1
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Hong W, Wu Y, Sun Z, Yang S, Cheng Q, Liu H, Lin X, Ni R, Yao Y, Wang S, Zheng Z, Sun A, Xi C, Song L. Sterile Diet Causes Gut Microbiome Collapse of Cancer Patients Post Hematopoietic Cell Transplantation, But Normal Diet Recovers Them. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2403991. [PMID: 38973355 DOI: 10.1002/advs.202403991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 06/07/2024] [Indexed: 07/09/2024]
Abstract
Though sterile diet, post-transplantation surgery is a clinical strategy for patient care to prevent the infiltration of gut pathogens, less is known about its effects on the gut microbiome. Here, the gut microbiome dynamics of leukemia patients following a 120-day "sterile-normal" diet strategy posthematopoietic cell transplantation are examined. In contrast to the traditional idea, a sterile diet leads to the lowest gut microbiota diversity (p < 0.05) and short-chain fatty acids, promoted the proliferation of potential pathogens such as Streptococcus (up by 16.93%) and Lactobacillus (up by 40.30%), and 43.32% reduction in nodes and an 85.33% reduction in edges within the microbial interaction's network. Interestingly, a normal diet allows the gut microbiome recovery and significantly promotes the abundance of beneficial bacteria. These results indicate that a sterile diet leads to a collapse of the patient's gut microbiome and promoted the proliferation of potential pathogens. This assay is a starting point for a more sophisticated assessment of the effects of a sterile diet. The work also suggests a basic principle for the re-establishment of microbial equilibrium that supplementation of microbial taxa may be the key to the restoration of the degraded ecosystem.
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Affiliation(s)
- Wenqing Hong
- School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China
| | - Yun Wu
- Department of Hematology, The First Affiliated Hospital of University of Science and Technology of China, Hefei, 230001, China
| | - Zimin Sun
- Department of Hematology, The First Affiliated Hospital of University of Science and Technology of China, Hefei, 230001, China
- Blood and Cell Therapy Institute, Division of Life Sciences and Medicine, Anhui Provincial Key Laboratory of Blood Research and Applications, University of Science and Technology of China, Hefei, 230027, China
| | - Shu Yang
- Institute of Public Health Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, 230026, China
| | - Qing Cheng
- Department of Hematology, The First Affiliated Hospital of University of Science and Technology of China, Hefei, 230001, China
| | - Huilan Liu
- Department of Hematology, The First Affiliated Hospital of University of Science and Technology of China, Hefei, 230001, China
| | - Xiaoxing Lin
- School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China
| | - Renjie Ni
- School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China
| | - Yuping Yao
- School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China
| | - Shuijing Wang
- School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China
| | - Zihao Zheng
- School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China
| | - Anyi Sun
- School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China
| | - Chuanwu Xi
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Liyan Song
- School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Science, Chongqing, 400714, China
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2
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Huang P, Dong Q, Wang Y, Tian Y, Wang S, Zhang C, Yu L, Tian F, Gao X, Guo H, Yi S, Li M, Liu Y, Zhang Q, Lu W, Wang G, Yang B, Cui S, Hua D, Wang X, Jiao Y, Liu L, Deng Q, Ma B, Wu T, Zou H, Shi J, Zhang H, Fan D, Sheng Y, Zhao J, Tang L, Zhang H, Sun W, Chen W, Kong X, Chen L, Zhai Q. Gut microbial genomes with paired isolates from China illustrate probiotic and cardiometabolic effects. CELL GENOMICS 2024; 4:100559. [PMID: 38740021 PMCID: PMC11228888 DOI: 10.1016/j.xgen.2024.100559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 02/04/2024] [Accepted: 04/15/2024] [Indexed: 05/16/2024]
Abstract
The gut microbiome displays genetic differences among populations, and characterization of the genomic landscape of the gut microbiome in China remains limited. Here, we present the Chinese Gut Microbial Reference (CGMR) set, comprising 101,060 high-quality metagenomic assembled genomes (MAGs) of 3,707 nonredundant species from 3,234 fecal samples across primarily rural Chinese locations, 1,376 live isolates mainly from lactic acid bacteria, and 987 novel species relative to worldwide databases. We observed region-specific coexisting MAGs and MAGs with probiotic and cardiometabolic functionalities. Preliminary mouse experiments suggest a probiotic effect of two Faecalibacillus intestinalis isolates in alleviating constipation, cardiometabolic influences of three Bacteroides fragilis_A isolates in obesity, and isolates from the genera Parabacteroides and Lactobacillus in host lipid metabolism. Our study expands the current microbial genomes with paired isolates and demonstrates potential host effects, contributing to the mechanistic understanding of host-microbe interactions.
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Affiliation(s)
- Pan Huang
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Quanbin Dong
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China; Department of Gastroenterology, Changzhou Medical Center, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Nanjing Medical University, Changzhou, China
| | - Yifeng Wang
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China; Cardiovascular Research Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Yunfan Tian
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China
| | - Shunhe Wang
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Chengcheng Zhang
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Leilei Yu
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Fengwei Tian
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Xiaoxiang Gao
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Hang Guo
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Shanrong Yi
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Mingyang Li
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Yang Liu
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Qingsong Zhang
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Wenwei Lu
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Gang Wang
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Bo Yang
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Shumao Cui
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Dongxu Hua
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China
| | - Xiuchao Wang
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China
| | - Yuwen Jiao
- Department of Gastroenterology, Changzhou Medical Center, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Nanjing Medical University, Changzhou, China
| | - Lu Liu
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China
| | - Qiufeng Deng
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China
| | - Beining Ma
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China
| | - Tingting Wu
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China
| | - Huayiyang Zou
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China
| | - Jing Shi
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China
| | - Haifeng Zhang
- Cardiovascular Research Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Daming Fan
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Yanhui Sheng
- Cardiovascular Research Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Liming Tang
- Department of Gastroenterology, Changzhou Medical Center, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Nanjing Medical University, Changzhou, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Wei Sun
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China
| | - Wei Chen
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Xiangqing Kong
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China; Cardiovascular Research Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China.
| | - Lianmin Chen
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China; Department of Gastroenterology, Changzhou Medical Center, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Nanjing Medical University, Changzhou, China.
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China.
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3
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Reshef N, Gophna U, Reshef L, Konikoff F, Gabay G, Zornitzki T, Knobler H, Maor Y. Prebiotic Treatment in Patients with Nonalcoholic Fatty Liver Disease (NAFLD)-A Randomized Pilot Trial. Nutrients 2024; 16:1571. [PMID: 38892505 PMCID: PMC11174003 DOI: 10.3390/nu16111571] [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: 03/20/2024] [Revised: 05/10/2024] [Accepted: 05/17/2024] [Indexed: 06/21/2024] Open
Abstract
Several studies show that gut microbiotas in patients with nonalcoholic fatty liver disease (NAFLD) differ from those in a healthy population, suggesting that this alteration plays a role in NAFLD pathogenesis. We investigated whether prebiotic administration affects liver fat content and/or liver-related and metabolic parameters. Patients with NAFLD and metabolic syndrome (age: 50 ± 11; 79% men) were randomized to receive either 16 g/day of prebiotic (ITFs-inulin-type fructans) (n = 8) or placebo (maltodextrin) (n = 11) for 12 weeks. Patients were instructed to maintain a stable weight throughout the study. Liver fat content (measured by H1MRS), fecal microbiota, and metabolic, inflammatory, and liver parameters were determined before and after intervention. Fecal samples from patients who received the prebiotic had an increased content of Bifidobacterium (p = 0.025), which was not observed with the placebo. However, the baseline and end-of-study liver fat contents did not change significantly in the prebiotic and placebo groups, neither did the liver function tests' metabolic and inflammatory mediators, including fibroblast growth factor-19 and lipopolysaccharide-binding protein. Body weight remained stable in both groups. These findings suggest that prebiotic treatment without weight reduction is insufficient to improve NAFLD.
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Affiliation(s)
- Naama Reshef
- Institute of Diabetes and Metabolism-Kaplan Medical Center, Rehovot 7661041, Israel; (T.Z.); (H.K.)
- School of Nutritional Sciences, Faculty of Agriculture, Food and Environment, The Hebrew University, Jerusalem 9112102, Israel
| | - Uri Gophna
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel-Aviv University, Tel Aviv 6423906, Israel; (U.G.); (L.R.)
| | - Leah Reshef
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel-Aviv University, Tel Aviv 6423906, Israel; (U.G.); (L.R.)
| | - Fred Konikoff
- Institute of Gastroenterology and Hepatology-Meir Medical Center, Kefar Sava 4428164, Israel; (F.K.)
- Faculty of Medicine, Tel-Aviv University, Tel Aviv 6423906, Israel
| | - Gila Gabay
- Institute of Gastroenterology and Hepatology-Meir Medical Center, Kefar Sava 4428164, Israel; (F.K.)
| | - Taiba Zornitzki
- Institute of Diabetes and Metabolism-Kaplan Medical Center, Rehovot 7661041, Israel; (T.Z.); (H.K.)
- Hadassah School of Medicine, The Hebrew University, Jerusalem 9112102, Israel;
| | - Hilla Knobler
- Institute of Diabetes and Metabolism-Kaplan Medical Center, Rehovot 7661041, Israel; (T.Z.); (H.K.)
- Hadassah School of Medicine, The Hebrew University, Jerusalem 9112102, Israel;
| | - Yaakov Maor
- Hadassah School of Medicine, The Hebrew University, Jerusalem 9112102, Israel;
- Institute of Gastroenterology and Hepatology-Kaplan Medical Center, Rehovot 7661043, Israel
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4
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Guerrieri F, Libert C. The invisible life. Front Microbiol 2024; 15:1401487. [PMID: 38832115 PMCID: PMC11144902 DOI: 10.3389/fmicb.2024.1401487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 04/29/2024] [Indexed: 06/05/2024] Open
Affiliation(s)
- Francesca Guerrieri
- Cancer Research Center of Lyon (CRCL), UMR Inserm 1052 - CNRS 5286, Lyon, France
| | - Cédric Libert
- Ecole Nationale Superieure d'Architecture de Saint-Etienne, Saint-Etienne, France
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5
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Bu S, Beavers AW, Sugino KY, Keller SF, Alaimo K, Comstock SS. Influence of Compost Amendments on Soil and Human Gastrointestinal Bacterial Communities during a Single Gardening Season. Microorganisms 2024; 12:928. [PMID: 38792758 PMCID: PMC11123992 DOI: 10.3390/microorganisms12050928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 04/24/2024] [Accepted: 04/29/2024] [Indexed: 05/26/2024] Open
Abstract
To measure associations between gardening with different compost amendments and the human gut microbiota composition, gardeners (n = 25) were provided with one of three types of compost: chicken manure (CM), dairy manure and plant material (DMP), or plant-based (P). Stool samples were collected before gardening (T1), after compost amendment (T2), and at peak garden harvest (T3). Compost and soil samples were collected. DNA was extracted, 16S rRNA libraries were established, and libraries were sequenced by Illumina MiSeq. Sequences were processed using mothur, and data were analyzed in R software version 4.2.2. Fast expectation-maximization microbial source tracking analysis was used to determine stool bacteria sources. At T2/T3, the gut microbiotas of P participants had the lowest Shannon alpha diversity, which was also the trend at T1. In stool from T2, Ruminococcus 1 were less abundant in the microbiotas of those using P compost as compared to those using CM or DMP. At T2, Prevotella 9 had the highest abundance in the microbiotas of those using CM compost. In participants who used CM compost to amend their gardening plots, a larger proportion of the human stool bacteria were sourced from CM compared to soil. Soil exposure through gardening was associated with a small but detectable change in the gardeners' gut microbiota composition. These results suggest that human interactions with soil through gardening could potentially impact health through alterations to the gut microbiota.
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Affiliation(s)
- Sihan Bu
- Department of Food Science and Human Nutrition, Michigan State University, East Lansing, MI 48824, USA; (S.B.); (K.Y.S.); (K.A.)
| | - Alyssa W. Beavers
- Department of Nutrition and Food Science, Wayne State University, Detroit, MI 48201, USA
| | - Kameron Y. Sugino
- Department of Food Science and Human Nutrition, Michigan State University, East Lansing, MI 48824, USA; (S.B.); (K.Y.S.); (K.A.)
| | - Sarah F. Keller
- Department of Food Science and Human Nutrition, Michigan State University, East Lansing, MI 48824, USA; (S.B.); (K.Y.S.); (K.A.)
| | - Katherine Alaimo
- Department of Food Science and Human Nutrition, Michigan State University, East Lansing, MI 48824, USA; (S.B.); (K.Y.S.); (K.A.)
| | - Sarah S. Comstock
- Department of Food Science and Human Nutrition, Michigan State University, East Lansing, MI 48824, USA; (S.B.); (K.Y.S.); (K.A.)
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6
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Rampelli S, Gallois S, D’Amico F, Turroni S, Fabbrini M, Scicchitano D, Candela M, Henry A. The gut microbiome of Baka forager-horticulturalists from Cameroon is optimized for wild plant foods. iScience 2024; 27:109211. [PMID: 38433907 PMCID: PMC10904984 DOI: 10.1016/j.isci.2024.109211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/21/2023] [Accepted: 02/07/2024] [Indexed: 03/05/2024] Open
Abstract
The human gut microbiome is losing biodiversity, due to the "microbiome modernization process" that occurs with urbanization. To keep track of it, here we applied shotgun metagenomics to the gut microbiome of the Baka, a group of forager-horticulturalists from Cameroon, who combine hunting and gathering with growing a few crops and working for neighboring Bantu-speaking farmers. We analyzed the gut microbiome of individuals with different access to and use of wild plant and processed foods, to explore the variation of their gut microbiome along the cline from hunter-gatherer to agricultural subsistence patterns. We found that 26 species-level genome bins from our cohort were pivotal for the degradation of the wild plant food substrates. These microbes include Old Friend species and are encoded for genes that are no longer present in industrialized gut microbiome. Our results highlight the potential relevance of these genes to human biology and health, in relation to lifestyle.
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Affiliation(s)
- Simone Rampelli
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum – University of Bologna, 40126 Bologna, Italy
| | - Sandrine Gallois
- Department of Archaeological Sciences, Faculty of Archaeology, Leiden University, 2311 Leiden, the Netherlands
- Institute of Environmental Science and Technology, ST, 08193 Bellaterra, Spain
| | - Federica D’Amico
- Microbiomics Unit, Department of Medical and Surgical Sciences (DiMeC), Alma Mater Studiorum – University of Bologna, 40138 Bologna, Italy
| | - Silvia Turroni
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum – University of Bologna, 40126 Bologna, Italy
| | - Marco Fabbrini
- Microbiomics Unit, Department of Medical and Surgical Sciences (DiMeC), Alma Mater Studiorum – University of Bologna, 40138 Bologna, Italy
| | - Daniel Scicchitano
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum – University of Bologna, 40126 Bologna, Italy
| | - Marco Candela
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum – University of Bologna, 40126 Bologna, Italy
| | - Amanda Henry
- Department of Archaeological Sciences, Faculty of Archaeology, Leiden University, 2311 Leiden, the Netherlands
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7
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Truter M, Koopman JE, Jordaan K, Tsamkxao LO, Cowan DA, Underdown SJ, Ramond JB, Rifkin RF. Documenting the diversity of the Namibian Ju|'hoansi intestinal microbiome. Cell Rep 2024; 43:113690. [PMID: 38244196 DOI: 10.1016/j.celrep.2024.113690] [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: 02/11/2022] [Revised: 10/27/2023] [Accepted: 01/04/2024] [Indexed: 01/22/2024] Open
Abstract
We investigate the bacterial and fungal composition and functionality of the Ju|'hoansi intestinal microbiome (IM). The Juǀ'hoansi are a hunter-gatherer community residing in northeastern Namibia. They formerly subsisted by hunting and gathering but have been increasingly exposed to industrial dietary sources, medicines, and lifestyle features. They present an opportunity to study the evolution of the human IM in situ, from a predominantly hunter-gatherer to an increasingly Western urban-forager-farmer lifestyle. Their bacterial IM resembles that of typical hunter-gatherers, being enriched for genera such as Prevotella, Blautia, Faecalibacterium, Succinivibrio, and Treponema. Fungal IM inhabitants include animal pathogens and plant saprotrophs such as Fusarium, Issatchenkia, and Panellus. Our results suggest that diet and culture exert a greater influence on Ju|'hoansi IM composition than age, self-identified biological sex, and medical history. The Ju|'hoansi exhibit a unique core IM composition that diverges from the core IMs of other populations.
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Affiliation(s)
- Mia Truter
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield 0028, South Africa; Scientific Computing Research Unit, Department of Chemistry, University of Cape Town, Rondebosch 7700, South Africa
| | - Jessica E Koopman
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield 0028, South Africa
| | - Karen Jordaan
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield 0028, South Africa
| | - Leon Oma Tsamkxao
- Juǀ'hoan Traditional Authority (JUTA), Tsumkwe, Otjozondjupa Region, Namibia
| | - Don A Cowan
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield 0028, South Africa
| | - Simon J Underdown
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield 0028, South Africa; Department of Anthropology and Geography, Human Origins and Palaeoenvironmental Research Group, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Jean-Baptiste Ramond
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield 0028, South Africa; Department of Anthropology and Geography, Human Origins and Palaeoenvironmental Research Group, Oxford Brookes University, Oxford OX3 0BP, UK; Extreme Ecosystem Microbiomics & Ecogenomics (E(2)ME) Lab., Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Riaan F Rifkin
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield 0028, South Africa; Juǀ'hoan Traditional Authority (JUTA), Tsumkwe, Otjozondjupa Region, Namibia; Department of Anthropology and Geography, Human Origins and Palaeoenvironmental Research Group, Oxford Brookes University, Oxford OX3 0BP, UK.
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8
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Rocafort M, Gootenberg DB, Luévano JM, Paer JM, Hayward MR, Bramante JT, Ghebremichael MS, Xu J, Rogers ZH, Munoz AR, Okello S, Kim JH, Sentongo R, Wagubi R, Lankowski A, Maruapula S, Zhao G, Handley SA, Mosepele M, Siedner MJ, Kwon DS. HIV-associated gut microbial alterations are dependent on host and geographic context. Nat Commun 2024; 15:1055. [PMID: 38316748 PMCID: PMC10844288 DOI: 10.1038/s41467-023-44566-4] [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: 02/03/2021] [Accepted: 12/19/2023] [Indexed: 02/07/2024] Open
Abstract
HIV-associated changes in intestinal microbiota are believed to be important drivers of disease progression. However, the majority of studies have focused on populations in high-income countries rather than in developing regions where HIV burden is greatest. To better understand the impact of HIV on fecal microbiota globally, we compare the fecal microbial community of individuals in the U.S., Uganda, and Botswana. We identify significant bacterial taxa alterations with both treated and untreated HIV infection with a high degree of uniqueness in each cohort. HIV-associated taxa alterations are also significantly different between populations that report men who have sex with men (MSM) behavior and non-MSM populations. Additionally, while we find that HIV infection is consistently associated with higher soluble markers of immune activation, most specific bacterial taxa associated with these markers in each region are not shared and none are shared across all three geographic locations in our study. Our findings demonstrate that HIV-associated changes in fecal microbiota are overall distinct among geographical locations and sexual behavior groups, although a small number of taxa shared between pairs of geographic locations warrant further investigation, highlighting the importance of considering host context to fully assess the impact of the gut microbiome on human health and disease.
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Affiliation(s)
- Muntsa Rocafort
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
| | - David B Gootenberg
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
- Harvard Medical School, Boston, MA, 02114, USA
| | - Jesús M Luévano
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
- Harvard Medical School, Boston, MA, 02114, USA
| | - Jeffrey M Paer
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
| | | | | | | | - Jiawu Xu
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
| | - Zoe H Rogers
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
| | | | - Samson Okello
- Department of Medicine, Mbarara University of Science and Technology, 1956, Mbarara, Uganda
| | - June-Ho Kim
- Harvard Medical School, Boston, MA, 02114, USA
| | - Ruth Sentongo
- Department of Medicine, Mbarara University of Science and Technology, 1956, Mbarara, Uganda
| | - Robert Wagubi
- Department of Medicine, Mbarara University of Science and Technology, 1956, Mbarara, Uganda
| | - Alex Lankowski
- Medical Practice Evaluation Center, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Segametsi Maruapula
- Department of Family & Consumer Sciences, University of Botswana, 0022, Gaborone, Botswana
| | - Guoyan Zhao
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Scott A Handley
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Mosepele Mosepele
- Faculty of Medicine, University of Botswana, 0022, Gaborone, Botswana
| | - Mark J Siedner
- Harvard Medical School, Boston, MA, 02114, USA
- Medical Practice Evaluation Center, Massachusetts General Hospital, Boston, MA, 02114, USA
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Douglas S Kwon
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA.
- Harvard Medical School, Boston, MA, 02114, USA.
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, 02114, USA.
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9
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Nezhadi J, Rezaee MA, Ozma MA, Ganbarov K, Kafil HS. Gut Microbiota Exchange in Domestic Animals and Rural-urban People Axis. Curr Pharm Biotechnol 2024; 25:825-837. [PMID: 37877143 DOI: 10.2174/0113892010261535230920062107] [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: 05/09/2023] [Revised: 08/13/2023] [Accepted: 08/25/2023] [Indexed: 10/26/2023]
Abstract
In recent years, one of the most critical topics in microbiology that can be addressed is microbiome and microbiota. The term microbiome contains both the microbiota and structural elements, metabolites/signal molecules, and the surrounding environmental conditions, and the microbiota consists of all living members forming the microbiome. Among; the intestinal microbiota is one of the most important microbiota, also called the gut microbiota. After colonization, the gut microbiota can have different functions, including resistance to pathogens, maintaining the intestinal epithelium, metabolizing dietary and pharmaceutical compounds, and controlling immune function. Recently, studies have shown that the gut microbiota can prevent the formation of fat in the body. In this study, we examined the gut microbiota in various animals, including dogs, cats, dairy cows, sheep, chickens, horses, and people who live in urban and rural areas. Based on the review of various studies, it has been determined that the population of microbiota in animals and humans is different, and various factors such as the environment, nutrition, and contact with animals can affect the microbiota of people living in urban and rural areas.
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Affiliation(s)
- Javad Nezhadi
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Mahdi Asghari Ozma
- Department of Microbiology, Research Center for Pharmaceutical Nanotechnology, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Khudaverdi Ganbarov
- Department of Microbiology, Research Laboratory of Microbiology and Virology, Baku State University, Baku, Azerbaijan
| | - Hossein Samadi Kafil
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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10
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Zhao Z, Xiao G, Xia J, Guo H, Yang X, Jiang Q, Wang H, Hu J, Zhang C. Effectiveness of probiotic/prebiotic/synbiotic treatments on anxiety: A systematic review and meta-analysis of randomized controlled trials. J Affect Disord 2023; 343:9-21. [PMID: 37734624 DOI: 10.1016/j.jad.2023.09.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 08/18/2023] [Accepted: 09/17/2023] [Indexed: 09/23/2023]
Abstract
BACKGROUND Anxiety can adversely affect human well-being. This meta-analysis aimed to evaluate the effects of interventions that alter the gut microbes (including probiotics, prebiotics, and synbiotics) on anxiety. METHODS A systematic meta-analysis of the effects of probiotics, prebiotics, and synbiotics on anxiety was conducted by searching randomized controlled trials (RCTs) in 13 databases. The primary outcomes were the pre- and post-intervention anxiety scores in the intervention and placebo groups. Anxiety scores were extracted as standard mean differences (SMDs) and pooled based on a random effects model. Subgroup analyses of anxiety scales, health status, gastrointestinal symptoms, flora strains, treatment type, probiotic dose, region, and treatment duration were also performed. RESULTS 29 RCTs (2035 participants) were included, revealing that both probiotics and synbiotics significantly reduced anxiety scores. Additionally, anxiety scores did not significantly reduce when comparing prebiotics and placebos. LIMITATIONS Owing to the small combined effect size of probiotic/prebiotic/synbiotic treatments and the relatively few studies on prebiotics and synbiotics included in the analysis, the findings of probiotic/prebiotic/synbiotic treatments are preliminary. CONCLUSIONS Our study indicated that probiotics and synbiotics can reduce anxiety scores; however, it might be premature to conclude their clinical efficacy in alleviating anxiety due to the small effect size. There is no consensus regarding the optimal dose, treatment duration, treatment type, or probiotic strain to improve anxiety. Moreover, the mechanisms by which probiotics and synbiotics improve anxiety remain unclear. More RCTs are needed to determine the mechanisms of action and to identify appropriate markers to clarify their effects.
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Affiliation(s)
- Ziran Zhao
- International Nursing School, Hainan Medical University, Haikou, China
| | - Gui Xiao
- Xiangya Nursing School, Central South University, Changsha, China
| | - Jieqiong Xia
- International Nursing School, Hainan Medical University, Haikou, China
| | - Honghua Guo
- International Nursing School, Hainan Medical University, Haikou, China
| | - Xiaoli Yang
- International Nursing School, Hainan Medical University, Haikou, China
| | - Qian Jiang
- International Nursing School, Hainan Medical University, Haikou, China
| | - Hu Wang
- Xiangya Nursing School, Central South University, Changsha, China
| | - Jiaji Hu
- Xiangya Nursing School, Central South University, Changsha, China
| | - Caihong Zhang
- International Nursing School, Hainan Medical University, Haikou, China.
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11
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Yersin S, Garneau JR, Schneeberger PHH, Osman KA, Cercamondi CI, Muhummed AM, Tschopp R, Zinsstag J, Vonaesch P. Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits. Sci Rep 2023; 13:21342. [PMID: 38049420 PMCID: PMC10696028 DOI: 10.1038/s41598-023-47748-8] [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: 09/01/2023] [Accepted: 11/17/2023] [Indexed: 12/06/2023] Open
Abstract
The composition and function of the intestinal microbiota are major determinants of human health and are strongly influenced by diet, antibiotic treatment, lifestyle and geography. Nevertheless, we currently have only little data on microbiomes of non-westernized communities. We assess the stool microbiota composition in 59 children aged 2-5 years from the Adadle district of Ethiopia, Somali Regional State. Here, milk and starch-rich food are predominant components of the local diet, where the inhabitants live a remote, traditional agropastoral lifestyle. Microbiota composition, function and the resistome were characterized by both 16S rRNA gene amplicon and shotgun metagenomic sequencing and compared to 1471 publicly available datasets from children living in traditional, transitional, and industrial communities with different subsistence strategies. Samples from the Adadle district are low in Bacteroidaceae, and Prevotellaceae, the main bacterial representatives in the feces of children living in industrialized and non-industrialized communities, respectively. In contrast, they had a higher relative abundance in Streptococcaceae, Bifidobacteriaceae and Erysipelatoclostridiaceae. Further, genes involved in degradation pathways of lactose, D-galactose and simple carbohydrates were enriched. Overall, our study revealed a unique composition of the fecal microbiota of these agropastoral children, highlighting the need to further characterize the fecal bacterial composition of human populations living different lifestyles.
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Affiliation(s)
- Simon Yersin
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Julian R Garneau
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Pierre H H Schneeberger
- Helminth Drug Development Unit, Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123, Allschwil, Switzerland
- University of Basel, Petersplatz 1, 4001, Basel, Switzerland
| | | | - Colin Ivano Cercamondi
- Department of Health Sciences and Technology, ETHZ, Rämistrasse 101, 8092, Zurich, Switzerland
| | - Abdifatah Muktar Muhummed
- University of Basel, Petersplatz 1, 4001, Basel, Switzerland
- Jigjiga University, Jigjiga, Ethiopia
- Human and Animal Health Unit, Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123, Allschwil, Switzerland
| | - Rea Tschopp
- University of Basel, Petersplatz 1, 4001, Basel, Switzerland
- Human and Animal Health Unit, Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123, Allschwil, Switzerland
- Armauer Hansen Research Institute, Jimma Road, 1005, Addis Ababa, Ethiopia
| | - Jakob Zinsstag
- University of Basel, Petersplatz 1, 4001, Basel, Switzerland
- Human and Animal Health Unit, Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123, Allschwil, Switzerland
| | - Pascale Vonaesch
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland.
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12
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Morandini F, Perez K, Brot L, Seck SM, Tibère L, Grill JP, Macia E, Seksik P. Urbanization associates with restricted gut microbiome diversity and delayed maturation in infants. iScience 2023; 26:108136. [PMID: 37876823 PMCID: PMC10590973 DOI: 10.1016/j.isci.2023.108136] [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: 03/26/2023] [Revised: 07/16/2023] [Accepted: 10/02/2023] [Indexed: 10/26/2023] Open
Abstract
Alterations of the microbiome are linked to increasingly common diseases such as obesity, allergy, and inflammatory bowel disease. Post-industrial lifestyles are thought to contribute to the gut microbiome alterations that cause or aggravate these diseases. Comparing communities across the industrialization spectrum can reveal associations between gut microbiome alterations and lifestyle and health, and help pinpoint which specific aspect of the post-industrial lifestyle is linked to microbiome alterations. Here, we compare the gut microbiomes of 60 mother and infant pairs from rural and urban areas of Senegal over two time points. We find that urban mothers, who were more frequently overweight, had different gut microbiome compositions than rural mothers, showing an expansion of Lachnospiraceae and Enterobacter. Urban infants, on the other hand, showed a delayed gut microbiome maturation and a higher susceptibility to infectious diseases. Thus, we identify new microbiome features associated with industrialization, whose association with disease may be further investigated.
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Affiliation(s)
| | - Kevin Perez
- Biomedical Sciences department, University of Lausanne, 1005 Lausanne, Vaud, Switzerland
| | - Loic Brot
- Centre de Recherche Saint-Antoine, Assistance Publique-Hôpitaux de Paris, Hôpital Saint Antoine, Service de Gastroentérologie, Inserm, Sorbonne Université, 75012 Paris, France
- Sorbonne Université, INSERM UMRS-938, Centre de Recherche Saint-Antoine, CRSA, AP-HP, 75012 Paris, France
| | - Sidy Mohammed Seck
- Internal medicine/Nephrology department, Faculty of Health Sciences and IRL-3189 “Environnement, Santé, Sociétés”, University Gaston Berger, Saint-Louis 00234, Senegal
| | - Laurence Tibère
- Centre d'Études et de Recherche: Travail, Organisation, Pouvoir (CERTOP) UMR CNRS 5044, Université de Toulouse, 31013 Toulouse, France
| | - Jean-Pierre Grill
- Sorbonne Université, INSERM UMRS-938, Centre de Recherche Saint-Antoine, CRSA, AP-HP, 75012 Paris, France
| | - Enguerran Macia
- International Research Laboratory "Environnement, Sant, Socits" (CNRS / UCAD / UGB / USTTB / CNRST), Dakar, Senegal
- Unit Mixte de Recherche 7268 Anthropologie bio-culturelle, Droit, Ethique et Sant (CNRS / AMU / EFS), Aix-Marseille, France
| | - Philippe Seksik
- Centre de Recherche Saint-Antoine, Assistance Publique-Hôpitaux de Paris, Hôpital Saint Antoine, Service de Gastroentérologie, Inserm, Sorbonne Université, 75012 Paris, France
- Sorbonne Université, INSERM UMRS-938, Centre de Recherche Saint-Antoine, CRSA, AP-HP, 75012 Paris, France
- Paris Center for Microbiome Medicine (PaCeMM) FHU, 75571 Paris, France
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13
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Kortman GAM, Timmerman HM, Schaafsma A, Stoutjesdijk E, Muskiet FAJ, Nhien NV, van Hoffen E, Boekhorst J, Nauta A. Mothers' Breast Milk Composition and Their Respective Infant's Gut Microbiota Differ between Five Distinct Rural and Urban Regions in Vietnam. Nutrients 2023; 15:4802. [PMID: 38004196 PMCID: PMC10675055 DOI: 10.3390/nu15224802] [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: 10/23/2023] [Revised: 11/10/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
Microbiota colonization and development in early life is impacted by various host intrinsic (genetic) factors, but also diet, lifestyle, as well as environmental and residential factors upon and after birth. To characterize the impact of maternal nutrition and environmental factors on vaginally born infant gut microbiota composition, we performed an observational study in five distinct geographical areas in Vietnam. Fecal samples of infants (around 39 days old) and fecal and breast milk samples of their mothers (around 28 years) were collected. The microbiota composition of all samples was analyzed by 16S rRNA gene Illumina sequencing and a bioinformatics workflow based on QIIME. In addition, various breast milk components were determined. Strong associations between the geographically determined maternal diet and breast milk composition as well as infant fecal microbiota were revealed. Most notable was the association of urban Ha Noi with relatively high abundances of taxa considered pathobionts, such as Klebsiella and Citrobacter, at the expense of Bifidobacterium. Breast milk composition was most distinct in rural Ha Long Bay, characterized by higher concentrations of, e.g., docosahexaenoic acid (DHA), eicosapentaenoic acid (EPA), selenium, and vitamin B12, while it was characterized by, e.g., iron, zinc, and α-linolenic acid (ALA) in Ha Noi. Breast milk iron levels were positively associated with infant fecal Klebsiella and negatively with Bifidobacterium, while the EPA and DHA levels were positively associated with Bifidobacterium. In conclusion, differences between five regions in Vietnam with respect to both maternal breast milk and infant gut microbiota composition were revealed, most likely in part due to maternal nutrition. Thus, there could be opportunities to beneficially steer infant microbiota development in a more desired (rural instead of urban) direction through the mother's diet.
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Affiliation(s)
| | | | - Anne Schaafsma
- Friesland Campina, Stationsplein 4, 3818 LE Amersfoort, The Netherlands
| | - Eline Stoutjesdijk
- Department of Laboratory Medicine, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands
| | - Frits A. J. Muskiet
- Department of Laboratory Medicine, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands
| | - Nguyen V. Nhien
- National Institute of Food Control, No. 65 Pham Than Duat Str., Mai Dich Ward., Cau Giay Dist., Ha Noi 100000, Vietnam
| | | | - Jos Boekhorst
- NIZO Food Research B.V., 6718 ZB Ede, The Netherlands
| | - Arjen Nauta
- Friesland Campina, Stationsplein 4, 3818 LE Amersfoort, The Netherlands
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14
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Parizadeh M, Arrieta MC. The global human gut microbiome: genes, lifestyles, and diet. Trends Mol Med 2023; 29:789-801. [PMID: 37516570 DOI: 10.1016/j.molmed.2023.07.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/03/2023] [Accepted: 07/07/2023] [Indexed: 07/31/2023]
Abstract
A growing number of human gut microbiome studies consistently describe differences between human populations. Here, we review how factors related to host genetics, ethnicity, lifestyle, and geographic location help explain this variation. Studies from contrasting environmental scenarios point to diet and lifestyle as the most influential. The effect of human migration and displacement demonstrates how the microbiome adapts to newly adopted lifestyles and contributes to the profound biological and health consequences attributed to migration. This information strongly suggests against a universal scale for healthy or dysbiotic gut microbiomes, and prompts for additional microbiome population surveys, particularly from less industrialized nations. Considering these important differences will be critical for designing strategies to diagnose and restore dysbiosis in various human populations.
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Affiliation(s)
- Mona Parizadeh
- Department of Physiology and Pharmacology, University of Calgary, Calgary, Alberta, Canada; Department of Pediatrics, University of Calgary, Calgary, Alberta, Canada; International Microbiome Center, University of Calgary, Calgary, Alberta, Canada
| | - Marie-Claire Arrieta
- Department of Physiology and Pharmacology, University of Calgary, Calgary, Alberta, Canada; Department of Pediatrics, University of Calgary, Calgary, Alberta, Canada; International Microbiome Center, University of Calgary, Calgary, Alberta, Canada.
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15
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Pheeha SM, Tamuzi JL, Chale-Matsau B, Manda S, Nyasulu PS. A Scoping Review Evaluating the Current State of Gut Microbiota Research in Africa. Microorganisms 2023; 11:2118. [PMID: 37630678 PMCID: PMC10458939 DOI: 10.3390/microorganisms11082118] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 08/15/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
The gut microbiota has emerged as a key human health and disease determinant. However, there is a significant knowledge gap regarding the composition, diversity, and function of the gut microbiota, specifically in the African population. This scoping review aims to examine the existing literature on gut microbiota research conducted in Africa, providing an overview of the current knowledge and identifying research gaps. A comprehensive search strategy was employed to identify relevant studies. Databases including MEDLINE (PubMed), African Index Medicus (AIM), CINAHL (EBSCOhost), Science Citation index (Web of Science), Embase (Ovid), Scopus (Elsevier), WHO International Clinical Trials Registry Platform (ICTRP), and Google Scholar were searched for relevant articles. Studies investigating the gut microbiota in African populations of all age groups were included. The initial screening included a total of 2136 articles, of which 154 were included in this scoping review. The current scoping review revealed a limited number of studies investigating diseases of public health significance in relation to the gut microbiota. Among these studies, HIV (14.3%), colorectal cancer (5.2%), and diabetes mellitus (3.9%) received the most attention. The top five countries that contributed to gut microbiota research were South Africa (16.2%), Malawi (10.4%), Egypt (9.7%), Kenya (7.1%), and Nigeria (6.5%). The high number (n = 66) of studies that did not study any specific disease in relation to the gut microbiota remains a gap that needs to be filled. This scoping review brings attention to the prevalent utilization of observational study types (38.3%) in the studies analysed and emphasizes the importance of conducting more experimental studies. Furthermore, the findings reflect the need for more disease-focused, comprehensive, and population-specific gut microbiota studies across diverse African regions and ethnic groups to better understand the factors shaping gut microbiota composition and its implications for health and disease. Such knowledge has the potential to inform targeted interventions and personalized approaches for improving health outcomes in African populations.
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Affiliation(s)
- Sara M. Pheeha
- Division of Epidemiology and Biostatistics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7500, South Africa; (S.M.P.)
- Department of Chemical Pathology, Faculty of Medicine and Health Sciences, Sefako Makgatho Health Sciences University, Pretoria 0208, South Africa
- National Health Laboratory Service, Dr George Mukhari Academic Hospital, Pretoria 0208, South Africa
| | - Jacques L. Tamuzi
- Division of Epidemiology and Biostatistics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7500, South Africa; (S.M.P.)
| | - Bettina Chale-Matsau
- Department of Chemical Pathology, Faculty of Health Sciences, University of Pretoria, Pretoria 0028, South Africa
- National Health Laboratory Service, Steve Biko Academic Hospital, Pretoria 0002, South Africa
| | - Samuel Manda
- Department of Statistics, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0028, South Africa
| | - Peter S. Nyasulu
- Division of Epidemiology and Biostatistics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7500, South Africa; (S.M.P.)
- Division of Epidemiology and Biostatistics, School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa
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16
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Young T, Laroche O, Walker SP, Miller MR, Casanovas P, Steiner K, Esmaeili N, Zhao R, Bowman JP, Wilson R, Bridle A, Carter CG, Nowak BF, Alfaro AC, Symonds JE. Prediction of Feed Efficiency and Performance-Based Traits in Fish via Integration of Multiple Omics and Clinical Covariates. BIOLOGY 2023; 12:1135. [PMID: 37627019 PMCID: PMC10452023 DOI: 10.3390/biology12081135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 08/07/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023]
Abstract
Fish aquaculture is a rapidly expanding global industry, set to support growing demands for sources of marine protein. Enhancing feed efficiency (FE) in farmed fish is required to reduce production costs and improve sector sustainability. Recognising that organisms are complex systems whose emerging phenotypes are the product of multiple interacting molecular processes, systems-based approaches are expected to deliver new biological insights into FE and growth performance. Here, we establish 14 diverse layers of multi-omics and clinical covariates to assess their capacities to predict FE and associated performance traits in a fish model (Oncorhynchus tshawytscha) and uncover the influential variables. Inter-omic relatedness between the different layers revealed several significant concordances, particularly between datasets originating from similar material/tissue and between blood indicators and some of the proteomic (liver), metabolomic (liver), and microbiomic layers. Single- and multi-layer random forest (RF) regression models showed that integration of all data layers provide greater FE prediction power than any single-layer model alone. Although FE was among the most challenging of the traits we attempted to predict, the mean accuracy of 40 different FE models in terms of root-mean square errors normalized to percentage was 30.4%, supporting RF as a feature selection tool and approach for complex trait prediction. Major contributions to the integrated FE models were derived from layers of proteomic and metabolomic data, with substantial influence also provided by the lipid composition layer. A correlation matrix of the top 27 variables in the models highlighted FE trait-associations with faecal bacteria (Serratia spp.), palmitic and nervonic acid moieties in whole body lipids, levels of free glycerol in muscle, and N-acetylglutamic acid content in liver. In summary, we identified subsets of molecular characteristics for the assessment of commercially relevant performance-based metrics in farmed Chinook salmon.
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Affiliation(s)
- Tim Young
- Aquaculture Biotechnology Research Group, Department of Environmental Science, School of Science, Private Bag 92006, Auckland 1142, New Zealand
- The Centre for Biomedical and Chemical Sciences, School of Science, Auckland University of Technology, Private Bag 92006, Auckland 1142, New Zealand
| | | | | | - Matthew R. Miller
- Cawthron Institute, Nelson 7010, New Zealand
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart Private Bag 49, Hobart 7005, Australia
| | | | | | - Noah Esmaeili
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart Private Bag 49, Hobart 7005, Australia
| | - Ruixiang Zhao
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart Private Bag 49, Hobart 7005, Australia
| | - John P. Bowman
- Tasmanian Institute of Agricultural Research, University of Tasmania, Hobart 7005, Australia
| | - Richard Wilson
- Central Science Laboratory, Research Division, University of Tasmania, Hobart 7001, Australia
| | - Andrew Bridle
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart Private Bag 49, Hobart 7005, Australia
| | - Chris G. Carter
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart Private Bag 49, Hobart 7005, Australia
- Blue Economy Cooperative Research Centre, Launceston 7250, Australia
| | - Barbara F. Nowak
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart Private Bag 49, Hobart 7005, Australia
| | - Andrea C. Alfaro
- Aquaculture Biotechnology Research Group, Department of Environmental Science, School of Science, Private Bag 92006, Auckland 1142, New Zealand
| | - Jane E. Symonds
- Cawthron Institute, Nelson 7010, New Zealand
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart Private Bag 49, Hobart 7005, Australia
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17
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Zhang YD, Fan SJ, Zhang Z, Li JX, Liu XX, Hu LX, Knibbs LD, Dadvand P, Jalaludin B, Browning MH, Zhao T, Heinrich J, He Z, Chen CZ, Zhou Y, Dong GH, Yang BY. Association between Residential Greenness and Human Microbiota: Evidence from Multiple Countries. ENVIRONMENTAL HEALTH PERSPECTIVES 2023; 131:87010. [PMID: 37585351 PMCID: PMC10431502 DOI: 10.1289/ehp12186] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 07/06/2023] [Accepted: 07/17/2023] [Indexed: 08/18/2023]
Abstract
BACKGROUND Greenness, referring to a measurement of the density of vegetated land (e.g., gardens, parks, grasslands), has been linked with many human health outcomes. However, the evidence on greenness exposure and human microbiota remains limited, inconclusive, drawn from specific regions, and based on only modest sample size. OBJECTIVES We aimed to study the association between greenness exposure and human microbial diversity and composition in a large sample across 34 countries and regions. METHODS We explored associations between residential greenness and human microbial alpha-diversity, composition, and genus abundance using data from 34 countries. Greenness exposure was assessed using the normalized difference vegetation index and the enhanced vegetation index mean values in the month before sampling. We used linear regression models to estimate the association between greenness and microbial alpha-diversity and tested the effect modification of age, sex, climate zone, and pet ownership of participants. Differences in microbial composition were tested by permutational multivariate analysis of variance based on Bray-Curtis distance and differential taxa were detected using the DESeq2 R package between two greenness exposure groups split by median values of greenness. RESULTS We found that higher greenness was significantly associated with greater richness levels in the palm and gut microbiota but decreased evenness in the gut microbiota. Pet ownership and climate zone modified some associations between greenness and alpha-diversity. Palm and gut microbial composition at the genus level also varied by greenness. Higher abundances of the genera Lactobacillus and Bifidobacterium, and lower abundances of the genera Anaerotruncus and Streptococcus, were observed in people with higher greenness levels. DISCUSSION These findings suggest that residential greenness was associated with microbial richness and composition in the human skin and gut samples, collected across different geographic contexts. Future studies may validate the observed associations and determine whether they correspond to improvements in human health. https://doi.org/10.1289/EHP12186.
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Affiliation(s)
- Yi-Dan Zhang
- Guangdong Provincial Engineering Technology Research Center of Environmental Pollution and Health Risk Assessment, Department of Occupational and Environmental Health, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Shu-Jun Fan
- Department of Environmental Health, Guangzhou Center for Disease Control and Prevention, Guangzhou, China
- Institute of Public Health, Guangzhou Medical University and Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Zheng Zhang
- Department of Central Laboratory, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing, China
| | - Jia-Xin Li
- Guangdong Provincial Engineering Technology Research Center of Environmental Pollution and Health Risk Assessment, Department of Occupational and Environmental Health, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Xiao-Xuan Liu
- Guangdong Provincial Engineering Technology Research Center of Environmental Pollution and Health Risk Assessment, Department of Occupational and Environmental Health, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Li-Xin Hu
- Department of Maternal and Child Health, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Luke D. Knibbs
- School of Public Health, University of Sydney, Camperdown, New South Wales, Australia
| | - Payam Dadvand
- ISGlobal, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- CIBER Epidemiología y Salud Pública, Madrid, Spain
| | - Bin Jalaludin
- School of Population Health, University of New South Wales, Kensington, New South Wales, Australia
| | - Matthew H.E.M. Browning
- Department of Park, Recreation, and Tourism Management, Clemson University, Clemson, South Carolina, USA
| | - Tianyu Zhao
- Institute and Clinic for Occupational, Social and Environmental Medicine, Hospital of the Ludwig-Maximilians-Universität München (LMU Munich), Munich, Germany
- Comprehensive Pneumology Center Munich, LMU Munich, Munich, Germany
- German Center for Lung Research, Justus Liebig University Giessen, Giessen, Germany
- Institute of Epidemiology, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany
| | - Joachim Heinrich
- Institute and Clinic for Occupational, Social and Environmental Medicine, LMU Munich, Munich, Germany
- Allergy and Lung Health Unit, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Zhini He
- Food Safety and Health Research Center, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Cheng-Zhi Chen
- School of Public Health and Management, Research Center for Medicine and Social Development, Innovation Center for Social Risk Governance in Health, Chongqing Medical University, Chongqing, China
| | - Yuanzhong Zhou
- Department of Epidemiology, School of Public Health, Zunyi Medical University, Zunyi, China
| | - Guang-Hui Dong
- Guangdong Provincial Engineering Technology Research Center of Environmental Pollution and Health Risk Assessment, Department of Occupational and Environmental Health, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Bo-Yi Yang
- Guangdong Provincial Engineering Technology Research Center of Environmental Pollution and Health Risk Assessment, Department of Occupational and Environmental Health, School of Public Health, Sun Yat-sen University, Guangzhou, China
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18
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Zhao G, Xie L, Wu Y, Wang B, Teng W, Sun Z, Kao Q, Liu W, Pi X, Ma H. Effects of urbanization and lifestyle habits on the intestinal microbiota of adolescents in eastern China. Front Microbiol 2023; 14:989303. [PMID: 37378282 PMCID: PMC10291051 DOI: 10.3389/fmicb.2023.989303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 05/23/2023] [Indexed: 06/29/2023] Open
Abstract
Introduction Owing to urbanization, living habits have changed widely, leading to alterations in the intestinal microbiota of urban residents. However, there are few studies on the characteristics of intestinal microbiota of adolescents living in different urbanized areas in China. Methods A total of 302 fecal samples collected from adolescent students in eastern China were examined. 16S rRNA high-throughput sequencing was used to identify the fecal microbiota. These data were combined with questionnaire survey results to investigate the effect of urbanization on the intestinal microbiota of adolescents in eastern China. Moreover, the role of lifestyle habits in this relationship was also evaluated. Results The results revealed significant differences in the structure of the intestinal microbiota among adolescents living in regions with different levels of urbanization. Adolescents living in urban regions had a significantly higher proportion of Bacteroides (p < 0.001, FDR = 0.004), whereas those living in towns and rural regions had higher proportions of Bifidobacterium (p < 0.001, FDR < 0.001) and Prevotella (p < 0.05, FDR = 0.019). The diversity of the intestinal microbiota was higher in urban residents than in adolescents living in towns and rural regions (p < 0.05). In addition, the differences in intestinal microbiota across individuals living in cities, towns, and rural regions were related to dietary preferences, flavor preferences, and sleep and exercise durations. Adolescents who ate more meat had more Dorea (LDA = 3.622, p = 0.04), while the abundance of Escherichia-Shigella is higher among adolescents who ate more condiments (LDA = 4.285, p = 0.02). The abundance of Dialister was significantly increased in adolescents with longer sleep durations (LDA = 4.066, p = 0.03). Adolescents who exercised for a long duration had more Faecalibacterium than those who exercised for a shorter duration (LDA = 4.303, p = 0.04). Discussion Our research has preliminarily demonstrated that there were differences in the composition of Gut microbiome in stool samples of adolescents living in different urbanized areas, and provide a scientific basis for the maintenance of a healthy intentional microbota in adolescences.
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Affiliation(s)
- Gang Zhao
- Department of Infectious Disease Control and Prevention, Hangzhou Center for Disease Control and Prevention, Hangzhou, China
| | - Lu Xie
- School of Public Health, Hangzhou Normal University, Hangzhou, China
| | - Yan Wu
- Department of Infectious Disease Control and Prevention, Hangzhou Center for Disease Control and Prevention, Hangzhou, China
| | - Bing Wang
- Department of Infectious Disease Control and Prevention, Hangzhou Center for Disease Control and Prevention, Hangzhou, China
| | - Weilin Teng
- Department of Infectious Disease Control and Prevention, Hangzhou Center for Disease Control and Prevention, Hangzhou, China
| | - Zhou Sun
- Department of Infectious Disease Control and Prevention, Hangzhou Center for Disease Control and Prevention, Hangzhou, China
| | - Qingjun Kao
- Department of Infectious Disease Control and Prevention, Hangzhou Center for Disease Control and Prevention, Hangzhou, China
| | - Wei Liu
- Zhejiang Academy of Agriculture Sciences, Institute of Plant Protection and Microbiology, Hangzhou, China
| | - Xionge Pi
- Zhejiang Academy of Agriculture Sciences, Institute of Plant Protection and Microbiology, Hangzhou, China
| | - Haiyan Ma
- School of Public Health, Hangzhou Normal University, Hangzhou, China
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19
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van der Vossen EWJ, Davids M, Bresser LRF, Galenkamp H, van den Born BJH, Zwinderman AH, Levin E, Nieuwdorp M, de Goffau MC. Gut microbiome transitions across generations in different ethnicities in an urban setting-the HELIUS study. MICROBIOME 2023; 11:99. [PMID: 37158898 PMCID: PMC10165778 DOI: 10.1186/s40168-023-01488-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 02/03/2023] [Indexed: 05/10/2023]
Abstract
BACKGROUND During the course of history, various important lifestyle changes have caused profound transitions of the gut microbiome. These include the introduction of agriculture and animal husbandry, a shift from a nomadic to a more sedentary lifestyle, and recently increased levels of urbanization and a transition towards a more Western lifestyle. The latter is linked with shifts in the gut microbiome that have a reduced fermentative capability and which are commonly associated with diseases of affluence. In this study, in which 5193 subjects are included, we investigated the direction of microbiome shifts that occur in various ethnicities living in Amsterdam by comparing 1st and 2nd generation participants. We furthermore validated part of these findings with a cohort of subjects that moved from rural Thailand to the USA. RESULTS The abundance of the Prevotella cluster, which includes P. copri and the P. stercorea trophic network, diminished in the 2nd generation Moroccans and Turks but also in younger Dutch, whilst the Western-associated Bacteroides/Blautia/Bifidobacterium (BBB) cluster, which has an inverse correlation with α-diversity, increased. At the same time, the Christensenellaceae/Methanobrevibacter/Oscillibacter trophic network, which is positively associated with α-diversity and a healthy BMI, decreased in younger Turks and Dutch. Large compositional shifts were not observed in South-Asian and African Surinamese, in whom the BBB cluster is already dominant in the 1st generation, but ASV-level shifts towards certain species, associated amongst others with obesity, were observed. CONCLUSION The Moroccan and Turkish populations, but also the Dutch population are transitioning towards a less complex and fermentative less capable configuration of the gut microbiota, which includes a higher abundance of the Western-associated BBB cluster. The Surinamese, whom have the highest prevalence of diabetes and other diseases of affluence, are already dominated by the BBB cluster. Given the continuous increase in diseases of affluence, this devolution towards low-diversity and fermentatively less capable gut microbiome compositions in urban environments is a worrying development. Video Abstract.
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Affiliation(s)
- Eduard W J van der Vossen
- Department of Experimental Vascular Medicine, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Mark Davids
- Department of Experimental Vascular Medicine, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Lucas R F Bresser
- Department of Experimental Vascular Medicine, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
- Horaizon BV, Marshalllaan 2, 2625 GZ, Delft, The Netherlands
| | - Henrike Galenkamp
- Department of Public and Occupational Health, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Bert-Jan H van den Born
- Department of Public and Occupational Health, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
- Department of Vascular Medicine, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Aeilko H Zwinderman
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Vascular Medicine, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Evgeni Levin
- Department of Experimental Vascular Medicine, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
- Horaizon BV, Marshalllaan 2, 2625 GZ, Delft, The Netherlands
| | - Max Nieuwdorp
- Department of Experimental Vascular Medicine, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands.
- Department of Vascular Medicine, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands.
| | - Marcus C de Goffau
- Department of Experimental Vascular Medicine, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands.
- Sanger Institute, Cambridge, UK.
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20
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Awan I, Schultz E, Sterrett JD, Dawud LM, Kessler LR, Schoch D, Lowry CA, Feldman-Winter L, Phadtare S. A Pilot Study Exploring Temporal Development of Gut Microbiome/Metabolome in Breastfed Neonates during the First Week of Life. Pediatr Gastroenterol Hepatol Nutr 2023; 26:99-115. [PMID: 36950061 PMCID: PMC10025571 DOI: 10.5223/pghn.2023.26.2.99] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/08/2022] [Accepted: 01/07/2023] [Indexed: 03/24/2023] Open
Abstract
Purpose Exclusive breastfeeding promotes gut microbial compositions associated with lower rates of metabolic and autoimmune diseases. Its cessation is implicated in increased microbiome-metabolome discordance, suggesting a vulnerability to dietary changes. Formula supplementation is common within our low-income, ethnic-minority community. We studied exclusively breastfed (EBF) neonates' early microbiome-metabolome coupling in efforts to build foundational knowledge needed to target this inequality. Methods Maternal surveys and stool samples from seven EBF neonates at first transitional stool (0-24 hours), discharge (30-48 hours), and at first appointment (days 3-5) were collected. Survey included demographics, feeding method, medications, medical history and tobacco and alcohol use. Stool samples were processed for 16S rRNA gene sequencing and lipid analysis by gas chromatography-mass spectrometry. Alpha and beta diversity analyses and Procrustes randomization for associations were carried out. Results Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria were the most abundant taxa. Variation in microbiome composition was greater between individuals than within (p=0.001). Palmitic, oleic, stearic, and linoleic acids were the most abundant lipids. Variation in lipid composition was greater between individuals than within (p=0.040). Multivariate composition of the metabolome, but not microbiome, correlated with time (p=0.030). Total lipids, saturated lipids, and unsaturated lipids concentrations increased over time (p=0.012, p=0.008, p=0.023). Alpha diversity did not correlate with time (p=0.403). Microbiome composition was not associated with each samples' metabolome (p=0.450). Conclusion Neonate gut microbiomes were unique to each neonate; respective metabolome profiles demonstrated generalizable temporal developments. The overall variability suggests potential interplay between influences including maternal breastmilk composition, amount consumed and living environment.
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Affiliation(s)
- Imad Awan
- Department of Medicine, Loma Linda University Medical Center, Loma Linda, CA, USA
| | - Emily Schultz
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, NJ, USA
| | - John D. Sterrett
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
| | - Lamya’a M. Dawud
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
| | - Lyanna R. Kessler
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
| | - Deborah Schoch
- Cooper Medical School of Rowan University and Cooper University Hospital, Camden, NJ, USA
| | - Christopher A. Lowry
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
| | - Lori Feldman-Winter
- Cooper Medical School of Rowan University and Cooper University Hospital, Camden, NJ, USA
| | - Sangita Phadtare
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, NJ, USA
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21
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Ouyang R, Ding J, Huang Y, Zheng F, Zheng S, Ye Y, Li Q, Wang X, Ma X, Zou Y, Chen R, Zhuo Z, Li Z, Xin Q, Zhou L, Lu X, Ren Z, Liu X, Kovatcheva-Datchary P, Xu G. Maturation of the gut metabolome during the first year of life in humans. Gut Microbes 2023; 15:2231596. [PMID: 37424334 PMCID: PMC10334852 DOI: 10.1080/19490976.2023.2231596] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 06/23/2023] [Accepted: 06/27/2023] [Indexed: 07/11/2023] Open
Abstract
The gut microbiota is involved in the production of numerous metabolites that maintain host wellbeing. The assembly of the gut microbiome is highly dynamic, and influenced by many postnatal factors, moreover, little is known about the development of the gut metabolome. We showed that geography has an important influence on the microbiome dynamics in the first year of life based on two independent cohorts from China and Sweden. Major compositional differences since birth were the high relative abundance of Bacteroides in the Swedish cohort and Streptococcus in the Chinese cohort. We analyzed the development of the fecal metabolome in the first year of life in the Chinese cohort. Lipid metabolism, especially acylcarnitines and bile acids, was the most abundant metabolic pathway in the newborn gut. Delivery mode and feeding induced particular differences in the gut metabolome since birth. In contrast to C-section newborns, medium- and long-chain acylcarnitines were abundant at newborn age only in vaginally delivered infants, associated by the presence of bacteria such as Bacteroides vulgatus and Parabacteroides merdae. Our data provide a basis for understanding the maturation of the fecal metabolome and the metabolic role of gut microbiota in infancy.
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Affiliation(s)
- Runze Ouyang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
- University of Chinese Academy of Sciences, Beijing, China
- Liaoning Province Key Laboratory of Metabolomics, Dalian, China
| | - Juan Ding
- Department of Quality Control, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yan Huang
- University of Chinese Academy of Sciences, Beijing, China
| | - Fujian Zheng
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
- University of Chinese Academy of Sciences, Beijing, China
- Liaoning Province Key Laboratory of Metabolomics, Dalian, China
| | - Sijia Zheng
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
- University of Chinese Academy of Sciences, Beijing, China
- Liaoning Province Key Laboratory of Metabolomics, Dalian, China
| | - Yaorui Ye
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
- Liaoning Province Key Laboratory of Metabolomics, Dalian, China
| | - Qi Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
- Liaoning Province Key Laboratory of Metabolomics, Dalian, China
| | - Xiaolin Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
- Liaoning Province Key Laboratory of Metabolomics, Dalian, China
| | - Xiao Ma
- Department of Nursing, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yuxin Zou
- Department of Pediatrics, Liaocheng People’s Hospital, Liaocheng, China
| | - Rong Chen
- Department of Respiratory Medicine, Dalian Municipal Women and Children’s Medical Center (Group), Dalian, China
| | - Zhihong Zhuo
- Department of Pediatric, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhen Li
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Qi Xin
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Lina Zhou
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
- University of Chinese Academy of Sciences, Beijing, China
- Liaoning Province Key Laboratory of Metabolomics, Dalian, China
| | - Xin Lu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
- University of Chinese Academy of Sciences, Beijing, China
- Liaoning Province Key Laboratory of Metabolomics, Dalian, China
| | - Zhigang Ren
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xinyu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
- University of Chinese Academy of Sciences, Beijing, China
- Liaoning Province Key Laboratory of Metabolomics, Dalian, China
| | - Petia Kovatcheva-Datchary
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
- University of Chinese Academy of Sciences, Beijing, China
- Institute for Molecular Infection Biology, University of Wurzburg, Wurzburg, Germany
- Department of Pediatrics, University of Wurzburg, Wurzburg, Germany
| | - Guowang Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
- University of Chinese Academy of Sciences, Beijing, China
- Liaoning Province Key Laboratory of Metabolomics, Dalian, China
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22
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Untargeted Fecal Metabolomic Analyses across an Industrialization Gradient Reveal Shared Metabolites and Impact of Industrialization on Fecal Microbiome-Metabolome Interactions. mSystems 2022; 7:e0071022. [PMID: 36416540 PMCID: PMC9765122 DOI: 10.1128/msystems.00710-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The metabolome is a central determinant of human phenotypes and includes the plethora of small molecules produced by host and microbiome or taken up from exogenous sources. However, studies of the metabolome have so far focused predominantly on urban, industrialized populations. Through an untargeted metabolomic analysis of 90 fecal samples from human individuals from Africa and the Americas-the birthplace and the last continental expansion of our species, respectively-we characterized a shared human fecal metabolome. The majority of detected metabolite features were ubiquitous across populations, despite any geographic, dietary, or behavioral differences. Such shared metabolite features included hyocholic acid and cholesterol. However, any characterization of the shared human fecal metabolome is insufficient without exploring the influence of industrialization. Here, we show chemical differences along an industrialization gradient, where the degree of industrialization correlates with metabolomic changes. We identified differential metabolite features such as amino acid-conjugated bile acids and urobilin as major metabolic correlates of these behavioral shifts. Additionally, coanalyses with over 5,000 publicly available human fecal samples and cooccurrence probability analyses with the gut microbiome highlight connections between the human fecal metabolome and gut microbiome. Our results indicate that industrialization significantly influences the human fecal metabolome, but diverse human lifestyles and behavior still maintain a shared human fecal metabolome. This study represents the first characterization of the shared human fecal metabolome through untargeted analyses of populations along an industrialization gradient. IMPORTANCE As the world becomes increasingly industrialized, understanding the biological consequences of these lifestyle shifts and what it means for past, present, and future human health is critical. Indeed, industrialization is associated with rises in allergic and autoimmune health conditions and reduced microbial diversity. Exploring these health effects on a chemical level requires consideration of human lifestyle diversity, but understanding the significance of any differences also requires knowledge of what molecular components are shared between human groups. Our study reveals the key chemistry of the human gut as defined by varied industrialization-based differences and ubiquitous shared features. Ultimately, these novel findings extend our knowledge of human molecular biology, especially as it is influenced by lifestyle and behavior, and provide steps toward understanding how human biology has changed over our species' history.
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23
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Li W, Li H, Wang S, Han K, Liu Y, An Z, Wu H, Li J, Song J, Wu W. Regional pattern and signatures of gut microbiota in rural residents with coronary heart disease: A metagenomic analysis. Front Cell Infect Microbiol 2022; 12:1007161. [PMID: 36519129 PMCID: PMC9742380 DOI: 10.3389/fcimb.2022.1007161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 10/25/2022] [Indexed: 11/29/2022] Open
Abstract
Coronary heart disease (CHD) is tightly associated with gut microbiota, but microbiota heterogeneity limits the application of microbial biomarkers and personalized interventions demand regional-specific features. The purpose of this study was to comprehensively characterize the regional pattern of gut microbiota in rural residents with CHD and assess the predictive value and clinical correlations of local microbial signatures. We profiled the gut microbiota by shotgun metagenomic sequencing from 19 CHD and 19 healthy residents in rural Xinxiang, China, and tested the physiological parameters. The results indicated that microbial diversity, as well as KEGG orthology (KO) and carbohydrate-active enzymes (CAZymes) functions, deserved no significant disparities between CHD and healthy residents. The relative abundance of Bacteroidetes phylum was significantly lower and unclassified Lachnospiraceae genus, and Eubacterium rectale species were markedly higher in CHD residents compared with the healthy control. Co-occurrence network revealed a more diverse and scattered ecology in CHD residents. LEfSe identified 39 potential biomarkers and butanoate metabolism and glycosyltransferases families were the enhanced KO and CAZymes in CHD residents, respectively. Twenty key signatures were determined by the random forest algorithm and most of them belonged to the Clostridium cluster. These key signatures harbored a superior accuracy of 83.9% to distinguish CHD and healthy residents and, fasting serum insulin, diastolic blood pressure, and body mass index were the top three clinical parameters influencing the gut bacterial community. Furthermore, we also found that low-density lipoprotein and waist circumference had significantly positive correlations with the members of the Clostridium cluster. These findings expand our knowledge in the regional-specific pattern of gut microbiota for rural CHD residents and highlight the non-invasive diagnostic value and clinical correlations of microbial signatures.
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Affiliation(s)
- Wenlong Li
- School of Public Health, Xinxiang Medical University, Xinxiang, Henan, China,Institute of Infectious Disease Prevention and Control, Zhengzhou Center for Disease Control and Prevention, Zhengzhou, Henan, China
| | - Huijun Li
- School of Public Health, Xinxiang Medical University, Xinxiang, Henan, China
| | - Shaolan Wang
- School of Public Health, Xinxiang Medical University, Xinxiang, Henan, China
| | - Keyang Han
- School of Public Health, Xinxiang Medical University, Xinxiang, Henan, China
| | - Yuan Liu
- School of Public Health, Xinxiang Medical University, Xinxiang, Henan, China
| | - Zhen An
- School of Public Health, Xinxiang Medical University, Xinxiang, Henan, China
| | - Hui Wu
- School of Public Health, Xinxiang Medical University, Xinxiang, Henan, China
| | - Juan Li
- School of Public Health, Xinxiang Medical University, Xinxiang, Henan, China
| | - Jie Song
- School of Public Health, Xinxiang Medical University, Xinxiang, Henan, China
| | - Weidong Wu
- School of Public Health, Xinxiang Medical University, Xinxiang, Henan, China,*Correspondence: Weidong Wu,
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Saleem A, Ikram A, Dikareva E, Lahtinen E, Matharu D, Pajari AM, de Vos WM, Hasan F, Salonen A, Jian C. Unique Pakistani gut microbiota highlights population-specific microbiota signatures of type 2 diabetes mellitus. Gut Microbes 2022; 14:2142009. [PMID: 36322821 PMCID: PMC9635555 DOI: 10.1080/19490976.2022.2142009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Biogeographic variations in the gut microbiota are pivotal to understanding the global pattern of host-microbiota interactions in prevalent lifestyle-related diseases. Pakistani adults, having an exceptionally high prevalence of type 2 diabetes mellitus (T2D), are one of the most understudied populations in microbiota research to date. The aim of the present study is to examine the gut microbiota across individuals from Pakistan and other populations of non-industrialized and industrialized lifestyles with a focus on T2D. The fecal samples from 94 urban-dwelling Pakistani adults with and without T2D were profiled by bacterial 16S ribosomal RNA gene and fungal internal transcribed spacer (ITS) region amplicon sequencing and eubacterial qPCR, and plasma samples quantified for circulating levels of lipopolysaccharide-binding protein (LBP) and the activation ability of Toll-like receptor (TLR)-signaling. Publicly available datasets generated with comparable molecular methods were retrieved for comparative analysis of the bacterial microbiota. Overall, urbanized Pakistanis' gut microbiota was similar to that of transitional or non-industrialized populations, depleted in Akkermansiaceae and enriched in Prevotellaceae (dominated by the non-Westernized clades of Prevotella copri). The relatively high proportion of Atopobiaceae appeared to be a unique characteristic of the Pakistani gut microbiota. The Pakistanis with T2D had elevated levels of LBP and TLR-signaling in circulation as well as gut microbial signatures atypical of other populations, e.g., increased relative abundance of Libanicoccus/Parolsenella, limiting the inter-population extrapolation of gut microbiota-based classifiers for T2D. Taken together, our findings call for a more global representation of understudied populations to extend the applicability of microbiota-based diagnostics and therapeutics.
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Affiliation(s)
- Afshan Saleem
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland,Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan,Department of Microbiology, Faculty of Basic and Applied Sciences, University of Haripur, Haripur, Pakistan
| | - Aamer Ikram
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | - Evgenia Dikareva
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Emilia Lahtinen
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Dollwin Matharu
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Anne-Maria Pajari
- Department of Food and Nutrition, University of Helsinki, Helsinki, Finland
| | - Willem M. de Vos
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland,Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Fariha Hasan
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Anne Salonen
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Ching Jian
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland,CONTACT Ching Jian Haartmaninkatu 3, PO box 21, FI-00014Helsinki, Finland
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25
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Early-life chemical exposome and gut microbiome development: African research perspectives within a global environmental health context. Trends Microbiol 2022; 30:1084-1100. [PMID: 35697586 DOI: 10.1016/j.tim.2022.05.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 01/13/2023]
Abstract
The gut microbiome of neonates, infants, and toddlers (NITs) is very dynamic, and only begins to stabilize towards the third year of life. Within this period, exposure to xenobiotics may perturb the gut environment, thereby driving or contributing to microbial dysbiosis, which may negatively impact health into adulthood. Despite exposure of NITs globally, but especially in Africa, to copious amounts and types of xenobiotics - such as mycotoxins, pesticide residues, and heavy metals - little is known about their influence on the early-life microbiome or their effects on acute or long-term health. Within the African context, the influence of fermented foods, herbal mixtures, and the delivery environment on the early-life microbiome are often neglected, despite being potentially important factors that influence the microbiome. Consequently, data on in-depth understanding of the microbiome-exposome interactions is lacking in African cohorts. Collecting and evaluating such data is important because exposome-induced gut dysbiosis could potentially favor disease progression.
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26
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Sarfraz MH, Shahid A, Asghar S, Aslam B, Ashfaq UA, Raza H, Prieto MA, Simal-Gandara J, Barba FJ, Rajoka MSR, Khurshid M, Nashwan AJ. Personalized nutrition, microbiota, and metabolism: A triad for eudaimonia. Front Mol Biosci 2022; 9:1038830. [PMID: 36330221 PMCID: PMC9623024 DOI: 10.3389/fmolb.2022.1038830] [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: 09/07/2022] [Accepted: 10/06/2022] [Indexed: 11/28/2022] Open
Abstract
During the previous few years, the relationship between the gut microbiota, metabolic disorders, and diet has come to light, especially due to the understanding of the mechanisms that particularly link the gut microbiota with obesity in animal models and clinical trials. Research has led to the understanding that the responses of individuals to dietary inputs vary remarkably therefore no single diet can be suggested to every individual. The variations are attributed to differences in the microbiome and host characteristics. In general, it is believed that the immanent nature of host-derived factors makes them difficult to modulate. However, diet can more easily shape the microbiome, potentially influencing human physiology through modulation of digestion, absorption, mucosal immune response, and the availability of bioactive compounds. Thus, diet could be useful to influence the physiology of the host, as well as to ameliorate various disorders. In the present study, we have described recent developments in understanding the disparities of gut microbiota populations between individuals and the primary role of diet-microbiota interactions in modulating human physiology. A deeper understanding of these relationships can be useful for proposing personalized nutrition strategies and nutrition-based therapeutic interventions to improve human health.
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Affiliation(s)
| | - Aqsa Shahid
- Department of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan
- Faculty of Rehabilitation and Allied Health Sciences, Riphah International University, Faisalabad, Pakistan
| | - Samra Asghar
- Faculty of Rehabilitation and Allied Health Sciences, Riphah International University, Faisalabad, Pakistan
| | - Bilal Aslam
- Department of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Hammad Raza
- Department of Biochemistry, Government College University Faisalabad, Faisalabad, Pakistan
| | - Miguel A. Prieto
- Nutrition and Bromatology Group, Faculty of Food Science and Technology, University of Vigo, Ourense, Spain
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Bragança, Portugal
| | - Jesus Simal-Gandara
- Nutrition and Bromatology Group, Faculty of Food Science and Technology, University of Vigo, Ourense, Spain
| | - Francisco J. Barba
- Nutrition and Bromatology Group, Faculty of Food Science and Technology, University of Vigo, Ourense, Spain
- Nutrition and Food Science Area, Preventive Medicine and Public Health, Food Science, Toxicology and Forensic Medicine Department, Faculty of Pharmacy, Universitat de València, Burjassot, València, Spain
| | - Muhammad Shahid Riaz Rajoka
- Nutrition and Bromatology Group, Faculty of Food Science and Technology, University of Vigo, Ourense, Spain
- Food and Feed Immunology Group, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Mohsin Khurshid
- Department of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan
- *Correspondence: Mohsin Khurshid, ; Abdulqadir J. Nashwan,
| | - Abdulqadir J. Nashwan
- Nursing Department, Hazm Mebaireek General Hospital (HMGH), Hamad Medical Corporation (HMC), Doha, Qatar
- *Correspondence: Mohsin Khurshid, ; Abdulqadir J. Nashwan,
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Eow SY, Gan WY, Jiang T, Loh SP, Lee LJ, Chin YS, Than LTL, How KN, Thong PL, Liu Y, Zhao J, Chen L. MYBIOTA: A birth cohort on maternal and infant microbiota and its impact on infant health in Malaysia. Front Nutr 2022; 9:994607. [PMID: 36238465 PMCID: PMC9552002 DOI: 10.3389/fnut.2022.994607] [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: 07/15/2022] [Accepted: 09/12/2022] [Indexed: 11/15/2022] Open
Abstract
Background The microbiota plays a key role in early immunity maturation that affects infant health and is associated with the development of non-communicable diseases and allergies in later life. Objective The MYBIOTA is a prospective mother-infant cohort study in Malaysia aiming to determine the association between gut microbiota with infant health (temperament, gastrointestinal disorders, eczema, asthma, and developmental delays) in Selangor, Malaysia. Methods Pregnant mothers will be enrolled in their first trimester of pregnancy, and follow-ups will be done for infants during their first year of life. Maternal-infant biological samples (blood, feces, saliva, urine, and breast milk), anthropometric, dietary, and clinical information will be collected at different time points from early pregnancy to 12 months postpartum. Discussion This study could provide a better understanding of the colonization and development of the gut microbiome during early life and its impact on infant health. Clinical trial registration https://clinicaltrials.gov/, identifier NCT04919265.
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Affiliation(s)
- Shiang Yen Eow
- Department of Nutrition, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Wan Ying Gan
- Department of Nutrition, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Tiemin Jiang
- National Engineering Research Center of Dairy Health for Maternal and Child, Beijing Sanyuan Foods Co. Ltd., Yinghai, Beijing, China
- South Asia Branch of National Engineering Center of Dairy for Maternal and Child Health, Guilin University of Technology, Guilin, China
| | - Su Peng Loh
- Department of Nutrition, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Ling Jun Lee
- Department of Nutrition, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Yit Siew Chin
- Department of Nutrition, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Research Center of Excellence, Nutrition and Non-communicable Diseases, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Leslie Thian Lung Than
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Kang Nien How
- Unit of Dermatology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Pui Ling Thong
- Department of Pediatrics, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Yanpin Liu
- National Engineering Research Center of Dairy Health for Maternal and Child, Beijing Sanyuan Foods Co. Ltd., Yinghai, Beijing, China
- Beijing Engineering Research Center of Dairy, Beijing Technical Innovation Center of Human Milk Research, Beijing Sanyuan Foods Co. Ltd., Yinghai, Beijing, China
| | - Junying Zhao
- National Engineering Research Center of Dairy Health for Maternal and Child, Beijing Sanyuan Foods Co. Ltd., Yinghai, Beijing, China
- Beijing Engineering Research Center of Dairy, Beijing Technical Innovation Center of Human Milk Research, Beijing Sanyuan Foods Co. Ltd., Yinghai, Beijing, China
| | - Lijun Chen
- National Engineering Research Center of Dairy Health for Maternal and Child, Beijing Sanyuan Foods Co. Ltd., Yinghai, Beijing, China
- Beijing Engineering Research Center of Dairy, Beijing Technical Innovation Center of Human Milk Research, Beijing Sanyuan Foods Co. Ltd., Yinghai, Beijing, China
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Pinacho-Guendulain B, Montiel-Castro AJ, Ramos-Fernández G, Pacheco-López G. Social complexity as a driving force of gut microbiota exchange among conspecific hosts in non-human primates. Front Integr Neurosci 2022; 16:876849. [PMID: 36110388 PMCID: PMC9468716 DOI: 10.3389/fnint.2022.876849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
The emergent concept of the social microbiome implies a view of a highly connected biological world, in which microbial interchange across organisms may be influenced by social and ecological connections occurring at different levels of biological organization. We explore this idea reviewing evidence of whether increasing social complexity in primate societies is associated with both higher diversity and greater similarity in the composition of the gut microbiota. By proposing a series of predictions regarding such relationship, we evaluate the existence of a link between gut microbiota and primate social behavior. Overall, we find that enough empirical evidence already supports these predictions. Nonetheless, we conclude that studies with the necessary, sufficient, explicit, and available evidence are still scarce. Therefore, we reflect on the benefit of founding future analyses on the utility of social complexity as a theoretical framework.
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Affiliation(s)
- Braulio Pinacho-Guendulain
- Doctorado en Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana (UAM), Ciudad de México, Mexico
| | - Augusto Jacobo Montiel-Castro
- Department of Health Sciences, Metropolitan Autonomous University (UAM), Lerma, Mexico
- *Correspondence: Augusto Jacobo Montiel-Castro,
| | - Gabriel Ramos-Fernández
- Institute for Research on Applied Mathematics and Systems (IIMAS), National Autonomous University of Mexico (UNAM), Mexico City, Mexico
- Center for Complexity Sciences, National Autonomous University of Mexico, Mexico City, Mexico
| | - Gustavo Pacheco-López
- Department of Health Sciences, Metropolitan Autonomous University (UAM), Lerma, Mexico
- Gustavo Pacheco-López,
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Sharon I, Quijada NM, Pasolli E, Fabbrini M, Vitali F, Agamennone V, Dötsch A, Selberherr E, Grau JH, Meixner M, Liere K, Ercolini D, de Filippo C, Caderni G, Brigidi P, Turroni S. The Core Human Microbiome: Does It Exist and How Can We Find It? A Critical Review of the Concept. Nutrients 2022; 14:nu14142872. [PMID: 35889831 PMCID: PMC9323970 DOI: 10.3390/nu14142872] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/06/2022] [Accepted: 07/08/2022] [Indexed: 11/16/2022] Open
Abstract
The core microbiome, which refers to a set of consistent microbial features across populations, is of major interest in microbiome research and has been addressed by numerous studies. Understanding the core microbiome can help identify elements that lead to dysbiosis, and lead to treatments for microbiome-related health states. However, defining the core microbiome is a complex task at several levels. In this review, we consider the current state of core human microbiome research. We consider the knowledge that has been gained, the factors limiting our ability to achieve a reliable description of the core human microbiome, and the fields most likely to improve that ability. DNA sequencing technologies and the methods for analyzing metagenomics and amplicon data will most likely facilitate higher accuracy and resolution in describing the microbiome. However, more effort should be invested in characterizing the microbiome’s interactions with its human host, including the immune system and nutrition. Other components of this holobiontic system should also be emphasized, such as fungi, protists, lower eukaryotes, viruses, and phages. Most importantly, a collaborative effort of experts in microbiology, nutrition, immunology, medicine, systems biology, bioinformatics, and machine learning is probably required to identify the traits of the core human microbiome.
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Affiliation(s)
- Itai Sharon
- Migal-Galilee Research Institute, P.O. Box 831, Kiryat Shmona 11016, Israel
- Faculty of Sciences and Technology, Tel-Hai Academic College, Upper Galilee 1220800, Israel
- Correspondence:
| | - Narciso Martín Quijada
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, A-1210 Vienna, Austria; (N.M.Q.); (E.S.)
- Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, FFoQSI GmbH, A-3430 Tulln an der Donau, Austria
| | - Edoardo Pasolli
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, 80055 Portici, Italy; (E.P.); (D.E.)
- Task Force on Microbiome Studies, University of Naples Federico II, 80055 Portici, Italy
| | - Marco Fabbrini
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy; (M.F.); (S.T.)
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Italy;
| | - Francesco Vitali
- Institute of Agricultural Biology and Biotechnology (IBBA), National Research Council (CNR), Via Moruzzi 1, 56124 Pisa, Italy; (F.V.); (C.d.F.)
| | - Valeria Agamennone
- Microbiology and Systems Biology, Netherlands Organization for Applied Scientific Research (TNO), Utrechtseweg 48, 3704 HE Zeist, The Netherlands;
| | - Andreas Dötsch
- Department of Physiology and Biochemistry of Nutrition, Max Rubner-Institut (MRI)-Federal Research Institute of Nutrition and Food, 76131 Karlsruhe, Germany;
| | - Evelyne Selberherr
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, A-1210 Vienna, Austria; (N.M.Q.); (E.S.)
| | - José Horacio Grau
- Amedes Genetics, Amedes Medizinische Dienstleistungen GmbH, 10117 Berlin, Germany; (J.H.G.); (M.M.); (K.L.)
- Center for Species Survival, Smithsonian Conservation Biology Institute, Washington, DC 20008, USA
| | - Martin Meixner
- Amedes Genetics, Amedes Medizinische Dienstleistungen GmbH, 10117 Berlin, Germany; (J.H.G.); (M.M.); (K.L.)
| | - Karsten Liere
- Amedes Genetics, Amedes Medizinische Dienstleistungen GmbH, 10117 Berlin, Germany; (J.H.G.); (M.M.); (K.L.)
| | - Danilo Ercolini
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, 80055 Portici, Italy; (E.P.); (D.E.)
- Task Force on Microbiome Studies, University of Naples Federico II, 80055 Portici, Italy
| | - Carlotta de Filippo
- Institute of Agricultural Biology and Biotechnology (IBBA), National Research Council (CNR), Via Moruzzi 1, 56124 Pisa, Italy; (F.V.); (C.d.F.)
| | - Giovanna Caderni
- NEUROFARBA Department, Pharmacology and Toxicology Section, University of Florence, Viale Pieraccini 6, 50139 Florence, Italy;
| | - Patrizia Brigidi
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Italy;
| | - Silvia Turroni
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy; (M.F.); (S.T.)
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Li J, Zhu Y, Yang L, Wang Z. Effect of gut microbiota in the colorectal cancer and potential target therapy. Discov Oncol 2022; 13:51. [PMID: 35749000 PMCID: PMC9232688 DOI: 10.1007/s12672-022-00517-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 06/15/2022] [Indexed: 02/05/2023] Open
Abstract
The symbiotic interaction between gut microbiota and the digestive tract is an important factor in maintaining the intestinal environment balance. Colorectal cancer (CRC) is a complex disease involving the interaction between tumour cells and a large number of microorganisms. The microbiota is involved in the occurrence, development and prognosis of colorectal cancer. Several microbiota species have been studied, such as Fusobacterium nucleatum (F. nucleatum), Enterotoxigenic Bacteroides fragilis (ETBF), Streptococcus bovis (S. bovis), Lactobacillus, and Bifidobacterium. Studies about the interaction between microbiota and CRC were retrieved from Embase, PubMed, Ovid and Web of Science up to 21 Oct 2021. This review expounded on the effect of microbiota on CRC, especially the dysregulation of bacteria and carcinogenicity. The methods of gut microbiota modifications representing novel prognostic markers and innovative therapeutic strategies were also described.
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Affiliation(s)
- Junchuan Li
- Gastrointestinal Center, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Yuzhou Zhu
- Gastrointestinal Center, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Lie Yang
- Gastrointestinal Center, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Ziqiang Wang
- Gastrointestinal Center, West China Hospital, Sichuan University, Chengdu, Sichuan China
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31
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Olm MR, Dahan D, Carter MM, Merrill BD, Yu FB, Jain S, Meng XD, Tripathi S, Wastyk H, Neff N, Holmes S, Sonnenburg ED, Jha AR, Sonnenburg JL. Robust variation in infant gut microbiome assembly across a spectrum of lifestyles. Science 2022; 376:1220-1223. [PMID: 35679413 PMCID: PMC9894631 DOI: 10.1126/science.abj2972] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Infant microbiome assembly has been intensely studied in infants from industrialized nations, but little is known about this process in nonindustrialized populations. We deeply sequenced infant stool samples from the Hadza hunter-gatherers of Tanzania and analyzed them in a global meta-analysis. Infant microbiomes develop along lifestyle-associated trajectories, with more than 20% of genomes detected in the Hadza infant gut representing novel species. Industrialized infants-even those who are breastfed-have microbiomes characterized by a paucity of Bifidobacterium infantis and gene cassettes involved in human milk utilization. Strains within lifestyle-associated taxonomic groups are shared between mother-infant dyads, consistent with early life inheritance of lifestyle-shaped microbiomes. The population-specific differences in infant microbiome composition and function underscore the importance of studying microbiomes from people outside of wealthy, industrialized nations.
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Affiliation(s)
- Matthew R. Olm
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Dylan Dahan
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Matthew M. Carter
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Bryan D. Merrill
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Sunit Jain
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | - Surya Tripathi
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Hannah Wastyk
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Norma Neff
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Susan Holmes
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Statistics, Stanford University, Stanford, CA, USA
| | - Erica D. Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Aashish R. Jha
- Genetic Heritage Group, Program in Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Justin L. Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA.,Corresponding author:
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32
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Samara J, Moossavi S, Alshaikh B, Ortega VA, Pettersen VK, Ferdous T, Hoops SL, Soraisham A, Vayalumkal J, Dersch-Mills D, Gerber JS, Mukhopadhyay S, Puopolo K, Tompkins TA, Knights D, Walter J, Amin H, Arrieta MC. Supplementation with a probiotic mixture accelerates gut microbiome maturation and reduces intestinal inflammation in extremely preterm infants. Cell Host Microbe 2022; 30:696-711.e5. [PMID: 35550672 DOI: 10.1016/j.chom.2022.04.005] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/08/2022] [Accepted: 04/11/2022] [Indexed: 11/19/2022]
Abstract
Probiotics are increasingly administered to premature infants to prevent necrotizing enterocolitis and neonatal sepsis. However, their effects on gut microbiome assembly and immunity are poorly understood. Using a randomized intervention trial in extremely premature infants, we tested the effects of a probiotic product containing four strains of Bifidobacterium species autochthonous to the infant gut and one Lacticaseibacillus strain on the compositional and functional trajectory of microbiome. Daily administration of the mixture accelerated the transition into a mature, term-like microbiome with higher stability and species interconnectivity. Besides infant age, Bifidobacterium strains and stool metabolites were the best predictors of microbiome maturation, and structural equation modeling confirmed probiotics as a major determinant for the trajectory of microbiome assembly. Bifidobacterium-driven microbiome maturation was also linked to an anti-inflammatory intestinal immune milieu. This demonstrates that Bifidobacterium strains are ecosystem engineers that lead to an acceleration of microbiome maturation and immunological consequences in extremely premature infants.
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Affiliation(s)
- Jumana Samara
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada; Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; International Microbiome Centre, University of Calgary, Calgary, AB, Canada; Health Sciences Centre, Winnipeg, MB, Canada
| | - Shirin Moossavi
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada; Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; International Microbiome Centre, University of Calgary, Calgary, AB, Canada; Microbiome and Microbial Ecology Interest Group (MMEIG), Universal Scientific Education and Research Network (USERN), Calgary, Canada
| | - Belal Alshaikh
- Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; Calgary Zone Section of Neonatology, Calgary, AB, Canada
| | - Van A Ortega
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada; Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; International Microbiome Centre, University of Calgary, Calgary, AB, Canada
| | - Veronika Kuchařová Pettersen
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada; Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; International Microbiome Centre, University of Calgary, Calgary, AB, Canada; Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Tahsin Ferdous
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada; Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; International Microbiome Centre, University of Calgary, Calgary, AB, Canada
| | - Suzie L Hoops
- Biotechnology Institute and Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Amuchou Soraisham
- Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; Calgary Zone Section of Neonatology, Calgary, AB, Canada
| | - Joseph Vayalumkal
- Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| | - Deonne Dersch-Mills
- Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; Calgary Zone Section of Neonatology, Calgary, AB, Canada
| | - Jeffrey S Gerber
- Division of Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Sagori Mukhopadhyay
- Newborn Care at Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Karen Puopolo
- Newborn Care at Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | | | - Dan Knights
- Biotechnology Institute and Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Jens Walter
- School of Microbiology, Department of Medicine, and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Harish Amin
- Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; Calgary Zone Section of Neonatology, Calgary, AB, Canada
| | - Marie-Claire Arrieta
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada; Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; International Microbiome Centre, University of Calgary, Calgary, AB, Canada.
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Rosas-Plaza S, Hernández-Terán A, Navarro-Díaz M, Escalante AE, Morales-Espinosa R, Cerritos R. Human Gut Microbiome Across Different Lifestyles: From Hunter-Gatherers to Urban Populations. Front Microbiol 2022; 13:843170. [PMID: 35558108 PMCID: PMC9087276 DOI: 10.3389/fmicb.2022.843170] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 02/25/2022] [Indexed: 12/13/2022] Open
Abstract
Human lifestyle and its relationship with the human microbiome has been a line of research widely studied. This is because, throughout human history, civilizations have experienced different environments and lifestyles that could have promoted changes in the human microbiome. The comparison between industrialized and non-industrialized human populations in several studies has allowed to observe variation in the microbiome structure due to the population lifestyle. Nevertheless, the lifestyle of human populations is a gradient where several subcategories can be described. Yet, it is not known how these different lifestyles of human populations affect the microbiome structure on a large scale. Therefore, the main goal of this work was the collection and comparison of 16S data from the gut microbiome of populations that have different lifestyles around the world. With the data obtained from 14 studies, it was possible to compare the gut microbiome of 568 individuals that represent populations of hunter-gatherers, agricultural, agropastoral, pastoral, and urban populations. Results showed that industrialized populations present less diversity than those from non-industrialized populations, as has been described before. However, by separating traditional populations into different categories, we were able to observe patterns that cannot be appreciated by encompassing the different traditional lifestyles in a single category. In this sense, we could confirm that different lifestyles exhibit distinct alpha and beta diversity. In particular, the gut microbiome of pastoral and agropastoral populations seems to be more similar to those of urban populations according to beta diversity analysis. Beyond that, beta diversity analyses revealed that bacterial composition reflects the different lifestyles, representing a transition from hunters-gatherers to industrialized populations. Also, we found that certain groups such as Bacteoidaceae, Lanchospiraceae, and Rickenellaceae have been favored in the transition to modern societies, being differentially abundant in urban populations. Thus, we could hypothesize that due to adaptive/ecological processes; multifunctional bacterial groups (e.g., Bacteroidaceae) could be replacing some functions lost in the transition to modern lifestyle.
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Affiliation(s)
- Santiago Rosas-Plaza
- Centro de Investigación en Políticas, Población y Salud, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Posgrado en Ciencias Biológicas, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Alejandra Hernández-Terán
- Departamento de Investigación en Tabaquismo y EPOC, Instituto Nacional de Enfermedades Respiratorias Ismael Cosìo Villegas, México City, Mexico
| | - Marcelo Navarro-Díaz
- Laboratorio Nacional de Ciencias de la Sostenibilidad (LANCIS), Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Ana E. Escalante
- Laboratorio Nacional de Ciencias de la Sostenibilidad (LANCIS), Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Rosario Morales-Espinosa
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - René Cerritos
- Centro de Investigación en Políticas, Población y Salud, Universidad Nacional Autónoma de México, Mexico City, Mexico
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Shi Y, Wang P, Zhou D, Huang L, Zhang L, Gao X, Maitiabula G, Wang S, Wang X. Multi-Omics Analyses Characterize the Gut Microbiome and Metabolome Signatures of Soldiers Under Sustained Military Training. Front Microbiol 2022; 13:827071. [PMID: 35401452 PMCID: PMC8990768 DOI: 10.3389/fmicb.2022.827071] [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: 12/01/2021] [Accepted: 02/22/2022] [Indexed: 11/15/2022] Open
Abstract
Exercise can directly alter the gut microbiome at the compositional and functional metabolic levels, which in turn may beneficially influence physical performance. However, data how the gut microbiome and fecal metabolome change, and how they interact in soldiers who commonly undergo sustained military training are limited. To address this issue, we first performed 16S rRNA sequencing to assess the gut microbial community patterns in a cohort of 80 soldiers separated into elite soldiers (ES, n = 40) and non-elite soldiers (N-ES, n = 40). We observed that the α-diversities of the ES group were higher than those of the N-ES group. As for both taxonomical structure and phenotypic compositions, elite soldiers were mainly characterized by an increased abundance of bacteria producing short-chain fatty acids (SCFAs), including Ruminococcaceae_UCG-005, Prevotella_9, and Veillonella, as well as a higher proportion of oxidative stress tolerant microbiota. The taxonomical signatures of the gut microbiome were significantly correlated with soldier performance. To further investigate the metabolic activities of the gut microbiome, using an untargeted metabolomic method, we found that the ES and N-ES groups displayed significantly different metabolic profiles and differential metabolites were primarily involved in the metabolic network of carbohydrates, energy, and amino acids, which might contribute to an enhanced exercise phenotype. Furthermore, these differences in metabolites were strongly correlated with the altered abundance of specific microbes. Finally, by integrating multi-omics data, we identified a shortlist of bacteria-metabolites associated with physical performance, following which a random forest classifier was established based on the combinatorial biomarkers capable of distinguishing between elite and non-elite soldiers with high accuracy. Our findings suggest possible future modalities for improving physical performance through targeting specific bacteria associated with more energetically efficient metabolic patterns.
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Affiliation(s)
- Yifan Shi
- Department of General Surgery, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China.,Department of Gastrointestinal Surgery, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Peng Wang
- Department of General Surgery, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Da Zhou
- Department of General Surgery, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Longchang Huang
- Department of General Surgery, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Li Zhang
- Department of General Surgery, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Xuejin Gao
- Department of General Surgery, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Gulisudumu Maitiabula
- Department of General Surgery, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Siwen Wang
- Department of General Surgery, Jinling Hospital, The First School of Clinical Medicine, Southern Medical University, Nanjing, China
| | - Xinying Wang
- Department of General Surgery, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
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Oyedemi OT, Shaw S, Martin JC, Ayeni FA, Scott KP. Changes in the gut microbiota of Nigerian infants within the first year of life. PLoS One 2022; 17:e0265123. [PMID: 35298505 PMCID: PMC8929609 DOI: 10.1371/journal.pone.0265123] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 02/23/2022] [Indexed: 11/19/2022] Open
Abstract
The composition of the gut microbiota plays an important role in maintaining the balance between health and disease. However, there is considerably less information on the composition of the gut microbiota of non-Western communities. This study was designed to investigate the evolution in the gut microbiota in a cohort of Nigerian infants within the first year of life. Faecal samples were obtained monthly from 28 infants from birth for one year. The infants had been born by a mix of natural birth and caesarean section and were either breast-fed or mixed fed. Sequencing of the V1-V2 region of the 16S rRNA gene was used to characterise the microbiota. Short chain fatty acids and lactate present in each faecal sample were identified by gas chromatography. Microbial differences were observed between the vaginal and caesarean section delivered infants in samples collected within 7 days of life, although these differences were not observed in later samples. Exclusively breastfed infants had predominance of Ruminococcus gnavus, Collinsella, and Sutterella species. Different Bifidobacterium species dominated breast-fed compared to mixed fed infants. Clostridium, Enterococcus, Roseburia, and Coprococcus species were observed once the infants commenced weaning. Butyrate was first detected when weaning started between months 4–6 in the majority of the infants while total short chain fatty acid concentrations increased, and acetate and lactate remained high following the introduction of solid foods. The observed taxonomic differences in the gut microbiota between Nigerian infants, as well as butyrate production during weaning, were strongly influenced by diet, and not by birthing method. Introduction of local/solid foods encouraged the colonisation and evolution of specific marker organisms associated with carbohydrate metabolism.
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Affiliation(s)
- Omolanke T. Oyedemi
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Nigeria
| | - Sophie Shaw
- Centre for Genome Enabled Biology and Medicine, University of Aberdeen, Aberdeen, Scotland, United Kingdom
| | - Jennifer C. Martin
- The Rowett Institute, University of Aberdeen, Aberdeen, Scotland, United Kingdom
| | - Funmilola A. Ayeni
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Nigeria
- Department of Biology, Simmons University, Fenway, Boston, United States of America
- * E-mail: (KPS); (FAA)
| | - Karen P. Scott
- The Rowett Institute, University of Aberdeen, Aberdeen, Scotland, United Kingdom
- * E-mail: (KPS); (FAA)
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Bauermeister A, Mannochio-Russo H, Costa-Lotufo LV, Jarmusch AK, Dorrestein PC. Mass spectrometry-based metabolomics in microbiome investigations. Nat Rev Microbiol 2022; 20:143-160. [PMID: 34552265 PMCID: PMC9578303 DOI: 10.1038/s41579-021-00621-9] [Citation(s) in RCA: 150] [Impact Index Per Article: 75.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2021] [Indexed: 02/08/2023]
Abstract
Microbiotas are a malleable part of ecosystems, including the human ecosystem. Microorganisms affect not only the chemistry of their specific niche, such as the human gut, but also the chemistry of distant environments, such as other parts of the body. Mass spectrometry-based metabolomics is one of the key technologies to detect and identify the small molecules produced by the human microbiota, and to understand the functional role of these microbial metabolites. This Review provides a foundational introduction to common forms of untargeted mass spectrometry and the types of data that can be obtained in the context of microbiome analysis. Data analysis remains an obstacle; therefore, the emphasis is placed on data analysis approaches and integrative analysis, including the integration of microbiome sequencing data.
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Affiliation(s)
- Anelize Bauermeister
- Institute of Biomedical Science, Universidade de São Paulo, São Paulo, SP, Brazil,Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, USA
| | - Helena Mannochio-Russo
- Department of Biochemistry and Organic Chemistry, Institute of Chemistry, São Paulo State University, Araraquara, SP, Brazil,Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, USA
| | | | - Alan K. Jarmusch
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, USA
| | - Pieter C. Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, USA.,Department of Pediatrics, University of California, San Diego, CA, USA.,Center for Microbiome Innovation, University of California, San Diego, CA, USA
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37
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Reynoso-García J, Narganes-Storde Y, Santiago-Rodriguez TM, Toranzos GA. Mycobiome-Host Coevolution? The Mycobiome of Ancestral Human Populations Seems to Be Different and Less Diverse Than Those of Extant Native and Urban-Industrialized Populations. Microorganisms 2022; 10:microorganisms10020459. [PMID: 35208912 PMCID: PMC8877467 DOI: 10.3390/microorganisms10020459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/24/2021] [Accepted: 12/07/2021] [Indexed: 02/06/2023] Open
Abstract
Few data exist on the human gut mycobiome in relation to lifestyle, ethnicity, and dietary habits. To understand the effect of these factors on the structure of the human gut mycobiome, we analyzed sequences belonging to two extinct pre-Columbian cultures inhabiting Puerto Rico (the Huecoid and Saladoid) and compared them to coprolite samples found in Mexico and Ötzi, the Iceman’s large intestine. Stool mycobiome samples from extant populations in Peru and urban cultures from the United States were also included. The ancient Puerto Rican cultures exhibited a lower fungal diversity in comparison to the extant populations. Dissimilarity distances showed that the Huecoid gut mycobiome resembled that from ancient Mexico. Fungal genera including Aspergillus spp., Penicillium spp., Rasamsonia spp., Byssochlamys spp., Talaromyces spp., Blastomyces spp., Monascus spp., and Penicilliopsis spp. were differentially abundant in the ancient and extant populations. Despite cultural differences, certain fungal taxa were present in all samples. These results suggest that culture and diet may impact the gut mycobiome and emphasize that modern lifestyles could be associated with the alteration of gut mycobiome diversity. The present study presents data on ancient and extant human gut mycobiomes in terms of lifestyle, ethnicity, and diet in the Americas.
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Affiliation(s)
- Jelissa Reynoso-García
- Environmental Microbiology Laboratory, Biology Department, University of Puerto Rico, San Juan 00931, Puerto Rico;
- Correspondence:
| | - Yvonne Narganes-Storde
- Center for Archaeological Research, Río Piedras Campus, University of Puerto Rico, San Juan 00931, Puerto Rico;
| | | | - Gary A. Toranzos
- Environmental Microbiology Laboratory, Biology Department, University of Puerto Rico, San Juan 00931, Puerto Rico;
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38
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Zhang C, Hansen MEB, Tishkoff SA. Advances in integrative African genomics. Trends Genet 2022; 38:152-168. [PMID: 34740451 PMCID: PMC8752515 DOI: 10.1016/j.tig.2021.09.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 09/16/2021] [Accepted: 09/28/2021] [Indexed: 12/16/2022]
Abstract
There has been a rapid increase in human genome sequencing in the past two decades, resulting in the identification of millions of previously unknown genetic variants. However, African populations are under-represented in sequencing efforts. Additional sequencing from diverse African populations and the construction of African-specific reference genomes is needed to better characterize the full spectrum of variation in humans. However, sequencing alone is insufficient to address the molecular and cellular mechanisms underlying variable phenotypes and disease risks. Determining functional consequences of genetic variation using multi-omics approaches is a fundamental post-genomic challenge. We discuss approaches to close the knowledge gaps about African genomic diversity and review advances in African integrative genomic studies and their implications for precision medicine.
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Affiliation(s)
- Chao Zhang
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew E B Hansen
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sarah A Tishkoff
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
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de Goffau MC, Jallow AT, Sanyang C, Prentice AM, Meagher N, Price DJ, Revill PA, Parkhill J, Pereira DIA, Wagner J. Gut microbiomes from Gambian infants reveal the development of a non-industrialized Prevotella-based trophic network. Nat Microbiol 2022; 7:132-144. [PMID: 34972822 PMCID: PMC8727306 DOI: 10.1038/s41564-021-01023-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 11/11/2021] [Indexed: 02/07/2023]
Abstract
Distinct bacterial trophic networks exist in the gut microbiota of individuals in industrialized and non-industrialized countries. In particular, non-industrialized gut microbiomes tend to be enriched with Prevotella species. To study the development of these Prevotella-rich compositions, we investigated the gut microbiota of children aged between 7 and 37 months living in rural Gambia (616 children, 1,389 stool samples, stratified by 3-month age groups). These infants, who typically eat a high-fibre, low-protein diet, were part of a double-blind, randomized iron intervention trial (NCT02941081) and here we report the secondary outcome. We found that child age was the largest discriminating factor between samples and that anthropometric indices (collection time points, season, geographic collection site, and iron supplementation) did not significantly influence the gut microbiome. Prevotella copri, Faecalibacterium prausnitzii and Prevotella stercorea were, on average, the most abundant species in these 1,389 samples (35%, 11% and 7%, respectively). Distinct bacterial trophic network clusters were identified, centred around either P. stercorea or F. prausnitzii and were found to develop steadily with age, whereas P. copri, independently of other species, rapidly became dominant after weaning. This dataset, set within a critical gut microbial developmental time frame, provides insights into the development of Prevotella-rich gut microbiomes, which are typically understudied and are underrepresented in western populations.
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Affiliation(s)
- Marcus C de Goffau
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
- Department of Vascular Medicine, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Amadou T Jallow
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Chilel Sanyang
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Andrew M Prentice
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Niamh Meagher
- Department of Infectious Diseases at the Doherty Institute for Infection & Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, VIC, Australia
- Centre for Epidemiology & Biostatistics, Melbourne School of Population & Global Health, The University of Melbourne, Melbourne, Australia
| | - David J Price
- Department of Infectious Diseases at the Doherty Institute for Infection & Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, VIC, Australia
- Centre for Epidemiology & Biostatistics, Melbourne School of Population & Global Health, The University of Melbourne, Melbourne, Australia
| | - Peter A Revill
- Victorian Infectious Disease Reference Laboratory, the Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Dora I A Pereira
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Josef Wagner
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK.
- Victorian Infectious Disease Reference Laboratory, the Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia.
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40
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Romano-Keeler J, Sun J. The First 1000 Days: Assembly of the Neonatal Microbiome and Its Impact on Health Outcomes. NEWBORN (CLARKSVILLE, MD.) 2022; 1:219-226. [PMID: 36237439 PMCID: PMC9555117 DOI: 10.5005/jp-journals-11002-0028] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Early life microbial colonization is critical for the development of the immune system, postnatal growth, and long-term health and disease. The dynamic and nascent microbiomes of children are highly individualized and are characterized by low bacterial diversity. Any disruptions in microbial colonization can contribute to shifts in normal microbial colonization that persist past the first 1000 days of life and result in intestinal dysbiosis. Here, we focus on microbiome-host interactions during fetal, newborn, and infant microbiome development. We summarize the roles of bacterial communities in fetal development and adverse health outcomes due to dysbiosis. We also discuss how internal and external factors program the microbiome's metabolic machinery as it evolves into an adult-like microbiome. Finally, we discuss the limits of current studies and future directions. Studies on the early-life microbiome will be critical for a better understanding of childhood health and diseases, as well as restorative methods for the prevention and treatment of diseases in adulthood.
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Affiliation(s)
- Joann Romano-Keeler
- Division of Neonatology, Department of Pediatrics, University of Illinois, Chicago, Illinois, United States of America
| | - Jun Sun
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois, Chicago, Illinois, United States of America; University of Illinois Cancer Center, Chicago, Illinois, United States of America; Jesse Brown VA Medical Center, Chicago, Illinois, United States of America
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41
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Helminth-Induced Human Gastrointestinal Dysbiosis: a Systematic Review and Meta-Analysis Reveals Insights into Altered Taxon Diversity and Microbial Gradient Collapse. mBio 2021; 12:e0289021. [PMID: 34933444 PMCID: PMC8689561 DOI: 10.1128/mbio.02890-21] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
High-throughput 16S rRNA sequencing has allowed the characterization of helminth-uninfected (HU) and helminth-infected (HI) gut microbiomes, revealing distinct profiles. However, there have been no qualitative or quantitative syntheses of these studies, which show marked variation in participant age, diet, pathogen of interest, and study location. A predefined minimally biased search strategy identified 23 studies in humans. For each of these studies, we qualitatively addressed the effects of helminth infection on within-individual (alpha) and between-individual (beta) fecal microbiome diversity, infection-associated microbial taxa, the effect of helminth clearance on microbiome composition, microbiome composition as a predictor of infection status or treatment outcome, and treatment-specific effects on the fecal microbiome. Concomitantly, we performed a meta-analysis on a subset of 7 of these studies containing raw, paired-end 16S reads and individual-level metadata, comprising 424 pretreatment or untreated HI individuals and 497 HU controls. After reducing the batch effect and adjusting for age, our data demonstrated that intestinal helminth parasites can alter the host gut microbiome by increasing alpha diversity and promoting taxonomic reassortment and gradient collapse. Most strongly influencing the microbiome composition were the helminths found in the large intestine, Enterobius vermicularis and Trichuris trichiura, suggesting that this influence appears to be specific to soil-transmitted helminths (STH) species and host anatomical niche. In summary, using a large and diverse sample set captured in the meta-analysis, we were able to evaluate the influence of individual helminth species as well as species-species interactions, each of which explained a significant portion of the variation in the microbiome.
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Allali I, Abotsi RE, Tow LA, Thabane L, Zar HJ, Mulder NM, Nicol MP. Human microbiota research in Africa: a systematic review reveals gaps and priorities for future research. MICROBIOME 2021; 9:241. [PMID: 34911583 PMCID: PMC8672519 DOI: 10.1186/s40168-021-01195-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 11/14/2021] [Indexed: 05/11/2023]
Abstract
BACKGROUND The role of the human microbiome in health and disease is an emerging and important area of research; however, there is a concern that African populations are under-represented in human microbiome studies. We, therefore, conducted a systematic survey of African human microbiome studies to provide an overview and identify research gaps. Our secondary objectives were: (i) to determine the number of peer-reviewed publications; (ii) to identify the extent to which the researches focused on diseases identified by the World Health Organization [WHO] State of Health in the African Region Report as being the leading causes of morbidity and mortality in 2018; (iii) to describe the extent and pattern of collaborations between researchers in Africa and the rest of the world; and (iv) to identify leadership and funders of the studies. METHODOLOGY We systematically searched Medline via PubMed, Scopus, CINAHL, Academic Search Premier, Africa-Wide Information through EBSCOhost, and Web of Science from inception through to 1st April 2020. We included studies that characterized samples from African populations using next-generation sequencing approaches. Two reviewers independently conducted the literature search, title and abstract, and full-text screening, as well as data extraction. RESULTS We included 168 studies out of 5515 records retrieved. Most studies were published in PLoS One (13%; 22/168), and samples were collected from 33 of the 54 African countries. The country where most studies were conducted was South Africa (27/168), followed by Kenya (23/168) and Uganda (18/168). 26.8% (45/168) focused on diseases of significant public health concern in Africa. Collaboration between scientists from the United States of America and Africa was most common (96/168). The first and/or last authors of 79.8% of studies were not affiliated with institutions in Africa. Major funders were the United States of America National Institutes of Health (45.2%; 76/168), Bill and Melinda Gates Foundation (17.8%; 30/168), and the European Union (11.9%; 20/168). CONCLUSIONS There are significant gaps in microbiome research in Africa, especially those focusing on diseases of public health importance. There is a need for local leadership, capacity building, intra-continental collaboration, and national government investment in microbiome research within Africa. Video Abstract.
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Affiliation(s)
- Imane Allali
- Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, and Genomic Centre of Human Pathologies, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Rabat, Morocco
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Regina E Abotsi
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Department of Molecular and Cell Biology, Faculty of Science, University of Cape Town, Cape Town, South Africa
- Department of Pharmaceutical Microbiology, School of Pharmacy, University of Health and Allied Sciences, Ho, Ghana
| | - Lemese Ah Tow
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Lehana Thabane
- Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, Ontario, Canada
- Biostatistics Unit, Father Sean O'Sullivan Research Centre, St Joseph's Healthcare, Hamilton, Ontario, Canada
- Departments of Paediatrics and Anaesthesia, McMaster University, Hamilton, Ontario, Canada
- Centre for Evaluation of Medicine, St Joseph's Healthcare, Hamilton, Ontario, Canada
- Population Health Research Institute, Hamilton Health Sciences, Hamilton, Ontario, Canada
- Centre for Evidence-based Health Care, Faculty of Health Sciences, Stellenbosch University, Tygerberg, South Africa
- Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Heather J Zar
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, Cape Town, South Africa
- MRC Unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Nicola M Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Mark P Nicol
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
- School of Biomedical Sciences, University of Western Australia, M504, Perth, WA, 6009, Australia.
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Afolayan AO, Biagi E, Rampelli S, Candela M, Brigidi P, Turroni S, Ayeni FA. The Gut Microbiota of an Individual Varies With Intercontinental Four-Month Stay Between Italy and Nigeria: A Pilot Study. Front Cell Infect Microbiol 2021; 11:725769. [PMID: 34881191 PMCID: PMC8646098 DOI: 10.3389/fcimb.2021.725769] [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: 06/15/2021] [Accepted: 11/03/2021] [Indexed: 11/13/2022] Open
Abstract
Despite well-established knowledge of the role of diet and the geographic effect on the gut microbiota of human populations, the temporal dynamics of the individual microbiota profile across changes associated with intercontinental short residence are still far from being understood. This pilot study sought to provide insights into the trajectory of the gut microbiota of an individual during a two-month stay in Italy and a subsequent two-month stay in Nigeria, by 16S rRNA gene sequencing and inferred metagenomics. The gut microbiota underwent massive but temporary changes, both taxonomically and based on predicted functionality. The faecal microbiota associated with the short stay in Italy progressively lost diversity and showed a dominance of Firmicutes, while after returning to Nigeria, the microbial community quickly regained the typical profile, in terms of biodiversity and bacterial signatures of traditional lifestyle, i.e., Prevotella and Treponema. Predicted pathways involved in glycolysis, fermentation and N-acetylneuraminate degradation were enriched during the subsequent two-month stay in Nigeria, whereas pathways associated with amino acid and peptidoglycan synthesis and maturation became over-represented during short stay in Italy. Our findings stress the plasticity of the individual gut microbiota even during a short-term travel, with loss/gain of taxonomic and functional features that mirror those of the gut microbiota of indigenous people dwelling therein.
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Affiliation(s)
- Ayorinde O Afolayan
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Nigeria
| | - Elena Biagi
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Simone Rampelli
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Marco Candela
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Patrizia Brigidi
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Silvia Turroni
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Funmilola A Ayeni
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Nigeria.,Department of Biology, Simmons University, Boston, MA, United States
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Barone M, D'Amico F, Fabbrini M, Rampelli S, Brigidi P, Turroni S. Over-feeding the gut microbiome: A scoping review on health implications and therapeutic perspectives. World J Gastroenterol 2021; 27:7041-7064. [PMID: 34887627 PMCID: PMC8613651 DOI: 10.3748/wjg.v27.i41.7041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/02/2021] [Accepted: 10/14/2021] [Indexed: 02/06/2023] Open
Abstract
The human gut microbiome has gained increasing attention over the past two decades. Several findings have shown that this complex and dynamic microbial ecosystem can contribute to the maintenance of host health or, when subject to imbalances, to the pathogenesis of various enteric and non-enteric diseases. This scoping review summarizes the current knowledge on how the gut microbiota and microbially-derived compounds affect host metabolism, especially in the context of obesity and related disorders. Examples of microbiome-based targeted intervention strategies that aim to restore and maintain an eubiotic layout are then discussed. Adjuvant therapeutic interventions to alleviate obesity and associated comorbidities are traditionally based on diet modulation and the supplementation of prebiotics, probiotics and synbiotics. However, these approaches have shown only moderate ability to induce sustained changes in the gut microbial ecosystem, making the development of innovative and tailored microbiome-based intervention strategies of utmost importance in clinical practice. In this regard, the administration of next-generation probiotics and engineered microbiomes has shown promising results, together with more radical intervention strategies based on the replacement of the dysbiotic ecosystem by means of fecal microbiota transplantation from healthy donors or with the introduction of synthetic communities specifically designed to achieve the desired therapeutic outcome. Finally, we provide a perspective for future translational investigations through the implementation of bioinformatics approaches, including machine and deep learning, to predict health risks and therapeutic outcomes.
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Affiliation(s)
- Monica Barone
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, Bologna 40138, Italy
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | - Federica D'Amico
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, Bologna 40138, Italy
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | - Marco Fabbrini
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, Bologna 40138, Italy
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | - Simone Rampelli
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | - Patrizia Brigidi
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, Bologna 40138, Italy
| | - Silvia Turroni
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
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Vanhaecke T, Bretin O, Poirel M, Tap J. Drinking Water Source and Intake Are Associated with Distinct Gut Microbiota Signatures in US and UK Populations. J Nutr 2021; 152:171-182. [PMID: 34642755 PMCID: PMC8754568 DOI: 10.1093/jn/nxab312] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/28/2021] [Accepted: 08/25/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The microbiome of the digestive tract exerts fundamental roles in host physiology. Extrinsic factors including lifestyle and diet are widely recognized as key drivers of gut and oral microbiome compositions. Although drinking water is among the food items consumed in the largest amount, little is known about its potential impact on the microbiome. OBJECTIVES We explored the associations of plain drinking water source and intake with gut and oral microbiota compositions in a population-based cohort. METHODS Microbiota, health, lifestyle, and food intake data were extracted from the American Gut Project public database. Associations of drinking water source (bottled, tap, filtered, or well water) and intake with global microbiota composition were evaluated using linear and logistic models adjusted for anthropometric, diet, and lifestyle factors in 3413 and 3794 individuals, respectively (fecal samples; 56% female, median [IQR] age: 48 [36-59] y; median [IQR] BMI: 23.3 [20.9-26.3] kg/m2), and in 283 and 309 individuals, respectively (oral samples). RESULTS Drinking water source ranked among the key contributing factors explaining the gut microbiota variation, accounting for 13% [Faith's phylogenetic diversity (Faith's PD)] and 47% (Bray-Curtis dissimilarity) of the age effect size. Drinking water source was associated with differences in gut microbiota signatures, as revealed by β diversity analyses (P < 0.05; Bray-Curtis dissimilarity, weighted UniFrac distance). Subjects drinking mostly well water had higher fecal α diversity (P < 0.05; Faith's PD, observed amplicon sequence variants), higher Dorea, and lower Bacteroides, Odoribacter, and Streptococcus than the other groups. Low water drinkers also exhibited gut microbiota differences compared with high water drinkers (P < 0.05; Bray-Curtis dissimilarity, unweighted UniFrac distance) and a higher abundance of Campylobacter. No associations were found between oral microbiota composition and drinking water consumption. CONCLUSIONS Our results indicate that drinking water may be an important factor in shaping the human gut microbiome and that integrating drinking water source and intake as covariates in future microbiome analyses is warranted.
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Prasoodanan P K V, Sharma AK, Mahajan S, Dhakan DB, Maji A, Scaria J, Sharma VK. Western and non-western gut microbiomes reveal new roles of Prevotella in carbohydrate metabolism and mouth-gut axis. NPJ Biofilms Microbiomes 2021; 7:77. [PMID: 34620880 PMCID: PMC8497558 DOI: 10.1038/s41522-021-00248-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 09/09/2021] [Indexed: 01/22/2023] Open
Abstract
The abundance and diversity of host-associated Prevotella species have a profound impact on human health. To investigate the composition, diversity, and functional roles of Prevotella in the human gut, a population-wide analysis was carried out on 586 healthy samples from western and non-western populations including the largest Indian cohort comprising of 200 samples, and 189 Inflammatory Bowel Disease samples from western populations. A higher abundance and diversity of Prevotella copri species enriched in complex plant polysaccharides metabolizing enzymes, particularly pullulanase containing polysaccharide-utilization-loci (PUL), were found in Indian and non-western populations. A higher diversity of oral inflammations-associated Prevotella species and an enrichment of virulence factors and antibiotic resistance genes in the gut microbiome of western populations speculates an existence of a mouth-gut axis. The study revealed the landscape of Prevotella composition in the human gut microbiome and its impact on health in western and non-western populations.
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Affiliation(s)
- Vishnu Prasoodanan P K
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh, 462066, India
| | - Ashok K Sharma
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh, 462066, India
- Department of Animal Science, Department of Food Science and Nutrition, University of Minnesota, Saint Paul, MN, 55455, USA
| | - Shruti Mahajan
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh, 462066, India
| | - Darshan B Dhakan
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh, 462066, India
- Behaviour and Metabolism Laboratory, Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, 1400-038, Lisboa, Portugal
| | - Abhijit Maji
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh, 462066, India
- Animal Disease Research & Diagnostic Laboratory, South Dakota State University, Brookings, SD, 57007, USA
| | - Joy Scaria
- Animal Disease Research & Diagnostic Laboratory, South Dakota State University, Brookings, SD, 57007, USA
| | - Vineet K Sharma
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh, 462066, India.
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47
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Bramble MS, Vashist N, Ko A, Priya S, Musasa C, Mathieu A, Spencer DA, Lupamba Kasendue M, Mamona Dilufwasayo P, Karume K, Nsibu J, Manya H, Uy MNA, Colwell B, Boivin M, Mayambu JPB, Okitundu D, Droit A, Mumba Ngoyi D, Blekhman R, Tshala-Katumbay D, Vilain E. The gut microbiome in konzo. Nat Commun 2021; 12:5371. [PMID: 34508085 PMCID: PMC8433213 DOI: 10.1038/s41467-021-25694-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 08/24/2021] [Indexed: 02/08/2023] Open
Abstract
Konzo, a distinct upper motor neuron disease associated with a cyanogenic diet and chronic malnutrition, predominately affects children and women of childbearing age in sub-Saharan Africa. While the exact biological mechanisms that cause this disease have largely remained elusive, host-genetics and environmental components such as the gut microbiome have been implicated. Using a large study population of 180 individuals from the Democratic Republic of the Congo, where konzo is most frequent, we investigate how the structure of the gut microbiome varied across geographical contexts, as well as provide the first insight into the gut flora of children affected with this debilitating disease using shotgun metagenomic sequencing. Our findings indicate that the gut microbiome structure is highly variable depending on region of sampling, but most interestingly, we identify unique enrichments of bacterial species and functional pathways that potentially modulate the susceptibility of konzo in prone regions of the Congo.
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Affiliation(s)
- Matthew S Bramble
- Center for Genetic Medicine Research, Children's Research Institute, Children's National Hospital, Washington, DC, USA
| | - Neerja Vashist
- Center for Genetic Medicine Research, Children's Research Institute, Children's National Hospital, Washington, DC, USA
- Department of Genomics and Precision Medicine, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Arthur Ko
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Sambhawa Priya
- Departments of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
| | - Céleste Musasa
- Center for Genetic Medicine Research, Children's Research Institute, Children's National Hospital, Washington, DC, USA
| | - Alban Mathieu
- Computational Biology Laboratory, CHU de Québec - Université Laval Research Center, Québec City, QC, Canada
| | - D' Andre Spencer
- Center for Genetic Medicine Research, Children's Research Institute, Children's National Hospital, Washington, DC, USA
| | | | - Patrick Mamona Dilufwasayo
- Center for Genetic Medicine Research, Children's Research Institute, Children's National Hospital, Washington, DC, USA
- Institut National de Recherche Biomédicale (INRB), Kinshasa, DR, Congo
| | - Kevin Karume
- Center for Genetic Medicine Research, Children's Research Institute, Children's National Hospital, Washington, DC, USA
- Institut National de Recherche Biomédicale (INRB), Kinshasa, DR, Congo
| | - Joanna Nsibu
- Institut National de Recherche Biomédicale (INRB), Kinshasa, DR, Congo
| | - Hans Manya
- Center for Genetic Medicine Research, Children's Research Institute, Children's National Hospital, Washington, DC, USA
- Institut National de Recherche Biomédicale (INRB), Kinshasa, DR, Congo
| | - Mary N A Uy
- Center for Genetic Medicine Research, Children's Research Institute, Children's National Hospital, Washington, DC, USA
- College of Medicine, University of the Philippines, Manila, Manila, Philippines
| | - Brian Colwell
- School of Public Health, Texas A&M University, College Station, TX, USA
| | - Michael Boivin
- Department of Psychiatry and Neurology & Ophthalmology, Michigan State University, East Lansing, MI, USA
| | - J P Banae Mayambu
- Ministry of Health National Program on Nutrition (PRONANUT), Kinshasa, DR, Congo
| | - Daniel Okitundu
- Centre Neuro-Psychopathologique (CNPP), University of Kinshasa, Kinshasa, Congo
| | - Arnaud Droit
- Computational Biology Laboratory, CHU de Québec - Université Laval Research Center, Québec City, QC, Canada
| | - Dieudonné Mumba Ngoyi
- Institut National de Recherche Biomédicale (INRB), Kinshasa, DR, Congo
- Department of Tropical Medicine, University of Kinshasa, Kinshasa, DR, Congo
| | - Ran Blekhman
- Departments of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
| | - Desire Tshala-Katumbay
- Institut National de Recherche Biomédicale (INRB), Kinshasa, DR, Congo.
- Department of Neurology and School of Public Health, Oregon Health & Science University, Portland, OR, USA.
| | - Eric Vilain
- Center for Genetic Medicine Research, Children's Research Institute, Children's National Hospital, Washington, DC, USA.
- Department of Genomics and Precision Medicine, George Washington University School of Medicine and Health Sciences, Washington, DC, USA.
- International Research Laboratory of Epigenetics, Data, Politics, Centre National de la Recherche Scientifique, Washington, DC, USA.
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Lu J, Zhang L, Zhai Q, Zhao J, Zhang H, Lee YK, Lu W, Li M, Chen W. Chinese gut microbiota and its associations with staple food type, ethnicity, and urbanization. NPJ Biofilms Microbiomes 2021; 7:71. [PMID: 34489454 PMCID: PMC8421333 DOI: 10.1038/s41522-021-00245-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 08/11/2021] [Indexed: 02/06/2023] Open
Abstract
The gut microbiota could affect human health and disease. Although disease-associated microbiota alteration has been extensively investigated in the Chinese population, a nationwide Chinese gut microbiota baseline is still lacking. Here we performed 16 S rRNA gene sequencing on fecal samples from 2678 healthy Chinese individuals, who belonged to eight ethnic groups and resided in 63 counties/cities of 28 provinces. We identified four enterotypes, three of which were enriched for Prevotella, Bacteroides, and Escherichia, respectively, whereas the fourth one had no dominant genus. By assessing the association between the gut microbiota and 20 variables belonging to six categories, geography, demography, diet, urbanization, lifestyle, and sampling month, we revealed that geography explained the largest microbiota variation, and clarified the distinct patterns in the associations with staple food type, ethnicity, and urban/rural residence. Specifically, the gut microbiota of Han Chinese and ethnic minority groups from the same sites was more alike than that of the same ethnic minority groups from different sites. Individuals consuming wheat as staple food were predicted to have more microbial genes involving in glucan 1,3-beta-glucosidase and S-adenosyl-L-methionine biosynthesis than those who consumed rice, based on functional prediction. Besides, an appreciable effect of urbanization on decreased intra-individual diversity, increased inter-individual diversity, and increased proportion of the Bacteroides enterotype was observed. Collectively, our study provided a nationwide gut microbiota baseline of the Chinese population and knowledge on important covariates, which are fundamental to translational microbiota research.
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Affiliation(s)
- Jing Lu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Li Zhang
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, China
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China
| | - Yuan-Kun Lee
- International Joint Research Laboratory for Pharmabiotics & Antibiotic Resistance, Jiangnan University, Wuxi, China
- Department of Microbiology & Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Wenwei Lu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.
- School of Food Science and Technology, Jiangnan University, Wuxi, China.
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China.
- International Joint Research Laboratory for Pharmabiotics & Antibiotic Resistance, Jiangnan University, Wuxi, China.
| | - Mingkun Li
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.
- School of Food Science and Technology, Jiangnan University, Wuxi, China.
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China.
- International Joint Research Laboratory for Pharmabiotics & Antibiotic Resistance, Jiangnan University, Wuxi, China.
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Nguyen QP, Karagas MR, Madan JC, Dade E, Palys TJ, Morrison HG, Pathmasiri WW, McRitche S, Sumner SJ, Frost HR, Hoen AG. Associations between the gut microbiome and metabolome in early life. BMC Microbiol 2021; 21:238. [PMID: 34454437 PMCID: PMC8400760 DOI: 10.1186/s12866-021-02282-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 07/14/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The infant intestinal microbiome plays an important role in metabolism and immune development with impacts on lifelong health. The linkage between the taxonomic composition of the microbiome and its metabolic phenotype is undefined and complicated by redundancies in the taxon-function relationship within microbial communities. To inform a more mechanistic understanding of the relationship between the microbiome and health, we performed an integrative statistical and machine learning-based analysis of microbe taxonomic structure and metabolic function in order to characterize the taxa-function relationship in early life. RESULTS Stool samples collected from infants enrolled in the New Hampshire Birth Cohort Study (NHBCS) at approximately 6-weeks (n = 158) and 12-months (n = 282) of age were profiled using targeted and untargeted nuclear magnetic resonance (NMR) spectroscopy as well as DNA sequencing of the V4-V5 hypervariable region from the bacterial 16S rRNA gene. There was significant inter-omic concordance based on Procrustes analysis (6 weeks: p = 0.056; 12 months: p = 0.001), however this association was no longer significant when accounting for phylogenetic relationships using generalized UniFrac distance metric (6 weeks: p = 0.376; 12 months: p = 0.069). Sparse canonical correlation analysis showed significant correlation, as well as identifying sets of microbe/metabolites driving microbiome-metabolome relatedness. Performance of machine learning models varied across different metabolites, with support vector machines (radial basis function kernel) being the consistently top ranked model. However, predictive R2 values demonstrated poor predictive performance across all models assessed (avg: - 5.06% -- 6 weeks; - 3.7% -- 12 months). Conversely, the Spearman correlation metric was higher (avg: 0.344-6 weeks; 0.265-12 months). This demonstrated that taxonomic relative abundance was not predictive of metabolite concentrations. CONCLUSIONS Our results suggest a degree of overall association between taxonomic profiles and metabolite concentrations. However, lack of predictive capacity for stool metabolic signatures reflects, in part, the possible role of functional redundancy in defining the taxa-function relationship in early life as well as the bidirectional nature of the microbiome-metabolome association. Our results provide evidence in favor of a multi-omic approach for microbiome studies, especially those focused on health outcomes.
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Affiliation(s)
- Quang P. Nguyen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth College, Hanover, NH USA
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth College, Hanover, NH USA
| | - Margaret R. Karagas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth College, Hanover, NH USA
- Children’s Environmental Health & Disease Prevention Research Center at Dartmouth, Lebanon, NH USA
| | - Juliette C. Madan
- Department of Epidemiology, Geisel School of Medicine at Dartmouth College, Hanover, NH USA
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth College, Hanover, NH USA
- Children’s Environmental Health & Disease Prevention Research Center at Dartmouth, Lebanon, NH USA
- Department of Pediatrics, Children’s Hospital at Dartmouth, Hanover, NH USA
| | - Erika Dade
- Department of Epidemiology, Geisel School of Medicine at Dartmouth College, Hanover, NH USA
| | - Thomas J. Palys
- Department of Epidemiology, Geisel School of Medicine at Dartmouth College, Hanover, NH USA
| | - Hilary G. Morrison
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA USA
| | - Wimal W. Pathmasiri
- Department of Nutrition, Nutrition Research Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Susan McRitche
- Department of Nutrition, Nutrition Research Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Susan J. Sumner
- Department of Nutrition, Nutrition Research Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - H. Robert Frost
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth College, Hanover, NH USA
| | - Anne G. Hoen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth College, Hanover, NH USA
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth College, Hanover, NH USA
- Children’s Environmental Health & Disease Prevention Research Center at Dartmouth, Lebanon, NH USA
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50
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Di Cristanziano V, Farowski F, Berrilli F, Santoro M, Di Cave D, Glé C, Daeumer M, Thielen A, Wirtz M, Kaiser R, Eberhardt KA, Vehreschild MJGT, D’Alfonso R. Analysis of Human Gut Microbiota Composition Associated to the Presence of Commensal and Pathogen Microorganisms in Côte d'Ivoire. Microorganisms 2021; 9:microorganisms9081763. [PMID: 34442844 PMCID: PMC8400437 DOI: 10.3390/microorganisms9081763] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/12/2021] [Accepted: 08/14/2021] [Indexed: 12/11/2022] Open
Abstract
Background: The human gut microbiota is a microbial ecosystem contributing to the maintenance of host health with functions related to immune and metabolic aspects. Relations between microbiota and enteric pathogens in sub-Saharan Africa are scarcely investigated. The present study explored gut microbiota composition associated to the presence of common enteric pathogens and commensal microorganisms, e.g., Blastocystis and Entamoeba species, in children and adults from semi-urban and non-urban localities in Côte d’Ivoire. Methods: Seventy-six stool samples were analyzed for microbiota composition by 16S rRDNA sequencing. The presence of adeno-, entero-, parechoviruses, bacterial and protozoal pathogens, Blastocystis, and commensal Entamoeba species, was analyzed by different molecular assays. Results: Twelve individuals resulted negative for any tested microorganisms, 64 subjects were positive for one or more microorganisms. Adenovirus, enterovirus, enterotoxigenic Escherichia coli (ETEC), and Blastocystis were frequently detected. Conclusions: The bacterial composition driven by Prevotellaceae and Ruminococcaceae confirmed the biotype related to the traditional dietary and cooking practices in low-income countries. Clear separation in UniFrac distance in subjects co-harboring Entamoeba hartmanni and Blastocystis was evidenced. Alpha diversity variation in negative control group versus only Blastocystis positive suggested its possible regulatory contribution on intestinal microbiota. Pathogenic bacteria and virus did not affect the positive outcome of co-harbored Blastocystis.
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Affiliation(s)
- Veronica Di Cristanziano
- Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50935 Cologne, Germany; (M.W.); (R.K.)
- Correspondence: ; Tel.: +49-221-478-85828
| | - Fedja Farowski
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50937 Cologne, Germany; (F.F.); (M.J.G.T.V.)
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University Frankfurt, 60590 Frankfurt am Main, Germany
| | - Federica Berrilli
- Department of Clinical Sciences and Translational Medicine, University of Rome Tor Vergata, 00133 Rome, Italy; (F.B.); (M.S.); (D.D.C.)
| | - Maristella Santoro
- Department of Clinical Sciences and Translational Medicine, University of Rome Tor Vergata, 00133 Rome, Italy; (F.B.); (M.S.); (D.D.C.)
| | - David Di Cave
- Department of Clinical Sciences and Translational Medicine, University of Rome Tor Vergata, 00133 Rome, Italy; (F.B.); (M.S.); (D.D.C.)
| | - Christophe Glé
- Centre Don Orione Pour Handicapés Physiques, Bonoua BP 21, Côte d’Ivoire; (C.G.); (R.D.)
| | - Martin Daeumer
- Seq-IT GmbH & Co KG, 67655 Kaiserslautern, Germany; (M.D.); (A.T.)
| | | | - Maike Wirtz
- Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50935 Cologne, Germany; (M.W.); (R.K.)
| | - Rolf Kaiser
- Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50935 Cologne, Germany; (M.W.); (R.K.)
| | - Kirsten Alexandra Eberhardt
- Department of Tropical Medicine, Bernhard Nocht Institute for Tropical Medicine & I. Department of Medicine, University Medical Center Hamburg-Eppendorf, 20359 Hamburg, Germany;
- Institute for Transfusion Medicine, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Maria J. G. T. Vehreschild
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50937 Cologne, Germany; (F.F.); (M.J.G.T.V.)
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University Frankfurt, 60590 Frankfurt am Main, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn, 50937 Cologne, Germany
| | - Rossella D’Alfonso
- Centre Don Orione Pour Handicapés Physiques, Bonoua BP 21, Côte d’Ivoire; (C.G.); (R.D.)
- Department of Systems Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
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