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Chang X, Zhang Y, Chen X, Li S, Mei H, Xiao H, Ma X, Liu Z, Li R. Gut microbiome and serum amino acid metabolome alterations in autism spectrum disorder. Sci Rep 2024; 14:4037. [PMID: 38369656 PMCID: PMC10874930 DOI: 10.1038/s41598-024-54717-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 02/15/2024] [Indexed: 02/20/2024] Open
Abstract
Gut microbiota and their metabolic products might play important roles in regulating the pathogenesis of autism spectrum disorder (ASD). The purpose of this study was to characterize gut microbiota and serum amino acid metabolome profiles in children with ASD. A non-randomized controlled study was carried out to analyze the alterations in the intestinal microbiota and their metabolites in patients with ASD (n = 30) compared with neurotypical controls (NC) (n = 30) by metagenomic sequencing to define the gut microbiota community and liquid chromatography/mass spectrometry (LC/MS) analysis to characterize the metabolite profiles. Compared with children in the NC group, those in the ASD group showed lower richness, higher evenness, and an altered microbial community structure. At the class level, Deinococci and Holophagae were significantly lower in children with ASD compared with TD. At the phylum level, Deinococcus-Thermus was significantly lower in children with ASD compared with TD. In addition, the functional properties (such as galactose metabolism) displayed significant differences between the ASD and NC groups. Five dominant altered species were identified and analyzed (LDA score > 2.0, P < 0.05), including Subdoligranulum, Faecalibacterium_praushitzii, Faecalibacterium, Veillonellaceae, and Rumminococcaceae. The peptides/nickel transport system was the main metabolic pathway involved in the differential species in the ASD group. Decreased ornithine levels and elevated valine levels may increase the risk of ASD through a metabolic pathway known as the nickel transport system. The microbial metabolism in diverse environments was negatively correlated with phascolarctobacterium succinatutens. Our study provides novel insights into compositional and functional alterations in the gut microbiome and metabolite profiles in ASD and the underlying mechanisms between metabolite and ASD.
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Affiliation(s)
- Xuening Chang
- Department of Child Health Care, Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430016, China
| | - Yuchen Zhang
- School of Medicine, Wuhan University of Science and Technology, Wuhan, 430081, China
| | - Xue Chen
- School of Medicine, Wuhan University of Science and Technology, Wuhan, 430081, China
| | - Shihan Li
- Department of Child Health Care, Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430016, China
| | - Hong Mei
- Department of Maternal and Child Health, Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430016, China
| | - Han Xiao
- Department of Maternal and Child Health, Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430016, China.
| | - Xinyu Ma
- Department of Radiology, Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430016, China.
| | - Zhisheng Liu
- Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430016, China.
| | - Ruizhen Li
- Department of Child Health Care, Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430016, China.
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Li C, Li X, Guo R, Ni W, Liu K, Liu Z, Dai J, Xu Y, Abduriyim S, Wu Z, Zeng Y, Lei B, Zhang Y, Wang Y, Zeng W, Zhang Q, Chen C, Qiao J, Liu C, Hu S. Expanded catalogue of metagenome-assembled genomes reveals resistome characteristics and athletic performance-associated microbes in horse. MICROBIOME 2023; 11:7. [PMID: 36631912 PMCID: PMC9835274 DOI: 10.1186/s40168-022-01448-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 12/14/2022] [Indexed: 06/12/2023]
Abstract
BACKGROUND As a domesticated species vital to humans, horses are raised worldwide as a source of mechanical energy for sports, leisure, food production, and transportation. The gut microbiota plays an important role in the health, diseases, athletic performance, and behaviour of horses. RESULTS Here, using approximately 2.2 Tb of metagenomic sequencing data from gut samples from 242 horses, including 110 samples from the caecum and 132 samples from the rectum (faeces), we assembled 4142 microbial metagenome-assembled genomes (MAG), 4015 (96.93%) of which appear to correspond to new species. From long-read data, we successfully assembled 13 circular whole-chromosome bacterial genomes representing novel species. The MAG contained over 313,568 predicted carbohydrate-active enzymes (CAZy), over 59.77% of which had low similarity match in CAZy public databases. High abundance and diversity of antibiotic resistance genes (ARG) were identified in the MAG, likely showing the wide use of antibiotics in the management of horse. The abundances of at least 36 MAG (e.g. MAG belonging to Lachnospiraceae, Oscillospiraceae, and Ruminococcus) were higher in racehorses than in nonracehorses. These MAG enriched in racehorses contained every gene in a major pathway for producing acetate and butyrate by fibre fermentation, presenting potential for greater amount of short-chain fatty acids available to fuel athletic performance. CONCLUSION Overall, we assembled 4142 MAG from short- and long-read sequence data in the horse gut. Our dataset represents an exhaustive microbial genome catalogue for the horse gut microbiome and provides a valuable resource for discovery of performance-enhancing microbes and studies of horse gut microbiome. Video Abstract.
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Affiliation(s)
- Cunyuan Li
- College of Life Science, Shihezi University, Shihezi, 832003 Xinjiang China
- Key Laboratory of Ecological Corps for Oasis City and Mountain Basin System, Shihezi University, Shihezi, 832003 Xinjiang China
- College of Animal Science and Technology, Shihezi University, Shihezi, 832003 Xinjiang China
| | - Xiaoyue Li
- College of Life Science, Shihezi University, Shihezi, 832003 Xinjiang China
- Key Laboratory of Ecological Corps for Oasis City and Mountain Basin System, Shihezi University, Shihezi, 832003 Xinjiang China
| | - Rongjun Guo
- Novogene Bioinformatics Institute, Beijing, 100000 China
| | - Wei Ni
- College of Life Science, Shihezi University, Shihezi, 832003 Xinjiang China
- Key Laboratory of Ecological Corps for Oasis City and Mountain Basin System, Shihezi University, Shihezi, 832003 Xinjiang China
| | - Kaiping Liu
- College of Life Science, Shihezi University, Shihezi, 832003 Xinjiang China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, 830003 Xinjiang China
| | - Zhuang Liu
- College of Life Science, Shihezi University, Shihezi, 832003 Xinjiang China
| | - Jihong Dai
- College of Life Science, Shihezi University, Shihezi, 832003 Xinjiang China
| | - Yueren Xu
- College of Life Science, Shihezi University, Shihezi, 832003 Xinjiang China
| | | | - Zhuangyuan Wu
- Xinjiang Altay Animal Husbandry and Veterinary Station, Altay, 836501 Xinjiang China
| | - Yaqi Zeng
- College of Animal Science, Xinjiang Agricultural University, Urumqi, 830000 Xinjiang China
| | - Bingbing Lei
- College of Life Science, Shihezi University, Shihezi, 832003 Xinjiang China
| | - Yunfeng Zhang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, 830003 Xinjiang China
| | - Yue Wang
- College of Life Science, Shihezi University, Shihezi, 832003 Xinjiang China
| | - Weibin Zeng
- College of Animal Science and Technology, Shihezi University, Shihezi, 832003 Xinjiang China
| | - Qiang Zhang
- College of Animal Science and Technology, Shihezi University, Shihezi, 832003 Xinjiang China
| | - Chuangfu Chen
- College of Animal Science and Technology, Shihezi University, Shihezi, 832003 Xinjiang China
| | - Jun Qiao
- College of Animal Science and Technology, Shihezi University, Shihezi, 832003 Xinjiang China
| | - Chen Liu
- Novogene Bioinformatics Institute, Beijing, 100000 China
| | - Shengwei Hu
- College of Life Science, Shihezi University, Shihezi, 832003 Xinjiang China
- Key Laboratory of Ecological Corps for Oasis City and Mountain Basin System, Shihezi University, Shihezi, 832003 Xinjiang China
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Tian B, Yao JH, Lin X, Lv WQ, Jiang LD, Wang ZQ, Shen J, Xiao HM, Xu H, Xu LL, Cheng X, Shen H, Qiu C, Luo Z, Zhao LJ, Yan Q, Deng HW, Zhang LS. Metagenomic study of the gut microbiota associated with cow milk consumption in Chinese peri-/postmenopausal women. Front Microbiol 2022; 13:957885. [PMID: 36051762 PMCID: PMC9425034 DOI: 10.3389/fmicb.2022.957885] [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: 05/31/2022] [Accepted: 07/22/2022] [Indexed: 11/17/2022] Open
Abstract
Cow milk consumption (CMC) and alterations of gut bacterial composition are proposed to be closely related to human health and disease. Our research aims to investigate the changes in human gut microbial composition in Chinese peri-/postmenopausal women with different CMC habits. A total of 517 subjects were recruited and questionnaires about their CMC status were collected; 394 subjects were included in the final analyses. Fecal samples were used for studying gut bacterial composition. All the subjects were divided into a control group (n = 248) and a CMC group (n = 146) according to their CMC status. Non-parametric tests and LEfSe at different taxonomic levels were used to reveal differentially abundant taxa and functional categories across different CMC groups. Relative abundance (RA) of one phylum (p_Actinobacteria), three genera (g_Bifidobacterium, g_Anaerostipes, and g_Bacteroides), and 28 species diversified significantly across groups. Specifically, taxa g_Anaerostipes (p < 0.01), g_Bacteroides (p < 0.05), s_Anaerostipes_hadrus (p < 0.01), and s_Bifidobacterium_pseudocatenulatum (p < 0.01) were positively correlated with CMC levels, but p_Actinobacteria (p < 0.01) and g_Bifidobacterium (p < 0.01) were negatively associated with CMC levels. KEGG module analysis revealed 48 gut microbiome functional modules significantly (p < 0.05) associated with CMC, including Vibrio cholerae pathogenicity signature, cholera toxins (p = 9.52e-04), and cephamycin C biosynthesis module (p = 0.0057), among others. In conclusion, CMC was associated with changes in gut microbiome patterns including beta diversity and richness of some gut microbiota. The alterations of certain bacteria including g_Anaerostipes and s_Bifidobacterium_pseudocatenulatum in the CMC group should be important for human health. This study further supports the biological value of habitual cow milk consumption.
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Affiliation(s)
- Bo Tian
- School of Physical Science and Engineering, College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, China
| | - Jia-Heng Yao
- School of Physical Science and Engineering, College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, China
| | - Xu Lin
- Department of Endocrinology and Metabolism, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
| | - Wan-Qiang Lv
- Center for System Biology, Data Sciences, and Reproductive Health, School of Basic Medical Science, Central South University, Changsha, China
| | - Lin-Dong Jiang
- Tulane Center for Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States
| | - Zhuo-Qi Wang
- School of Physical Science and Engineering, College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, China
| | - Jie Shen
- Department of Endocrinology and Metabolism, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China,Shunde Hospital of Southern Medical University (The First People’s Hospital of Shunde), Foshan, China
| | - Hong-Mei Xiao
- Center for System Biology, Data Sciences, and Reproductive Health, School of Basic Medical Science, Central South University, Changsha, China
| | - Hanli Xu
- School of Physical Science and Engineering, College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, China
| | - Lu-Lu Xu
- School of Physical Science and Engineering, College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, China
| | - Xiyu Cheng
- School of Physical Science and Engineering, College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, China
| | - Hui Shen
- Tulane Center for Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States
| | - Chuan Qiu
- Tulane Center for Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States
| | - Zhe Luo
- Tulane Center for Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States
| | - Lan-Juan Zhao
- Tulane Center for Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States
| | - Qiong Yan
- School of Physical Science and Engineering, College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, China
| | - Hong-Wen Deng
- Tulane Center for Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States,*Correspondence: Li-Shu Zhang,
| | - Li-Shu Zhang
- School of Physical Science and Engineering, College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, China,Hong-Wen Deng,
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