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Park G, Kim S, Lee W, Kim G, Shin H. Deciphering the Impact of Defecation Frequency on Gut Microbiome Composition and Diversity. Int J Mol Sci 2024; 25:4657. [PMID: 38731876 PMCID: PMC11083994 DOI: 10.3390/ijms25094657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/02/2024] [Accepted: 04/18/2024] [Indexed: 05/13/2024] Open
Abstract
This study explores the impact of defecation frequency on the gut microbiome structure by analyzing fecal samples from individuals categorized by defecation frequency: infrequent (1-3 times/week, n = 4), mid-frequent (4-6 times/week, n = 7), and frequent (daily, n = 9). Utilizing 16S rRNA gene-based sequencing and LC-MS/MS metabolome profiling, significant differences in microbial diversity and community structures among the groups were observed. The infrequent group showed higher microbial diversity, with community structures significantly varying with defecation frequency, a pattern consistent across all sampling time points. The Ruminococcus genus was predominant in the infrequent group, but decreased with more frequent defecation, while the Bacteroides genus was more common in the frequent group, decreasing as defecation frequency lessened. The infrequent group demonstrated enriched biosynthesis genes for aromatic amino acids and branched-chain amino acids (BCAAs), in contrast to the frequent group, which had a higher prevalence of genes for BCAA catabolism. Metabolome analysis revealed higher levels of metabolites derived from aromatic amino acids and BCAA metabolism in the infrequent group, and lower levels of BCAA-derived metabolites in the frequent group, consistent with their predicted metagenomic functions. These findings underscore the importance of considering stool consistency/frequency in understanding the factors influencing the gut microbiome.
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Affiliation(s)
- Gwoncheol Park
- Department of Food Science & Biotechnology, College of Life Science, Sejong University, Seoul 05006, Republic of Korea; (G.P.); (S.K.); (W.L.); (G.K.)
- Carbohydrate Bioproduct Research Center, Sejong University, Seoul 05006, Republic of Korea
- Department of Health, Nutrition & Food Sciences, College of Education, Health & Human Sciences, Florida State University, Tallahassee, FL 32306, USA
| | - Seongok Kim
- Department of Food Science & Biotechnology, College of Life Science, Sejong University, Seoul 05006, Republic of Korea; (G.P.); (S.K.); (W.L.); (G.K.)
- Carbohydrate Bioproduct Research Center, Sejong University, Seoul 05006, Republic of Korea
| | - WonJune Lee
- Department of Food Science & Biotechnology, College of Life Science, Sejong University, Seoul 05006, Republic of Korea; (G.P.); (S.K.); (W.L.); (G.K.)
- Carbohydrate Bioproduct Research Center, Sejong University, Seoul 05006, Republic of Korea
| | - Gyungcheon Kim
- Department of Food Science & Biotechnology, College of Life Science, Sejong University, Seoul 05006, Republic of Korea; (G.P.); (S.K.); (W.L.); (G.K.)
- Carbohydrate Bioproduct Research Center, Sejong University, Seoul 05006, Republic of Korea
| | - Hakdong Shin
- Department of Food Science & Biotechnology, College of Life Science, Sejong University, Seoul 05006, Republic of Korea; (G.P.); (S.K.); (W.L.); (G.K.)
- Carbohydrate Bioproduct Research Center, Sejong University, Seoul 05006, Republic of Korea
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Lazar L, Eshel A, Moadi L, Yackobovitch-Gavan M, Bar-Maisels M, Shtaif B, Nevo M, Phillip M, Turjeman S, Koren O, Gat-Yablonski G. Children with idiopathic short stature have significantly different gut microbiota than their normal height siblings: a case-control study. Front Endocrinol (Lausanne) 2024; 15:1343337. [PMID: 38464968 PMCID: PMC10920232 DOI: 10.3389/fendo.2024.1343337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 01/31/2024] [Indexed: 03/12/2024] Open
Abstract
Objectives To investigate the role of gut microbiota (GM) in pathogenesis of idiopathic short stature (ISS) by comparing GM of ISS children to their normal-height siblings. Methods This case-control study, conducted at the Schneider Children's Medical Center's Institute for Endocrinology and Diabetes between 4/2018-11/2020, involved 30 pairs of healthy pre-pubertal siblings aged 3-10 years, each comprising one sibling with ISS and one with normal height. Outcome measures from fecal analysis of both siblings included GM composition analyzed by 16S rRNA sequencing, fecal metabolomics, and monitoring the growth of germ-free (GF) mice after fecal transplantation. Results Fecal analysis of ISS children identified higher predicted levels of genes encoding enzymes for pyrimidine, purine, flavin, coenzyme B, and thiamine biosynthesis, lower levels of several amino acids, and a significantly higher prevalence of the phylum Euryarchaeota compared to their normal-height siblings (p<0.001). ISS children with higher levels of Methanobrevibacter, the dominant species in the archaeal gut community, were significantly shorter in stature than those with lower levels (p=0.022). Mice receiving fecal transplants from ISS children did not experience stunted growth, probably due to the eradication of Methanobrevibacter caused by exposure to oxygen during fecal collection. Discussion Our findings suggest that different characteristics in the GM may explain variations in linear growth. The varying levels of Methanobrevibacter demonstrated within the ISS group reflect the multifactorial nature of ISS and the potential ability of the GM to partially explain growth variations. The targeting of specific microbiota could provide personalized therapies to improve growth in children with ISS.
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Affiliation(s)
- Liora Lazar
- School of Medicine, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel
- The Jesse Z and Sara Lea Shafer Institute for Endocrinology and Diabetes, National Center for Childhood Diabetes, Schneider Children’s Medical Center of Israel, Petach Tikva, Israel
| | - Adi Eshel
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Lelyan Moadi
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Michal Yackobovitch-Gavan
- School of Medicine, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel
- The Jesse Z and Sara Lea Shafer Institute for Endocrinology and Diabetes, National Center for Childhood Diabetes, Schneider Children’s Medical Center of Israel, Petach Tikva, Israel
- Department of Epidemiology and Preventive Medicine, School of Public Health, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Meytal Bar-Maisels
- The Jesse Z and Sara Lea Shafer Institute for Endocrinology and Diabetes, National Center for Childhood Diabetes, Schneider Children’s Medical Center of Israel, Petach Tikva, Israel
- Felsenstein Medical Research Center, Tel Aviv University, Petach Tikva, Israel
| | - Biana Shtaif
- School of Medicine, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel
- Felsenstein Medical Research Center, Tel Aviv University, Petach Tikva, Israel
| | - Michal Nevo
- The Jesse Z and Sara Lea Shafer Institute for Endocrinology and Diabetes, National Center for Childhood Diabetes, Schneider Children’s Medical Center of Israel, Petach Tikva, Israel
| | - Moshe Phillip
- School of Medicine, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel
- The Jesse Z and Sara Lea Shafer Institute for Endocrinology and Diabetes, National Center for Childhood Diabetes, Schneider Children’s Medical Center of Israel, Petach Tikva, Israel
- Felsenstein Medical Research Center, Tel Aviv University, Petach Tikva, Israel
| | - Sondra Turjeman
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Omry Koren
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Galia Gat-Yablonski
- School of Medicine, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel
- The Jesse Z and Sara Lea Shafer Institute for Endocrinology and Diabetes, National Center for Childhood Diabetes, Schneider Children’s Medical Center of Israel, Petach Tikva, Israel
- Felsenstein Medical Research Center, Tel Aviv University, Petach Tikva, Israel
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Cai Y, Luo Y, Dai N, Yang Y, He Y, Chen H, Zhao M, Fu X, Chen T, Xing Z. Corrigendum: Functional metagenomic and metabolomics analysis of gut dysbiosis induced by hyperoxia. Front Microbiol 2024; 15:1382290. [PMID: 38426055 PMCID: PMC10904077 DOI: 10.3389/fmicb.2024.1382290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 03/02/2024] Open
Abstract
[This corrects the article DOI: 10.3389/fmicb.2023.1197970.].
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Affiliation(s)
- Yulan Cai
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital of Zunyi Medical University, Zunyi, China
- Department of Endocrinology and Metabolism, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- Kweichow Moutai Hospital, Renhuai, China
| | - Yanhong Luo
- The First Clinical College, Zunyi Medical University, Zunyi, China
| | - Ninan Dai
- Department of Critical Care Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Yan Yang
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital of Zunyi Medical University, Zunyi, China
- Department of Endocrinology and Metabolism, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Ying He
- Department of Critical Care Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Huajun Chen
- Department of Critical Care Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Manlu Zhao
- The First Clinical College, Zunyi Medical University, Zunyi, China
| | - Xiaoyun Fu
- Department of Critical Care Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Tao Chen
- Department of Critical Care Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Zhouxiong Xing
- Department of Critical Care Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, China
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Wang D, Liu X, Shi S, Ren T, Wang W. Gut microbiota and metabolite variations in a migraine mouse model. Front Cell Infect Microbiol 2024; 13:1322059. [PMID: 38357211 PMCID: PMC10864585 DOI: 10.3389/fcimb.2023.1322059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 12/27/2023] [Indexed: 02/16/2024] Open
Abstract
Migraine is a prevalent clinical disorder characterized by recurrent unilateral throbbing headache episodes accompanied by symptoms such as nausea, vomiting, photophobia, and phonophobia. Despite its common occurrence, the diagnosis, pathophysiology, and treatment of migraine remain controversial. Extensive research has implicated the gut microbiota in various central nervous system disorders, including anxiety disorders, depression, and Parkinson's disease. Some studies have also suggested that migraine may stem from disruptions to neurohormones and metabolism. This study aimed to investigate the disparities in gut microbiota and metabolites between migraine mice model and normal mice to shed light on the underlying mechanisms and potential therapeutic approaches. Distinct differences in gut microbial composition were observed between the migraine mouse model and normal mouse, indicating a potential correlation between these variations and the pathogenesis of migraine. This study provides evidence of differences in gut microbiota composition and metabolites between a migraine mouse model and normal mice, which showed that Akkermansiaceae constituted the most abundant taxon in the sham injection mouse group, while Lachnospiraceae constituted the most prevalent group in the migraine mouse model group. The associations between the abundances of Akkermansia muciniphila and Lachnospiraceae bacteria and metabolites suggested their potential roles in the pathogenesis of migraine. The altered abundance of Lachnospiraceae observed in migraine-afflicted mice and its correlations with changes in metabolites suggest that it may affect the host's health. Thus, probiotic therapy emerges as a possible treatment for migraine. Moreover, significant disparities in gut metabolites were observed between the migraine mouse model and normal mice. These alterations encompass multiple metabolic pathways, suggesting that metabolic disturbances may also contribute to the development of migraines.
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Affiliation(s)
- Dan Wang
- Ear, Nose, and Throat (ENT) Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, Fudan University, Shanghai, China
- National Health Council (NHC) Key Laboratory of Hearing Medicine, Fudan University, Shanghai, sChina
| | - Xu Liu
- Ear, Nose, and Throat (ENT) Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, Fudan University, Shanghai, China
- National Health Council (NHC) Key Laboratory of Hearing Medicine, Fudan University, Shanghai, sChina
| | - Suming Shi
- Ear, Nose, and Throat (ENT) Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, Fudan University, Shanghai, China
- National Health Council (NHC) Key Laboratory of Hearing Medicine, Fudan University, Shanghai, sChina
| | - Tongli Ren
- Ear, Nose, and Throat (ENT) Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, Fudan University, Shanghai, China
- National Health Council (NHC) Key Laboratory of Hearing Medicine, Fudan University, Shanghai, sChina
| | - Wuqing Wang
- Ear, Nose, and Throat (ENT) Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, Fudan University, Shanghai, China
- National Health Council (NHC) Key Laboratory of Hearing Medicine, Fudan University, Shanghai, sChina
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Hayes JA, Lunger AW, Sharma AS, Fernez MT, Carrier RL, Koppes AN, Koppes R, Woolston BM. Engineered bacteria titrate hydrogen sulfide and induce concentration-dependent effects on the host in a gut microphysiological system. Cell Rep 2023; 42:113481. [PMID: 37980564 PMCID: PMC10791167 DOI: 10.1016/j.celrep.2023.113481] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 10/05/2023] [Accepted: 11/06/2023] [Indexed: 11/21/2023] Open
Abstract
Hydrogen sulfide (H2S) is a gaseous microbial metabolite whose role in gut diseases is debated, with contradictory results stemming from experimental difficulties associated with accurate dosing and measuring H2S and the use of model systems that do not accurately represent the human gut environment. Here, we engineer Escherichia coli to titrate H2S across the physiological range in a gut microphysiological system (chip) supportive of the co-culture of microbes and host cells. The chip is engineered to maintain H2S gas tension and enables visualization of co-culture in real time with confocal microscopy. Engineered strains colonize the chip and are metabolically active for 2 days, during which they produce H2S across a 16-fold range and induce changes in host gene expression and metabolism in an H2S-concentration-dependent manner. These results validate a platform for studying the mechanisms underlying microbe-host interactions by enabling experiments that are infeasible with current animal and in vitro models.
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Affiliation(s)
- Justin A Hayes
- Department of Chemical Engineering, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA
| | - Anna W Lunger
- Department of Chemical Engineering, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA
| | - Aayushi S Sharma
- Department of Mechanical and Industrial Engineering, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA; Department of Bioengineering, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA
| | - Matthew T Fernez
- Department of Chemical Engineering, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA
| | - Rebecca L Carrier
- Department of Chemical Engineering, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA; Department of Bioengineering, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA; Department of Biology, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA
| | - Abigail N Koppes
- Department of Chemical Engineering, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA; Department of Bioengineering, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA
| | - Ryan Koppes
- Department of Chemical Engineering, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA.
| | - Benjamin M Woolston
- Department of Chemical Engineering, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA.
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Nishimoto Y, Salim F, Yama K, Kumagai K, Jo R, Harada M, Maruyama Y, Aita Y, Fujii N, Inokuchi T, Kawamata R, Sako M, Ichiba Y, Tsutsumi K, Kimura M, Mori Y, Murakami S, Kakizawa Y, Kumagai T, Fukuda S. Integrated analysis of the oral and intestinal microbiome and metabolome of elderly people with more than 26 original teeth: a pilot study. Front Microbiol 2023; 14:1233460. [PMID: 37901820 PMCID: PMC10600518 DOI: 10.3389/fmicb.2023.1233460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 09/22/2023] [Indexed: 10/31/2023] Open
Abstract
Elderly subjects with more than 20 natural teeth have a higher healthy life expectancy than those with few or no teeth. The oral microbiome and its metabolome are associated with oral health, and they are also associated with systemic health via the oral-gut axis. Here, we analyzed the oral and gut microbiome and metabolome profiles of elderly subjects with more than 26 natural teeth. Salivary samples collected as mouth-rinsed water and fecal samples were obtained from 22 healthy individuals, 10 elderly individuals with more than 26 natural teeth and 24 subjects with periodontal disease. The oral microbiome and metabolome profiles of elderly individuals resembled those of subjects with periodontal disease, with the metabolome showing a more substantial differential abundance of components. Despite the distinct oral metabolome profiles, there was no differential abundance of components in the gut microbiome and metabolomes, except for enrichment of short-chain fatty acids in elderly subjects. Finally, to investigate the relationship between the oral and gut microbiome and metabolome, we analyzed bacterial coexistence in the oral cavity and gut and analyzed the correlation of metabolite levels between the oral cavity and gut. However, there were few associations between oral and gut for bacteria and metabolites in either elderly or healthy subjects. Overall, these results indicate distinct oral microbiome and metabolome profiles, as well as the lack of an oral-gut axis in elderly subjects with a high number of natural teeth.
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Affiliation(s)
| | - Felix Salim
- Metagen Inc., Tsuruoka, Yamagata, Japan
- Department of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Kazuma Yama
- Research and Development Headquarters, Lion Corporation, Tokyo, Japan
| | - Kota Kumagai
- Hiyoshi Oral Health Clinics, Sakata, Yamagata, Japan
| | - Ryutaro Jo
- Research and Development Headquarters, Lion Corporation, Tokyo, Japan
| | - Minori Harada
- Hiyoshi Oral Health Clinics, Sakata, Yamagata, Japan
| | - Yuki Maruyama
- Research and Development Headquarters, Lion Corporation, Tokyo, Japan
| | - Yuto Aita
- Research and Development Headquarters, Lion Corporation, Tokyo, Japan
| | - Narumi Fujii
- Research and Development Headquarters, Lion Corporation, Tokyo, Japan
| | - Takuya Inokuchi
- Research and Development Headquarters, Lion Corporation, Tokyo, Japan
| | - Ryosuke Kawamata
- Research and Development Headquarters, Lion Corporation, Tokyo, Japan
| | - Misato Sako
- Research and Development Headquarters, Lion Corporation, Tokyo, Japan
| | - Yuko Ichiba
- Research and Development Headquarters, Lion Corporation, Tokyo, Japan
| | - Kota Tsutsumi
- Research and Development Headquarters, Lion Corporation, Tokyo, Japan
| | - Mitsuo Kimura
- Research and Development Headquarters, Lion Corporation, Tokyo, Japan
| | - Yuka Mori
- Metagen Inc., Tsuruoka, Yamagata, Japan
| | - Shinnosuke Murakami
- Metagen Inc., Tsuruoka, Yamagata, Japan
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Yasushi Kakizawa
- Research and Development Headquarters, Lion Corporation, Tokyo, Japan
| | | | - Shinji Fukuda
- Metagen Inc., Tsuruoka, Yamagata, Japan
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
- Laboratory for Regenerative Microbiology, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Gut Environmental Design Group, Kanagawa Institute of Industrial Science and Technology, Kawasaki, Kanagawa, Japan
- Transborder Medical Research Center, University of Tsukuba, Tsukuba, Ibaraki, Japan
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Cai Y, Luo Y, Dai N, Yang Y, He Y, Chen H, Zhao M, Fu X, Chen T, Xing Z. Functional metagenomic and metabolomics analysis of gut dysbiosis induced by hyperoxia. Front Microbiol 2023; 14:1197970. [PMID: 37840730 PMCID: PMC10569423 DOI: 10.3389/fmicb.2023.1197970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 09/11/2023] [Indexed: 10/17/2023] Open
Abstract
Background Inhaled oxygen is the first-line therapeutic approach for maintaining tissue oxygenation in critically ill patients, but usually exposes patients to damaging hyperoxia. Hyperoxia adversely increases the oxygen tension in the gut lumen which harbors the trillions of microorganisms playing an important role in host metabolism and immunity. Nevertheless, the effects of hyperoxia on gut microbiome and metabolome remain unclear, and metagenomic and metabolomics analysis were performed in this mouse study. Methods C57BL/6 mice were randomly divided into a control (CON) group exposed to room air with fractional inspired oxygen (FiO2) of 21% and a hyperoxia (OXY) group exposed to FiO2 of 80% for 7 days, respectively. Fecal pellets were collected on day 7 and subjected to metagenomic sequencing. Another experiment with the same design was performed to explore the impact of hyperoxia on gut and serum metabolome. Fecal pellets and blood were collected and high-performance liquid chromatography with mass spectrometric analysis was carried out. Results At the phylum level, hyperoxia increased the ratio of Firmicutes/Bacteroidetes (p = 0.049). At the species level, hyperoxia reduced the abundance of Muribaculaceae bacterium Isolate-037 (p = 0.007), Isolate-114 (p = 0.010), and Isolate-043 (p = 0.011) etc. Linear discriminant analysis effect size (LEfSe) revealed that Muribaculaceae and Muribaculaceae bacterium Isolate-037, both belonging to Bacteroidetes, were the marker microbes of the CON group, while Firmicutes was the marker microbes of the OXY group. Metagenomic analysis using Kyoto Encyclopedia of Genes and Genomes (KEGG) and Carbohydrate-Active enZYmes (CAZy) revealed that hyperoxia provoked disturbances in carbohydrate and lipid metabolism. Fecal metabolomics analysis showed hyperoxia reduced 11-dehydro Thromboxane B2-d4 biosynthesis (p = 1.10 × 10-11). Hyperoxia blunted fecal linoleic acid metabolism (p = 0.008) and alpha-linolenic acid metabolism (p = 0.014). We showed that 1-docosanoyl-glycer-3-phosphate (p = 1.58 × 10-10) was the most significant differential serum metabolite inhibited by hyperoxia. In addition, hyperoxia suppressed serum hypoxia-inducible factor-1 (HIF-1, p = 0.007) and glucagon signaling pathways (p = 0.007). Conclusion Hyperoxia leads to gut dysbiosis by eliminating beneficial and oxygen strictly intolerant Muribaculaceae with genomic dysfunction of carbohydrate and lipid metabolism. In addition, hyperoxia suppresses unsaturated fatty acid metabolism in the gut and inhibits the HIF-1 and glucagon signaling pathways in the serum.
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Affiliation(s)
- Yulan Cai
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital of Zunyi Medical University, Zunyi, China
- Department of Endocrinology and Metabolism, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- Kweichow Moutai Hospital, Renhuai, China
| | - Yanhong Luo
- The First Clinical College, Zunyi Medical University, Zunyi, China
| | - Ninan Dai
- Department of Critical Care Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Yan Yang
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital of Zunyi Medical University, Zunyi, China
- Department of Endocrinology and Metabolism, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Ying He
- Department of Critical Care Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Huajun Chen
- Department of Critical Care Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Manlu Zhao
- The First Clinical College, Zunyi Medical University, Zunyi, China
| | - Xiaoyun Fu
- Department of Critical Care Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Tao Chen
- Department of Critical Care Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Zhouxiong Xing
- Department of Critical Care Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, China
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Zhou L, Qiu W, Wang J, Zhao A, Zhou C, Sun T, Xiong Z, Cao P, Shen W, Chen J, Lai X, Zhao LH, Wu Y, Li M, Qiu F, Yu Y, Xu ZZ, Zhou H, Jia W, Liao Y, Retnakaran R, Krewski D, Wen SW, Clemente JC, Chen T, Xie RH, He Y. Effects of vaginal microbiota transfer on the neurodevelopment and microbiome of cesarean-born infants: A blinded randomized controlled trial. Cell Host Microbe 2023; 31:1232-1247.e5. [PMID: 37327780 DOI: 10.1016/j.chom.2023.05.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 03/22/2023] [Accepted: 05/19/2023] [Indexed: 06/18/2023]
Abstract
The microbiomes of cesarean-born infants differ from vaginally delivered infants and are associated with increased disease risks. Vaginal microbiota transfer (VMT) to newborns may reverse C-section-related microbiome disturbances. Here, we evaluated the effect of VMT by exposing newborns to maternal vaginal fluids and assessing neurodevelopment, as well as the fecal microbiota and metabolome. Sixty-eight cesarean-delivered infants were randomly assigned a VMT or saline gauze intervention immediately after delivery in a triple-blind manner (ChiCTR2000031326). Adverse events were not significantly different between the two groups. Infant neurodevelopment, as measured by the Ages and Stages Questionnaire (ASQ-3) score at 6 months, was significantly higher with VMT than saline. VMT significantly accelerated gut microbiota maturation and regulated levels of certain fecal metabolites and metabolic functions, including carbohydrate, energy, and amino acid metabolisms, within 42 days after birth. Overall, VMT is likely safe and may partially normalize neurodevelopment and the fecal microbiome in cesarean-delivered infants.
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Affiliation(s)
- Lepeng Zhou
- School of Nursing, Affiliated Foshan Maternity & Child Healthcare Hospital, Department of Laboratory Medicine in Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China; School of Nursing; Department of Nursing, Foshan Fetal Medicine Research Institute, Affiliated Foshan Maternity & Child Healthcare Hospital, Southern Medical University, Foshan, Guangdong 528100, China; Department of Nursing, The Seventh Affiliated Hospital, Southern Medical University, Foshan, Guangdong 528244, China
| | - Wen Qiu
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510280, China
| | - Jie Wang
- School of Nursing; Department of Nursing, Foshan Fetal Medicine Research Institute, Affiliated Foshan Maternity & Child Healthcare Hospital, Southern Medical University, Foshan, Guangdong 528100, China
| | - Aihua Zhao
- Center for Translational Medicine and Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Jiao Tong University School of Medicine Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Chuhui Zhou
- School of Nursing; Department of Nursing, Foshan Fetal Medicine Research Institute, Affiliated Foshan Maternity & Child Healthcare Hospital, Southern Medical University, Foshan, Guangdong 528100, China
| | - Tao Sun
- Center for Translational Medicine and Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Jiao Tong University School of Medicine Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Ziyu Xiong
- Department of Nursing, The Seventh Affiliated Hospital, Southern Medical University, Foshan, Guangdong 528244, China
| | - Peihua Cao
- Clinical Research Center, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510280, China; Department of Biostatistics, School of Public Health, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Wei Shen
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510280, China; Department of Neonatology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Jingfen Chen
- School of Nursing; Department of Nursing, Foshan Fetal Medicine Research Institute, Affiliated Foshan Maternity & Child Healthcare Hospital, Southern Medical University, Foshan, Guangdong 528100, China
| | - Xiaolu Lai
- School of Nursing; Department of Nursing, Foshan Fetal Medicine Research Institute, Affiliated Foshan Maternity & Child Healthcare Hospital, Southern Medical University, Foshan, Guangdong 528100, China
| | - Liu-Hong Zhao
- School of Nursing; Department of Nursing, Foshan Fetal Medicine Research Institute, Affiliated Foshan Maternity & Child Healthcare Hospital, Southern Medical University, Foshan, Guangdong 528100, China
| | - Yue Wu
- Department of Cardiology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Meng Li
- Department of Obstetrics, The Seventh Affiliated Hospital, Southern Medical University, Foshan, Guangdong 528244, China
| | - Feng Qiu
- Department of Laboratory Medicine, The Seventh Affiliated Hospital, Southern Medical University, Foshan, Guangdong 528244, China
| | - Yanhong Yu
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Zhenjiang Zech Xu
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510280, China; State Key Laboratory of Food Science and Technology, Institute of Nutrition and College of Food Science and Technology, Nanchang University, Nanchang, Jiangxi 330047, China
| | - Hongwei Zhou
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510280, China; State Key Laboratory of Organ Failure Research, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Wei Jia
- Center for Translational Medicine and Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Jiao Tong University School of Medicine Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Yan Liao
- Ottawa Hospital Research Institute, Ottawa, ON K1H8L6, Canada
| | - Ravi Retnakaran
- Leadership Sinai Centre for Diabetes, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Division of Endocrinology, University of Toronto, Toronto, ON M5S 2E8, Canada
| | - Daniel Krewski
- McLaughlin Centre for Population Health Risk Assessment, Faculty of Medicine, University of Ottawa, Ottawa, ON K1N 6N5, Canada; Risk Science International, Ottawa, ON K1P 5J6, Canada; School of Epidemiology and Public Health, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Shi Wu Wen
- Ottawa Hospital Research Institute, Ottawa, ON K1H8L6, Canada; School of Epidemiology and Public Health, University of Ottawa, Ottawa, ON K1N 6N5, Canada; Department of Obstetrics and Gynecology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Jose C Clemente
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Tianlu Chen
- Center for Translational Medicine and Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Jiao Tong University School of Medicine Affiliated Sixth People's Hospital, Shanghai 200233, China.
| | - Ri-Hua Xie
- School of Nursing; Department of Nursing, Foshan Fetal Medicine Research Institute, Affiliated Foshan Maternity & Child Healthcare Hospital, Southern Medical University, Foshan, Guangdong 528100, China.
| | - Yan He
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510280, China; State Key Laboratory of Organ Failure Research, Southern Medical University, Guangzhou, Guangdong 510515, China; Guangdong Provincial Clinical Research Center for Laboratory Medicine, Guangzhou, Guangdong 510033, China.
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Jenickova E, Andrén Aronsson C, Mascellani Bergo A, Cinek O, Havlik J, Agardh D. Effects of Lactiplantibacillus plantarum and Lacticaseibacillus paracasei supplementation on the faecal metabolome in children with coeliac disease autoimmunity: a randomised, double-blinded placebo-controlled clinical trial. Front Nutr 2023; 10:1183963. [PMID: 37485388 PMCID: PMC10359497 DOI: 10.3389/fnut.2023.1183963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 06/08/2023] [Indexed: 07/25/2023] Open
Abstract
Introduction Coeliac disease is a lifelong immune-mediated enteropathy manifested as gluten intolerance in individuals carrying specific human leukocyte antigen (HLA) molecules. Other factors than genetics and gluten intake, however, may play a role in triggering the disease. The gut internal environment is thought to be one of these potential contributing factors, and it can be influenced throughout life. Methods We examine the impact of Lactiplantibacillus plantarum HEAL9 and Lacticaseibacillus paracasei 8700:2 supplementation on the faecal metabolome in genetically predisposed children having tissue transglutaminase autoantibodies, i.e., coeliac disease autoimmunity. Probiotic strains were selected based on their beneficial properties, including mucosal permeability and immune modulation effects. The intervention group (n = 40) and control group (n = 38) took the probiotics or placebo daily for 6 months in a double-blinded randomised trial. Faecal samples were collected at baseline and after 3 and 6 months and analysed using the 1H NMR for metabolome. The incorporation of 16S rRNA sequencing as a supportive dataset complemented the analysis of the metabolome data. Results During the 6 months of intervention, the stool concentrations of 4-hydroxyphenylacetate increased in the intervention group as compared to controls, whereas concentrations of threonine, valine, leucine, isoleucine, methionine, phenylalanine, aspartate, and fumarate decreased. Additionally, a noteworthy effect on the glycine, serine, and threonine metabolic pathway has been observed. Conclusion The findings suggest a modest yet significant impact of the probiotics on the faecal metabolome, primarily influencing proteolytic processes in the gut. Clinical trial registration ClinicalTrials.gov, NCT03176095.
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Affiliation(s)
- Eliska Jenickova
- Department of Food Science, Czech University of Life Sciences Prague, Prague, Czechia
| | | | - Anna Mascellani Bergo
- Department of Food Science, Czech University of Life Sciences Prague, Prague, Czechia
| | - Ondrej Cinek
- Department of Pediatrics and Department of Medical Microbiology, Charles University in Prague and University Hospital Motol, Prague, Czechia
| | - Jaroslav Havlik
- Department of Food Science, Czech University of Life Sciences Prague, Prague, Czechia
| | - Daniel Agardh
- Department of Clinical Sciences, Lund University, Malmö, Sweden
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Vacca M, Celano G, Calabrese FM, Rocchetti MT, Iacobellis I, Serale N, Calasso M, Gesualdo L, De Angelis M. In vivo evaluation of an innovative synbiotics on stage IIIb-IV chronic kidney disease patients. Front Nutr 2023; 10:1215836. [PMID: 37396126 PMCID: PMC10311028 DOI: 10.3389/fnut.2023.1215836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 05/30/2023] [Indexed: 07/04/2023] Open
Abstract
Background Microbiota unbalance has been proven to affect chronic kidney disease (CKD) patients and, noteworthy, microbiota composition and activity are implicated in CKD worsening. The progression of kidney failure implies an exceeding accumulation of waste compounds deriving from the nitrogenous metabolism in the intestinal milieu. Therefore, in the presence of an altered intestinal permeability, gut-derived uremic toxins, i.e., indoxyl sulfate (IS) and p-cresyl sulfate (PCS), can accumulate in the blood. Methods In a scenario facing the nutritional management as adjuvant therapy, the present study assessed the effectiveness of an innovative synbiotics for its ability to modulate the patient gut microbiota and metabolome by setting a randomized, single-blind, placebo-controlled, pilot trial accounting for IIIb-IV stage CKD patients and healthy controls. Metataxonomic fecal microbiota and fecal volatilome were analyzed at the run-in, after 2 months of treatment, and after 1 month of wash out. Results Significant changes in microbiota profile, as well as an increase of the saccharolytic metabolism, in feces were found for those CKD patients that were allocated in the synbiotics arm. Conclusions Noteworthy, the here analyzed data emphasized a selective efficacy of the present synbiotics on a stage IIIb-IV CKD patients. Nonetheless, a further validation of this trial accounting for an increased patient number should be considered. Clinical trial registration https://clinicaltrials.gov/, identifier NCT03815786.
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Affiliation(s)
- Mirco Vacca
- Department of Soil Plant and Food Sciences, University of Bari, Bari, Italy
| | - Giuseppe Celano
- Department of Soil Plant and Food Sciences, University of Bari, Bari, Italy
| | | | | | - Ilaria Iacobellis
- Department of Soil Plant and Food Sciences, University of Bari, Bari, Italy
| | - Nadia Serale
- Department of Soil Plant and Food Sciences, University of Bari, Bari, Italy
| | - Maria Calasso
- Department of Soil Plant and Food Sciences, University of Bari, Bari, Italy
| | - Loreto Gesualdo
- Department of Precision and Regenerative Medicine and Ionian Area, University of Bari Aldo Moro, Bari, Italy
| | - Maria De Angelis
- Department of Soil Plant and Food Sciences, University of Bari, Bari, Italy
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11
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Li S, Xu K, Cheng Y, Chen L, Yi A, Xiao Z, Zhao X, Chen M, Tian Y, Meng W, Tang Z, Zhou S, Ruan G, Wei Y. The role of complex interactions between the intestinal flora and host in regulating intestinal homeostasis and inflammatory bowel disease. Front Microbiol 2023; 14:1188455. [PMID: 37389342 PMCID: PMC10303177 DOI: 10.3389/fmicb.2023.1188455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 05/10/2023] [Indexed: 07/01/2023] Open
Abstract
Pharmacological treatment of inflammatory bowel disease (IBD) is inefficient and difficult to discontinue appropriately, and enterobacterial interactions are expected to provide a new target for the treatment of IBD. We collected recent studies on the enterobacterial interactions among the host, enterobacteria, and their metabolite products and discuss potential therapeutic options. Intestinal flora interactions in IBD are affected in the reduced bacterial diversity, impact the immune system and are influenced by multiple factors such as host genetics and diet. Enterobacterial metabolites such as SCFAs, bile acids, and tryptophan also play important roles in enterobacterial interactions, especially in the progression of IBD. Therapeutically, a wide range of sources of probiotics and prebiotics exhibit potential therapeutic benefit in IBD through enterobacterial interactions, and some have gained wide recognition as adjuvant drugs. Different dietary patterns and foods, especially functional foods, are novel therapeutic modalities that distinguish pro-and prebiotics from traditional medications. Combined studies with food science may significantly improve the therapeutic experience of patients with IBD. In this review, we provide a brief overview of the role of enterobacteria and their metabolites in enterobacterial interactions, discuss the advantages and disadvantages of the potential therapeutic options derived from such metabolites, and postulate directions for further research.
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Affiliation(s)
- Siyu Li
- Department of Gastroenterology, Chongqing Key Laboratory of Digestive Malignancies, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
- Basic Medicine College of Army Medical University, Army Medical University, Chongqing, China
| | - Kan Xu
- Department of Gastroenterology, Chongqing Key Laboratory of Digestive Malignancies, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
- Basic Medicine College of Army Medical University, Army Medical University, Chongqing, China
| | - Yi Cheng
- Department of Gastroenterology, Chongqing Key Laboratory of Digestive Malignancies, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Lu Chen
- Department of Gastroenterology, Chongqing Key Laboratory of Digestive Malignancies, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Ailin Yi
- Department of Gastroenterology, Chongqing Key Laboratory of Digestive Malignancies, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Zhifeng Xiao
- Department of Gastroenterology, Chongqing Key Laboratory of Digestive Malignancies, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Xuefei Zhao
- Department of Gastroenterology, Chongqing Key Laboratory of Digestive Malignancies, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Minjia Chen
- Department of Gastroenterology, Chongqing Key Laboratory of Digestive Malignancies, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Yuting Tian
- Department of Gastroenterology, Chongqing Key Laboratory of Digestive Malignancies, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Wei Meng
- Department of Gastroenterology, Chongqing Key Laboratory of Digestive Malignancies, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Zongyuan Tang
- Department of Gastroenterology, Chongqing Key Laboratory of Digestive Malignancies, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Shuhong Zhou
- Department of Laboratory Animal Center, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Guangcong Ruan
- Department of Gastroenterology, Chongqing Key Laboratory of Digestive Malignancies, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Yanling Wei
- Department of Gastroenterology, Chongqing Key Laboratory of Digestive Malignancies, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
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Anderson GM. Determination of Indolepropionic Acid and Related Indoles in Plasma, Plasma Ultrafiltrate, and Saliva. Metabolites 2023; 13:metabo13050602. [PMID: 37233643 DOI: 10.3390/metabo13050602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/19/2023] [Accepted: 04/24/2023] [Indexed: 05/27/2023] Open
Abstract
The microbial metabolite indolepropionic acid (IPA) and related indolic metabolites, including indolecarboxylic acid (ICA), indolelactic acid (ILA), indoleacetic acid (IAA), indolebutyric acid (IBA), indoxylsulfate (ISO4), and indole, were determined in human plasma, plasma ultrafiltrate (UF), and saliva. The compounds were separated on a 150 × 3 mm column of 3 μm Hypersil C18 eluted with a mobile phase of 80% pH 5 0.01 M sodium acetate containing 1.0 g/L of tert-butylammonium chloride/20% acetonitrile and then detected fluorometrically. Levels of IPA in human plasma UF and of ILA in saliva are reported for the first time. The determination of IPA in plasma UF enables the first report of free plasma IPA, the presumed physiologically active pool of this important microbial metabolite of tryptophan. Plasma and salivary ICA and IBA were not detected, consistent with the absence of any prior reported values. Observed levels or limits of detection for other indolic metabolites usefully supplement limited prior reports.
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Affiliation(s)
- George M Anderson
- Department of Laboratory Medicine, The Child Study Center, Yale University School of Medicine, 230 S. Frontage Rd., New Haven, CT 06519, USA
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13
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Liu H, Xu J, Yeung C, Chen Q, Li J. Effects of hemicellulose on intestinal mucosal barrier integrity, gut microbiota, and metabolomics in a mouse model of type 2 diabetes mellitus. Front Microbiol 2023; 14:1096471. [PMID: 36825092 PMCID: PMC9942597 DOI: 10.3389/fmicb.2023.1096471] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 01/10/2023] [Indexed: 02/10/2023] Open
Abstract
Background and objective Impaired gut barrier contributes to the progression of type 2 diabetes mellitus (T2DM), and the gut microbiota and metabolome play an important role in it. Hemicellulose, a potential prebiotics, how its supplementation impacted the glucose level, the impaired gut barrier, and the gut microbiota and metabolome in T2DM remained unclear. Methods In this study, some mice were arranged randomly into four groups: db/db mice fed by a compositionally defined diet (CDD), db/db mice fed by a CDD with 10% and 20% hemicellulose supplementation, and control mice fed by a CDD. Body weight and fasting blood glucose levels were monitored weekly. The gut barrier was evaluated. Fresh stool samples were analyzed using metagenomic sequencing and liquid chromatography-mass spectrometry to detect gut microbiota and metabolome changes. Systemic and colonic inflammation were evaluated. Results Better glycemic control, restoration of the impaired gut barrier, and lowered systemic inflammation levels were observed in db/db mice with the supplementation of 10 or 20% hemicellulose. The gut microbiota showed significant differences in beta diversity among the four groups. Fifteen genera with differential relative abundances and 59 significantly different metabolites were found. In the db/db group, hemicellulose eliminated the redundant Faecalibaculum and Enterorhabdus. The increased succinate and ursodeoxycholic acid (UDCA) after hemicellulose treatment were negatively correlated with Bifidobacterium, Erysipelatoclostridium, and Faecalibaculum. In addition, hemicellulose reduced the colonic expressions of TLR2/4 and TNF-α in db/db mice. Conclusion Hemicellulose may serve as a potential therapeutic intervention for T2DM by improving impaired intestinal mucosal barrier integrity, modulating gut microbiota composition, and altering the metabolic profile.
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Affiliation(s)
| | | | - Chiuwing Yeung
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
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14
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Nishimoto Y, Kawai J, Mori K, Hartanto T, Komatsu K, Kudo T, Fukuda S. Dietary supplement of mushrooms promotes SCFA production and moderately associates with IgA production: A pilot clinical study. Front Nutr 2023; 9:1078060. [PMID: 36698463 PMCID: PMC9868702 DOI: 10.3389/fnut.2022.1078060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 12/21/2022] [Indexed: 01/11/2023] Open
Abstract
Background Mushrooms are rich in dietary fiber, and fiber intake has been reported to increase the levels of short-chain fatty acids (SCFAs). It has also been reported that SCFAs promote immunoglobulin A (IgA) production, indicating involvement in systemic immunity. Objectives The objective of this study was to evaluate the effects of mushroom consumption on the amount of intestinal IgA. We also aimed to comprehensively evaluate the gut microbiota and intestinal metabolome and to conduct an exploratory analysis of their relationship with IgA. Methods Healthy adults (n = 80) were enrolled in a parallel group trial. Participants consumed a diet with mushrooms or a placebo diet once daily for 4 weeks. Gut microbiota profiles were assessed by sequencing the bacterial 16S ribosomal RNA-encoding gene. Intestinal metabolome profiles were analyzed using capillary electrophoresis-time of flight mass spectrometry (CE-TOFMS). Results Mushroom consumption tended to increase IgA levels at 4 weeks of consumption compared to those in the control group (p = 0.0807; Hedges' g = 0.480). The mushroom group had significantly higher levels of intestinal SCFAs, such as butyrate and propionate, than the control group (p = 0.001 and 0.020; Hedges' g = 0.824 and 0.474, respectively). Correlation analysis between the changes in the amount of intestinal IgA and the baseline features of the intestinal environment showed that the increasing amount of intestinal IgA was positively correlated with the baseline levels of SCFAs (Spearman's R = 0.559 and 0.419 for butyrate and propionate, respectively). Conclusion Consumption of mushrooms significantly increased the intestinal SCFAs and IgA in some subjects. The increase in intestinal IgA levels was more prominent in subjects with higher SCFA levels at baseline. This finding provides evidence that mushroom alters the intestinal environment, but the intensity of the effect still depends on the baseline intestinal environment. This trial was registered at www.umin.ac.jp as UMIN000043979.
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Affiliation(s)
| | - Junya Kawai
- Mushroom Research Laboratory, Hokuto Corporation, Nagano, Japan
| | - Koichiro Mori
- Mushroom Research Laboratory, Hokuto Corporation, Nagano, Japan
| | | | | | | | - Shinji Fukuda
- Metagen Inc., Tsuruoka, Japan,Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan,Gut Environmental Design Group, Kanagawa Institute of Industrial Science and Technology, Kawasaki, Japan,Transborder Medical Research Center, University of Tsukuba, Tsukuba, Japan,Laboratory for Regenerative Microbiology, Juntendo University Graduate School of Medicine, Tokyo, Japan,*Correspondence: Shinji Fukuda,
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15
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He J, Zhang Y, Li H, Xie Y, Huang G, Peng C, Zhao P, Wang Z. Hybridization alters the gut microbial and metabolic profile concurrent with modifying intestinal functions in Tunchang pigs. Front Microbiol 2023; 14:1159653. [PMID: 37152756 PMCID: PMC10157192 DOI: 10.3389/fmicb.2023.1159653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 03/15/2023] [Indexed: 05/09/2023] Open
Abstract
Introduction Hybridization has been widely used among Chinese wild boars to improve their growth performance and maintain meat quality. Most studies have focused on the genetic basis for such variation. However, the differences in the gut environment between hybrid and purebred boars, which can have significant impacts on their health and productivity, have been poorly understood. Methods In the current study, metagenomics was used to detect the gut microbial diversity and composition in hybrid Batun (BT, Berkshire × Tunchang) pigs and purebred Tunchang (TC) pigs. Additionally, untargeted metabolomic analysis was used to detect differences in gut metabolic pathways. Furthermore, multiple molecular experiments were conducted to demonstrate differences in intestinal functions. Results As a result of hybridization in TC pigs, a microbial change was observed, especially in Prevotella and Lactobacillus. Significant differences were found in gut metabolites, including fatty acyls, steroids, and steroid derivatives. Furthermore, the function of the intestinal barrier was decreased by hybridization, while the function of nutrient metabolism was increased. Discussion Evidences were shown that hybridization changed the gut microbiome, gut metabolome, and intestinal functions of TC pigs. These findings supported our hypothesis that hybridization altered the gut microbial composition, thereby modifying the intestinal functions, even the host phenotypes. Overall, our study highlights the importance of considering the gut microbiome as a key factor in the evaluation of animal health and productivity, particularly in the context of genetic selection and breeding programs.
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Affiliation(s)
- Jiayi He
- Hainan Institute of Zhejiang University, Sanya, China
- College of Animal Science, Zhejiang University, Hangzhou, China
| | - Yunchao Zhang
- Hainan Institute of Zhejiang University, Sanya, China
- College of Animal Science, Zhejiang University, Hangzhou, China
| | - Hui Li
- Long Jian Animal Husbandry Company, Haikou, China
| | - Yanshe Xie
- Hainan Institute of Zhejiang University, Sanya, China
- College of Animal Science, Zhejiang University, Hangzhou, China
| | - Guiqing Huang
- Hainan Institute of Zhejiang University, Sanya, China
- College of Animal Science, Zhejiang University, Hangzhou, China
| | - Chen Peng
- Hainan Institute of Zhejiang University, Sanya, China
- College of Animal Science, Zhejiang University, Hangzhou, China
| | - Pengju Zhao
- Hainan Institute of Zhejiang University, Sanya, China
- College of Animal Science, Zhejiang University, Hangzhou, China
- *Correspondence: Pengju Zhao,
| | - Zhengguang Wang
- Hainan Institute of Zhejiang University, Sanya, China
- College of Animal Science, Zhejiang University, Hangzhou, China
- Zhengguang Wang,
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16
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Peng Y, Chiu ATG, Li VWY, Zhang X, Yeung WL, Chan SHS, Tun HM. The role of the gut-microbiome-brain axis in metabolic remodeling amongst children with cerebral palsy and epilepsy. Front Neurol 2023; 14:1109469. [PMID: 36923492 PMCID: PMC10009533 DOI: 10.3389/fneur.2023.1109469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 02/08/2023] [Indexed: 03/02/2023] Open
Abstract
Background Epilepsy-associated dysbiosis in gut microbiota has been previously described, but the mechanistic roles of the gut microbiome in epileptogenesis among children with cerebral palsy (CP) have yet to be illustrated. Methods Using shotgun metagenomic sequencing coupled with untargeted metabolomics analysis, this observational study compared the gut microbiome and metabolome of eight children with non-epileptic cerebral palsy (NECP) to those of 13 children with cerebral palsy with epilepsy (CPE). Among children with CPE, 8 had drug-sensitive epilepsy (DSE) and five had drug-resistant epilepsy (DRE). Characteristics at enrollment, medication history, and 7-day dietary intake were compared between groups. Results At the species level, CPE subjects had significantly lower abundances of Bacteroides fragilis and Dialister invisus but higher abundances of Phascolarctobacterium faecium and Eubacterium limosum. By contrast, DRE subjects had a significantly higher colonization of Veillonella parvula. Regarding microbial functional pathways, CPE subjects had decreased abundances of pathways for serine degradation, quinolinic acid degradation, glutamate degradation I, glycerol degradation, sulfate reduction, and nitrate reduction but increased abundances of pathways related to ethanol production. As for metabolites, CPE subjects had higher concentrations of kynurenic acid, 2-oxindole, dopamine, 2-hydroxyphenyalanine, 3,4-dihydroxyphenylglycol, L-tartaric acid, and D-saccharic acid; DRE subjects had increased concentrations of indole and homovanilic acid. Conclusions In this study, we found evidence of gut dysbiosis amongst children with cerebral palsy and epilepsy in terms of gut microbiota species, functional pathways, and metabolites. The combined metagenomic and metabolomic analyses have shed insights on the potential roles of B. fragilis and D. invisus in neuroprotection. The combined analyses have also provided evidence for the involvement of GMBA in the epilepsy-related dysbiosis of kynurenine, serotonin, and dopamine pathways and their complex interplay with neuroimmune and neuroendocrinological pathways.
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Affiliation(s)
- Ye Peng
- The Jockey Club School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.,Microbiota I-Center (MagIC), The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.,Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Annie T G Chiu
- Department of Paediatrics and Adolescent Medicine, Hong Kong Children's Hospital, Kowloon City, Hong Kong SAR, China
| | - Vivien W Y Li
- Department of Paediatrics and Adolescent Medicine, Queen Mary Hospital and Duchess of Kent Children's Hospital, Pokfulam, Hong Kong SAR, China
| | - Xi Zhang
- The Jockey Club School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.,Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Wai L Yeung
- Department of Paediatrics and Adolescent Medicine, Hong Kong Children's Hospital, Kowloon City, Hong Kong SAR, China
| | - Sophelia H S Chan
- Department of Paediatrics and Adolescent Medicine, Hong Kong Children's Hospital, Kowloon City, Hong Kong SAR, China.,Department of Paediatrics and Adolescent Medicine, Queen Mary Hospital and Duchess of Kent Children's Hospital, Pokfulam, Hong Kong SAR, China.,Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Hein M Tun
- The Jockey Club School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.,Microbiota I-Center (MagIC), The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.,Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
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17
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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18
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Vatanen T, Jabbar KS, Ruohtula T, Honkanen J, Avila-Pacheco J, Siljander H, Stražar M, Oikarinen S, Hyöty H, Ilonen J, Mitchell CM, Yassour M, Virtanen SM, Clish CB, Plichta DR, Vlamakis H, Knip M, Xavier RJ. Mobile genetic elements from the maternal microbiome shape infant gut microbial assembly and metabolism. Cell 2022; 185:4921-4936.e15. [PMID: 36563663 PMCID: PMC9869402 DOI: 10.1016/j.cell.2022.11.023] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 09/30/2022] [Accepted: 11/11/2022] [Indexed: 12/24/2022]
Abstract
The perinatal period represents a critical window for cognitive and immune system development, promoted by maternal and infant gut microbiomes and their metabolites. Here, we tracked the co-development of microbiomes and metabolomes from late pregnancy to 1 year of age using longitudinal multi-omics data from a cohort of 70 mother-infant dyads. We discovered large-scale mother-to-infant interspecies transfer of mobile genetic elements, frequently involving genes associated with diet-related adaptations. Infant gut metabolomes were less diverse than maternal but featured hundreds of unique metabolites and microbe-metabolite associations not detected in mothers. Metabolomes and serum cytokine signatures of infants who received regular-but not extensively hydrolyzed-formula were distinct from those of exclusively breastfed infants. Taken together, our integrative analysis expands the concept of vertical transmission of the gut microbiome and provides original insights into the development of maternal and infant microbiomes and metabolomes during late pregnancy and early life.
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Affiliation(s)
- Tommi Vatanen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Liggins Institute, University of Auckland, Auckland, New Zealand
| | | | - Terhi Ruohtula
- New Children's Hospital, Helsinki University Hospital, Helsinki, Finland
| | - Jarno Honkanen
- New Children's Hospital, Helsinki University Hospital, Helsinki, Finland
| | | | - Heli Siljander
- New Children's Hospital, Helsinki University Hospital, Helsinki, Finland; Centre for Military Medicine, Finnish Defence Forces, Riihimäki, Finland
| | - Martin Stražar
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sami Oikarinen
- Department of Virology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Heikki Hyöty
- Department of Virology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland; Fimlab Laboratories, Tampere, Finland
| | - Jorma Ilonen
- Immunogenetics Laboratory, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Caroline M Mitchell
- Vincent Obstetrics & Gynecology Department, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Moran Yassour
- Microbiology & Molecular Genetics Department, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel; The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Suvi M Virtanen
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland; Unit of Health Sciences, Faculty of Social Sciences, Tampere University, Tampere, Finland; Center for Child Health Research and Development and Innovation Center, Tampere University Hospital, Tampere, Finland
| | - Clary B Clish
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Damian R Plichta
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA 02139, USA
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA 02139, USA
| | - Mikael Knip
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland; New Children's Hospital, Helsinki University Hospital, Helsinki, Finland; Tampere Center for Child Health Research, Tampere University Hospital, Tampere, Finland
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA 02139, USA; Center for Computational and Integrative Biology, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
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19
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Vatanen T, Ang QY, Siegwald L, Sarker SA, Le Roy CI, Duboux S, Delannoy-Bruno O, Ngom-Bru C, Boulangé CL, Stražar M, Avila-Pacheco J, Deik A, Pierce K, Bullock K, Dennis C, Sultana S, Sayed S, Rahman M, Ahmed T, Modesto M, Mattarelli P, Clish CB, Vlamakis H, Plichta DR, Sakwinska O, Xavier RJ. A distinct clade of Bifidobacterium longum in the gut of Bangladeshi children thrives during weaning. Cell 2022; 185:4280-4297.e12. [PMID: 36323316 DOI: 10.1016/j.cell.2022.10.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 08/17/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022]
Abstract
The gut microbiome has an important role in infant health and development. We characterized the fecal microbiome and metabolome of 222 young children in Dhaka, Bangladesh during the first two years of life. A distinct Bifidobacterium longum clade expanded with introduction of solid foods and harbored enzymes for utilizing both breast milk and solid food substrates. The clade was highly prevalent in Bangladesh, present globally (at lower prevalence), and correlated with many other gut taxa and metabolites, indicating an important role in gut ecology. We also found that the B. longum clades and associated metabolites were implicated in childhood diarrhea and early growth, including positive associations between growth measures and B. longum subsp. infantis, indolelactate and N-acetylglutamate. Our data demonstrate geographic, cultural, seasonal, and ecological heterogeneity that should be accounted for when identifying microbiome factors implicated in and potentially benefiting infant development.
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20
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Roussel C, Chabaud S, Lessard-Lord J, Cattero V, Pellerin FA, Feutry P, Bochard V, Bolduc S, Desjardins Y. UPEC Colonic-Virulence and Urovirulence Are Blunted by Proanthocyanidins-Rich Cranberry Extract Microbial Metabolites in a Gut Model and a 3D Tissue-Engineered Urothelium. Microbiol Spectr 2022; 10:e0243221. [PMID: 35972287 PMCID: PMC9603664 DOI: 10.1128/spectrum.02432-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 07/27/2022] [Indexed: 01/04/2023] Open
Abstract
Uropathogenic Escherichia coli (UPEC) ecology-pathophysiology from the gut reservoir to its urothelium infection site is poorly understood, resulting in equivocal benefits in the use of cranberry as prophylaxis against urinary tract infections. To add further understanding from the previous findings on PAC antiadhesive properties against UPEC, we assessed in this study the effects of proanthocyanidins (PAC) rich cranberry extract microbial metabolites on UTI89 virulence and fitness in contrasting ecological UPEC's environments. For this purpose, we developed an original model combining a colonic fermentation system (SHIME) with a dialysis cassette device enclosing UPEC and a 3D tissue-engineered urothelium. Two healthy fecal donors inoculated the colons. Dialysis cassettes containing 7log10 CFU/mL UTI89 were immersed for 2h in the SHIME colons to assess the effect of untreated (7-day control diet)/treated (14-day PAC-rich extract) metabolomes on UPEC behavior. Engineered urothelium were then infected with dialysates containing UPEC for 6 h. This work demonstrated for the first time that in the control fecal microbiota condition without added PAC, the UPEC virulence genes were activated upstream the infection site, in the gut. However, PAC microbial-derived cranberry metabolites displayed a remarkable propensity to blunt activation of genes encoding toxin, adhesin/invasins in the gut and on the urothelium, in a donor-dependent manner. Variability in subjects' gut microbiota and ensuing contrasting cranberry PAC metabolism affects UPEC virulence and should be taken into consideration when designing cranberry efficacy clinical trials. IMPORTANCE Uropathogenic Escherichia coli (UPEC) are the primary cause of recurrent urinary tract infections (UTI). The poor understanding of UPEC ecology-pathophysiology from its reservoir-the gut, to its infection site-the urothelium, partly explains the inadequate and abusive use of antibiotics to treat UTI, which leads to a dramatic upsurge in antibiotic-resistance cases. In this context, we evaluated the effect of a cranberry proanthocyanidins (PAC)-rich extract on the UPEC survival and virulence in a bipartite model of a gut microbial environment and a 3D urothelium model. We demonstrated that PAC-rich cranberry extract microbial metabolites significantly blunt activation of UPEC virulence genes at an early stage in the gut reservoir. We also showed that altered virulence in the gut affects infectivity on the urothelium in a microbiota-dependent manner. Among the possible mechanisms, we surmise that specific microbial PAC metabolites may attenuate UPEC virulence, thereby explaining the preventative, yet contentious properties of cranberry against UTI.
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Affiliation(s)
- Charlène Roussel
- Institute of Nutrition and Functional Foods (INAF), Faculty of Agriculture and Food Sciences, Laval University, Québec, Quebec, Canada
| | - Stéphane Chabaud
- Centre de Recherche en Organogenèse Expérimentale de l Université Laval/LOEX, Centre de Recherche du CHU de Québec‐Université Laval, Axe Médecine Régénératrice, Québec, Quebec, Canada
| | - Jacob Lessard-Lord
- Institute of Nutrition and Functional Foods (INAF), Faculty of Agriculture and Food Sciences, Laval University, Québec, Quebec, Canada
| | - Valentina Cattero
- Institute of Nutrition and Functional Foods (INAF), Faculty of Agriculture and Food Sciences, Laval University, Québec, Quebec, Canada
| | - Félix-Antoine Pellerin
- Centre de Recherche en Organogenèse Expérimentale de l Université Laval/LOEX, Centre de Recherche du CHU de Québec‐Université Laval, Axe Médecine Régénératrice, Québec, Quebec, Canada
| | - Perrine Feutry
- Institute of Nutrition and Functional Foods (INAF), Faculty of Agriculture and Food Sciences, Laval University, Québec, Quebec, Canada
| | | | - Stéphane Bolduc
- Centre de Recherche en Organogenèse Expérimentale de l Université Laval/LOEX, Centre de Recherche du CHU de Québec‐Université Laval, Axe Médecine Régénératrice, Québec, Quebec, Canada
| | - Yves Desjardins
- Institute of Nutrition and Functional Foods (INAF), Faculty of Agriculture and Food Sciences, Laval University, Québec, Quebec, Canada
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21
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He W, Xie Z, Wittig NK, Zachariassen LF, Andersen A, Andersen HJ, Birkedal H, Nielsen DS, Hansen AK, Bertram HC. Yogurt Benefits Bone Mineralization in Ovariectomized Rats with Concomitant Modulation of the Gut Microbiome. Mol Nutr Food Res 2022; 66:e2200174. [PMID: 36039478 PMCID: PMC9788323 DOI: 10.1002/mnfr.202200174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 07/04/2022] [Indexed: 12/30/2022]
Abstract
SCOPE Evidence supports that gut-modulating foods potentially can suppress bone loss in postmenopausal women. This study aims to investigate the effect of milk calcium-enriched milk, yogurt, and yogurt-inulin combination on the gut-bone association. METHODS AND RESULTS A 6-week intervention study is conducted in ovariectomized rats. Four pastes containing milk calcium-fortified milk (M-Ca), milk calcium-fortified yogurt (Y-Ca), inulin-fortified Y-Ca (Y-I-Ca), or an isoconcentration of calcium carbonate (Ca-N), and a calcium-deficient paste are provided. M-Ca does not influence bone mineral density and content (BMD and BMC), femur mechanical strength, or femoral microstructure compared to Ca-N, but Y-Ca increases spine BMD. The serum metabolome reveals that Y-Ca modulated glycine-related pathways with reduced glycine, serine, and threonine. No additive effects of yogurt and inulin are found on bone parameters. Correlation analysis shows that increased lactobacilli and reduced Clostridiaceae members in Y-Ca is associated with an increased spine BMD. Increases in Bifidobacterium pseudolongum, Turicibacter, Blautia, and Allobaculum and gut short-chain fatty acids in Y-I-Ca are not reflected in bone parameters. CONCLUSION Yogurt as calcium vehicle contributes to increased spine BMD concomitant with changes in the gut microbiome and glycine-related pathways, while adding inulin to yogurt does not affect bone mineralization in ovariectomized rats.
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Affiliation(s)
- Weiwei He
- Department of Food ScienceAarhus UniversityAgro Food Park 48Aarhus N8200Denmark
| | - Zhuqing Xie
- Department of Food ScienceUniversity of CopenhagenDK‐1958FrederiksbergDenmark
| | - Nina Kølln Wittig
- Department of Chemistry and iNANOAarhus UniversityDK‐8000Aarhus CDenmark
| | - Line F. Zachariassen
- Department of Veterinary and Animal SciencesFaculty of Health and Medical SciencesUniversity of CopenhagenDK‐1958FrederiksbergDenmark
| | | | | | - Henrik Birkedal
- Department of Chemistry and iNANOAarhus UniversityDK‐8000Aarhus CDenmark
| | - Dennis S. Nielsen
- Department of Food ScienceUniversity of CopenhagenDK‐1958FrederiksbergDenmark
| | - Axel K. Hansen
- Department of Veterinary and Animal SciencesFaculty of Health and Medical SciencesUniversity of CopenhagenDK‐1958FrederiksbergDenmark
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22
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Nabavi-Rad A, Sadeghi A, Asadzadeh Aghdaei H, Yadegar A, Smith SM, Zali MR. The double-edged sword of probiotic supplementation on gut microbiota structure in Helicobacter pylori management. Gut Microbes 2022; 14:2108655. [PMID: 35951774 PMCID: PMC9373750 DOI: 10.1080/19490976.2022.2108655] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
As Helicobacter pylori management has become more challenging and less efficient over the last decade, the interest in innovative interventions is growing by the day. Probiotic co-supplementation to antibiotic therapies is reported in several studies, presenting a moderate reduction in drug-related side effects and a promotion in positive treatment outcomes. However, the significance of gut microbiota involvement in the competence of probiotic co-supplementation is emphasized by a few researchers, indicating the alteration in the host gastrointestinal microbiota following probiotic and drug uptake. Due to the lack of long-term follow-up studies to determine the efficiency of probiotic intervention in H. pylori eradication, and the delicate interaction of the gut microbiota with the host wellness, this review aims to discuss the gut microbiota alteration by probiotic co-supplementation in H. pylori management to predict the comprehensive effectiveness of probiotic oral administration.Abbreviations: acyl-CoA- acyl-coenzyme A; AMP- antimicrobial peptide; AMPK- AMP-activated protein kinase; AP-1- activator protein 1; BA- bile acid; BAR- bile acid receptor; BCAA- branched-chain amino acid; C2- acetate; C3- propionate; C4- butyrate; C5- valeric acid; CagA- Cytotoxin-associated gene A; cAMP- cyclic adenosine monophosphate; CD- Crohn's disease; CDI- C. difficile infection; COX-2- cyclooxygenase-2; DC- dendritic cell; EMT- epithelial-mesenchymal transition; FMO- flavin monooxygenases; FXR- farnesoid X receptor; GPBAR1- G-protein-coupled bile acid receptor 1; GPR4- G protein-coupled receptor 4; H2O2- hydrogen peroxide; HCC- hepatocellular carcinoma; HSC- hepatic stellate cell; IBD- inflammatory bowel disease; IBS- irritable bowel syndrome; IFN-γ- interferon-gamma; IgA immunoglobulin A; IL- interleukin; iNOS- induced nitric oxide synthase; JAK1- janus kinase 1; JAM-A- junctional adhesion molecule A; LAB- lactic acid bacteria; LPS- lipopolysaccharide; MALT- mucosa-associated lymphoid tissue; MAMP- microbe-associated molecular pattern; MCP-1- monocyte chemoattractant protein-1; MDR- multiple drug resistance; mTOR- mammalian target of rapamycin; MUC- mucin; NAFLD- nonalcoholic fatty liver disease; NF-κB- nuclear factor kappa B; NK- natural killer; NLRP3- NLR family pyrin domain containing 3; NOC- N-nitroso compounds; NOD- nucleotide-binding oligomerization domain; PICRUSt- phylogenetic investigation of communities by reconstruction of unobserved states; PRR- pattern recognition receptor; RA- retinoic acid; RNS- reactive nitrogen species; ROS- reactive oxygen species; rRNA- ribosomal RNA; SCFA- short-chain fatty acids; SDR- single drug resistance; SIgA- secretory immunoglobulin A; STAT3- signal transducer and activator of transcription 3; T1D- type 1 diabetes; T2D- type 2 diabetes; Th17- T helper 17; TLR- toll-like receptor; TMAO- trimethylamine N-oxide; TML- trimethyllysine; TNF-α- tumor necrosis factor-alpha; Tr1- type 1 regulatory T cell; Treg- regulatory T cell; UC- ulcerative colitis; VacA- Vacuolating toxin A.
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Affiliation(s)
- Ali Nabavi-Rad
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amir Sadeghi
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Abbas Yadegar
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran,CONTACT Abbas Yadegar ; Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Shahid Arabi Ave., Yemen St., Velenjak, Tehran, Iran
| | - Sinéad Marian Smith
- Department of Clinical Medicine, School of Medicine, Trinity College Dublin, Dublin, Ireland,Sinéad Marian Smith Department of Clinical Medicine, School of Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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23
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Li J, Li Y, Duan W, Zhao Z, Yang L, Wei W, Li J, Li Y, Yu Y, Dai B, Guo R. Shugan granule contributes to the improvement of depression-like behaviors in chronic restraint stress-stimulated rats by altering gut microbiota. CNS Neurosci Ther 2022; 28:1409-1424. [PMID: 35713215 PMCID: PMC9344086 DOI: 10.1111/cns.13881] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 05/16/2022] [Accepted: 05/24/2022] [Indexed: 12/14/2022] Open
Abstract
Aim The investigation aims to evaluate the potential effect of Shugan Granule (SGKL) on the gut, brain, and behaviors in rats exposed to chronic restraint stress (CRS). Methods The fecal microbiota and metabolite changes were studied in rats exposed to CRS and treated with SGKL (0.1 mg/kg/day). Depressive behaviors of these rats were determined through an open‐field experiment, forced swimming test, sucrose preference, and weighing. Moreover, LPS‐stimulated microglia and CRS‐stimulated rats were treated with SGKL to investigate the regulation between SGKL and the PI3K/Akt/pathway, which is inhibited by LY294002, a PI3K inhibitor. Results (i) SGKL improved the altered behaviors in CRS‐stimulated rats; (ii) SGKL ameliorated the CRS‐induced neuronal degeneration and tangled nerve fiber and also contributed to the recovery of intestinal barrier injury in these rats; (iii) SGKL inhibited the hippocampus elevations of TNF‐α, IL‐1β, and IL‐6 in response to CRS modeling; (iv) based on the principal coordinates analysis (PCoA), SGKL altered α‐diversity indices and shifted β‐diversity in CRS‐stimulated rats; (v) at the genus level, SGKL decreased the CRS‐enhanced abundance of Bacteroides; (vi) Butyricimonas and Candidatus Arthromitus were enriched in SGKL‐treated rats; (vii) altered gut microbiota and metabolites were correlated with behaviors, inflammation, and PI3K/Akt/mTOR pathway; (viii) SGKL increased the LPS‐decreased phosphorylation of the PI3K/Akt/mTOR pathway in microglia and inhibited the LPS‐induced microglial activation; (ix) PI3K/Akt/mTOR pathway inactivation reversed the SGKL effects in CRS rats. Conclusion SGKL targets the PI3K/Akt/mTOR pathway by altering gut microbiota and metabolites, which ameliorates altered behavior and inflammation in the hippocampus.
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Affiliation(s)
- Junnan Li
- Second Clinical Medical College, Beijing University of Chinese Medicine, Beijing, China
| | - Yannan Li
- Second Clinical Medical College, Beijing University of Chinese Medicine, Beijing, China
| | - Wenzhe Duan
- Second Clinical Medical College, Beijing University of Chinese Medicine, Beijing, China
| | - Zhonghui Zhao
- Second Clinical Medical College, Beijing University of Chinese Medicine, Beijing, China
| | - Lixuan Yang
- Second Clinical Medical College, Beijing University of Chinese Medicine, Beijing, China
| | - Wei Wei
- Second Clinical Medical College, Beijing University of Chinese Medicine, Beijing, China
| | - Jingchun Li
- Second Clinical Medical College, Beijing University of Chinese Medicine, Beijing, China
| | - Yang Li
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Yao Yu
- Beijing Changping Hospital of Integrated Chinese and Western Medicine, Beijing, China
| | - Baoan Dai
- Second Clinical Medical College, Beijing University of Chinese Medicine, Beijing, China
| | - Rongjuan Guo
- Department of Neurology, Dongfang Hospital Beijing University of Chinese Medicine, Beijing, China
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24
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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25
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Byerley LO, Gallivan KM, Christopher CJ, Taylor CM, Luo M, Dowd SE, Davis GM, Castro HF, Campagna SR, Ondrak KS. Gut Microbiome and Metabolome Variations in Self-Identified Muscle Builders Who Report Using Protein Supplements. Nutrients 2022; 14:nu14030533. [PMID: 35276896 PMCID: PMC8839395 DOI: 10.3390/nu14030533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 01/21/2022] [Accepted: 01/23/2022] [Indexed: 12/03/2022] Open
Abstract
Muscle builders frequently consume protein supplements, but little is known about their effect on the gut microbiota. This study compared the gut microbiome and metabolome of self-identified muscle builders who did or did not report consuming a protein supplement. Twenty-two participants (14 males and 8 females) consumed a protein supplement (PS), and seventeen participants (12 males and 5 females) did not (No PS). Participants provided a fecal sample and completed a 24-h food recall (ASA24). The PS group consumed significantly more protein (118 ± 12 g No PS vs. 169 ± 18 g PS, p = 0.02). Fecal metabolome and microbiome were analyzed by using untargeted metabolomics and 16S rRNA gene sequencing, respectively. Metabolomic analysis identified distinct metabolic profiles driven by allantoin (VIP score = 2.85, PS 2.3-fold higher), a catabolic product of uric acid. High-protein diets contain large quantities of purines, which gut microbes degrade to uric acid and then allantoin. The bacteria order Lactobacillales was higher in the PS group (22.6 ± 49 No PS vs. 136.5 ± 38.1, PS (p = 0.007)), and this bacteria family facilitates purine absorption and uric acid decomposition. Bacterial genes associated with nucleotide metabolism pathways (p < 0.001) were more highly expressed in the No PS group. Both fecal metagenomic and metabolomic analyses revealed that the PS group’s higher protein intake impacted nitrogen metabolism, specifically altering nucleotide degradation.
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Affiliation(s)
- Lauri O. Byerley
- Sports and Health Sciences, School of Health Sciences, American Public University System, Charles Town, WV 25414, USA; (K.M.G.); (K.S.O.)
- Department of Physiology, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
- Correspondence: or
| | - Karyn M. Gallivan
- Sports and Health Sciences, School of Health Sciences, American Public University System, Charles Town, WV 25414, USA; (K.M.G.); (K.S.O.)
| | - Courtney J. Christopher
- Department of Chemistry, University of Tennessee at Knoxville, Knoxville, TN 37996, USA; (C.J.C.); (H.F.C.); (S.R.C.)
| | - Christopher M. Taylor
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA; (C.M.T.); (M.L.)
| | - Meng Luo
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA; (C.M.T.); (M.L.)
| | - Scot E. Dowd
- Molecular Research LP, 503 Clovis Rd, Shallowater, TX 79363, USA;
| | - Gregory M. Davis
- Kinesiology and Health Studies, Southeastern Louisiana University, Hammond, LA 70401, USA;
| | - Hector F. Castro
- Department of Chemistry, University of Tennessee at Knoxville, Knoxville, TN 37996, USA; (C.J.C.); (H.F.C.); (S.R.C.)
- Biological and Small Molecule Mass Spectrometry Core, University of Tennessee at Knoxville, Knoxville, TN 37996, USA
| | - Shawn R. Campagna
- Department of Chemistry, University of Tennessee at Knoxville, Knoxville, TN 37996, USA; (C.J.C.); (H.F.C.); (S.R.C.)
- Biological and Small Molecule Mass Spectrometry Core, University of Tennessee at Knoxville, Knoxville, TN 37996, USA
| | - Kristin S. Ondrak
- Sports and Health Sciences, School of Health Sciences, American Public University System, Charles Town, WV 25414, USA; (K.M.G.); (K.S.O.)
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26
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Zhen W, Liu Y, Shao Y, Ma Y, Wu Y, Guo F, Abbas W, Guo Y, Wang Z. Yeast β-Glucan Altered Intestinal Microbiome and Metabolome in Older Hens. Front Microbiol 2022; 12:766878. [PMID: 34975793 PMCID: PMC8718749 DOI: 10.3389/fmicb.2021.766878] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 11/11/2021] [Indexed: 12/31/2022] Open
Abstract
The prebiotics- and probiotics-mediated positive modulation of the gut microbiota composition is considered a useful approach to improve gut health and food safety in chickens. This study explored the effects of yeast β-glucan (YG) supplementation on intestinal microbiome and metabolites profiles as well as mucosal immunity in older hens. A total of 256 43-week-old hens were randomly assigned to two treatments, with 0 and 200 mg/kg of YG. Results revealed YG-induced downregulation of toll-like receptors (TLRs) and cytokine gene expression in the ileum without any effect on the intestinal barrier. 16S rRNA analysis claimed that YG altered α- and β-diversity and enriched the relative abundance of class Bacilli, orders Lactobacillales and Enterobacteriales, families Lactobacillaceae and Enterobacteriaceae, genera Lactobacillus and Escherichia–Shigella, and species uncultured bacterium-Lactobacillus. Significant downregulation of cutin and suberin, wax biosynthesis, atrazine degradation, vitamin B6 metabolism, phosphotransferase system (PTS), steroid degradation, biosynthesis of unsaturated fatty acids, aminobenzoate degradation and quorum sensing and upregulation of ascorbate and aldarate metabolism, C5-branched dibasic acid metabolism, glyoxylate and dicarboxylate metabolism, pentose and glucuronate interconversions, steroid biosynthesis, carotenoid biosynthesis, porphyrin and chlorophyll metabolism, sesquiterpenoid and triterpenoid biosynthesis, lysine degradation, and ubiquinone and other terpenoid-quinone biosyntheses were observed in YG-treated hens, as substantiated by the findings of untargeted metabolomics analysis. Overall, YG manifests prebiotic properties by altering gut microbiome and metabolite profiles and can downregulate the intestinal mucosal immune response of breeder hens.
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Affiliation(s)
- Wenrui Zhen
- Henan International Joint Laboratory of Animal Welfare and Health Breeding, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China.,State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yuchen Liu
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yujing Shao
- College of Biology, China Agricultural University, Beijing, China
| | - Yanbo Ma
- Henan International Joint Laboratory of Animal Welfare and Health Breeding, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Yuanyuan Wu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Fangshen Guo
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Waseem Abbas
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yuming Guo
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhong Wang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
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27
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Mujagic Z, Kasapi M, Jonkers DMAE, Garcia-Perez I, Vork L, Weerts ZZR, Serrano-Contreras JI, Zhernakova A, Kurilshikov A, Scotcher J, Holmes E, Wijmenga C, Keszthelyi D, Nicholson JK, Posma JM, Masclee AAM. Integrated fecal microbiome-metabolome signatures reflect stress and serotonin metabolism in irritable bowel syndrome. Gut Microbes 2022; 14:2063016. [PMID: 35446234 PMCID: PMC9037519 DOI: 10.1080/19490976.2022.2063016] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
To gain insight into the complex microbiome-gut-brain axis in irritable bowel syndrome (IBS), several modalities of biological and clinical data must be combined. We aimed to identify profiles of fecal microbiota and metabolites associated with IBS and to delineate specific phenotypes of IBS that represent potential pathophysiological mechanisms. Fecal metabolites were measured using proton nuclear magnetic resonance (1H-NMR) spectroscopy and gut microbiome using shotgun metagenomic sequencing (MGS) in a combined dataset of 142 IBS patients and 120 healthy controls (HCs) with extensive clinical, biological and phenotype information. Data were analyzed using support vector classification and regression and kernel t-SNE. Microbiome and metabolome profiles could distinguish IBS and HC with an area-under-the-receiver-operator-curve of 77.3% and 79.5%, respectively, but this could be improved by combining microbiota and metabolites to 83.6%. No significant differences in predictive ability of the microbiome-metabolome data were observed between the three classical, stool pattern-based, IBS subtypes. However, unsupervised clustering showed distinct subsets of IBS patients based on fecal microbiome-metabolome data. These clusters could be related plasma levels of serotonin and its metabolite 5-hydroxyindoleacetate, effects of psychological stress on gastrointestinal (GI) symptoms, onset of IBS after stressful events, medical history of previous abdominal surgery, dietary caloric intake and IBS symptom duration. Furthermore, pathways in metabolic reaction networks were integrated with microbiota data, that reflect the host-microbiome interactions in IBS. The identified microbiome-metabolome signatures for IBS, associated with altered serotonin metabolism and unfavorable stress response related to GI symptoms, support the microbiota-gut-brain link in the pathogenesis of IBS.
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Affiliation(s)
- Zlatan Mujagic
- Division Gastroenterology-Hepatology, Maastricht University Medical Center+, Maastricht, The Netherlands,Nutrim School for Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands,Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, South Kensington Campus, Imperial College London, London, UK,CONTACT Zlatan Mujagic Division Gastroenterology-Hepatology, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Melpomeni Kasapi
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, South Kensington Campus, Imperial College London, London, UK
| | - Daisy MAE Jonkers
- Division Gastroenterology-Hepatology, Maastricht University Medical Center+, Maastricht, The Netherlands,Nutrim School for Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands
| | - Isabel Garcia-Perez
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Hammersmith Campus, Imperial College London, London, UK
| | - Lisa Vork
- Division Gastroenterology-Hepatology, Maastricht University Medical Center+, Maastricht, The Netherlands,Nutrim School for Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands
| | - Zsa Zsa R.M. Weerts
- Division Gastroenterology-Hepatology, Maastricht University Medical Center+, Maastricht, The Netherlands,Nutrim School for Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands
| | - Jose Ivan Serrano-Contreras
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, South Kensington Campus, Imperial College London, London, UK
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jamie Scotcher
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, South Kensington Campus, Imperial College London, London, UK
| | - Elaine Holmes
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Hammersmith Campus, Imperial College London, London, UK,The Australian National Phenome Center, Harry Perkins Institute, Murdoch University, Perth, Australia
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Daniel Keszthelyi
- Division Gastroenterology-Hepatology, Maastricht University Medical Center+, Maastricht, The Netherlands,Nutrim School for Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands
| | - Jeremy K Nicholson
- The Australian National Phenome Center, Harry Perkins Institute, Murdoch University, Perth, Australia
| | - Joram M Posma
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, South Kensington Campus, Imperial College London, London, UK
| | - Ad AM Masclee
- Division Gastroenterology-Hepatology, Maastricht University Medical Center+, Maastricht, The Netherlands,Nutrim School for Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands
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28
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Gojda J, Cahova M. Gut Microbiota as the Link between Elevated BCAA Serum Levels and Insulin Resistance. Biomolecules 2021; 11:1414. [PMID: 34680047 DOI: 10.3390/biom11101414] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 09/21/2021] [Accepted: 09/23/2021] [Indexed: 12/17/2022] Open
Abstract
The microbiota-harboring human gut is an exquisitely active ecosystem that has evolved in a constant symbiosis with the human host. It produces numerous compounds depending on its metabolic capacity and substrates availability. Diet is the major source of the substrates that are metabolized to end-products, further serving as signal molecules in the microbiota-host cross-talk. Among these signal molecules, branched-chain amino acids (BCAAs) has gained significant scientific attention. BCAAs are abundant in animal-based dietary sources; they are both produced and degraded by gut microbiota and the host circulating levels are associated with the risk of type 2 diabetes. This review aims to summarize the current knowledge on the complex relationship between gut microbiota and its functional capacity to handle BCAAs as well as the host BCAA metabolism in insulin resistance development. Targeting gut microbiota BCAA metabolism with a dietary modulation could represent a promising approach in the prevention and treatment of insulin resistance related states, such as obesity and diabetes.
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29
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Nishimoto Y, Nomaguchi T, Mori Y, Ito M, Nakamura Y, Fujishima M, Murakami S, Yamada T, Fukuda S. The Nutritional Efficacy of Chlorella Supplementation Depends on the Individual Gut Environment: A Randomised Control Study. Front Nutr 2021; 8:648073. [PMID: 34136514 PMCID: PMC8200412 DOI: 10.3389/fnut.2021.648073] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 05/06/2021] [Indexed: 01/04/2023] Open
Abstract
Recent studies have accumulated evidence that the intestinal environment is strongly correlated with host diet, which influences host health. A number of dietary products whose mechanisms of influence operate via the gut microbiota have been revealed, but they are still limited. Here, we investigated the dietary influence of Chlorella, a green alga commercially available as a dietary supplement. A randomised, double-blind, placebo-controlled crossover trial including 40 Japanese participants with constipation was performed. In this study, the primary outcome and secondary outcome were set as defecation frequency and blood folate level, respectively. In both outcomes, no significant differences were detected compared to the control intake. Therefore, we analysed the gut microbiome, gut metabolome, and blood parameters in an integrated manner as an exploratory analysis. We revealed that the consumption of Chlorella increased the level of several dicarboxylic acids in faeces. Furthermore, the analysis showed that individuals with low concentrations of faecal propionate showed an increase in propionate concentration upon Chlorella intake. In addition, increasing blood folate levels were negatively correlated with defecation frequency at baseline. Our study suggested that the effect of Chlorella consumption varies among individuals depending on their intestinal environment, which illustrates the importance of stratified dietary management based on the intestinal environment in individuals.
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Affiliation(s)
| | | | - Yuka Mori
- Metabologenomics, Inc., Tsuruoka, Japan
| | | | | | | | - Shinnosuke Murakami
- Metabologenomics, Inc., Tsuruoka, Japan
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Takuji Yamada
- Metabologenomics, Inc., Tsuruoka, Japan
- Department of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Shinji Fukuda
- Metabologenomics, Inc., Tsuruoka, Japan
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Intestinal Microbiota Project, Kanagawa Institute of Industrial Science and Technology, Kawasaki, Japan
- Transborder Medical Research Center, University of Tsukuba, Tsukuba, Japan
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30
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Ta LDH, Chan JCY, Yap GC, Purbojati RW, Drautz-Moses DI, Koh YM, Tay CJX, Huang CH, Kioh DYQ, Woon JY, Tham EH, Loo EXL, Shek LP, Karnani N, Goh A, Van Bever HP, Teoh OH, Chan YH, Lay C, Knol J, Yap F, Tan KH, Chong YS, Godfrey KM, Kjelleberg S, Schuster SC, Chan ECY, Lee BW. A compromised developmental trajectory of the infant gut microbiome and metabolome in atopic eczema. Gut Microbes 2020; 12:1-22. [PMID: 33023370 PMCID: PMC7553750 DOI: 10.1080/19490976.2020.1801964] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Evidence is accumulating that the establishment of the gut microbiome in early life influences the development of atopic eczema. In this longitudinal study, we used integrated multi-omics analyses to infer functional mechanisms by which the microbiome modulates atopic eczema risk. We measured the functionality of the gut microbiome and metabolome of 63 infants between ages 3 weeks and 12 months with well-defined eczema cases and controls in a sub-cohort from the Growing Up in Singapore Toward healthy Outcomes (GUSTO) mother-offspring cohort. At 3 weeks, the microbiome and metabolome of allergen-sensitized atopic eczema infants were characterized by an enrichment of Escherichia coli and Klebsiella pneumoniae, associated with increased stool D-glucose concentration and increased gene expression of associated virulence factors. A delayed colonization by beneficial Bacteroides fragilis and subsequent delayed accumulation of butyrate and propionate producers after 3 months was also observed. Here, we describe an aberrant developmental trajectory of the gut microbiome and stool metabolome in allergen sensitized atopic eczema infants. The infographic describes an impaired developmental trajectory of the gut microbiome and metabolome in allergen-sensitized atopic eczema (AE) infants and infer its contribution in modulating allergy risk in the Singaporean mother-offspring GUSTO cohort. The key microbial signature of AE is characterized by (1) an enrichment of Escherichia coli and Klebsiella pneumoniae which are associated with accumulation of pre-glycolysis intermediates (D-glucose) via the trehalose metabolic pathway, increased gene expression of associated virulence factors (invasin, adhesin, flagellin and lipopolysaccharides) by utilizing ATP from oxidative phosphorylation and delayed production of butyrate and propionate, (2) depletion of Bacteroides fragilis which resulted in lower expression of immunostimulatory bacterial cell envelope structure and folate (vitamin B9) biosynthesis pathway, and (3) accompanied depletion of bacterial groups with the ability to derive butyrate and propionate through direct or indirect pathways which collectively resulted in reduced glycolysis, butyrate and propionate biosynthesis.
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Affiliation(s)
- Le Duc Huy Ta
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - James Chun Yip Chan
- Skin Research Institute of Singapore, A*STAR, Singapore,Innovations in Food & Chemical Safety Programme, A*STAR
| | - Gaik Chin Yap
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Rikky W. Purbojati
- Singapore Centre For Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore
| | - Daniela I. Drautz-Moses
- Singapore Centre For Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore
| | - Yanqing Michelle Koh
- Singapore Centre For Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore
| | - Carina Jing Xuan Tay
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Chiung-Hui Huang
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Dorinda Yan Qin Kioh
- Department of Pharmacy, Faculty of Science, National University of Singapore, Singapore
| | - Jia Yun Woon
- Department of Pharmacy, Faculty of Science, National University of Singapore, Singapore
| | - Elizabeth Huiwen Tham
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore,Khoo Teck Puat-National University Children’s Medical Institute, National University Health System, Singapore
| | - Evelyn Xiu Ling Loo
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Lynette P.C. Shek
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore,Khoo Teck Puat-National University Children’s Medical Institute, National University Health System, Singapore
| | - Neerja Karnani
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Anne Goh
- Department of Paediatrics, KK Women’s and Children’s Hospital, Singapore
| | - Hugo P.S. Van Bever
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore,Khoo Teck Puat-National University Children’s Medical Institute, National University Health System, Singapore
| | - Oon Hoe Teoh
- Department of Paediatrics, KK Women’s and Children’s Hospital, Singapore
| | - Yiong Huak Chan
- Biostatistics Unit, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Christophe Lay
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore,Danone Nutricia Research, Singapore
| | - Jan Knol
- Danone Nutricia Research, Utrecht, The Netherlands,Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Fabian Yap
- Department of Paediatrics, KK Women’s and Children’s Hospital, Singapore
| | - Kok Hian Tan
- Department of Paediatrics, KK Women’s and Children’s Hospital, Singapore
| | - Yap-Seng Chong
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore,Department of Obstetrics & Gynaecology, National University of Singapore, Singapore
| | - Keith M. Godfrey
- MRC Lifecourse Epidemiology Unit and NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Staffan Kjelleberg
- Singapore Centre For Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore
| | - Stephan C. Schuster
- Singapore Centre For Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore
| | - Eric Chun Yong Chan
- Innovations in Food & Chemical Safety Programme, A*STAR,Department of Pharmacy, Faculty of Science, National University of Singapore, Singapore,Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore,Eric Chun Yong Chan Department of Paediatrics, National University of Singapore (NUS) Tahir Foundation Building (MD1), Level 15, 12 Science Drive 2, Singapore, Singapore 117549
| | - Bee Wah Lee
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore,CONTACT Bee Wah Lee
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31
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Vernocchi P, Marini F, Capuani G, Tomassini A, Conta G, Del Chierico F, Malattia C, De Benedetti F, Martini A, Dallapiccola B, van Dijkhuizen EHP, Miccheli A, Putignani L. Fused Omics Data Models Reveal Gut Microbiome Signatures Specific of Inactive Stage of Juvenile Idiopathic Arthritis in Pediatric Patients. Microorganisms 2020; 8:E1540. [PMID: 33036309 DOI: 10.3390/microorganisms8101540] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/01/2020] [Accepted: 10/02/2020] [Indexed: 01/15/2023] Open
Abstract
Juvenile idiopathic arthritis (JIA) is the most common rheumatic disease in children. Herein, we evaluated the relationship between the gut microbiome (GM) and disease phenotype by an integrated omics fused approach. In a multicenter, observational cohort study, stools from Italian JIA patients were collected at baseline, active, and inactive disease stages, and their GM compared to healthy controls (CTRLs). The microbiota metabolome was analyzed to detect volatile- and non-volatile organic compounds (VOCs); the data were fused with operational taxonomic units (OTUs) from 16S RNA targeted-metagenomics and classified by chemometric models. Non-VOCs did not characterize JIA patients nor JIA activity stages compared to CTRLs. The core of VOCs, (Ethanol, Methyl-isobutyl-ketone, 2,6-Dimethyl-4-heptanone and Phenol) characterized patients at baseline and inactive disease stages, while the OTUs represented by Ruminococcaceae, Lachnospiraceae and Clostridiacea discriminated between JIA inactive stage and CTRLs. No differences were highlighted amongst JIA activity stages. Finally, the fused data discriminated inactive and baseline stages versus CTRLs, based on the contribution of the invariant core of VOCs while Ruminococcaceae concurred for the inactive stage versus CTRLs comparison. In conclusion, the GM signatures enabled to distinguish the inactive disease stage from CTRLs.
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Pilla R, Suchodolski JS. The Role of the Canine Gut Microbiome and Metabolome in Health and Gastrointestinal Disease. Front Vet Sci 2020; 6:498. [PMID: 31993446 PMCID: PMC6971114 DOI: 10.3389/fvets.2019.00498] [Citation(s) in RCA: 174] [Impact Index Per Article: 43.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 12/17/2019] [Indexed: 12/22/2022] Open
Abstract
The gut microbiome contributes to host metabolism, protects against pathogens, educates the immune system, and, through these basic functions, affects directly or indirectly most physiologic functions of its host. Molecular techniques have allowed us to expand our knowledge by unveiling a wide range of unculturable bacteria that were previously unknown. Most bacterial sequences identified in the canine gastrointestinal (GI) tract fall into five phyla: Firmicutes, Fusobacteria, Bacteroidetes, Proteobacteria, and Actinobacteria. While there are variations in the microbiome composition along the GI tract, most clinical studies concentrate on fecal microbiota. Age, diet, and many other environmental factors may play a significant role in the maintenance of a healthy microbiome, however, the alterations they cause pale in comparison with the alterations found in diseased animals. GI dysfunctions are the most obvious association with gut dysbiosis. In dogs, intestinal inflammation, whether chronic or acute, is associated with significant differences in the composition of the intestinal microbiota. Gut dysbiosis happens when such alterations result in functional changes in the microbial transcriptome, proteome, or metabolome. Commonly affected metabolites include short-chain fatty acids, and amino acids, including tryptophan and its catabolites. A recently developed PCR-based algorithm termed “Dysbiosis Index” is a tool that allows veterinarians to quantify gut dysbiosis and can be used to monitor disease progression and response to treatment. Alterations or imbalances in the microbiota affect immune function, and strategies to manipulate the gut microbiome may be useful for GI related diseases. Antibiotic usage induces a rapid and significant drop in taxonomic richness, diversity, and evenness. For that reason, a renewed interest has been put on probiotics, prebiotics, and fecal microbiota transplantation (FMT). Although probiotics are typically unable to colonize the gut, the metabolites they produce during their transit through the GI tract can ameliorate clinical signs and modify microbiome composition. Another interesting development is FMT, which may be a promising tool to aid recovery from dysbiosis, but further studies are needed to evaluate its potential and limitations.
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Affiliation(s)
- Rachel Pilla
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, Texas A&M University, College Station, TX, United States
| | - Jan S Suchodolski
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, Texas A&M University, College Station, TX, United States
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Hsu BB, Gibson TE, Yeliseyev V, Liu Q, Lyon L, Bry L, Silver PA, Gerber GK. Dynamic Modulation of the Gut Microbiota and Metabolome by Bacteriophages in a Mouse Model. Cell Host Microbe 2019; 25:803-814.e5. [PMID: 31175044 DOI: 10.1101/454579] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 03/09/2019] [Accepted: 04/30/2019] [Indexed: 05/18/2023]
Abstract
The human gut microbiome is comprised of densely colonizing microorganisms including bacteriophages, which are in dynamic interaction with each other and the mammalian host. To address how bacteriophages impact bacterial communities in the gut, we investigated the dynamic effects of phages on a model microbiome. Gnotobiotic mice were colonized with defined human gut commensal bacteria and subjected to predation by cognate lytic phages. We found that phage predation not only directly impacts susceptible bacteria but also leads to cascading effects on other bacterial species via interbacterial interactions. Metabolomic profiling revealed that shifts in the microbiome caused by phage predation have a direct consequence on the gut metabolome. Our work provides insight into the ecological importance of phages as modulators of bacterial colonization, and it additionally suggests the potential impact of gut phages on the mammalian host with implications for their therapeutic use to precisely modulate the microbiome.
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Affiliation(s)
- Bryan B Hsu
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Travis E Gibson
- Massachusetts Host-Microbiome Center, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Vladimir Yeliseyev
- Massachusetts Host-Microbiome Center, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Qing Liu
- Massachusetts Host-Microbiome Center, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Lorena Lyon
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Lynn Bry
- Massachusetts Host-Microbiome Center, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Pamela A Silver
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA.
| | - Georg K Gerber
- Massachusetts Host-Microbiome Center, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
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Hsu BB, Gibson TE, Yeliseyev V, Liu Q, Lyon L, Bry L, Silver PA, Gerber GK. Dynamic Modulation of the Gut Microbiota and Metabolome by Bacteriophages in a Mouse Model. Cell Host Microbe 2019; 25:803-814.e5. [PMID: 31175044 PMCID: PMC6579560 DOI: 10.1016/j.chom.2019.05.001] [Citation(s) in RCA: 272] [Impact Index Per Article: 54.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 03/09/2019] [Accepted: 04/30/2019] [Indexed: 02/07/2023]
Abstract
The human gut microbiome is comprised of densely colonizing microorganisms including bacteriophages, which are in dynamic interaction with each other and the mammalian host. To address how bacteriophages impact bacterial communities in the gut, we investigated the dynamic effects of phages on a model microbiome. Gnotobiotic mice were colonized with defined human gut commensal bacteria and subjected to predation by cognate lytic phages. We found that phage predation not only directly impacts susceptible bacteria but also leads to cascading effects on other bacterial species via interbacterial interactions. Metabolomic profiling revealed that shifts in the microbiome caused by phage predation have a direct consequence on the gut metabolome. Our work provides insight into the ecological importance of phages as modulators of bacterial colonization, and it additionally suggests the potential impact of gut phages on the mammalian host with implications for their therapeutic use to precisely modulate the microbiome.
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Affiliation(s)
- Bryan B Hsu
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Travis E Gibson
- Massachusetts Host-Microbiome Center, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Vladimir Yeliseyev
- Massachusetts Host-Microbiome Center, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Qing Liu
- Massachusetts Host-Microbiome Center, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Lorena Lyon
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Lynn Bry
- Massachusetts Host-Microbiome Center, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Pamela A Silver
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA.
| | - Georg K Gerber
- Massachusetts Host-Microbiome Center, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
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Abstract
Antibiotics disturb the gastrointestinal tract microbiota and in turn reduce colonization resistance against Clostridium difficile. The mechanism for this loss of colonization resistance is still unknown but likely reflects structural (microbial) and functional (metabolic) changes to the gastrointestinal tract. Members of the gut microbial community shape intestinal metabolism that provides nutrients and ultimately supports host immunity. This review will discuss how antibiotics alter the structure of the gut microbiota and how this impacts bacterial metabolism in the gut. It will also explore the chemical requirements for C. difficile germination, growth, toxin production and sporulation. Many of the metabolites that influence C. difficile physiology are products of gut microbial metabolism including bile acids, carbohydrates and amino acids. To restore colonization resistance against C. difficile after antibiotics a targeted approach restoring both the structure and function of the gastrointestinal tract is needed.
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