiang, China. Illumina sequencing of the V3–V4 region of the 16S rRNA gene was used to investigate gut microbiota profiles while Bio-Plex Pro Human Cytokine 27-plex Panel was employed to explore host immune response. We found that, compared with healthy controls, children with depression had greater bacterial richness and altered β-diversity. Pro-inflammatory genera such as Streptococcus were enriched in the depression group, whereas anti-inflammatory genera such as Faecalibacterium were reduced, as determined by linear discriminant analysis effect size. These changes corresponded to altered bacterial functions, especially the production of immunomodulatory metabolites. We also identified the presence of a complex inflammatory condition in children with depression, characterized by increased levels of pro-inflammatory cytokines such as IL-17 and decreased levels of anti-inflammatory cytokines such as IFN-γ. Correlation analysis demonstrated that the differential cytokine abundance was closely linked to changes in gut microbiota of children with depression. In summary, key functional genera, such as Streptococcus and Faecalibacterium, alone or in combination, could serve as novel and powerful non-invasive biomarkers to distinguish between children with depression from healthy ones. This study was the first to demonstrate that, in Chinese children with depression, gut microbiota homeostasis is disrupted, concomitant with the activation of a complex pro-inflammatory response. These findings suggest that gut microbiota might play an important role in the pathogenesis of depression in school-aged children, while key functional bacteria in gut may serve as novel targets for non-invasive diagnosis and patient-tailored early precise intervention in children with depression.
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Affiliation(s)
- Zongxin Ling
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
- *Correspondence: Zongxin Ling, ; Longyou Zhao, ; Qinghai Song,
| | - Yiwen Cheng
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Feng Chen
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xiumei Yan
- Department of Laboratory Medicine, Lishui Second People’s Hospital, Lishui, China
| | - Xia Liu
- Department of Intensive Care Unit, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Li Shao
- Institute of Hepatology and Metabolic Diseases, Hangzhou Normal University, Hangzhou, China
- Institute of Translational Medicine, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
| | - Guolin Jin
- Department of Psychiatry, Lishui Second People’s Hospital, Lishui, China
| | - Dajin Zhou
- Department of Laboratory Medicine, Lishui Second People’s Hospital, Lishui, China
| | - Guizhen Jiang
- Department of Laboratory Medicine, Lishui Second People’s Hospital, Lishui, China
| | - He Li
- Department of Psychiatry, Lishui Second People’s Hospital, Lishui, China
| | - Longyou Zhao
- Department of Laboratory Medicine, Lishui Second People’s Hospital, Lishui, China
- *Correspondence: Zongxin Ling, ; Longyou Zhao, ; Qinghai Song,
| | - Qinghai Song
- Department of Psychiatry, Lishui Second People’s Hospital, Lishui, China
- *Correspondence: Zongxin Ling, ; Longyou Zhao, ; Qinghai Song,
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Leveraging Existing 16SrRNA Microbial Data to Define a Composite Biomarker for Autism Spectrum Disorder. Microbiol Spectr 2022; 10:e0033122. [PMID: 35762814 PMCID: PMC9431227 DOI: 10.1128/spectrum.00331-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Cumulative studies have utilized high-throughput sequencing of the 16SrRNA gene to characterize the composition and structure of the microbiota in autism spectrum disorder (ASD). However, they do not always obtain consistent results; thus, conducting cross-study comparisons is necessary. This study sought to analyze the alteration of fecal microbiota and the diagnostic capabilities of gut microbiota biomarkers in individuals with ASD using the existing 16SrRNA microbial data and explore heterogeneity among studies. The raw sequence and metadata from 10 studies, including 1,019 samples, were reanalyzed. Results showed no significant difference in alpha diversity of fecal microbiota between ASD and the control group. However, a significant difference in the composition structure of fecal microbiota was observed. Given the large differences in sample selection and technical differences, the separation of fecal microbiota between ASD and controls was not observed. Subgroup analysis was performed on the basis of different country of origin, hypervariable regions, and sequencing platforms, and the dominant genera in ASD and healthy control groups were determined by linear discriminant analysis (LDA) of the effect size (LEfSe) algorithm and Wilcoxon rank-sum test. Machine learning analyses were carried out to determine the diagnostic capabilities of potential microbial biomarkers. A total of 12 genera were identified to distinguish ASD from control, and the AUC of the training set and verification set was 0.757 and 0.761, respectively. Despite cohort heterogeneity, gut microbial dysbiosis of ASD has been proven to be a widespread phenomenon. Therefore, fecal microbial markers are of great significance in diagnosing ASD diseases and possible candidates for further mechanistic study of the role of intestinal microbiota in ASD. IMPORTANCE This study provides an updated analysis to characterize the gut microbiota in ASD using 16SrRNA gene high-throughput sequencing data from 10 publicly available studies. Our analysis suggests an association between the fecal microbiota and ASD. Sample selection and technical differences between studies may interfere with the species composition analysis of the ASD group and control group. By summarizing the results of 16SrRNA gene sequencing from multiple fecal samples, we can provide evidence to support the use of microbial biomarkers to diagnose the occurrence of ASD. Our study provides a new perspective for further revealing the correlation between gut microbiota and ASD from the perspective of 16SrRNA sequencing in larger samples.
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Analysis of Faecal Microbiota and Small ncRNAs in Autism: Detection of miRNAs and piRNAs with Possible Implications in Host-Gut Microbiota Cross-Talk. Nutrients 2022; 14:nu14071340. [PMID: 35405953 PMCID: PMC9000903 DOI: 10.3390/nu14071340] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/07/2022] [Accepted: 03/21/2022] [Indexed: 02/01/2023] Open
Abstract
Intestinal microorganisms impact health by maintaining gut homeostasis and shaping the host immunity, while gut dysbiosis associates with many conditions, including autism, a complex neurodevelopmental disorder with multifactorial aetiology. In autism, gut dysbiosis correlates with symptom severity and is characterised by a reduced bacterial variability and a diminished beneficial commensal relationship. Microbiota can influence the expression of host microRNAs that, in turn, regulate the growth of intestinal bacteria by means of bidirectional host-gut microbiota cross-talk. We investigated possible interactions among intestinal microbes and between them and host transcriptional modulators in autism. To this purpose, we analysed, by "omics" technologies, faecal microbiome, mycobiome, and small non-coding-RNAs (particularly miRNAs and piRNAs) of children with autism and neurotypical development. Patients displayed gut dysbiosis related to a reduction of healthy gut micro- and mycobiota as well as up-regulated transcriptional modulators. The targets of dysregulated non-coding-RNAs are involved in intestinal permeability, inflammation, and autism. Furthermore, microbial families, underrepresented in patients, participate in the production of human essential metabolites negatively influencing the health condition. Here, we propose a novel approach to analyse faeces as a whole, and for the first time, we detected miRNAs and piRNAs in faecal samples of patients with autism.
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