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Tan Z, Li J, He Y, Wang F, Xiao Q. Characteristics of gut microbiota and metabolomic of Hainan Tunchang pigs at various growth stages. Gene 2024; 900:148161. [PMID: 38219876 DOI: 10.1016/j.gene.2024.148161] [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: 09/18/2023] [Revised: 01/03/2024] [Accepted: 01/11/2024] [Indexed: 01/16/2024]
Abstract
Numerous gut microorganisms residing in the gut tract and their metabolites play an important role in animal growth. Diet, as the main factor, affects the changes of gut microbiota, and host genetics also have a significant impact on gut microbiota, including growth stages. However, the differences of gut microbiota and its metabolites at various growth stages in local pig breed remains unclear. We used 16S rRNA gene sequencing and untargeted metabolomics to investigate the fecal microbiota and metabolites in different developmental stages of Hainan Tunchang pigs. The relative proportions of dominant bacteria Firmicutes and Spirochaetes increased, Bacteroidetes and Proteobacteria decreased with the development. As age increased, different physiological states led to structural and functional changes in animal nutrition metabolism and immune needs, as well as changes in gut microbiota and its metabolites. We have detected several statistically different microbial and metabolic biomarkers at different growth stages. Meanwhile, through correlation analysis between differential bacteria and metabolites, it was found that the bacteria forming networks with their significant related metabolites were different at various growth stages, Holdemanella, Sharpea, Subdoligranulum, and uncultured_bacterium_o_Bacteroidales were enriched between preweaning piglets and weaning piglets, and they all positive correlated with related metabolites. We also found that the differential bacteria were significantly related to short-chain fatty acid. These findings might provide new insights into the developmental changes of gut microbiota in local pig breeds and the interaction mechanism between the body, and improve pig growth performance and efficiency by regulating the composition of gut microbiota and metabolites.
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Affiliation(s)
- Zhen Tan
- School of Tropical Agriculture and Forestry, Hainan University, 571737 Danzhou, PR China.
| | - Jie Li
- School of Tropical Agriculture and Forestry, Hainan University, 571737 Danzhou, PR China
| | - Yingzhi He
- School of Tropical Agriculture and Forestry, Hainan University, 571737 Danzhou, PR China
| | - Feifan Wang
- School of Tropical Agriculture and Forestry, Hainan University, 571737 Danzhou, PR China
| | - Qian Xiao
- School of Tropical Agriculture and Forestry, Hainan University, 571737 Danzhou, PR China.
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Shen Y, Li Y, Wu T, Dong Q, Deng Q, Liu L, Guo Y, Cao Y, Li Q, Shi J, Zou H, Jiao Y, Ding L, Li J, Gao Y, Hu S, Wang Y, Chen L. Early microbial intervention reshapes phenotypes of newborn Bos taurus through metabolic regulations. Gigascience 2024; 13:giad118. [PMID: 38217406 PMCID: PMC10787367 DOI: 10.1093/gigascience/giad118] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 08/29/2023] [Accepted: 12/23/2023] [Indexed: 01/15/2024] Open
Abstract
BACKGROUND The rumen of neonatal calves has limited functionality, and establishing intestinal microbiota may play a crucial role in their health and performance. Thus, we aim to explore the temporal colonization of the gut microbiome and the benefits of early microbial transplantation (MT) in newborn calves. RESULTS We followed 36 newborn calves for 2 months and found that the composition and ecological interactions of their gut microbiomes likely reached maturity 1 month after birth. Temporal changes in the gut microbiome of newborn calves are widely associated with changes in their physiological statuses, such as growth and fiber digestion. Importantly, we observed that MT reshapes the gut microbiome of newborns by altering the abundance and interaction of Bacteroides species, as well as amino acid pathways, such as arginine biosynthesis. Two-year follow-up of those calves further showed that MT improves their later milk production. Notably, MT improves fiber digestion and antioxidant capacity of newborns while reducing diarrhea. MT also contributes to significant changes in the metabolomic landscape, and with putative causal mediation analysis, we suggest that altered gut microbial composition in newborns may influence physiological status through microbial-derived metabolites. CONCLUSIONS Our study provides a metagenomic and metabolomic atlas of the temporal development of the gut microbiome in newborn calves. MT can alter the gut microbiome of newborns, leading to improved physiological status and later milk production. The data may help develop strategies to manipulate the gut microbiota during early life, which may be relevant to the health and production of newborn calves.
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Affiliation(s)
- Yizhao Shen
- College of Animal Science and Technology, Hebei Agricultural University, Baoding 071000, China
| | - Yan Li
- College of Animal Science and Technology, Hebei Agricultural University, Baoding 071000, China
| | - Tingting Wu
- Department of Gastrointestinal Surgery, Changzhou Medical Center, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Nanjing Medical University, Changzhou 213164, China
- Cardiovascular Research Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou 215006, China
- Department of Cardiology, Nanjing Medical University, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Quanbin Dong
- Cardiovascular Research Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou 215006, China
- Department of Cardiology, Nanjing Medical University, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Qiufeng Deng
- Department of Cardiology, Nanjing Medical University, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Lu Liu
- Department of Cardiology, Nanjing Medical University, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Yanfei Guo
- College of Animal Science and Technology, Hebei Agricultural University, Baoding 071000, China
| | - Yufeng Cao
- College of Animal Science and Technology, Hebei Agricultural University, Baoding 071000, China
| | - Qiufeng Li
- College of Animal Science and Technology, Hebei Agricultural University, Baoding 071000, China
| | - Jing Shi
- Department of Cardiology, Nanjing Medical University, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Huayiyang Zou
- Department of Cardiology, Nanjing Medical University, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Yuwen Jiao
- Department of Gastrointestinal Surgery, Changzhou Medical Center, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Nanjing Medical University, Changzhou 213164, China
| | - Luoyang Ding
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Jianguo Li
- College of Animal Science and Technology, Hebei Agricultural University, Baoding 071000, China
- Hebei Technology Innovation Center of Cattle and Sheep Embryo, Baoding 071000, China
- Hebei Research Institute of Dairy Industry Technology, Shijiazhuang 050221, China
| | - Yanxia Gao
- College of Animal Science and Technology, Hebei Agricultural University, Baoding 071000, China
- Hebei Technology Innovation Center of Cattle and Sheep Embryo, Baoding 071000, China
- Hebei Research Institute of Dairy Industry Technology, Shijiazhuang 050221, China
| | - Shixian Hu
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Yifeng Wang
- Cardiovascular Research Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou 215006, China
- Department of Cardiology, Nanjing Medical University, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Lianmin Chen
- Department of Gastrointestinal Surgery, Changzhou Medical Center, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Nanjing Medical University, Changzhou 213164, China
- Department of Cardiology, Nanjing Medical University, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
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Polygonatum sibiricum polysaccharides improve cognitive function in D-galactose-induced aging mice by regulating the microbiota-gut-brain axis. J Funct Foods 2023. [DOI: 10.1016/j.jff.2023.105476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023] Open
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4
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He Y, Li J, Wang F, Na W, Tan Z. Dynamic Changes in the Gut Microbiota and Metabolites during the Growth of Hainan Wenchang Chickens. Animals (Basel) 2023; 13:348. [PMID: 36766238 PMCID: PMC9913245 DOI: 10.3390/ani13030348] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/11/2023] [Accepted: 01/16/2023] [Indexed: 01/21/2023] Open
Abstract
Gut microbiota and their metabolites play important roles in animal growth by influencing the host's intake, storage, absorption, and utilization of nutrients. In addition to environmental factors, mainly diet, chicken breed and growth stage also affect changes in the gut microbiota. However, little research has been conducted on the development of gut microbiota and its metabolites in local chickens. In this study, the cecal microbiota and metabolites in different developmental stages of Hainan Wenchang chickens (a native breed of Bantam) were investigated using 16S rRNA sequencing and untargeted metabolomics. With aging, the structure of gut microbiota tended to be more stable. The relative proportions of dominant bacteria phyla Firmicutes, Bacteroidetes, and Proteobacteria showed stage changes with the development. With aging, gut microbiota and their metabolites may have structural and functional changes in response to nutrient metabolism and immune requirements in different physiological states. Several microbial and metabolic biomarkers with statistical differences were detected in different development stages. The bacteria that form networks with their significant related metabolites were different in various growth stages, including uncultured_bacterium_f_Ruminococcaceae, Ruminococcaceae_UCG-014, Faecalibacterium, uncultured_bacterium_o_Bacteroidales, and uncultured_bacterium_f_Lachnospiraceae. Partially differential bacteria were significantly correlated with short-chain fatty acids such as butyric acid. These findings may provide new insights into the physiological and molecular mechanisms of developmental changes of local chicken breeds, as well as resources for microbial and metabolic biomarker identification to improve growth efficiency.
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Affiliation(s)
| | | | | | - Wei Na
- School of Animal Science and Technology, Hainan University, Haikou 570228, China
| | - Zhen Tan
- School of Animal Science and Technology, Hainan University, Haikou 570228, China
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Tang Y, Chen B, Huang X, He X, Yi J, Zhao H, Tian F, Liu Y, Liu B. Fu brick tea alleviates high fat induced non-alcoholic fatty liver disease by remodeling the gut microbiota and liver metabolism. Front Nutr 2022; 9:1062323. [PMID: 36618677 PMCID: PMC9815510 DOI: 10.3389/fnut.2022.1062323] [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: 10/05/2022] [Accepted: 12/01/2022] [Indexed: 12/24/2022] Open
Abstract
Fu brick tea (FBT) and its extracts have good lipid-lowering effects and have been used in the treatment of obesity in previous studies. Unfortunately, the therapeutic effect of FBT on non-alcoholic fatty liver disease (NAFLD) has not been thoroughly studied. In this study, we explored the mechanism by which FBT alleviates NAFLD from the perspective of the gut microbiota and liver metabolites. The results showed that FBT could reduce the body weight, liver weight and abdominal fat of NAFLD mice, and improve liver pathological morphology, liver lipid deposition, blood lipids and liver function. Moreover, FBT improved the diversity of the gut microbiota and changed the profile of liver metabolism in NAFLD mice. Further studies showed that FBT could ameliorate the cecum barrier, and regulate the effects of factors related to lipid synthesis in the cecum and liver of NAFLD mice. In conclusion, the present study confirmed that FBT can alleviate high fat induced NAFLD by regulating the homeostasis of the gut microbiota and liver metabolites.
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Affiliation(s)
- Yan Tang
- Department of Basic Medicine, Yiyang Medical College, Yiyang, China
| | - Bowei Chen
- The First Hospital, Hunan University of Chinese Medicine, Changsha, China
- MOE Key Laboratory of Research and Translation on Prevention and Treatment of Major Diseases in Internal Medicine of Traditional Chinese Medicine, Hunan University of Chinese Medicine, Changsha, China
| | - Xin Huang
- Department of Clinical Medicine, Yiyang Medical College, Yiyang, China
| | - Xu He
- Department of Basic Medicine, Yiyang Medical College, Yiyang, China
| | - Jian Yi
- The First Hospital, Hunan University of Chinese Medicine, Changsha, China
- MOE Key Laboratory of Research and Translation on Prevention and Treatment of Major Diseases in Internal Medicine of Traditional Chinese Medicine, Hunan University of Chinese Medicine, Changsha, China
| | - Hong Zhao
- Department of Basic Medicine, Yiyang Medical College, Yiyang, China
| | - Fengming Tian
- The First Hospital, Hunan University of Chinese Medicine, Changsha, China
- MOE Key Laboratory of Research and Translation on Prevention and Treatment of Major Diseases in Internal Medicine of Traditional Chinese Medicine, Hunan University of Chinese Medicine, Changsha, China
| | - Yingfei Liu
- The First Hospital, Hunan University of Chinese Medicine, Changsha, China
- MOE Key Laboratory of Research and Translation on Prevention and Treatment of Major Diseases in Internal Medicine of Traditional Chinese Medicine, Hunan University of Chinese Medicine, Changsha, China
| | - Baiyan Liu
- Hunan Academy of Chinese Medicine, Changsha, China
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Shi T, Feng Y, Liu W, Liu H, Li T, Wang M, Li Z, Lu J, Abudurexiti A, Maimaitireyimu A, Hu J, Gao F. Characteristics of gut microbiota and fecal metabolomes in patients with celiac disease in Northwest China. Front Microbiol 2022; 13:1020977. [PMID: 36519162 PMCID: PMC9742481 DOI: 10.3389/fmicb.2022.1020977] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/14/2022] [Indexed: 06/30/2024] Open
Abstract
Celiac disease (CD) is an autoimmune small bowel disease. The pattern of gut microbiota is closely related to dietary habits, genetic background, and geographical factors. There is a lack of research on CD-related gut microbiota in China. This study aimed to use 16S rDNA sequencing and metabolomics to analyze the fecal microbial composition and metabolome characteristics in patients diagnosed with CD in Northwest China, and to screen potential biomarkers that could be used for its diagnosis. A significant difference in the gut microbiota composition was observed between the CD and healthy controls groups. At the genus level, the abundance of Streptococcus, Lactobacillus, Veillonella, and Allisonella communities in the CD group were increased (Q < 0.05). Furthermore, the abundance of Ruminococcus, Faecalibacterium, Blautia, Gemmiger, and Anaerostipes community in this group were decreased (Q < 0.05). A total of 222 different fecal metabolites were identified in the two groups, suggesting that CD patients have a one-carbon metabolism defect. Four species of bacteria and six metabolites were selected as potential biomarkers using a random forest model. Correlation analysis showed that changes in the gut microbiota were significantly correlated with changes in fecal metabolite levels. In conclusion, the patterns of distribution of gut microbiota and metabolomics in patients with CD in Northwest China were found to be unique to these individuals. This has opened up a new way to explore potential beneficial effects of supplementing specific nutrients and potential diagnostic and therapeutic targets in the future.
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Affiliation(s)
- Tian Shi
- Department of Gastroenterology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
- Xinjiang Clinical Research Center for Digestive Diseases, Urumqi, China
| | - Yan Feng
- Department of Gastroenterology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
- Xinjiang Clinical Research Center for Digestive Diseases, Urumqi, China
| | - Weidong Liu
- Department of Gastroenterology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
- Xinjiang Clinical Research Center for Digestive Diseases, Urumqi, China
| | - Huan Liu
- Department of Gastroenterology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
- Xinjiang Clinical Research Center for Digestive Diseases, Urumqi, China
| | - Ting Li
- Department of Gastroenterology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
- Xinjiang Clinical Research Center for Digestive Diseases, Urumqi, China
| | - Man Wang
- Department of Gastroenterology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
- Xinjiang Clinical Research Center for Digestive Diseases, Urumqi, China
| | - Ziqiong Li
- Department of Gastroenterology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
- Xinjiang Clinical Research Center for Digestive Diseases, Urumqi, China
| | - Jiajie Lu
- Department of Gastroenterology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
- Xinjiang Clinical Research Center for Digestive Diseases, Urumqi, China
| | - Adilai Abudurexiti
- Department of Gastroenterology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
- Xinjiang Clinical Research Center for Digestive Diseases, Urumqi, China
| | - Ayinuer Maimaitireyimu
- Department of Gastroenterology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
- Xinjiang Clinical Research Center for Digestive Diseases, Urumqi, China
| | - Jiali Hu
- Department of Gastroenterology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
- Xinjiang Clinical Research Center for Digestive Diseases, Urumqi, China
| | - Feng Gao
- Department of Gastroenterology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
- Xinjiang Clinical Research Center for Digestive Diseases, Urumqi, China
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Sishen Pill Ameliorates Dextran Sulfate Sodium (DSS)-Induced Colitis with Spleen-Kidney Yang Deficiency Syndromes: Role of Gut Microbiota, Fecal Metabolites, Inflammatory Dendritic Cells, and TLR4/NF- κB Pathway. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:6132289. [PMID: 36310616 PMCID: PMC9605852 DOI: 10.1155/2022/6132289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/08/2022] [Accepted: 09/13/2022] [Indexed: 11/17/2022]
Abstract
Sishen pill (SSP) is an old Chinese medicine used to treat colitis with spleen-kidney-yang deficiency (SKYD) syndromes. However, its exact mechanism of action has not yet been fully elucidated. The aim of this study was to evaluate the effects and potential mechanisms of SSP on colitis with SKYD syndromes in mice. Colitis with SKYD syndromes was induced by rhubarb, hydrocortisone, and dextran sulfate sodium (DSS), and treatment was provided with SSP. Flow cytometry was performed to examine the inflammatory dendritic cell (infDC) regulations of SSP. The changes in the gut microbiota (GM) and fecal metabolites post-SSP treatment were investigated using the combination of 16S rRNA sequencing and untargeted metabolomics. Additionally, we also examined whether SSPs could regulate the infDCs by modifying TLR4/NF-κB signaling pathways. Compared with the DSS group, the disease activity index, colonic weight, index of colonic weight, and colonic injury scores, as well as the levels of tumor necrosis factor (TNF)-α, interleukin (IL)-1β, IL-6, and IL-12p70 decreased significantly in the DSS + SSP group, while free triiodothyronine (FT3), free tetraiodothyronine (FT4), testosterone (TESTO), body weight change, colonic length, and the levels of IL-10 increased. Also, SSP decreased the amounts of CD103+CD11c+iNOS+, CD103+CD11c+TNF-α +, CD11c+CD103+CD324+, CD103+CD11c+MHC-II+, and CD103+CD11c+CD115+. Interestingly, 16S rRNA sequencing and untargeted metabolomics showed that SSP treatment restored the dysbiosis of GM and improved the dysfunction in fecal metabolism in colitis mice with SKYD syndromes. Correlation analysis indicated that the modulatory effects of SSP on FT3, FT4, IL-10, colonic weight index, CD103+CD11c+TNF-α +, CD103+CD11c+MHC-II+, and 13 common differential metabolites were related to alterations in the abundance of Parvibacter, Aerococcus, norank_f_Lachnospiraceae, Lachnospiraceae_UCG-006, Akkermansia, and Rhodococcus in the GM. In addition, SSP markedly inhibited the activation of the TLR4, MyD88, TRAF6, TAB2, and NF-κBp65 proteins and activated IκB. These results indicate that SSP can effectively alleviate colitis mice with SKYD syndrome by regulating infDCs, GM, fecal metabolites, and TLR4/NF-κB signaling pathways.
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Chatterjee G, Negi S, Basu S, Faintuch J, O'Donovan A, Shukla P. Microbiome systems biology advancements for natural well-being. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:155915. [PMID: 35568180 DOI: 10.1016/j.scitotenv.2022.155915] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 05/09/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
Throughout the years all data from epidemiological, physiological and omics have suggested that the microbial communities play a considerable role in modulating human health. The population of microorganisms residing in the human intestine collectively known as microbiota presents a genetic repertoire that is higher in magnitude than the human genome. They play an essential role in host immunity and neuronal signaling. Rapid enhancement of sequence based screening and development of humanized gnotobiotic model has sparked a great deal of interest among scientists to probe the dynamic interactions of the commensal bacteria. This review focuses on systemic analysis of the gut microbiome to decipher the complexity of the host-microbe intercommunication and gives a special emphasis on the evolution of targeted precision medicine through microbiome engineering. In addition, we have also provided a comprehensive description of how interconnection between metabolism and biochemical reactions in a specific organism can be obtained from a metabolic network or a flux balance analysis and combining multiple datasets helps in the identification of a particular metabolite. The review highlights how genetic modification of the critical components and programming the resident microflora can be employed for targeted precision medicine. Inspite of the ongoing debate on the utility of gut microbiome we have explored on the probable new therapeutic avenues like FMT (Fecal microbiota transplant) can be utilized. This review also recapitulates integrating human-relevant 3D cellular models coupled with computational models and the metadata obtained from interventional and epidemiological studies may decipher the complex interactome of diet-microbiota-disease pathophysiology. In addition, it will also open new avenues for the development of therapeutics derived from microbiome or implementation of personalized nutrition. In addition, the identification of biomarkers can also help towards the development of new diagnostic tools and eventually will lead to strategic management of the disease. Inspite of the ongoing debate on the utility of the gut microbiome we have explored how probable new therapeutic avenues like FMT (Fecal microbiota transplant) can be utilized. This review also summarises integrating human-relevant 3D cellular models coupled with computational models and the metadata obtained from interventional and epidemiological studies may decipher the complex interactome of diet- microbiota-disease pathophysiology. In addition, it will also open new avenues for the development of therapeutics derived from the microbiome or implementation of personalized nutrition. In addition, the identification of biomarkers can also help towards the development of new diagnostic tools and eventually will lead to strategic management of disease.
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Affiliation(s)
| | - Sangeeta Negi
- NMC Biolab, New Mexico Consortium, Los Alamos, NM, USA; Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | - Supratim Basu
- NMC Biolab, New Mexico Consortium, Los Alamos, NM, USA
| | - Joel Faintuch
- Department of Gastroenterology, Sao Paulo University Medical School, São Paulo, SP 01246-903, Brazil
| | | | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, India.
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Dynamic description of temporal changes of gut microbiota in broilers. Poult Sci 2022; 101:102037. [PMID: 35901643 PMCID: PMC9334346 DOI: 10.1016/j.psj.2022.102037] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/19/2022] [Accepted: 06/22/2022] [Indexed: 12/09/2022] Open
Abstract
The diversity of bacteria and fungi in the gut microbiota of commercial broilers that raised in cages from hatch to the end of the production cycle were examined by an analysis of 3,592 and 3,899 amplicon sequence variants (ASVs), respectively. More than 90% sequences in bacterial communities were related to Firmicutes and Proteobacteria. More than 90% sequences in fungal communities were related to Ascomycota, Basidiomycota, and Glomeromycota. A statistical analysis of the microbiota composition succession showed that age was one of the main factors affecting the intestinal microbial communities of broilers. The increasingly complex community succession of transient microbiota occurred along with an increase of age. This dynamic change was observed to be similar between bacteria and fungi. The gut microbiota had a special structure in the first 3 d after birth of broiler. The microbiota structure was quite stable in the period of rapid skeletal growth (d 14–21), and then changed significantly in the period of rapid gaining weight (d 35–42), thus indicating the composition of gut microbiota in broilers had unique structures at different developmental stages. We observed that several bacteria and fungi occupied key functions in the gut microbiota of broilers, suggesting that the gut homeostasis of broilers might be affected by losses of bacteria and fungi via altering interactions between microbiota. This study aimed to provide a data basis for manipulating the microbiota at different developmental stages, in order to improve production and the intestinal health of broilers.
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Liu B, Chen B, Yi J, Long H, Wen H, Tian F, Liu Y, Xiao L, Li L. Liuwei Dihuang Decoction Alleviates Cognitive Dysfunction in Mice With D-Galactose-Induced Aging by Regulating Lipid Metabolism and Oxidative Stress via the Microbiota-Gut-Brain Axis. Front Neurosci 2022; 16:949298. [PMID: 35844229 PMCID: PMC9283918 DOI: 10.3389/fnins.2022.949298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 06/15/2022] [Indexed: 11/24/2022] Open
Abstract
Background Aging is an important cause of cognitive dysfunction. Liuwei Dihuang decoction (LW), a commonly applied Chinese medicine formula, is widely used for the treatment of aging-related diseases in China. Previously, LW was confirmed to be effective in prolonging life span and reducing oxidative stress in aged mice. Unfortunately, the underlying mechanism of LW remains unclear. The aim of this study was to interpret the mechanism by which LW alleviates cognitive dysfunction related to aging from the perspective of the microbiota-gut-brain axis. Method All C57BL/6 mice (n = 60) were randomly divided into five groups: the control, model, vitamin E (positive control group), low-dose LW and high-dose LW groups (n = 12 in each group). Except for those in the control group, D-galactose was subcutaneously injected into mice in the other groups to induce the aging model. The antiaging effect of LW was evaluated by the water maze test, electron microscopy, 16S rRNA sequencing, combined LC–MS and GC–MS metabolomics, and ELISA. Results Liuwei Dihuang decoction ameliorated cognitive dysfunction and hippocampal synaptic ultrastructure damage in aging mice. Moreover, LW decreased Proteobacteria abundance and increased gut microbiota diversity in aging mice. Metabolomic analysis showed that LW treatment was associated with the significantly differential abundance of 14 metabolites, which were mainly enriched in apelin signaling, sphingolipid metabolism, glycerophospholipid and other metabolic pathways. Additionally, LW affected lipid metabolism and oxidative stress in aging mice. Finally, we also found that LW-regulated microbial species such as Proteobacteria and Fibrobacterota had potential relationships with lipid metabolism, oxidative stress and hippocampal metabolites. Conclusion In brief, LW improved cognitive function in aging mice by regulating lipid metabolism and oxidative stress through restoration of the homeostasis of the microbiota-gut-brain axis.
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Affiliation(s)
- Baiyan Liu
- The First Affiliated Hospital, Hunan University of Chinese Medicine, Changsha, China
- Hunan Academy of Chinese Medicine, Changsha, China
- *Correspondence: Baiyan Liu,
| | - Bowei Chen
- The First Affiliated Hospital, Hunan University of Chinese Medicine, Changsha, China
| | - Jian Yi
- The First Affiliated Hospital, Hunan University of Chinese Medicine, Changsha, China
- Hunan Academy of Chinese Medicine, Changsha, China
| | - Hongping Long
- The First Affiliated Hospital, Hunan University of Chinese Medicine, Changsha, China
| | - Huiqiao Wen
- The First Affiliated Hospital, Hunan University of Chinese Medicine, Changsha, China
| | - Fengming Tian
- The First Affiliated Hospital, Hunan University of Chinese Medicine, Changsha, China
| | - Yingfei Liu
- The First Affiliated Hospital, Hunan University of Chinese Medicine, Changsha, China
| | - Lan Xiao
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha, China
| | - Lisong Li
- College of Information Science and Engineering, Hunan University of Chinese Medicine, Changsha, China
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11
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de Castro Soares S, Sales-Campos H. Editorial: Probiotics and its Effects on Inflammatory and Infectious Disorders. Front Pharmacol 2022; 13:868044. [PMID: 35359870 PMCID: PMC8960446 DOI: 10.3389/fphar.2022.868044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 02/07/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
| | - Helioswilton Sales-Campos
- Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, Brazil
- *Correspondence: Helioswilton Sales-Campos,
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12
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Ladino L, Sánchez N, Vázquez-Frias R, Koletzko B. Latin American Considerations for Infant and Young Child Formulae. Nutrients 2021; 13:nu13113942. [PMID: 34836196 PMCID: PMC8620542 DOI: 10.3390/nu13113942] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 10/21/2021] [Accepted: 10/27/2021] [Indexed: 01/01/2023] Open
Abstract
Infant formula is the only acceptable substitute for breastmilk from 0 to 6 months old when human milk cannot be provided in sufficient amounts. Manufacturers have developed options that intend to meet the changing needs of the child aged from six to twelve months (follow-on formulae) and after the age of one year (young child formulae). The international code for marketing breast milk substitute stipulates standards for marketing practices of these products. In Latin America there are local variations of marketing practices. Novel marketing strategies such as advertising through social media and influencers pose new threats for breastfeeding success in Latin America. This review aims to examine variations in local regulations for marketing of infant formulae and to analyze the emerging phenomenon of influencer advertising. We reviewed the local norms for Latin American countries and examined differences and possible gaps. Emerging evidence of influencer marketing was explored. The results indicate that national regulations differ among Latin American countries, particularly with respect to product labelling and the requirement to use a local native language, highlighting the cost of the product, and different regulations prohibiting certain messages and illustrations. Regarding new marketing strategies, there is limited evidence on advertising infant formula through social media influencers, where different categories of marketing strategies can be described. More transparent reporting of social marketing by formula providers and more independent research on novel marketing strategies are needed.
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Affiliation(s)
- Liliana Ladino
- Faculty of Medicine, Research Institute on Nutrition, Genetics and Metabolism IINGM, Universidad El Bosque, Bogotá 110121, Colombia;
- Nutrition Working Group, Latin-American Society for Pediatric Gastroenterology Hepatology and Nutrition LASPGHAN, Mexico City 11560, Mexico;
| | - Nathalia Sánchez
- Research and Education Center on Nutrition, CIENutrition, Bogotá 110221, Colombia;
| | - Rodrigo Vázquez-Frias
- Nutrition Working Group, Latin-American Society for Pediatric Gastroenterology Hepatology and Nutrition LASPGHAN, Mexico City 11560, Mexico;
- Department of Gastroenterology and Nutrition, Hospital Infantil de México Federico Gómez, Mexico City 06720, Mexico
| | - Berthold Koletzko
- Department Pediatrics, Medical Centre of LMU Munich, Ludwig Maximilians University of Munich, Dr. von Hauner Children’s Hospital, 80539 München, Germany
- Correspondence: ; Tel.: +49-89-4400-52811
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13
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Xie M, Zhang S, Xu L, Wu Z, Yuan J, Chen X. Comparison of the Intestinal Microbiota During the Different Growth Stages of Red Swamp Crayfish ( Procambarus clarkii). Front Microbiol 2021; 12:696281. [PMID: 34589066 PMCID: PMC8473915 DOI: 10.3389/fmicb.2021.696281] [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: 04/16/2021] [Accepted: 08/12/2021] [Indexed: 12/21/2022] Open
Abstract
This study aimed to determine the effect of the growth stage of Procambarus clarkii on their intestinal microbiota. Intestinal samples of five different growth stages of P. clarkii (first instar, second instar, third instar, juvenile, and adult) from laboratory culture were analyzed through the Illumina MiSeq high-throughput sequencing platform to determine the intestinal microbiome of crayfish. The alpha diversity decreased along with the growth of the crayfish, with the relative abundance of the microbiota changing among stages; crayfish at closer development stages had a more comparable intestinal microbiota composition. A comparative analysis by principal component analysis and principal coordinate analysis showed that there were significant differences in the intestinal microbiota of crayfish among the different growth stages, except for the first two stages of larval crayfish, and the intestinal microbiota showed a consistent progression pattern from the larval stage to the juvenile stage. Some microbiota showed stage specificity, which might be the characteristic microbiota of different stages of growth. According to FAPROTAX functional clustering analysis, the three stages of larvae were clustered together, while the juvenile and adult stages were clustered separately according to the growth stage, indicating that, in the early stages of larval development, the function of the intestinal flora was similar; as the body grew and developed, the composition and function of the intestinal microbiota also changed.
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Affiliation(s)
- Mengqi Xie
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agriculture University, Wuhan, China.,Hubei Engineering Technology Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, China
| | - Shiyu Zhang
- Hubei Engineering Technology Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, China
| | - Lili Xu
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agriculture University, Wuhan, China
| | - Zhixin Wu
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agriculture University, Wuhan, China.,Hubei Engineering Technology Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, China
| | - Junfa Yuan
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agriculture University, Wuhan, China.,Hubei Engineering Technology Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, China
| | - Xiaoxuan Chen
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agriculture University, Wuhan, China
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14
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Qin T, Fu J, Verkade HJ. The role of the gut microbiome in graft fibrosis after pediatric liver transplantation. Hum Genet 2021; 140:709-724. [PMID: 32920649 PMCID: PMC8052232 DOI: 10.1007/s00439-020-02221-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 08/29/2020] [Indexed: 12/18/2022]
Abstract
Liver transplantation (LT) is a life-saving option for children with end-stage liver disease. However, about 50% of patients develop graft fibrosis in 1 year after LT, with normal liver function. Graft fibrosis may progress to cirrhosis, resulting in graft dysfunction and ultimately the need for re-transplantation. Previous studies have identified various risk factors for the post-LT fibrogenesis, however, to date, neither of the factors seems to fully explain the cause of graft fibrosis. Recently, evidence has accumulated on the important role of the gut microbiome in outcomes after solid organ transplantation. As an altered microbiome is present in pediatric patients with end-stage liver diseases, we hypothesize that the persisting alterations in microbial composition or function contribute to the development of graft fibrosis, for example by bacteria translocation due to increased intestinal permeability, imbalanced bile acids metabolism, and/or decreased production of short-chain fatty acids (SCFAs). Subsequently, an immune response can be activated in the graft, together with the stimulation of fibrogenesis. Here we review current knowledge about the potential mechanisms by which alterations in microbial composition or function may lead to graft fibrosis in pediatric LT and we provide prospective views on the efficacy of gut microbiome manipulation as a therapeutic target to alleviate the graft fibrosis and to improve long-term survival after LT.
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Affiliation(s)
- Tian Qin
- Pediatric Gastroenterology/Hepatology, Section of Nutrition and Metabolism, Research Laboratory of Pediatrics, Department of Pediatrics, Beatrix Children's Hospital/University Medical Center Groningen, P.O. Box 30.001, 9700 RB, Groningen, The Netherlands
| | - Jingyuan Fu
- Pediatric Gastroenterology/Hepatology, Section of Nutrition and Metabolism, Research Laboratory of Pediatrics, Department of Pediatrics, Beatrix Children's Hospital/University Medical Center Groningen, P.O. Box 30.001, 9700 RB, Groningen, The Netherlands
- Department of Genetics, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
| | - Henkjan J Verkade
- Pediatric Gastroenterology/Hepatology, Section of Nutrition and Metabolism, Research Laboratory of Pediatrics, Department of Pediatrics, Beatrix Children's Hospital/University Medical Center Groningen, P.O. Box 30.001, 9700 RB, Groningen, The Netherlands.
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15
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The long-term genetic stability and individual specificity of the human gut microbiome. Cell 2021; 184:2302-2315.e12. [PMID: 33838112 DOI: 10.1016/j.cell.2021.03.024] [Citation(s) in RCA: 154] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 12/02/2020] [Accepted: 03/11/2021] [Indexed: 12/11/2022]
Abstract
By following up the gut microbiome, 51 human phenotypes and plasma levels of 1,183 metabolites in 338 individuals after 4 years, we characterize microbial stability and variation in relation to host physiology. Using these individual-specific and temporally stable microbial profiles, including bacterial SNPs and structural variations, we develop a microbial fingerprinting method that shows up to 85% accuracy in classifying metagenomic samples taken 4 years apart. Application of our fingerprinting method to the independent HMP cohort results in 95% accuracy for samples taken 1 year apart. We further observe temporal changes in the abundance of multiple bacterial species, metabolic pathways, and structural variation, as well as strain replacement. We report 190 longitudinal microbial associations with host phenotypes and 519 associations with plasma metabolites. These associations are enriched for cardiometabolic traits, vitamin B, and uremic toxins. Finally, mediation analysis suggests that the gut microbiome may influence cardiometabolic health through its metabolites.
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16
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Leeming ER, Louca P, Gibson R, Menni C, Spector TD, Le Roy CI. The complexities of the diet-microbiome relationship: advances and perspectives. Genome Med 2021; 13:10. [PMID: 33472701 PMCID: PMC7819159 DOI: 10.1186/s13073-020-00813-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 11/25/2020] [Indexed: 02/07/2023] Open
Abstract
Personalised dietary modulation of the gut microbiota may be key to disease management. Current investigations provide a broad understanding of the impact of diet on the composition and activity of the gut microbiota, yet detailed knowledge in applying diet as an actionable tool remains limited. Further to the relative novelty of the field, approaches are yet to be standardised and extremely heterogeneous research outcomes have ensued. This may be related to confounders associated with complexities in capturing an accurate representation of both diet and the gut microbiota. This review discusses the intricacies and current methodologies of diet-microbial relations, the implications and limitations of these investigative approaches, and future considerations that may assist in accelerating applications. New investigations should consider improved collection of dietary data, further characterisation of mechanistic interactions, and an increased focus on -omic technologies such as metabolomics to describe the bacterial and metabolic activity of food degradation, together with its crosstalk with the host. Furthermore, clinical evidence with health outcomes is required before therapeutic dietary strategies for microbial amelioration can be made. The potential to reach detailed understanding of diet-microbiota relations may depend on re-evaluation, progression, and unification of research methodologies, which consider the complexities of these interactions.
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Affiliation(s)
- Emily R Leeming
- The Department of Twin Research, St Thomas' Hospital, King's College London, 3-4th Floor South Wing Block D, Westminster Bridge Road, London, SE1 7EH, UK
| | - Panayiotis Louca
- The Department of Twin Research, St Thomas' Hospital, King's College London, 3-4th Floor South Wing Block D, Westminster Bridge Road, London, SE1 7EH, UK
| | - Rachel Gibson
- Department of Nutritional Sciences, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, UK
| | - Cristina Menni
- The Department of Twin Research, St Thomas' Hospital, King's College London, 3-4th Floor South Wing Block D, Westminster Bridge Road, London, SE1 7EH, UK
| | - Tim D Spector
- The Department of Twin Research, St Thomas' Hospital, King's College London, 3-4th Floor South Wing Block D, Westminster Bridge Road, London, SE1 7EH, UK.
| | - Caroline I Le Roy
- The Department of Twin Research, St Thomas' Hospital, King's College London, 3-4th Floor South Wing Block D, Westminster Bridge Road, London, SE1 7EH, UK.
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17
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Scheid AD, Beadnell TC, Welch DR. Roles of mitochondria in the hallmarks of metastasis. Br J Cancer 2021; 124:124-135. [PMID: 33144695 PMCID: PMC7782743 DOI: 10.1038/s41416-020-01125-8] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 07/27/2020] [Accepted: 09/30/2020] [Indexed: 12/13/2022] Open
Abstract
Although mitochondrial contributions to cancer have been recognised for approximately a century, given that mitochondrial DNA (mtDNA) is dwarfed by the size of the nuclear genome (nDNA), nuclear genetics has represented a focal point in cancer biology, often at the expense of mtDNA and mitochondria. However, genomic sequencing and advances in in vivo models underscore the importance of mtDNA and mitochondria in cancer and metastasis. In this review, we explore the roles of mitochondria in the four defined 'hallmarks of metastasis': motility and invasion, microenvironment modulation, plasticity and colonisation. Biochemical processes within the mitochondria of both cancer cells and the stromal cells with which they interact are critical for each metastatic hallmark. We unravel complex dynamics in mitochondrial contributions to cancer, which are context-dependent and capable of either promoting metastasis or being leveraged to prevent it at various points of the metastatic cascade. Ultimately, mitochondrial contributions to cancer and metastasis are rooted in the capacity of these organelles to tune metabolic and genetic responses to dynamic microenvironmental cues.
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Affiliation(s)
- Adam D Scheid
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS, USA
- Heartland Center for Mitochondrial Medicine, Kansas City, KS, USA
| | - Thomas C Beadnell
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS, USA
- Heartland Center for Mitochondrial Medicine, Kansas City, KS, USA
| | - Danny R Welch
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS, USA.
- Heartland Center for Mitochondrial Medicine, Kansas City, KS, USA.
- University of Kansas Cancer Center, Kansas City, KS, USA.
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18
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Chen X, Xu J, Wang H, Luo J, Wang Z, Chen G, Jiang D, Cao R, Huang H, Luo D, Xiao X, Hu J. Profiling the differences of gut microbial structure between schizophrenia patients with and without violent behaviors based on 16S rRNA gene sequencing. Int J Legal Med 2020; 135:131-141. [PMID: 33067643 DOI: 10.1007/s00414-020-02439-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 09/30/2020] [Indexed: 02/07/2023]
Abstract
Understanding the violence behaviors in schizophrenia patients has always been the focus of forensic psychiatry. Although many studies show gut microbiota could regulate behavior, to our knowledge, no studies have profiled the gut microbiota structure in schizophrenia patients with violence. We profiled the characteristics of gut microbiota structure in 26 schizophrenia patients with violence (V.SCZ) by comparing with that of 16 schizophrenia patients without violence (NV.SCZ) under the control of confounders, and found the differences of gut microbiota structure between the two groups. Violence was assessed by the MacArthur Community Violence Instrument. Psychiatric symptoms were assessed by the Positive and Negative Syndrome Scale. The 16S rRNA gene sequencing was used to identify and relatively quantify gut microbial composition. Bioinformatics analysis was used to find differential gut microbial composition between the V.SCZ and NV.SCZ groups. Fifty-nine differential microbial taxonomic compositions were found between the two groups. Fifteen gut microbial compositions were the key microbial taxonomic compositions responsible for the differences between the V.SCZ and NV.SCZ groups, including five enriched microbial taxonomic compositions (p_Bacteroidetes, c_Bacteroidia, o_Bacteroidales, f_Prevotellaceae, s_Bacteroides_uniformis), and ten impoverished microbial taxonomic compositions (p_Actinobacteria, c_unidentified_Actinobacteria, o_Bifidobacteriales, f_ Enterococcaceae, f_Veillonellaceae, f_Bifidobacteriaceae, g_Enterococcus, g_Candidatus_Saccharimonas, g_Bifidobacterium, and s_Bifidobacterium_pseudocatenulatum). This study profiled the differences of gut microbiota between schizophrenia patients with violence and without violence. These results could enrich the etiological understanding of violence in schizophrenia and might be helpful to violence management in the future.
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Affiliation(s)
- Xiacan Chen
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Jiajun Xu
- Mental Health Center of West China Hospital, Sichuan University, Chengdu, China.
| | - Hongren Wang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Jiaguo Luo
- Jinxin Mental Health Center, Chengdu, China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Gang Chen
- Jinxin Mental Health Center, Chengdu, China
| | - Dan Jiang
- Jinxin Mental Health Center, Chengdu, China
| | - Ruochen Cao
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Haolan Huang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Dan Luo
- Mental Health Center of West China Hospital, Sichuan University, Chengdu, China
| | - Xiao Xiao
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University and the Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Junmei Hu
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China.
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19
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Chen L, van den Munckhof ICL, Schraa K, Ter Horst R, Koehorst M, van Faassen M, van der Ley C, Doestzada M, Zhernakova DV, Kurilshikov A, Bloks VW, Groen AK, Riksen NP, Rutten JHW, Joosten LAB, Wijmenga C, Zhernakova A, Netea MG, Fu J, Kuipers F. Genetic and Microbial Associations to Plasma and Fecal Bile Acids in Obesity Relate to Plasma Lipids and Liver Fat Content. Cell Rep 2020; 33:108212. [PMID: 33027657 DOI: 10.1016/j.celrep.2020.108212] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/31/2020] [Accepted: 09/09/2020] [Indexed: 12/21/2022] Open
Abstract
Bile acids (BAs) are implicated in the etiology of obesity-related conditions such as non-alcoholic fatty liver disease. Differently structured BA species display variable signaling activities via farnesoid X receptor (FXR) and Takeda G protein-coupled BA receptor 1 (TGR5). This study profiles plasma and fecal BAs and plasma 7α-hydroxy-4-cholesten-3-one (C4) in 297 persons with obesity, identifies underlying genetic and microbial determinants, and establishes BA correlations with liver fat and plasma lipid parameters. We identify 27 genetic associations (p < 5 × 10-8) and 439 microbial correlations (FDR < 0.05) for 50 BA entities. Additionally, we report 111 correlations between BA and 88 lipid parameters (FDR < 0.05), mainly for C4 reflecting hepatic BA synthesis. Inter-individual variability in the plasma BA profile does not reflect hepatic BA synthetic pathways, but rather transport and metabolism within the enterohepatic circulation. Our study reveals genetic and microbial determinants of BAs in obesity and their relationship to disease-relevant lipid parameters that are important for the design of personalized therapies targeting BA-signaling pathways.
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Affiliation(s)
- Lianmin Chen
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen 9713AV, the Netherlands; Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713AV, the Netherlands
| | - Inge C L van den Munckhof
- Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen 6500HB, the Netherlands
| | - Kiki Schraa
- Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen 6500HB, the Netherlands
| | - Rob Ter Horst
- Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen 6500HB, the Netherlands
| | - Martijn Koehorst
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen 9713AV, the Netherlands; Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen 9713AV, the Netherlands
| | - Martijn van Faassen
- Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen 9713AV, the Netherlands
| | - Claude van der Ley
- Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen 9713AV, the Netherlands
| | - Marwah Doestzada
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen 9713AV, the Netherlands; Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713AV, the Netherlands
| | - Daria V Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713AV, the Netherlands; Laboratory of Genomic Diversity, Center for Computer Technologies, ITMO University, St. Petersburg 197101, Russia
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713AV, the Netherlands
| | - Vincent W Bloks
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen 9713AV, the Netherlands
| | - Albert K Groen
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen 9713AV, the Netherlands; Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen 9713AV, the Netherlands; Department of Vascular Medicine, University of Amsterdam, Amsterdam University Medical Center, Amsterdam 1012WX, the Netherlands
| | | | - Niels P Riksen
- Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen 6500HB, the Netherlands
| | - Joost H W Rutten
- Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen 6500HB, the Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen 6500HB, the Netherlands; Department of Medical Genetics, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca 400000, Romania
| | - Cisca Wijmenga
- University of Groningen, Groningen 9712CP, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713AV, the Netherlands
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen 6500HB, the Netherlands; Department for Genomics & Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn 53113, Germany; Human Genomics Laboratory, Craiova University of Medicine and Pharmacy, Craiova 200349, Romania
| | - Jingyuan Fu
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen 9713AV, the Netherlands; Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713AV, the Netherlands.
| | - Folkert Kuipers
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen 9713AV, the Netherlands; Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen 9713AV, the Netherlands.
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20
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Chen L, Collij V, Jaeger M, van den Munckhof ICL, Vich Vila A, Kurilshikov A, Gacesa R, Sinha T, Oosting M, Joosten LAB, Rutten JHW, Riksen NP, Xavier RJ, Kuipers F, Wijmenga C, Zhernakova A, Netea MG, Weersma RK, Fu J. Gut microbial co-abundance networks show specificity in inflammatory bowel disease and obesity. Nat Commun 2020; 11:4018. [PMID: 32782301 PMCID: PMC7419557 DOI: 10.1038/s41467-020-17840-y] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 07/20/2020] [Indexed: 02/07/2023] Open
Abstract
The gut microbiome is an ecosystem that involves complex interactions. Currently, our knowledge about the role of the gut microbiome in health and disease relies mainly on differential microbial abundance, and little is known about the role of microbial interactions in the context of human disease. Here, we construct and compare microbial co-abundance networks using 2,379 metagenomes from four human cohorts: an inflammatory bowel disease (IBD) cohort, an obese cohort and two population-based cohorts. We find that the strengths of 38.6% of species co-abundances and 64.3% of pathway co-abundances vary significantly between cohorts, with 113 species and 1,050 pathway co-abundances showing IBD-specific effects and 281 pathway co-abundances showing obesity-specific effects. We can also replicate these IBD microbial co-abundances in longitudinal data from the IBD cohort of the integrative human microbiome (iHMP-IBD) project. Our study identifies several key species and pathways in IBD and obesity and provides evidence that altered microbial abundances in disease can influence their co-abundance relationship, which expands our current knowledge regarding microbial dysbiosis in disease. Gut microbiome alterations have been linked to inflammatory bowel disease (IBD) and obesity. Here, the authors characterize the metagenomes of four large human cohorts and perform co-abundance network analysis showing that dysbiosis in disease is marked by the altered co-abundance relationships, suggesting that pathway coabundance networks are more heterogeneous than species network.
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Affiliation(s)
- Lianmin Chen
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Valerie Collij
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Martin Jaeger
- Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Inge C L van den Munckhof
- Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Arnau Vich Vila
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Ranko Gacesa
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Trishla Sinha
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Marije Oosting
- Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands.,Department of Medical Genetics, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Joost H W Rutten
- Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Niels P Riksen
- Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Ramnik J Xavier
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Folkert Kuipers
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,University of Groningen, Groningen, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands.,Department for Genomics & Immunoregulation, Life and Medical Sciences Institute, University of Bonn, 53115, Bonn, Germany.,Human Genomics Laboratory, Craiova University of Medicine and Pharmacy, Craiova, Romania
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands. .,Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
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21
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Xia Y. Correlation and association analyses in microbiome study integrating multiomics in health and disease. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 171:309-491. [PMID: 32475527 DOI: 10.1016/bs.pmbts.2020.04.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Correlation and association analyses are one of the most widely used statistical methods in research fields, including microbiome and integrative multiomics studies. Correlation and association have two implications: dependence and co-occurrence. Microbiome data are structured as phylogenetic tree and have several unique characteristics, including high dimensionality, compositionality, sparsity with excess zeros, and heterogeneity. These unique characteristics cause several statistical issues when analyzing microbiome data and integrating multiomics data, such as large p and small n, dependency, overdispersion, and zero-inflation. In microbiome research, on the one hand, classic correlation and association methods are still applied in real studies and used for the development of new methods; on the other hand, new methods have been developed to target statistical issues arising from unique characteristics of microbiome data. Here, we first provide a comprehensive view of classic and newly developed univariate correlation and association-based methods. We discuss the appropriateness and limitations of using classic methods and demonstrate how the newly developed methods mitigate the issues of microbiome data. Second, we emphasize that concepts of correlation and association analyses have been shifted by introducing network analysis, microbe-metabolite interactions, functional analysis, etc. Third, we introduce multivariate correlation and association-based methods, which are organized by the categories of exploratory, interpretive, and discriminatory analyses and classification methods. Fourth, we focus on the hypothesis testing of univariate and multivariate regression-based association methods, including alpha and beta diversities-based, count-based, and relative abundance (or compositional)-based association analyses. We demonstrate the characteristics and limitations of each approaches. Fifth, we introduce two specific microbiome-based methods: phylogenetic tree-based association analysis and testing for survival outcomes. Sixth, we provide an overall view of longitudinal methods in analysis of microbiome and omics data, which cover standard, static, regression-based time series methods, principal trend analysis, and newly developed univariate overdispersed and zero-inflated as well as multivariate distance/kernel-based longitudinal models. Finally, we comment on current association analysis and future direction of association analysis in microbiome and multiomics studies.
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Affiliation(s)
- Yinglin Xia
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, United States.
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22
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Qian X, Chen L, Sui Y, Chen C, Zhang W, Zhou J, Dong W, Jiang M, Xin F, Ochsenreither K. Biotechnological potential and applications of microbial consortia. Biotechnol Adv 2020; 40:107500. [DOI: 10.1016/j.biotechadv.2019.107500] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 11/13/2019] [Accepted: 12/17/2019] [Indexed: 12/20/2022]
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23
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Grégoire H, Roncali L, Rousseau A, Chérel M, Delneste Y, Jeannin P, Hindré F, Garcion E. Targeting Tumor Associated Macrophages to Overcome Conventional Treatment Resistance in Glioblastoma. Front Pharmacol 2020; 11:368. [PMID: 32322199 PMCID: PMC7158850 DOI: 10.3389/fphar.2020.00368] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 03/10/2020] [Indexed: 12/11/2022] Open
Abstract
Glioblastoma (GB) is the most common and devastating form of brain cancer. Despite conventional treatments, progression or recurrences are systematic. In recent years, immunotherapies have emerged as an effective treatment in a number of cancers, leaving the question of their usefulness also faced with the particular case of brain tumors. The challenge here is major not only because the brain is the seat of our consciousness but also because of its isolation by the blood-brain barrier and the presence of a unique microenvironment that constitutes the central nervous system (CNS) with very specific constituent or patrolling cells. Much of the microenvironment is made up of immune cells or inflammation. Among these, tumor-associated macrophages (TAMs) are of significant interest as they are often involved in facilitating tumor progression as well as the development of resistance to standard therapies. In this review, the ubiquity of TAMs in GB will be discussed while the specific case of microglia resident in the brain will be also emphasized. In addition, the roles of TAMs as accomplices in the progression of GB and resistance to treatment will be presented. Finally, clinical trials targeting TAMs as a means of treating cancer will be discussed.
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Affiliation(s)
- Hélène Grégoire
- CRCINA, INSERM, Université de Nantes, Université d'Angers, Angers, France
| | - Loris Roncali
- CRCINA, INSERM, Université de Nantes, Université d'Angers, Angers, France
| | - Audrey Rousseau
- CRCINA, INSERM, Université de Nantes, Université d'Angers, Angers, France.,Département de Pathologie Cellulaire et Tissulaire, CHU Angers, Angers, France
| | - Michel Chérel
- CRCINA, INSERM, Université d'Angers, Université de Nantes, Nantes, France
| | - Yves Delneste
- CRCINA, INSERM, Université de Nantes, Université d'Angers, Angers, France.,Laboratoire d'Immunologie et Allergologie, CHU d'Angers, Angers, France
| | - Pascale Jeannin
- CRCINA, INSERM, Université de Nantes, Université d'Angers, Angers, France.,Laboratoire d'Immunologie et Allergologie, CHU d'Angers, Angers, France
| | - François Hindré
- CRCINA, INSERM, Université de Nantes, Université d'Angers, Angers, France.,PRIMEX, Plateforme de radiobiologie et d'imagerie expérimentale, SFR ICAT, Université d'Angers, Angers, France
| | - Emmanuel Garcion
- CRCINA, INSERM, Université de Nantes, Université d'Angers, Angers, France.,PACeM, Plateforme d'analyses cellulaires et moléculaires, SFR ICAT, Université d'Angers, Angers, France
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24
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Uren Webster TM, Rodriguez-Barreto D, Castaldo G, Gough P, Consuegra S, Garcia de Leaniz C. Environmental plasticity and colonisation history in the Atlantic salmon microbiome: A translocation experiment. Mol Ecol 2020; 29:886-898. [PMID: 32011775 PMCID: PMC7078932 DOI: 10.1111/mec.15369] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 01/11/2020] [Accepted: 01/29/2020] [Indexed: 12/20/2022]
Abstract
Microbial communities associated with the gut and the skin are strongly influenced by environmental factors, and can rapidly adapt to change. Historical processes may also affect the microbiome. In particular, variation in microbial colonisation in early life has the potential to induce lasting effects on microbial assemblages. However, little is known about the relative extent of microbiome plasticity or the importance of historical colonisation effects following environmental change, especially for nonmammalian species. To investigate this we performed a reciprocal translocation of Atlantic salmon between artificial and semi-natural conditions. Wild and hatchery-reared fry were transferred to three common garden experimental environments for 6 weeks: standard hatchery conditions, hatchery conditions with an enriched diet, and simulated wild conditions. We characterized the faecal and skin microbiome of individual fish before and after the environmental translocation, using a BACI (before-after-control-impact) design. We found evidence of extensive microbiome plasticity for both the gut and skin, with the greatest changes in alpha and beta diversity associated with the largest changes in environment and diet. Microbiome richness and diversity were entirely determined by environment, with no detectable effects of fish origin, and there was also a near-complete turnover in microbiome structure. However, we also identified, for the first time in fish, evidence of historical colonisation effects reflecting early-life experience, including ASVs characteristic of captive rearing. These results have important implications for host adaptation to local selective pressures, and highlight how conditions experienced during early life can have a long-term influence on the microbiome and, potentially, host health.
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Affiliation(s)
- Tamsyn M Uren Webster
- Centre for Sustainable Aquatic Research, College of Science, Swansea University, Swansea, UK
| | | | - Giovanni Castaldo
- Centre for Sustainable Aquatic Research, College of Science, Swansea University, Swansea, UK
| | - Peter Gough
- Cynrig Fish Culture Unit, Natural Resources Wales, Llanfrynach, UK
| | - Sofia Consuegra
- Centre for Sustainable Aquatic Research, College of Science, Swansea University, Swansea, UK
| | - Carlos Garcia de Leaniz
- Centre for Sustainable Aquatic Research, College of Science, Swansea University, Swansea, UK
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25
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O'Callaghan JL, Turner R, Dekker Nitert M, Barrett HL, Clifton V, Pelzer ES. Re-assessing microbiomes in the low-biomass reproductive niche. BJOG 2019; 127:147-158. [PMID: 31587490 DOI: 10.1111/1471-0528.15974] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2019] [Indexed: 12/21/2022]
Abstract
The female reproductive tract represents a continuum between the vagina and the upper genital tract. New evidence from cultivation-independent studies suggests that the female upper genital tract is not sterile; however, the significance of this for reproductive health and disease remains to be elucidated fully. Further, diagnosis and treatment of infectious reproductive tract pathologies using cultivation-independent technologies represents a largely unchartered area of modern medical science. The challenge now is to design well-controlled experiments to account for the ease of contamination known to confound molecular-based studies of low-biomass niches, including the uterus and placenta. This will support robust assessment of the potential function of microorganisms, microbial metabolites, and cell-free bacterial DNA on reproductive function in health and disease. TWEETABLE ABSTRACT: Molecular microbial studies of low-biomass niches require stringent experimental controls to reveal causal relations in reproductive health and disease.
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Affiliation(s)
- J L O'Callaghan
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Qld, Australia.,Institute of Health and Biomedical Innovation, Faculty of Health, Queensland University of Technology, Brisbane, Qld, Australia
| | - R Turner
- The Wesley Hospital, Auchenflower, Qld, Australia
| | - M Dekker Nitert
- School of Chemistry and Molecular Biosciences, Faculty of Science, University of Queensland, St Lucia, Qld, Australia
| | - H L Barrett
- Endocrinology, Mater Hospital, South Brisbane, Qld, Australia.,Mater Research, University of Queensland, St Lucia, Qld, Australia
| | - V Clifton
- Mater Research, Pregnancy and Development Group, South Brisbane, Qld, Australia
| | - E S Pelzer
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Qld, Australia.,Institute of Health and Biomedical Innovation, Faculty of Health, Queensland University of Technology, Brisbane, Qld, Australia
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26
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27
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van Oppen MJH, Blackall LL. Coral microbiome dynamics, functions and design in a changing world. Nat Rev Microbiol 2019; 17:557-567. [DOI: 10.1038/s41579-019-0223-4] [Citation(s) in RCA: 137] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2019] [Indexed: 12/20/2022]
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28
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Huang TT, Lai JB, Du YL, Xu Y, Ruan LM, Hu SH. Current Understanding of Gut Microbiota in Mood Disorders: An Update of Human Studies. Front Genet 2019; 10:98. [PMID: 30838027 PMCID: PMC6389720 DOI: 10.3389/fgene.2019.00098] [Citation(s) in RCA: 145] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 01/29/2019] [Indexed: 02/06/2023] Open
Abstract
Gut microbiota plays an important role in the bidirectional communication between the gut and the central nervous system. Mounting evidence suggests that gut microbiota can influence the brain function via neuroimmune and neuroendocrine pathways as well as the nervous system. Advances in gene sequencing techniques further facilitate investigating the underlying relationship between gut microbiota and psychiatric disorders. In recent years, researchers have preliminarily explored the gut microbiota in patients with mood disorders. The current review aims to summarize the published human studies of gut microbiota in mood disorders. The findings showed that microbial diversity and taxonomic compositions were significantly changed compared with healthy individuals. Most of these findings revealed that short-chain fatty acids-producing bacterial genera were decreased, while pro-inflammatory genera and those involved in lipid metabolism were increased in patients with depressive episodes. Interestingly, the abundance of Actinobacteria, Enterobacteriaceae was increased and Faecalibacterium was decreased consistently in patients with either bipolar disorder or major depressive disorder. Some studies further indicated that specific bacteria were associated with clinical characteristics, inflammatory profiles, metabolic markers, and pharmacological treatment. These studies present preliminary evidence of the important role of gut microbiota in mood disorders, through the brain-gut-microbiota axis, which emerges as a promising target for disease diagnosis and therapeutic interventions in the future.
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Affiliation(s)
- Ting-Ting Huang
- Department of Psychiatry, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jian-Bo Lai
- Department of Psychiatry, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,The Key Laboratory of Mental Disorder's Management of Zhejiang Province, Hangzhou, China.,Brain Research Institute of Zhejiang University, Hangzhou, China
| | - Yan-Li Du
- Department of Psychiatry, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yi Xu
- Department of Psychiatry, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,The Key Laboratory of Mental Disorder's Management of Zhejiang Province, Hangzhou, China.,Brain Research Institute of Zhejiang University, Hangzhou, China
| | - Lie-Min Ruan
- Department of Mental Health, Ningbo First Hospital, Ningbo, China
| | - Shao-Hua Hu
- Department of Psychiatry, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,The Key Laboratory of Mental Disorder's Management of Zhejiang Province, Hangzhou, China.,Brain Research Institute of Zhejiang University, Hangzhou, China
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