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Amin A, Mekadim C, Modrackova N, Bolechova P, Mrazek J, Neuzil-Bunesova V. Microbiome composition and presence of cultivable commensal groups of Southern Tamanduas (Tamandua tetradactyla) varies with captive conditions. Anim Microbiome 2024; 6:21. [PMID: 38698458 PMCID: PMC11064412 DOI: 10.1186/s42523-024-00311-w] [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: 09/08/2023] [Accepted: 04/18/2024] [Indexed: 05/05/2024] Open
Abstract
Southern Tamanduas (Tamandua tetradactyla) belong to the specialized placental myrmecophages. There is not much information about their intestinal microbiome. Moreover, due to their food specialization, it is difficult to create an adequate diet under breeding conditions. Therefore, we used 16S rDNA amplicon sequencing to analyze the fecal microbiome of captive Southern Tamanduas from four locations in the Czech Republic and evaluated the impact of the incoming diet and facility conditions on microbiome composition. Together with the microbiome analysis, we also quantified and identified cultivable commensals. The anteater fecal microbiome was dominated by the phyla Bacillota and Bacteroidota, while Pseudomonadota, Spirochaetota, and Actinobacteriota were less abundant. At the taxonomic family level, Lachnospiraceae, Prevotellaceae, Bacteroidaceae, Oscillospiraceae, Erysipelotrichaceae, Spirochaetaceae, Ruminococcaceae, Leuconostocaceae, and Streptococcaceae were mainly represented in the fecal microbiome of animals from all locations. Interestingly, Lactobacillaceae dominated in the location with a zoo-made diet. These animals also had significantly lower diversity of gut microbiome in comparison with animals from other locations fed mainly with a complete commercial diet. Moreover, captive conditions of analyzed anteater included other factors such as the enrichment of the diet with insect-based products, probiotic interventions, the presence of other animals in the exposure, which can potentially affect the composition of the microbiome and cultivable microbes. In total, 63 bacterial species from beneficial commensal to opportunistic pathogen were isolated and identified using MALDI-TOF MS in the set of more than one thousand selected isolates. Half of the detected species were present in the fecal microbiota of most animals, the rest varied across animals and locations.
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Affiliation(s)
- Ahmad Amin
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00, Prague 6, Czech Republic
| | - Chahrazed Mekadim
- Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, v. v. i., Videnska 1083, 142 20, Prague, Czech Republic
| | - Nikol Modrackova
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00, Prague 6, Czech Republic
| | - Petra Bolechova
- Department of Ethology and Companion Animal Science, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamycka 129, 165 00, Prague 6, Czech Republic
| | - Jakub Mrazek
- Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, v. v. i., Videnska 1083, 142 20, Prague, Czech Republic
| | - Vera Neuzil-Bunesova
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00, Prague 6, Czech Republic.
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Luo D, Yan L, Wang Z, Ji X, Pei N, Jia J, Luo Y, Ouyang H, Yang S, Feng Y. Pulchinenoside B4 ameliorates oral ulcers in rats by modulating gut microbiota and metabolites. Appl Microbiol Biotechnol 2024; 108:292. [PMID: 38592514 PMCID: PMC11003895 DOI: 10.1007/s00253-024-13099-1] [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: 12/28/2023] [Revised: 02/23/2024] [Accepted: 02/28/2024] [Indexed: 04/10/2024]
Abstract
Pulchinenoside B4, a natural saponin monomer from the Pulsatilla plant, plays an important role as an immunomodulator in the treatment of acute inflammation. Oral ulcer (OU) is a common ulcerative injury disease that occurs in the oral mucosa, including mucosal ulceration and abnormalities of lips and tongue. A close correlation exists between gut microbiota and circulating metabolites in patients with OU. However, the correlation between gut microbiota and serum metabolomics is not clear. Therefore, this study aimed to explore the changes in gut microbiota and metabolites in OU. The 16S ribosomal RNA (16S rRNA) gene sequencing was used to detect the changes in the composition of gut microbiota in OU rat model. Moreover, the endogenous small metabolites were explored by collecting the non-targeted serum metabolomics data. A total of 34 OU-related biomarkers were identified, mainly related to fatty acid metabolism and inflammatory pathways. The administration of B4 effectively reduced the occurrence of OU and restored the levels of multiple endogenous biomarkers and key gut microbial species to the normal level. This study demonstrated that the gut microbiota and metabolites were altered in the OU rat model, which were significantly restored to the normal level by B4, thereby showing good application prospects in the treatment of OU. KEY POINTS: • The first investigating the correlation between OU and gut microbiota. • A close correlation between metabolites and gut microbiota in OU disease was successfully identified. • Pulchinenoside B4 ameliorates oral ulcers in rats by modulating gut microbiota and metabolites.
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Affiliation(s)
- Dewei Luo
- Jiangxi University of Traditional Chinese Medicine, No. 818 Yunwan Road, Nanchang, 330002, People's Republic of China
| | - Li Yan
- Jiangxi University of Traditional Chinese Medicine, No. 818 Yunwan Road, Nanchang, 330002, People's Republic of China
| | - Zhujun Wang
- Jiangxi University of Traditional Chinese Medicine, No. 818 Yunwan Road, Nanchang, 330002, People's Republic of China
| | - Xiaofan Ji
- Jiangxi University of Traditional Chinese Medicine, No. 818 Yunwan Road, Nanchang, 330002, People's Republic of China
| | - Na Pei
- Xinyu University, No. 2666 Yangguang Road, Xinyu, 338004, People's Republic of China
| | - Jing Jia
- Jiangxi University of Traditional Chinese Medicine, No. 818 Yunwan Road, Nanchang, 330002, People's Republic of China
| | - Yingying Luo
- Jiangxi University of Traditional Chinese Medicine, No. 818 Yunwan Road, Nanchang, 330002, People's Republic of China.
| | - Hui Ouyang
- Jiangxi University of Traditional Chinese Medicine, No. 818 Yunwan Road, Nanchang, 330002, People's Republic of China.
- Research Center of Natural Resources of Chinese Medicinal Materials and Ethnic Medicine, Jiangxi University of Traditional Chinese Medicine, No. 818 Yunwan Road, Nanchang, 338004, People's Republic of China.
| | - Shilin Yang
- Jiangxi University of Traditional Chinese Medicine, No. 818 Yunwan Road, Nanchang, 330002, People's Republic of China
| | - Yulin Feng
- Jiangxi University of Traditional Chinese Medicine, No. 818 Yunwan Road, Nanchang, 330002, People's Republic of China.
- National Pharmaceutical Engineering Center for Solid Preparation in Chinese Herbal Medicine, No. 56 Yangming Road, Nanchang, 330006, People's Republic of China.
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Li J, Toyama H, Matsumoto T, Qasimi MI, Inoue R, Murase H, Yamamoto Y, Nagaoka K. Changes in fecal microbiota during estrous cycle in healthy thoroughbred mares. J Equine Vet Sci 2024; 135:105034. [PMID: 38428754 DOI: 10.1016/j.jevs.2024.105034] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 02/09/2024] [Accepted: 02/26/2024] [Indexed: 03/03/2024]
Abstract
Gut microbiota plays a crucial role in various physiological processes, including the regulation of the reproductive system and steroid sex hormones. Throughout the normal estrous cycle of healthy mares, the levels of estradiol-17β (E2) and progesterone (P4) in the blood exhibit periodic changes. To investigate the relationship between cyclic changes in steroid sex hormones and the gut microbiome of mares, we analyzed the fecal microbiota composition in healthy mares during the typical estrous cycle. Blood and fecal samples from five healthy mares were collected, E2 and P4 levels in serum were analyzed using radioimmunoassay (RIA), and the gut microbiome was analyzed by 16S rRNA sequencing. The overall richness and composition of the gut microbiota remained relatively stable during the normal estrous cycle in mares. The Linear Discriminant Analysis Effect Size analysis of the microbial composition during the follicular and luteal phases identified the Rhodococcus genus as differentially abundant. These findings indicate that the mare's gut microbiota's significant composition remains consistent throughout the estrous cycle. At the same time, specific low-abundance pathogenic bacteria exhibit changes that align with sexual hormonal fluctuations.
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Affiliation(s)
- Junjie Li
- Laboratory of Veterinary Physiology, Department of Veterinary Medicine, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
| | - Haruka Toyama
- Laboratory of Veterinary Physiology, Department of Veterinary Medicine, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
| | - Touko Matsumoto
- Laboratory of Veterinary Physiology, Department of Veterinary Medicine, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
| | - Mohammad Ibrahim Qasimi
- Laboratory of Veterinary Physiology, Department of Veterinary Medicine, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
| | - Ryo Inoue
- Laboratory of Animal Science, Department of Applied Biological Science, Setsunan University, Osaka, Japan
| | - Harutaka Murase
- Hidaka Training and Research Center, Japan Racing Association, Hokkaido 057-0171, Japan
| | - Yuki Yamamoto
- Laboratory of Veterinary Physiology, Department of Veterinary Medicine, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
| | - Kentaro Nagaoka
- Laboratory of Veterinary Physiology, Department of Veterinary Medicine, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan.
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Duong JT, Pope CE, Hayden HS, Miller C, Salipante SJ, Rowe SM, Solomon GM, Nichols D, Hoffman LR, Narkewicz MR, Green N. Alterations in the fecal microbiota in patients with advanced cystic fibrosis liver disease after 6 months of elexacaftor/tezacaftor/ivacaftor. J Cyst Fibros 2024:S1569-1993(24)00029-8. [PMID: 38448281 DOI: 10.1016/j.jcf.2024.02.015] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 02/23/2024] [Accepted: 02/28/2024] [Indexed: 03/08/2024]
Abstract
BACKGROUND Cystic fibrosis associated liver disease (CFLD) carries a significant disease burden with no effective preventive therapies. According to the gut-liver axis hypothesis for CFLD pathogenesis, dysbiosis and increased intestinal inflammation and permeability permit pathogenic bacterial translocation into the portal circulation, leading to hepatic inflammation and fibrosis. Evaluating the effect of CFTR (cystic fibrosis transmembrane conductance regulator) modulation with elexacaftor/tezacaftor/ivacaftor (ETI) may help determine the role of CFTR in CFLD and increase understanding of CFLD pathogenesis, which is critical for developing therapies. We aimed to characterize the fecal microbiota in participants with CF with and without advanced CFLD (aCFLD) before and after ETI. METHODS This is an ancillary analysis of stool samples from participants ages ≥12 y/o enrolled in PROMISE (NCT04038047). Included participants had aCFLD (cirrhosis with or without portal hypertension, or non-cirrhotic portal hypertension) or CF without liver disease (CFnoLD). Fecal microbiota were defined by shotgun metagenomic sequencing at baseline and 1 and 6 months post-ETI. RESULTS We analyzed 93 samples from 34 participants (11 aCFLD and 23 CFnoLD). Compared to CFnoLD, aCFLD had significantly higher baseline relative abundances of potential pathogens Streptococcus salivarius and Veillonella parvula. Four of 11 aCFLD participants had an initially abnormal fecal calprotectin that normalized 6 months post-ETI, correlating with a significant decrease in S. salivarius and a trend towards decreasing V. parvula. CONCLUSIONS These results support an association between dysbiosis and intestinal inflammation in CFLD with improvements in both post-ETI, lending further support to the gut-liver axis in aCFLD.
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Affiliation(s)
- Jennifer T Duong
- Department of Pediatrics, Division of Pediatric Gastroenterology, Hepatology, and Nutrition, University of California San Francisco School of Medicine, San Francisco, CA, USA.
| | - Christopher E Pope
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA, USA
| | - Hillary S Hayden
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA, USA
| | - Carson Miller
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA, USA
| | - Stephen J Salipante
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Steven M Rowe
- Department of Medicine and the Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - George M Solomon
- Department of Medicine and the Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - David Nichols
- Cystic Fibrosis Foundation Therapeutics Development Network Coordinating Center, Seattle Children's Research Institute, Seattle, WA, USA and Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
| | - Lucas R Hoffman
- Department of Microbiology and Department of Pediatrics, Division of Pulmonary and Sleep Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Michael R Narkewicz
- Digestive Health Institute, Children's Hospital Colorado and Section of Pediatric Gastroenterology, Hepatology and Nutrition, University of Colorado SOM, Aurora, CO, USA
| | - Nicole Green
- Department of Pediatrics, Division of Pediatric Gastroenterology, Hepatology, and Nutrition, University of Washington School of Medicine, Seattle, WA, USA
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Gaire TN, Scott HM, Noyes NR, Ericsson AC, Tokach MD, William H, Menegat MB, Vinasco J, Nagaraja TG, Volkova VV. Temporal dynamics of the fecal microbiome in female pigs from early life through estrus, parturition, and weaning of the first litter of piglets. Anim Microbiome 2024; 6:7. [PMID: 38383422 PMCID: PMC10882843 DOI: 10.1186/s42523-024-00294-8] [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: 09/09/2023] [Accepted: 02/07/2024] [Indexed: 02/23/2024] Open
Abstract
BACKGROUND Age-associated changes in the gastrointestinal microbiome of young pigs have been robustly described; however, the temporal dynamics of the fecal microbiome of the female pig from early life to first parity are not well understood. Our objective was to describe microbiome and antimicrobial resistance dynamics of the fecal microbiome of breeding sows from early life through estrus, parturition and weaning of the first litter of piglets (i.e., from 3 to 53 weeks of age). RESULTS Our analysis revealed that fecal bacterial populations in developing gilts undergo changes consistent with major maturation milestones. As the pigs progressed towards first estrus, the fecal bacteriome shifted from Rikenellaceae RC9 gut group- and UCG-002-dominated enterotypes to Treponema- and Clostridium sensu stricto 1-dominated enterotypes. After first estrus, the fecal bacteriome stabilized, with minimal changes in enterotype transition and associated microbial diversity from estrus to parturition and subsequent weaning of first litter piglets. Unlike bacterial communities, fecal fungal communities exhibited low diversity with high inter- and intra-pig variability and an increased relative abundance of certain taxa at parturition, including Candida spp. Counts of resistant fecal bacteria also fluctuated over time, and were highest in early life and subsequently abated as the pigs progressed to adulthood. CONCLUSIONS This study provides insights into how the fecal microbial community and antimicrobial resistance in female pigs change from three weeks of age throughout their first breeding lifetime. The fecal bacteriome enterotypes and diversity are found to be age-driven and established by the time of first estrus, with minimal changes observed during subsequent physiological stages, such as parturition and lactation, when compared to the earlier age-related shifts. The use of pigs as a model for humans is well-established, however, further studies are needed to understand how our results compare to the human microbiome dynamics. Our findings suggest that the fecal microbiome exhibited consistent changes across individual pigs and became more diverse with age, which is a beneficial characteristic for an animal model system.
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Affiliation(s)
- Tara N Gaire
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA
| | - H Morgan Scott
- Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Noelle R Noyes
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA
| | - Aaron C Ericsson
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO, 65211, USA
| | - Michael D Tokach
- Department of Animal Sciences and Industry, College of Agriculture, Kansas State University, Manhattan, KS, 66506, USA
| | - Hayden William
- Department of Animal Sciences and Industry, College of Agriculture, Kansas State University, Manhattan, KS, 66506, USA
| | - Mariana B Menegat
- Department of Animal Sciences and Industry, College of Agriculture, Kansas State University, Manhattan, KS, 66506, USA
| | - Javier Vinasco
- Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - T G Nagaraja
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA.
| | - Victoriya V Volkova
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA
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Romualdo GR, Valente LC, de Souza JLH, Rodrigues J, Barbisan LF. Modifying effects of 2,4-D and Glyphosate exposures on gut-liver-adipose tissue axis of diet-induced non-alcoholic fatty liver disease in mice. Ecotoxicol Environ Saf 2023; 268:115688. [PMID: 37992649 DOI: 10.1016/j.ecoenv.2023.115688] [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] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 11/03/2023] [Accepted: 11/11/2023] [Indexed: 11/24/2023]
Abstract
Nonalcoholic fatty liver disease (NAFLD), which is linked to western diet (WD) intake, affects 30% of the world's population and involves the crosstalk of liver steatosis, hypertrophy/inflammation of adipose tissue and deregulation of gut microbiome. Glyphosate and 2,4-D are some of the most applied herbicides worldwide, and their roles in NAFLD have not been investigated. Thus, the present study evaluated whether glyphosate and 2,4-D, in single or mixed exposure, alter WD-induced NAFLD in a mouse model. Male C57Bl/6 mice (n = 10/group) received a fat (30% lard, 0.02% cholesterol), and sucrose-rich diet (20%) and high sugar solution (23.1 and 18.9 g/L of fructose and glucose) for 6 months. Simultaneously, animals received glyphosate (0.05 or 5 mg/kg/day), 2,4-D (0.02 or 2 mg/kg/day), or their combination (0.05 +0.02 or 5 +2 mg/kg/day) by intragastrical administration (5 ×/week). Doses were based on the Acceptable Daily Intake (ADIs) or No Observed Adverse Effect Level (NOAEL) levels. Herbicide exposures featured differential responses. WD-induced obesity, hypercholesterolemia, and hyperglycemia remained unaltered. Compared to the group receiving only WD, only the concomitant exposure to WD and 2,4-D (2 mg) enhanced the percentage of mice with moderate/severe hepatic inflammation, CD68 macrophage infiltration, and malondialdehyde levels in the liver. In line, this herbicide modulated immune response- (including Cd4, C8b, Cd28, Cxcr3, Cxcr6) and oxidative stress-related (such as Gsta1, Gsta2, Gsta4, Gstm1, Gstm2, Gstm3, Gstm4, Nqo1, Gpx2) genes in the hepatic transcriptome analysis. This exposure also enriched pro-inflammatory Deferribacteres phylum in fecal microbiome. In general, the herbicide mixtures did not feature the same effects attributed to 2,4-D isolated exposure. Our findings indicate that 2,4-D, at a dose within the toxicological limits, was able to induce disturbances in mainly at the liver and gut axes involved in NAFLD development in male mice.
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Affiliation(s)
- Guilherme R Romualdo
- São Paulo State University (UNESP), Botucatu Medical School, Experimental Research Unit (UNIPEX), Multimodel Drug Screening Platform, Laboratory of Chemically Induced and Experimental Carcinogenesis (MDSP-LCQE), Botucatu, SP, Brazil; São Paulo State University (UNESP), Botucatu Medical School, Department of Pathology, Botucatu, SP, Brazil; São Paulo State University (UNESP), Biosciences Institute, Department of Structural and Functional Biology, Botucatu, SP, Brazil.
| | - Letícia Cardoso Valente
- São Paulo State University (UNESP), Botucatu Medical School, Experimental Research Unit (UNIPEX), Multimodel Drug Screening Platform, Laboratory of Chemically Induced and Experimental Carcinogenesis (MDSP-LCQE), Botucatu, SP, Brazil; São Paulo State University (UNESP), Botucatu Medical School, Department of Pathology, Botucatu, SP, Brazil; São Paulo State University (UNESP), Biosciences Institute, Department of Structural and Functional Biology, Botucatu, SP, Brazil; Federal University of Grande Dourados (UFGD), Faculty of Health Sciences, Dourados, MS, Brazil
| | - Jéssica Luri Hisano de Souza
- São Paulo State University (UNESP), Botucatu Medical School, Experimental Research Unit (UNIPEX), Multimodel Drug Screening Platform, Laboratory of Chemically Induced and Experimental Carcinogenesis (MDSP-LCQE), Botucatu, SP, Brazil; São Paulo State University (UNESP), Biosciences Institute, Department of Structural and Functional Biology, Botucatu, SP, Brazil
| | - Josias Rodrigues
- São Paulo State University (UNESP), Biosciences Institute, Department of Chemical and Biological Sciences, Botucatu, SP, Brazil
| | - Luís Fernando Barbisan
- São Paulo State University (UNESP), Botucatu Medical School, Experimental Research Unit (UNIPEX), Multimodel Drug Screening Platform, Laboratory of Chemically Induced and Experimental Carcinogenesis (MDSP-LCQE), Botucatu, SP, Brazil; São Paulo State University (UNESP), Biosciences Institute, Department of Structural and Functional Biology, Botucatu, SP, Brazil.
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Zhang Z, Lu W, Liu P, Li M, Ge X, Yu B, Wu Z, Liu G, Ding N, Cui B, Chen X. Microbial modifications with Lycium barbarum L. oligosaccharides decrease hepatic fibrosis and mitochondrial abnormalities in mice. Phytomedicine 2023; 120:155068. [PMID: 37690228 DOI: 10.1016/j.phymed.2023.155068] [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] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 09/03/2023] [Indexed: 09/12/2023]
Abstract
BACKGROUND Lycium barbarum L. is a typical Chinese herbal and edible plant and are now consumed globally. Low molecular weight L. barbarum L. oligosaccharides (LBO) exhibit better antioxidant activity and gastrointestinal digestibility in vitro than high molecular weight polysaccharides. However, the LBO on the treatment of liver disease is not studied. PURPOSE Modification of the gut microbial ecosystem by LBO is a promising treatment for liver fibrosis. STUDY DESIGN AND METHODS Herein, LBO were prepared and characterized. CCl4-treated mice were orally gavaged with LBO and the effects on hepatic fibrosis and mitochondrial abnormalities were evaluated according to relevant indicators (gut microbiota, faecal metabolites, and physiological and biochemical indices). RESULTS The results revealed that LBO, a potential prebiotic source, is a pyranose cyclic oligosaccharide possessing α-glycosidic and β-glycosidic bonds. Moreover, LBO supplementation restored the configuration of the bacterial community, enhanced the proliferation of beneficial species in the gastrointestinal tract (e.g., Bacillus, Tyzzerella, Fournierella and Coriobacteriaceae UCG-002), improved microbial metabolic alterations (i.e., carbohydrate metabolism, vitamin metabolism and entero-hepatic circulation), and increased antioxidants, including doxepin, in mice. Finally, LBO administration reduced serum inflammatory cytokine and hepatic hydroxyproline levels, improved intestinal and hepatic mitochondrial functions, and ameliorated mouse liver fibrosis. CONCLUSION These findings indicate that LBO can be utilized as a prebiotic and has a remarkable ability to mitigate liver fibrosis.
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Affiliation(s)
- Zheng Zhang
- State Key Laboratory of Biobased Material and Green Papermaking, School of Food Science and Engineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China
| | - Wenjia Lu
- State Key Laboratory of Biobased Material and Green Papermaking, School of Food Science and Engineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China
| | - Pengfei Liu
- State Key Laboratory of Biobased Material and Green Papermaking, School of Food Science and Engineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China
| | - Mengjie Li
- State Key Laboratory of Biobased Material and Green Papermaking, School of Food Science and Engineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China
| | - Xinyi Ge
- State Key Laboratory of Biobased Material and Green Papermaking, School of Food Science and Engineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China
| | - Bin Yu
- State Key Laboratory of Biobased Material and Green Papermaking, School of Food Science and Engineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China
| | - Zhengzong Wu
- State Key Laboratory of Biobased Material and Green Papermaking, School of Food Science and Engineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China
| | - Guimei Liu
- State Key Laboratory of Biobased Material and Green Papermaking, School of Food Science and Engineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China
| | - Nannan Ding
- Department of Nephrology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, China
| | - Bo Cui
- State Key Laboratory of Biobased Material and Green Papermaking, School of Food Science and Engineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China.
| | - Xiao Chen
- College of Health Sciences, Shandong University of Traditional Chinese Medicine, Jinan 250353, China.
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Niu LN, Zhang GN, Xuan DD, Lin C, Lu Z, Cao PP, Chen SW, Zhang Y, Cui XJ, Hu SK. Comparative analysis of the gut microbiota of wild adult rats from nine district areas in Hainan, China. World J Gastroenterol 2023; 29:3469-3481. [PMID: 37389235 PMCID: PMC10303509 DOI: 10.3748/wjg.v29.i22.3469] [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] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/19/2023] [Accepted: 05/16/2023] [Indexed: 06/06/2023] Open
Abstract
BACKGROUND Wild rats have the potential to hold zoonotic infectious agents that can spread to humans and cause disease.
AIM To better understand the composition of gut bacterial communities in rats is essential for preventing and treating such diseases. As a tropical island located in the south of China, Hainan province has abundant rat species. Here, we examined the gut bacterial composition in wild adult rats from Hainan province.
METHODS Fresh fecal samples were collected from 162 wild adult rats, including three species (Rattus norvegicus, Leopoldamys edwardsi, and Rattus losea), from nine regions of Hainan province between 2017-2018.
RESULTS We analyzed the composition of gut microbiota using the 16S rRNA gene amplicon sequencing. We identified 4903 bacterial operational taxonomic units (30 phyla, 175 families, and 498 genera), which vary between samples of different rat species in various habitats at various times of the year. In general, Firmicutes were the most abundant phyla, followed by Bacteroidetes (15.55%), Proteobacteria (6.13%), and Actinobacteria (4.02%). The genus Lactobacillus (20.08%), unidentified_Clostridiales (5.16%), Romboutsia (4.33%), unidentified_Ruminococcaceae (3.83%), Bacteroides (3.66%), Helicobacter (2.40%) and Streptococcus (2.37%) were dominant.
CONCLUSION The composition and abundance of the gut microbial communities varied between rat species and locations. This work provides fundamental information to identify microbial communities useful for disease control in Hainan province.
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Affiliation(s)
- Li-Na Niu
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou 571199, Hainan Province, China
- The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou 571199, Hainan Province, China
- Department of Pathogen Biology, Hainan Medical University, Haikou 571199, Hainan Province, China
| | - Guan-Nan Zhang
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou 571199, Hainan Province, China
- The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou 571199, Hainan Province, China
- Department of Pathogen Biology, Hainan Medical University, Haikou 571199, Hainan Province, China
| | - Duan-Duan Xuan
- Department of Laboratory, Xinxiang First People's Hospital, Xinxiang 453000, Henan Province, China
| | - Chong Lin
- Department of Laboratory, The Second Affiliated Hospital of Hainan Medical University, Haikou 570311, Hainan Province, China
| | - Zi Lu
- Department of Laboratory, The Second Affiliated Hospital of Hainan Medical University, Haikou 570311, Hainan Province, China
| | - Pei-Pei Cao
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou 571199, Hainan Province, China
- The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou 571199, Hainan Province, China
- Department of Pathogen Biology, Hainan Medical University, Haikou 571199, Hainan Province, China
| | - Shao-Wen Chen
- Department of Laboratory, The Second Affiliated Hospital of Hainan Medical University, Haikou 570311, Hainan Province, China
| | - Yong Zhang
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou 571199, Hainan Province, China
- The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou 571199, Hainan Province, China
- Department of Pathogen Biology, Hainan Medical University, Haikou 571199, Hainan Province, China
| | - Xiu-Ji Cui
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou 571199, Hainan Province, China
- The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou 571199, Hainan Province, China
- Department of Pathogen Biology, Hainan Medical University, Haikou 571199, Hainan Province, China
| | - Shou-Kui Hu
- Department of Clinical Laboratory, Peking University Shougang Hospital, Beijing 100144, China
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9
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Hou X, Du H, Deng Y, Wang H, Liu J, Qiao J, Liu W, Shu X, Sun B, Liu Y. Gut microbiota mediated the individualized efficacy of Temozolomide via immunomodulation in glioma. J Transl Med 2023; 21:198. [PMID: 36927689 PMCID: PMC10018922 DOI: 10.1186/s12967-023-04042-5] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 03/08/2023] [Indexed: 03/18/2023] Open
Abstract
BACKGROUND Temozolomide (TMZ) is the preferred chemotherapy strategy for glioma therapy. As a second-generation alkylating agent, TMZ provides superior oral bio-availability. However, limited response rate (less than 50%) and high incidence of drug resistance seriously restricts TMZ's application, there still lack of strategies to increase the chemotherapy sensitivity. METHODS Luci-GL261 glioma orthotopic xenograft model combined bioluminescence imaging was utilized to evaluate the anti-tumor effect of TMZ and differentiate TMZ sensitive (S)/non-sensitive (NS) individuals. Integrated microbiomics and metabolomics analysis was applied to disentangle the involvement of gut bacteria in TMZ sensitivity. Spearman's correlation analysis was applied to test the association between fecal bacteria levels and pharmacodynamics indices. Antibiotics treatment combined TMZ treatment was used to confirm the involvement of gut microbiota in TMZ response. Flow cytometry analysis, ELISA and histopathology were used to explore the potential role of immunoregulation in gut microbiota mediated TMZ response. RESULTS Firstly, gut bacteria composition was significantly altered during glioma development and TMZ treatment. Meanwhile, in vivo anti-cancer evaluation suggested a remarkable difference in chemotherapy efficacy after TMZ administration. Moreover, 16s rRNA gene sequencing and non-targeted metabolomics analysis revealed distinct different gut microbiota and immune infiltrating state between TMZ sensitive and non-sensitive mice, while abundance of differential gut bacteria and related metabolites was significantly correlated with TMZ pharmacodynamics indices. Further verification suggested that gut microbiota deletion by antibiotics treatment could accelerate glioma development, attenuate TMZ efficacy and inhibit immune cells (macrophage and CD8α+ T cell) recruitment. CONCLUSIONS The current study confirmed the involvement of gut microbiota in glioma development and individualized TMZ efficacy via immunomodulation, hence gut bacteria may serve as a predictive biomarker as well as a therapeutic target for clinical TMZ application.
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Affiliation(s)
- Xiaoying Hou
- Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China.,Cancer Institute, School of Medicine, Jianghan University, Wuhan, China
| | - Hongzhi Du
- School of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Yufei Deng
- Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China.,Cancer Institute, School of Medicine, Jianghan University, Wuhan, China
| | - Haiping Wang
- Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China.,Cancer Institute, School of Medicine, Jianghan University, Wuhan, China
| | - Jinmi Liu
- Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China.,Cancer Institute, School of Medicine, Jianghan University, Wuhan, China
| | - Jialu Qiao
- Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China
| | - Wei Liu
- Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China
| | - Xiji Shu
- Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China
| | - Binlian Sun
- Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China. .,Cancer Institute, School of Medicine, Jianghan University, Wuhan, China.
| | - Yuchen Liu
- Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China. .,Cancer Institute, School of Medicine, Jianghan University, Wuhan, China.
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10
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Centeno-Martinez RE, Dong W, Klopp RN, Yoon I, Boerman JP, Johnson TA. Effects of feeding Saccharomyces cerevisiae fermentation postbiotic on the fecal microbial community of Holstein dairy calves. Anim Microbiome 2023; 5:13. [PMID: 36803311 PMCID: PMC9938967 DOI: 10.1186/s42523-023-00234-y] [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: 06/08/2022] [Accepted: 02/10/2023] [Indexed: 02/21/2023] Open
Abstract
BACKGROUND The livestock industry is striving to identify antibiotic alternatives to reduce the need to use antibiotics. Postbiotics, such as Saccharomyces cerevisiae fermentation product (SCFP), have been studied and proposed as potential non-antibiotic growth promoters due to their effects on animal growth and the rumen microbiome; however, little is known of their effects on the hind-gut microbiome during the early life of calves. The objective of this study was to measure the effect of in-feed SCFP on the fecal microbiome of Holstein bull calves through 4 months of age. Calves (n = 60) were separated into two treatments: CON (no SCFP added) or SCFP (SmartCare®, Diamond V, Cedar Rapids, IA, in milk replacer and NutriTek®, Diamond V, Cedar Rapids, IA, incorporated into feed), and were blocked by body weight and serum total protein. Fecal samples were collected on d 0, 28, 56, 84, and 112 of the study to characterize the fecal microbiome community. Data were analyzed as a completely randomized block design with repeated measures when applicable. A random-forest regression method was implemented to more fully understand community succession in the calf fecal microbiome of the two treatment groups. RESULTS Richness and evenness of the fecal microbiota increased over time (P < 0.001), and SCFP calves tended to increase the evenness of the community (P = 0.06). Based on random-forest regression, calf age as predicted by microbiome composition was significantly correlated with the calf physiological age (R2 = 0.927, P < 1 × 10-15). Twenty-two "age-discriminatory" ASVs (amplicon sequence variants) were identified in the fecal microbiome that were shared between the two treatment groups. Of these, 6 ASVs (Dorea-ASV308, Lachnospiraceae-ASV288, Oscillospira-ASV311, Roseburia-ASV228, Ruminococcaceae-ASV89 and Ruminoccocaceae-ASV13) in the SCFP group reached their highest abundance in the third month, but they reached their highest abundance in the fourth month in the CON group. All other shared ASVs reached their highest abundance at the same timepoint in both treatment groups. CONCLUSIONS Supplementation of SCFP altered the abundance dynamics of age discriminatory ASVs, suggesting a faster maturation of some members of the fecal microbiota in SCFP calves compared to CON calves. These results demonstrate the value of analyzing microbial community succession as a continuous variable to identify the effects of a dietary treatment.
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Affiliation(s)
- Ruth Eunice Centeno-Martinez
- grid.169077.e0000 0004 1937 2197Department of Animal Science, Purdue University, 270 S Russell St., West Lafayette, IN USA
| | - Wenxuan Dong
- grid.169077.e0000 0004 1937 2197Department of Animal Science, Purdue University, 270 S Russell St., West Lafayette, IN USA
| | - Rebecca N. Klopp
- grid.169077.e0000 0004 1937 2197Department of Animal Science, Purdue University, 270 S Russell St., West Lafayette, IN USA
| | - Ilkyu Yoon
- grid.486943.40000 0004 0638 9395Diamond V, Cedar Rapids, IA USA
| | - Jacquelyn P. Boerman
- grid.169077.e0000 0004 1937 2197Department of Animal Science, Purdue University, 270 S Russell St., West Lafayette, IN USA
| | - Timothy A. Johnson
- grid.169077.e0000 0004 1937 2197Department of Animal Science, Purdue University, 270 S Russell St., West Lafayette, IN USA
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11
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Deepthi M, Arvind K, Saxena R, Pulikkan J, Sharma VK, Grace T. Exploring variation in the fecal microbial communities of Kasaragod Dwarf and Holstein crossbred cattle. Antonie Van Leeuwenhoek 2023; 116:53-65. [PMID: 36450879 DOI: 10.1007/s10482-022-01791-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 10/30/2022] [Indexed: 12/02/2022]
Abstract
The gut microbiota and its impact on health and nutrition in animals, including cattle has been of intense interest in recent times. Cattle, in particular indigenous varieties like Kasaragod Dwarf cow, have not received the due consideration given to other non-native cattle breeds, and the composition of their fecal microbiome is yet to be established. This study applied 16S rRNA high-throughput sequencing of fecal samples and compared the Kasaragod Dwarf with the highly prevalent Holstein crossbred cattle. Variation in their microbial composition was confirmed by marker gene-based taxonomic analysis. Principle Coordinate Analysis (PCoA) showed the distinct microbial architecture of the two cattle types. While the two cattle types possess unique signature taxa, in Kasaragod Dwarf cattle, many of the identified genera, including Anaerovibrio, Succinivibrio, Roseburia, Coprococcus, Paludibacter, Sutterella, Coprobacillus, and Ruminobacter, have previously been shown to be present in higher abundance in animals with higher feed efficiency. This is the first report of Kasaragod Dwarf cattle fecal microbiome profiling. Our findings highlight the predominance of specific taxa potentially associated with different fermentation products and feed efficiency phenotypes in Kasaragod Dwarf cattle compared to Holstein crossbred cattle.
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12
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Kothmann KH, Jons A, Wilhelmi B, Kasozi N, Graham L, Gent R, Atkin SL, Swart AC, Newell-Fugate AE. Non-invasive assessment of fecal glucocorticoid, progesterone, and androgen metabolites and microbiome in free-ranging southern white rhinoceros (Ceratotherium simum simum) in South Africa. Gen Comp Endocrinol 2022; 329:114099. [PMID: 35914652 DOI: 10.1016/j.ygcen.2022.114099] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 07/14/2022] [Accepted: 07/26/2022] [Indexed: 11/04/2022]
Abstract
Increased poaching in northern South Africa has necessitated relocation of large numbers of southern white rhinoceros (Ceratotherium simum simum) to the Eastern Cape Province. The climate and grassland ecology of this province differ from that of northern South Africa which may impact the health of this species. This assessment of fecal steroid levels and microbiome in 10 free-ranging southern white rhinoceros in the Eastern Cape will provide insights into white rhinoceros physiology in this biome. Fecal steroid metabolites were analyzed using enzyme immunoassay (EIA) and ultra-performance convergence chromatography tandem mass spectrometry (UPC2-MS/MS). Fecal microbial composition was assessed via next generation sequencing. EIAs with antibodies raised against progesterone (P4; mouse monoclonal - CL425 clone), testosterone (T; rabbit polyclonal), corticosterone (B; sheep polyclonal) were utilized. Pregnant females had large quantities of fecal progesterone metabolites (FPMs) detected by CL425 EIA. Pregnant females also had native P4 and 11α-hydroxydihydroprogesterone (11αOHDHP4; 4-pregnen-11α-ol-3,20-dione) detected by UPC2-MS/MS but these concentrations were 1000-fold less than the concentrations of FPMs detected by the CL425 EIA. By contrast, non-pregnant females had FPM concentrations detected by CL425 EIA which were similar to native P4 and 11αOHDHP4 concentrations detected by UPC2-MS/MS. Mean fecal androgen metabolite (FAM) concentrations detected by the T EIA were similar between males and females. 11-ketoandrostenedione (11KA4) detected by UPC2-MS/MS was higher in females than males. However, there was no difference between males and females in the concentration of fecal glucocorticoid metabolites (FGMs) detected by the B EIA. Bacteroidia, followed by Clostridia, was the most abundant classes of fecal microbes. The unfiltered microbiome of females was more diverse than that of males. The core fecal microbiome of young rhinoceros had a higher observed species richness (Shannon diversity index, and Simpson diversity index) than that of old rhinoceros. In the alpha male, immobilization was associated with an increase in FGMs detected by 11-deoxycortisol (S) detected by UPC2-MS/MS coupled with decreased abundance of Spirochaetia. We detected substantially different FAM and FPM concentrations from those previously reported for both captive and wild white rhinoceros. Comparison of our UPC2-MS/MS and EIA results underscores the fact that most EIAs are highly cross reactive for many steroid metabolites. Our data also demonstrates a distinct effect of stress not only on FGMs but also on the fecal microbiome. This is the first non-invasive assessment of fecal steroid metabolites by UPC2-MS/MS and the fecal microbiome in wild white rhinoceros.
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Affiliation(s)
- K H Kothmann
- Department of Veterinary Physiology and Pharmacology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
| | - A Jons
- Department of Molecular and Cellular Medicine, Health Science Center, Texas A&M University, College Station, TX 77843, USA
| | - B Wilhelmi
- Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140 South Africa
| | - N Kasozi
- Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140 South Africa
| | - L Graham
- Ikahala Veterinary Wildlife Services, Paterson 6131 South Africa
| | - R Gent
- Department of Biochemistry, Stellenbosch University, Stellenbosch 7600 South Africa
| | - S L Atkin
- Royal College of Surgeons in Ireland, Bahrain
| | - A C Swart
- Department of Biochemistry, Stellenbosch University, Stellenbosch 7600 South Africa; Department of Chemistry and Polymer Science, Stellenbosch University, Stellenbosch 7600 South Africa
| | - A E Newell-Fugate
- Department of Veterinary Physiology and Pharmacology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA.
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13
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George SE, James J, Devereux R, Wan Y, Diamond GL, Bradham KD, Scheckel KG, Thomas DJ. Ingestion of remediated lead-contaminated soils affects the fecal microbiome of mice. Sci Total Environ 2022; 837:155797. [PMID: 35561906 PMCID: PMC9830667 DOI: 10.1016/j.scitotenv.2022.155797] [Citation(s) in RCA: 2] [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] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/12/2022] [Accepted: 05/05/2022] [Indexed: 05/08/2023]
Abstract
The relationship between ingestion of diets amended with a Pb-contaminated soil and the composition of the fecal microbiome was examined in a mouse model. Mice consumed diets amended with a Pb-contaminated soil in its native (untreated) state or after treatment for remediation with phosphoric acid or triple superphosphate alone or in combination with iron-waste material or biosolids compost. Subacute dietary exposure of mice receiving treated soil resulted in modulation of the fecal intestinal flora, which coincided with reduced relative Pb bioavailability in the bone, blood and kidney and differences in Pb speciation compared to untreated soil. Shifts in the relative abundance of several phyla including Verrucomicrobia, Tenericutes, Firmicutes, Proteobacteria, and TM7 (Candidatus Saccharibacteria) were observed. Because the phyla persist in the presence of Pb, it is probable that they are resistant to Pb. This may enable members of the phyla to bind and limit Pb uptake in the intestine. Families Ruminococcaceae, Lachnospiraceae, Erysipelotrichaceae, Verrucomicrobiaceae, Prevotellaceae, Lactobacilaceae, and Bacteroidaceae, which have been linked to health or disease, also were modulated. This study is the first to explore the relationship between the murine fecal microbiome and ingested Pb contaminated soils treated with different remediation options designed to reduce bioavailability. Identifying commonalities in the microbiome that are correlated with more positive health outcomes may serve as biomarkers to assist in the selection of remediation approaches that are more effective and pose less risk.
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Affiliation(s)
- S Elizabeth George
- Center for Environmental Measurement & Modeling, Gulf Ecosystem Measurement & Modeling Division, U.S. Environmental Protection Agency, Office of Research & Development, Gulf Breeze, FL 32561, United States.
| | - Joseph James
- Center for Environmental Measurement & Modeling, Gulf Ecosystem Measurement & Modeling Division, U.S. Environmental Protection Agency, Office of Research & Development, Gulf Breeze, FL 32561, United States
| | - Richard Devereux
- Center for Environmental Measurement & Modeling, Gulf Ecosystem Measurement & Modeling Division, U.S. Environmental Protection Agency, Office of Research & Development, Gulf Breeze, FL 32561, United States
| | - Yongshan Wan
- Center for Environmental Measurement & Modeling, Gulf Ecosystem Measurement & Modeling Division, U.S. Environmental Protection Agency, Office of Research & Development, Gulf Breeze, FL 32561, United States
| | - Gary L Diamond
- SRC, Inc., North Syracuse, New York 13212, United States
| | - Karen D Bradham
- Center for Environmental Measurement & Modeling, Watershed & Ecosystem Characterization Division, U.S. Environmental Protection Agency, Office of Research & Development, Research Triangle Park, NC 27711, United States
| | - Kirk G Scheckel
- Center for Environmental Solutions and Emergency Response, Land Remediation & Technology Division, U.S. Environmental Protection Agency, Office of Research & Development, Cincinnati, OH 45224, United States
| | - David J Thomas
- Center for Computational Toxicology & Exposure, Chemical Characterization & Exposure Division, U.S. Environmental Protection Agency, Office of Research & Development, Research Triangle Park, NC 27711, United States
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14
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Bhattacharjee A, Dubey S, Sharma S. Storage of soil microbiome for application in sustainable agriculture: prospects and challenges. Environ Sci Pollut Res Int 2022; 29:3171-3183. [PMID: 34718953 DOI: 10.1007/s11356-021-17164-4] [Citation(s) in RCA: 2] [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] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 10/19/2021] [Indexed: 06/13/2023]
Abstract
Soil microbiome is a dynamic micro-ecosystem driving and fine-tuning several biological processes in the global macro-ecosystems. Its tremendous potential towards mediating sustainability in the ecosystem necessitates the urgent need to store it optimally and efficiently as "next-generation biologicals" for future applications via soil transplantation. The challenge, therefore, is to devise a strategy for the storage of soil microbiome such that its "functionality" is preserved for later application. This review discusses the current endeavours made towards storage of the soil microbiome. The methods for assessing the integrity of soil microbiome by targeting the structural diversity and functional potential of the preserved microbiomes have also been discussed. Further, the success stories related to the storage of fecal microbiome for application in transplants have also been highlighted. This is done primarily with the objective of learning lessons, and parallel application of the knowledge gained, in bringing about improvement in the research domain of soil microbiome storage. Subsequently, the limitations of current techniques of preservation have also been delineated. Further, the open questions in the area have been critically discussed. In conclusion, possible alternatives for storage, comprehensive analyses of the composition of the stored microbiome and their potential have been presented.
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Affiliation(s)
- Annapurna Bhattacharjee
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Shubham Dubey
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Shilpi Sharma
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India.
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15
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Chen Y, Lin H, Cole M, Morris A, Martinson J, Mckay H, Mimiaga M, Margolick J, Fitch A, Methe B, Srinivas VR, Peddada S, Rinaldo CR. Signature changes in gut microbiome are associated with increased susceptibility to HIV-1 infection in MSM. Microbiome 2021; 9:237. [PMID: 34879869 PMCID: PMC8656045 DOI: 10.1186/s40168-021-01168-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 09/14/2021] [Indexed: 05/12/2023]
Abstract
BACKGROUND Men who have sex with men (MSM) have been disproportionately affected by HIV-1 since the beginning of the AIDS pandemic, particularly in the USA and Europe. Compared to men who have sex with women (MSW), MSM have a distinct fecal microbiome regardless of HIV-1 infection. However, it is unclear whether the MSM-associated gut microbiome affects the susceptibility and progression of HIV-1 infection. We studied fecal microbiome profiles, short-chain fatty acids, and blood plasma inflammatory cytokines of 109 HIV-1 seroconverters (SC) from the early, 1984-1985 phase of the HIV-1 pandemic in the Multicenter AIDS Cohort Study (MACS) before and after HIV-1 infection compared to 156 HIV-1-negative MACS MSM (negative controls [NC]). RESULTS We found that family Succinivibrionaceae, S24-7, Mogibacteriaceae, Coriobacteriaceae, and Erysipelotrichaceae were significantly higher (p<0.05), whereas Odoribacteraceae, Verucomicrobiaceae, Bacteroidaceae, Barnesiellaceae, and Rikenellaceae were significantly lower (p<0.05), in SC before HIV-1 infection compared to NC. At the species level, Prevotella stercorea, Eubacterium biforme, and Collinsella aerofaciens were significantly higher (p<0.05), and Eubacterium dolichum, Desulfovibrio D168, Alistipes onderdonkii, Ruminococcus torques, Bacteroides fragilis, Bacteroides caccae, Alistipes putredinis, Akkermansia muciniphila, Bacteroides uniformis, and Bacteroides ovatus were significantly lower (p<0.05) in SC before HIV-1 infection compared to NC. After HIV-1 infection, family Prevotellaceae and Victivallaceae and species Bacteroides fragilis and Eubacterium cylindroides were significantly higher (p<0.05) in SC who developed AIDS within 5 years compared to the SC who were AIDS free for more than 10 years without antiretroviral therapy (ART). In addition, family Victivallaceae and species Prevotella stercorea, Coprococcus eutactus, and Butyrivibrio crossotus were significantly higher (p<0.05) and Gemmiger formicilis and Blautia obeum were significantly lower (p<0.05) after HIV-1 infection in SC who developed AIDS within 5-10 years compared to the SC who were AIDS-free for more than 10 years without ART. Furthermore, plasma inflammatory cytokine levels of sCD14, sCD163, interleukin 6, and lipopolysaccharide binding protein were significantly higher in SC with p<0.05 before HIV-1 infection compared to NC. CONCLUSIONS Our results suggest that pathogenic changes in the gut microbiome were present in MSM several months prior to infection with HIV-1 in the early phase of the AIDS pandemic in the USA. This was associated with increased inflammatory biomarkers in the blood and risk for development of AIDS. Video abstract.
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Affiliation(s)
- Yue Chen
- Department of Infectious Diseases and Microbiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA USA
| | - Huang Lin
- Current address: Biostatistics and Bioinformatics Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), NIH, Bethesda, MD USA
- Department of Biostatistics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA USA
| | - Mariah Cole
- Department of Infectious Diseases and Microbiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA USA
- Present address: Wilmot Cancer Center, University of Rochester Medical Center, Rochester, NY USA
| | - Alison Morris
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Jeremy Martinson
- Department of Infectious Diseases and Microbiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA USA
| | - Heather Mckay
- Department of Epidemiology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD USA
| | - Matthew Mimiaga
- Department of Epidemiology, Fielding School of Public Health, University of California at Los Angeles, Los Angeles, CA USA
| | - Joseph Margolick
- Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD USA
| | - Adam Fitch
- Present address: Wilmot Cancer Center, University of Rochester Medical Center, Rochester, NY USA
| | - Barbara Methe
- Present address: Wilmot Cancer Center, University of Rochester Medical Center, Rochester, NY USA
| | - Vatsala Rangachar Srinivas
- Department of Infectious Diseases and Microbiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA USA
| | - Shyamal Peddada
- Current address: Biostatistics and Bioinformatics Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), NIH, Bethesda, MD USA
- Department of Biostatistics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA USA
| | - Charles R. Rinaldo
- Department of Infectious Diseases and Microbiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA USA
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16
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Eng A, Hayden HS, Pope CE, Brittnacher MJ, Vo AT, Weiss EJ, Hager KR, Leung DH, Heltshe SL, Raftery D, Miller SI, Hoffman LR, Borenstein E. Infants with cystic fibrosis have altered fecal functional capacities with potential clinical and metabolic consequences. BMC Microbiol 2021; 21:247. [PMID: 34525965 PMCID: PMC8444586 DOI: 10.1186/s12866-021-02305-z] [Citation(s) in RCA: 6] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 08/20/2021] [Indexed: 12/11/2022] Open
Abstract
Background Infants with cystic fibrosis (CF) suffer from gastrointestinal (GI) complications, including pancreatic insufficiency and intestinal inflammation, which have been associated with impaired nutrition and growth. Recent evidence identified altered fecal microbiota taxonomic compositions in infants with CF relative to healthy infants that were characterized by differences in the abundances of taxa associated with GI health and nutrition. Furthermore, these taxonomic differences were more pronounced in low length infants with CF, suggesting a potential link to linear growth failure. We hypothesized that these differences would entail shifts in the microbiome’s functional capacities that could contribute to inflammation and nutritional failure in infants with CF. Results To test this hypothesis, we compared fecal microbial metagenomic content between healthy infants and infants with CF, supplemented with an analysis of fecal metabolomes in infants with CF. We identified notable differences in CF fecal microbial functional capacities, including metabolic and environmental response functions, compared to healthy infants that intensified during the first year of life. A machine learning-based longitudinal metagenomic age analysis of healthy and CF fecal metagenomic functional profiles further demonstrated that these differences are characterized by a CF-associated delay in the development of these functional capacities. Moreover, we found metagenomic differences in functions related to metabolism among infants with CF that were associated with diet and antibiotic exposure, and identified several taxa as potential drivers of these functional differences. An integrated metagenomic and metabolomic analysis further revealed that abundances of several fecal GI metabolites important for nutrient absorption, including three bile acids, correlated with specific microbes in infants with CF. Conclusions Our results highlight several metagenomic and metabolomic factors, including bile acids and other microbial metabolites, that may impact nutrition, growth, and GI health in infants with CF. These factors could serve as promising avenues for novel microbiome-based therapeutics to improve health outcomes in these infants. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02305-z.
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Affiliation(s)
- Alexander Eng
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Hillary S Hayden
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | | | | | - Anh T Vo
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Eli J Weiss
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Kyle R Hager
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Daniel H Leung
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Sonya L Heltshe
- Department of Pediatrics, University of Washington, Seattle, WA, USA.,Cystic Fibrosis Foundation Therapeutics Development Network Coordinating Center, Seattle Children's Research Institute, Seattle, WA, USA
| | - Daniel Raftery
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA, USA
| | - Samuel I Miller
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.,Department of Microbiology, University of Washington, Seattle, WA, USA.,Department of Medicine, University of Washington, Seattle, WA, USA
| | - Lucas R Hoffman
- Department of Microbiology, University of Washington, Seattle, WA, USA. .,Department of Pediatrics, University of Washington, Seattle, WA, USA. .,Pulmonary and Sleep Medicine, Seattle Children's Hospital, Seattle, WA, USA.
| | - Elhanan Borenstein
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel. .,Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel. .,Santa Fe Institute, Santa Fe, NM, USA.
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17
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Alemán JO, Henderson WA, Walker JM, Ronning A, Jones DR, Walter PJ, Daniel SG, Bittinger K, Vaughan R, MacArthur R, Chen K, Breslow JL, Holt PR. Excess dietary fructose does not alter gut microbiota or permeability in humans: A pilot randomized controlled study. J Clin Transl Sci 2021; 5:e143. [PMID: 34422323 DOI: 10.1017/cts.2021.801] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 02/21/2021] [Revised: 05/17/2021] [Accepted: 06/04/2021] [Indexed: 12/12/2022] Open
Abstract
Introduction: Non-alcoholic fatty liver disease (NAFLD) is an increasing cause of chronic liver disease that accompanies obesity and the metabolic syndrome. Excess fructose consumption can initiate or exacerbate NAFLD in part due to a consequence of impaired hepatic fructose metabolism. Preclinical data emphasized that fructose-induced altered gut microbiome, increased gut permeability, and endotoxemia play an important role in NAFLD, but human studies are sparse. The present study aimed to determine if two weeks of excess fructose consumption significantly alters gut microbiota or permeability in humans. Methods: We performed a pilot double-blind, cross-over, metabolic unit study in 10 subjects with obesity (body mass index [BMI] 30–40 mg/kg/m2). Each arm provided 75 grams of either fructose or glucose added to subjects’ individual diets for 14 days, substituted isocalorically for complex carbohydrates, with a 19-day wash-out period between arms. Total fructose intake provided in the fructose arm of the study totaled a mean of 20.1% of calories. Outcome measures included fecal microbiota distribution, fecal metabolites, intestinal permeability, markers of endotoxemia, and plasma metabolites. Results: Routine blood, uric acid, liver function, and lipid measurements were unaffected by the fructose intervention. The fecal microbiome (including Akkermansia muciniphilia), fecal metabolites, gut permeability, indices of endotoxemia, gut damage or inflammation, and plasma metabolites were essentially unchanged by either intervention. Conclusions: In contrast to rodent preclinical findings, excess fructose did not cause changes in the gut microbiome, metabolome, and permeability as well as endotoxemia in humans with obesity fed fructose for 14 days in amounts known to enhance NAFLD.
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18
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Cuscó A, Pérez D, Viñes J, Fàbregas N, Francino O. Long-read metagenomics retrieves complete single-contig bacterial genomes from canine feces. BMC Genomics 2021; 22:330. [PMID: 33957869 PMCID: PMC8103633 DOI: 10.1186/s12864-021-07607-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [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: 12/25/2020] [Accepted: 04/12/2021] [Indexed: 12/12/2022] Open
Abstract
Background Long-read sequencing in metagenomics facilitates the assembly of complete genomes out of complex microbial communities. These genomes include essential biologic information such as the ribosomal genes or the mobile genetic elements, which are usually missed with short-reads. We applied long-read metagenomics with Nanopore sequencing to retrieve high-quality metagenome-assembled genomes (HQ MAGs) from a dog fecal sample. Results We used nanopore long-read metagenomics and frameshift aware correction on a canine fecal sample and retrieved eight single-contig HQ MAGs, which were > 90% complete with < 5% contamination, and contained most ribosomal genes and tRNAs. At the technical level, we demonstrated that a high-molecular-weight DNA extraction improved the metagenomics assembly contiguity, the recovery of the rRNA operons, and the retrieval of longer and circular contigs that are potential HQ MAGs. These HQ MAGs corresponded to Succinivibrio, Sutterella, Prevotellamassilia, Phascolarctobacterium, Catenibacterium, Blautia, and Enterococcus genera. Linking our results to previous gastrointestinal microbiome reports (metagenome or 16S rRNA-based), we found that some bacterial species on the gastrointestinal tract seem to be more canid-specific –Succinivibrio, Prevotellamassilia, Phascolarctobacterium, Blautia_A sp900541345–, whereas others are more broadly distributed among animal and human microbiomes –Sutterella, Catenibacterium, Enterococcus, and Blautia sp003287895. Sutterella HQ MAG is potentially the first reported genome assembly for Sutterella stercoricanis, as assigned by 16S rRNA gene similarity. Moreover, we show that long reads are essential to detect mobilome functions, usually missed in short-read MAGs. Conclusions We recovered eight single-contig HQ MAGs from canine feces of a healthy dog with nanopore long-reads. We also retrieved relevant biological insights from these specific bacterial species previously missed in public databases, such as complete ribosomal operons and mobilome functions. The high-molecular-weight DNA extraction improved the assembly’s contiguity, whereas the high-accuracy basecalling, the raw read error correction, the assembly polishing, and the frameshift correction reduced the insertion and deletion errors. Both experimental and analytical steps ensured the retrieval of complete bacterial genomes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07607-0.
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Affiliation(s)
- Anna Cuscó
- Vetgenomics, Ed Eureka, Parc de Recerca UAB, Barcelona, Spain.
| | - Daniel Pérez
- Molecular Genetics Veterinary Service (SVGM), Veterinary School, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Joaquim Viñes
- Vetgenomics, Ed Eureka, Parc de Recerca UAB, Barcelona, Spain.,Molecular Genetics Veterinary Service (SVGM), Veterinary School, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Norma Fàbregas
- Vetgenomics, Ed Eureka, Parc de Recerca UAB, Barcelona, Spain
| | - Olga Francino
- Molecular Genetics Veterinary Service (SVGM), Veterinary School, Universitat Autònoma de Barcelona, Barcelona, Spain
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19
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Gonzalez A, Kapila N, Melendez-Rosado J, Liang H, Castro-Pavia F. An Evaluation of the Fecal Microbiome in Lynch Syndrome. J Gastrointest Cancer 2021; 52:365-368. [PMID: 33492618 DOI: 10.1007/s12029-021-00588-z] [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] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2021] [Indexed: 01/04/2023]
Abstract
PURPOSE There is limited data regarding the fecal microbiome findings in patients with Lynch syndrome. We aimed to study the fecal micobiome of patients with Lynch syndrome with and without cancer. METHODS We performed an observational study comparing the fecal microbiome of patients with Lynch syndrome (LS) with cancer with those without cancer. We included subjects older than 18 years with LS and excluded those with a history of colectomy or inflammatory bowel disease. We analyzed their fecal microbiome by 16S ribosomal subunit PCR amplification and performed comparative analyses. RESULTS Eight patients were included: 3 of these with LS and cancer (LS-C) and 5 patients with LS and no cancer (LS-NC). We found non-significant differences at the phyla and genera level between the LS-C and LS-NC groups. At the phyla level, LS-C patients had a higher percentage of Bacteroidetes (42.2% vs. 28.5%; P = 0.068) and Verrucomicrobia (0.644% vs 0.0007%; P = 0.10), and a lower percentage of Firmicutes (48.3% vs. 65.4%; P = 0.078). At the genus level, LS-C patients had a higher rate of Akkermania (0.766% vs. 0.001%; P = 0.11). LS-C patients with endometrial cancer had a higher rate of Bacteroides (37.4% vs 17.3%; P = 0.10). LS-C patients had a lower rate of Pseudobutyrvibrio (0.74% vs. 2.71%; P = 0.10). CONCLUSIONS The fecal microbiome of LS patients with extraintestinal cancer differs that of LS patients without cancer. Further studies are needed to explore microbiome changes in these high risk patients.
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Affiliation(s)
- Adalberto Gonzalez
- Department of Gastroenterology and Hepatology, Cleveland Clinic Florida, Weston, FL, 33331, USA
| | - Nikhil Kapila
- Department of Transplant Hepatology, Cleveland Clinic Florida, Weston, Florida, 33331, USA
| | | | - Hong Liang
- Department of Gastroenterology and Hepatology, Cleveland Clinic Florida, Weston, FL, 33331, USA
| | - Fernando Castro-Pavia
- Department of Gastroenterology and Hepatology, Cleveland Clinic Florida, Weston, FL, 33331, USA.
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20
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Jiang Y, Yuan Z, Shen Y, Rosa BA, Martin J, Cao S, Zhou Y, Mitreva M, Cao J. Alteration of the fecal microbiota in Chinese patients with Schistosoma japonicum infection. ACTA ACUST UNITED AC 2021; 28:1. [PMID: 33416489 PMCID: PMC7792497 DOI: 10.1051/parasite/2020074] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 07/31/2020] [Accepted: 12/14/2020] [Indexed: 12/13/2022]
Abstract
Schistosoma japonicum infection causes pathological injury to the host. Multiple studies have shown that intestinal helminth infection causes dysbiosis for the gut microbial community and impacts host immunology. However, the effect of acute S. japonicum infection on the gut microbiome structure (abundance and diversity) is still unclear. We collected fecal samples from healthy and infected patients from a single hospital in Hunan Province, China. The bacterial community was analyzed using 16S ribosomal RNA gene sequencing of the V4 hypervariable region using the HiSeq platform. Compared with healthy subjects, infected patients exhibited an increase in relative abundance of the TM7 phylum. At the genus level, there were seven differentially abundant genera between groups. The most significant finding was a Bacteroides enterotype in patients with acute schistosomiasis. These results suggest that S. japonicum infection has a significant effect on microbiome composition characterized by a higher abundance of the TM7 phylum and development of a Bacteroides enterotype.
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Affiliation(s)
- Yanyan Jiang
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, 200025 Shanghai, PR China - Chinese Center for Tropical Diseases Research, 200025 Shanghai, PR China - World Health Organization Collaborating Centre for Tropical Diseases, 200025 Shanghai, PR China - Key Laboratory of Parasite and Vector Biology, National Health Commission of the People's Republic of China, 200025 Shanghai, PR China
| | - Zhongying Yuan
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, 200025 Shanghai, PR China - Chinese Center for Tropical Diseases Research, 200025 Shanghai, PR China - World Health Organization Collaborating Centre for Tropical Diseases, 200025 Shanghai, PR China - Key Laboratory of Parasite and Vector Biology, National Health Commission of the People's Republic of China, 200025 Shanghai, PR China
| | - Yujuan Shen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, 200025 Shanghai, PR China - Chinese Center for Tropical Diseases Research, 200025 Shanghai, PR China - World Health Organization Collaborating Centre for Tropical Diseases, 200025 Shanghai, PR China - Key Laboratory of Parasite and Vector Biology, National Health Commission of the People's Republic of China, 200025 Shanghai, PR China
| | - Bruce A Rosa
- McDonnell Genome Institute, Washington University in St Louis, St Louis, 63001 MO, USA
| | - John Martin
- McDonnell Genome Institute, Washington University in St Louis, St Louis, 63001 MO, USA
| | - Shengkui Cao
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, 200025 Shanghai, PR China - Chinese Center for Tropical Diseases Research, 200025 Shanghai, PR China - World Health Organization Collaborating Centre for Tropical Diseases, 200025 Shanghai, PR China - Key Laboratory of Parasite and Vector Biology, National Health Commission of the People's Republic of China, 200025 Shanghai, PR China
| | - Yanjiao Zhou
- Department of Medicine, UConn Health, Farmington, 06023 CT, USA
| | - Makedonka Mitreva
- McDonnell Genome Institute, Washington University in St Louis, St Louis, 63001 MO, USA - Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St Louis, 63001 MO, USA
| | - Jianping Cao
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, 200025 Shanghai, PR China - Chinese Center for Tropical Diseases Research, 200025 Shanghai, PR China - World Health Organization Collaborating Centre for Tropical Diseases, 200025 Shanghai, PR China - Key Laboratory of Parasite and Vector Biology, National Health Commission of the People's Republic of China, 200025 Shanghai, PR China
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21
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Pope CE, Vo AT, Hayden HS, Weiss EJ, Durfey S, McNamara S, Ratjen A, Grogan B, Carter S, Nay L, Parsek MR, Singh PK, McKone EF, Aitken ML, Rosenfeld MR, Hoffman LR. Changes in fecal microbiota with CFTR modulator therapy: A pilot study. J Cyst Fibros 2021; 20:742-746. [PMID: 33390317 DOI: 10.1016/j.jcf.2020.12.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [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: 05/13/2020] [Revised: 11/18/2020] [Accepted: 12/03/2020] [Indexed: 11/28/2022]
Abstract
Studies have demonstrated that people with CF with pancreatic insufficiency (PI) have fecal dysbioses. Evidence suggests the causes of these dysbioses are multifactorial, and that important drivers include antibiotic exposure, dietary intake, and CF gastrointestinal tract dysfunction, including nutrient malabsorption. In this pilot study, we tested whether initiation of the CFTR modulator treatments ivacaftor (in a cohort of pancreatic sufficient (PS) people with CF and an R117H CFTR variant) or lumacaftor/ivacaftor (in a cohort of PI people with CF and an F508del variant) changed fecal measures of malabsorption or fecal microbiomes. While we identified no statistically significant fecal changes with either treatment, we detected trends in the PI cohort when initiating lumacaftor/ivacaftor towards decreased fecal fat content and towards fecal microbiomes that more closely resembled the fecal microbiota of people without PI. While these findings support a model in which nutrient malabsorption resulting from CF-induced PI drives fecal dysbiosis, they must be validated in future, larger studies of fecal microbiome and malabsorption outcomes with highly effective CFTR modulator therapies.
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Affiliation(s)
- C E Pope
- University of Washington, Seattle, USA
| | - A T Vo
- University of Washington, Seattle, USA
| | | | - E J Weiss
- University of Washington, Seattle, USA
| | - S Durfey
- University of Washington, Seattle, USA
| | | | - A Ratjen
- University of Washington, Seattle, USA
| | - B Grogan
- St. Vincent's University Hospital, Dublin, Ireland
| | - S Carter
- St. Vincent's University Hospital, Dublin, Ireland
| | - L Nay
- University of Washington, Seattle, USA
| | | | - P K Singh
- University of Washington, Seattle, USA
| | - E F McKone
- St. Vincent's University Hospital, Dublin, Ireland
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22
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Khine WWT, Rahayu ES, See TY, Kuah S, Salminen S, Nakayama J, Lee YK. Indonesian children fecal microbiome from birth until weaning was different from microbiomes of their mothers. Gut Microbes 2020; 12:1761240. [PMID: 32453977 PMCID: PMC7524161 DOI: 10.1080/19490976.2020.1761240] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [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: 02/03/2023] Open
Abstract
Gastrointestinal (GI) microbiota play an important role in human health and wellbeing and the first wave of gut microbes arrives mostly through vertical transmission from mother to child. This study has undertaken to understand the microbiota profile of healthy Southeast Asian mother-infant pairs. Here, we examined the fecal, vaginal and breast milk microbiota of Indonesian mothers and the fecal microbiota of their children from less than 1 month to 48 months old. To determine the immune status of children and the effect of diet at different ages, we examined the level of cytokines, bile acids in the fecal water and weaning food frequency. The fecal microbiota of the children before weaning contained mainly Bacteroides and Bifidobacterium, which presented at low abundance in the samples of mothers. After weaning, the fecal microbiome of children was mainly of the Prevotella type, with decreasing levels of Bifidobacterium, thus becoming more like the fecal microbiome of the mother. The abundance of infant fecal commensals generally correlated inversely with potential pathogens before weaning. The fecal Bifidobacterium in children correlated inversely with the consumption of complex carbohydrates and fruits after weaning. The specific cytokines related to the proliferation and maturation of immunity were found to increase after weaning. A decreasing level of primary bile acids and an increase of secondary bile acids were observed after weaning. This study highlights the change in the GI microbiota of infants to adult-type microbiota after weaning and identifies diet as a major contributing factor.
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Affiliation(s)
- Wei Wei Thwe Khine
- Department of Microbiology & Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore,Functional Foods Forum, Faculty of Medicine, University of Turku, Turku, Finland
| | - Endang Sutriswati Rahayu
- Faculty of Agricultural Technology and Center for Food & Nutrition Studies, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Ting Yi See
- Department of Microbiology & Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Sherwin Kuah
- Department of Microbiology & Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Seppo Salminen
- Functional Foods Forum, Faculty of Medicine, University of Turku, Turku, Finland
| | - Jiro Nakayama
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Yuan-Kun Lee
- Department of Microbiology & Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore,Department of Surgery, National University Hospital, Singapore,CONTACT Yuan-Kun Lee Department of Microbiology & Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2117545, Singapore
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23
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Gomez A, Sharma AK, Grev A, Sheaffer C, Martinson K. The Horse Gut Microbiome Responds in a Highly Individualized Manner to Forage Lignification. J Equine Vet Sci 2020; 96:103306. [PMID: 33349409 DOI: 10.1016/j.jevs.2020.103306] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 08/18/2020] [Revised: 10/13/2020] [Accepted: 10/13/2020] [Indexed: 12/30/2022]
Abstract
Although contributions of the equine gut microbiome to forage utilization are well recognized, the impact of alfalfa (Medicago sativa L.) lignification on the equine gut microbiome remains unknown; thus, we characterized microbial communities in the equine gut when feeding reduced lignin (RL) and conventional (CON) alfalfa hays to adult stock-type horses. Dietary treatments were fed to six horses in a crossover study. Experimental periods consisted of a 9-day dietary adaptation phase followed by a 5-day total fecal collection phase, during which horses were housed in individual box stalls and manure was removed on a continuous 24-hour basis. At 12-hour intervals, manure was mixed, frozen, and processed for V4, 16S rRNA amplicon MiSeq sequencing. Reduced lignin alfalfa did not shift microbiome composition equally across all horses; however, each subject's microbiome responded to hay lignin content in an individualized manner, mostly, in terms of beta diversity. Amplicon sequence variants affiliated to Akkermansia, Fibrobacter succinogenes, Treponema, and Paludibacter fluctuated significantly when RL alfalfa was fed, with abundance patterns unique to each horse. Horse-specific associations between individual gut microbiome traits and characteristics of the digested CON or RL alfalfa were also observed, mainly in regards to dry matter digestibility and mean fecal particle size. These results indicate that the horse gut microbiome responds in an individualized manner to changes in the amount of acid detergent lignin in alfalfa hay, potentially impacting several feed digestibility characteristics. The implications of these horse-specific responses to hay lignification, for metabolic health and performance, remain to be elucidated.
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Affiliation(s)
- Andres Gomez
- Department of Animal Science, University of Minnesota, St. Paul, MN.
| | | | - Amanda Grev
- Department of Animal Science, University of Minnesota, St. Paul, MN
| | - Craig Sheaffer
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN
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24
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Hu X, Xie Y, Xiao Y, Zeng W, Gong Z, Du J. Longitudinal analysis of fecal microbiome and metabolome during renal fibrotic progression in a unilateral ureteral obstruction animal model. Eur J Pharmacol 2020; 886:173555. [PMID: 32937112 DOI: 10.1016/j.ejphar.2020.173555] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 08/13/2020] [Revised: 09/04/2020] [Accepted: 09/12/2020] [Indexed: 02/02/2023]
Abstract
Renal fibrosis is a major pathological process in the progression of various chronic kidney diseases to end-stage renal disease (ESRD). Growing evidence has suggested that gut microbiota dysbiosis is closely related to ESRD. However, the interplay between altered fecal microbiome and metabolome during the renal fibrotic process remains unclear. Herein, an integrated approach of 16S ribosomal DNA sequencing combined with an ultra-high performance liquid chromatography-mass spectrometry-based metabolomics platform was applied to investigate the dynamic changes of fecal microbiota and metabolites throughout renal fibrosis progression in a mouse model of unilateral ureteral obstruction (UUO). The composition of gut microbiota changed markedly before and after UUO surgery. UUO mice showed a decrease in short-chain fatty acids-producing genera, including Bacteroides, Prevotellaceae_UCG-001, Roseburia, and Lachnospiraceae_NK4A136_group, as well as an increase in the genera Parasutterella and Alistipes, which changed dynamically over time. Additionally, 41 differential metabolites, mainly involved in 12 metabolic pathways, including inositol phosphate metabolism, primary bile acid biosynthesis, biosynthesis of unsaturated fatty acids, taurine and hypotaurine metabolism, purine metabolism, were identified in the UUO mice before and after surgery. Four fecal metabolites, myo-inositol, dodecanoic acid, N-acetylputrescine, and anthranilic acid, were positively associated with the progression of renal fibrosis. Moreover, by using multi-omics analyses, we found the alteration in UUO-related gut microbiota was correlated with a change in fecal metabolites. Therefore, our results provide insights into disturbances of the microbiome-metabolome interface in the progression of UUO-related renal fibrosis.
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Affiliation(s)
- Xiaofang Hu
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China; The Hunan Institute of Pharmacy Practice and Clinical Research, Changsha, 410008, Hunan, China
| | - Yuhong Xie
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China; The Hunan Institute of Pharmacy Practice and Clinical Research, Changsha, 410008, Hunan, China
| | - Yi Xiao
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China; The Hunan Institute of Pharmacy Practice and Clinical Research, Changsha, 410008, Hunan, China
| | - Wenjing Zeng
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China; The Hunan Institute of Pharmacy Practice and Clinical Research, Changsha, 410008, Hunan, China
| | - Zhicheng Gong
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China; The Hunan Institute of Pharmacy Practice and Clinical Research, Changsha, 410008, Hunan, China.
| | - Jie Du
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China; The Hunan Institute of Pharmacy Practice and Clinical Research, Changsha, 410008, Hunan, China.
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25
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Ramsteijn AS, Jašarević E, Houwing DJ, Bale TL, Olivier JDA. Antidepressant treatment with fluoxetine during pregnancy and lactation modulates the gut microbiome and metabolome in a rat model relevant to depression. Gut Microbes 2020; 11:735-753. [PMID: 31971855 PMCID: PMC7524305 DOI: 10.1080/19490976.2019.1705728] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [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: 02/03/2023] Open
Abstract
Up to 10% of women use selective serotonin reuptake inhibitor (SSRI) antidepressants during pregnancy and postpartum. Recent evidence suggests that SSRIs are capable of altering the gut microbiota. However, the interaction between maternal depression and SSRI use on bacterial community composition and the availability of microbiota-derived metabolites during pregnancy and lactation is not clear. We studied this using a rat model relevant to depression, where adult females with a genetic vulnerability and stressed as pups show depressive-like behaviors. Throughout pregnancy and lactation, females received the SSRI fluoxetine or vehicle. High-resolution 16S ribosomal RNA marker gene sequencing and targeted metabolomic analysis were used to assess the fecal microbiome and metabolite availability, respectively. Not surprisingly, we found that pregnancy and lactation segregate in terms of fecal microbiome diversity and composition, accompanied by changes in metabolite availability. However, we also showed that fluoxetine treatment altered important features of this transition from pregnancy to lactation most clearly in previously stressed dams, with lower fecal amino acid concentrations. Amino acid concentrations, in turn, correlated negatively with the relative abundance of bacterial taxa such as Prevotella and Bacteroides. Our study demonstrates an important relationship between antidepressant use during the perinatal period and maternal fecal metabolite availability in a rat model relevant to depression, possibly through parallel changes in the gut microbiome. Since microbial metabolites contribute to homeostasis and development, insults to the maternal microbiome by SSRIs might have health consequences for mother and offspring.
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Affiliation(s)
- Anouschka S Ramsteijn
- Department of Neurobiology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands,Center for Host-Microbial Interactions,Department of Biomedical Sciences, School of Veterinary Medicine and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Eldin Jašarević
- Center for Host-Microbial Interactions,Department of Biomedical Sciences, School of Veterinary Medicine and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA,Department of Pharmacology, Center for Epigenetic Research in Child Health and Brain Development, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Danielle J Houwing
- Department of Neurobiology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Tracy L Bale
- Center for Host-Microbial Interactions,Department of Biomedical Sciences, School of Veterinary Medicine and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA,Department of Pharmacology, Center for Epigenetic Research in Child Health and Brain Development, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Jocelien DA Olivier
- Department of Neurobiology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands,CONTACT Jocelien DA Olivier Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, Groningen9747 AG, The Netherlands
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26
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Li Y, Li RX, Du YT, Xu XJ, Xue Y, Gao D, Gao T, Sheng Z, Zhang LY, Tuo HZ. [Features of gut microbiota in patients with idiopathic Parkinson's disease]. Zhonghua Yi Xue Za Zhi 2020; 100:1017-1022. [PMID: 32294860 DOI: 10.3760/cma.j.cn112137-20190702-01480] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objectives: To investigate whether the fecal microbiome of Parkinson's disease patients differs from that of healthy population and explore the pathogenesis and new treatment of idiopathic Parkinson's disease. Methods: A total of 30 patients diagnosed as idiopathic Parkinson disease (PD group) in Beijing Friendship Hospital between April 2017 and June 2018 were enrolled and 30 healthy controls (NC group) were recruited at the same time.Medical records and score of unified Parkinson's disease rating scale (UPDRS) were collected and fresh fecal samples were obtained and stored in refrigerator (-80℃). The microbial compositions of fecal samples were investigated by 16S rRNA gene sequencing targeting the V3-V4 region. The taxa abundance and microbial composition were tested. Results: There was no difference of age and sex in PD and NC groups. Chao1 and Shannon indexes tended to be higher in PD group, yet failed to reach statistic significance (P=0.115 and 0.052). Relative abundance of gut microbiota differed in each taxonomic category. The relative abundance of Firmicutes in PD group was 53.6%(41.7%-64.8%), while that of Bacteroidetes in NC group was 51.7%(31.7%-65.3%). The ratios of Firmicutes to Bacteroidetes were significantly different between the two groups (1.6(0.9-3.4) vs 0.7(0.5-1.4), P=0.001). In Clostridia, Bacilli and Erysipelotrichia of Firmicutes, the relative abundances of Clostridiales, Christensenellaceae, Peptoclostridium, Lactobacillus and Erysipelatoclostridium were higher in PD group (P=0.024, 0.046, 0.036, 0.022 and 0.037). The relative abundance of Prevotella of Bacteroidales, was lower in PD group, yet failed to reach statistic significance (P=0.121). The relative abundances of Alistipes of Rikenellaceae and Butyricimonas of Marinilabiliales in PD group were significantly higher than those in NC group (P=0.047 and 0.033). The relative abundance of Bifidobacterium of Actinobacteria was significanly higher in PD group when compared with NC group (P=0.009). Despite the relatively low abundance, Akkermansia of Verrucomicrobia was significantly higher in PD group than in NC group (P=0.025). Conclusion: The structures of the fecal microbiota differ significantly between PD patients and healthy controls.
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Affiliation(s)
- Y Li
- Department of Neurology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
| | - R X Li
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
| | - Y T Du
- Department of Neurology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
| | - X J Xu
- Department of Neurology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
| | - Y Xue
- Department of Neurology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
| | - D Gao
- Department of Neurology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
| | - T Gao
- Department of Neurology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
| | - Z Sheng
- Department of Neurology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
| | - L Y Zhang
- Department of Neurology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
| | - H Z Tuo
- Department of Neurology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
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Holman DB, Yang W, Alexander TW. Antibiotic treatment in feedlot cattle: a longitudinal study of the effect of oxytetracycline and tulathromycin on the fecal and nasopharyngeal microbiota. Microbiome 2019; 7:86. [PMID: 31167657 PMCID: PMC6549328 DOI: 10.1186/s40168-019-0696-4] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 05/19/2019] [Indexed: 05/12/2023]
Abstract
BACKGROUND Beef cattle in North America frequently receive an antibiotic injection after feedlot placement to control and manage bovine respiratory disease. The potential collateral effect of these antibiotics on the bovine microbiome is largely unknown. Therefore, we determined the longitudinal impact of two commonly administered veterinary antibiotics, oxytetracycline and tulathromycin, on the fecal and nasopharyngeal (NP) microbiota of beef cattle that were transported to a feedlot. We also report the effect these antibiotics have on several antibiotic resistance determinants in both the fecal and NP microbiome. RESULTS Oxytetracycline and tulathromycin perturbation of the bovine fecal and NP microbiota was greatest at days 2 and 5. Although the NP microbiota of the tulathromycin-treated cattle had recovered by day 12, the NP microbiota of the oxytetracycline-treated group remained altered through day 34. Overall, the NP microbiota appeared to be more sensitive to antibiotic treatment than the fecal microbiota. Members of the bacterial Microbacteriaceae family were most notably affected by antibiotic administration in the NP microbiota. Both antibiotics protected against Pasteurella spp. in the nasopharynx at days 2 and 5. Despite very similar diets at both locations, the largest shift in the fecal and NP microbiota occurred after transport to the feedlot (P < 0.05). Antibiotic resistance determinants in the NP microbiome were also affected more strongly by antibiotic treatment than those in the fecal microbiome. Oxytetracycline increased the proportion of erm(X), sul2, tet(H), tet(M), and tet(W) in NP samples and tet(M) and tet(W) in fecal samples, at day 12 (P < 0.05). The effect of tulathromycin on the relative abundance of resistance genes in the NP microbiome was greatest at day 34 as erm(X), sul2, and tet(M) were enriched (P < 0.05). CONCLUSIONS Administration of a single injection of oxytetracycline and tulathromycin resulted in significant changes in the NP and fecal microbiota during the first 5 days after treatment. Antibiotic treatment also increased the relative abundance of several antibiotic resistance determinants in the fecal and NP microbiome at either day 12 or 34.
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Affiliation(s)
- Devin B Holman
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada
| | - Wenzhu Yang
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Trevor W Alexander
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada.
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Jiang X, Lu N, Xue Y, Liu S, Lei H, Tu W, Lu Y, Xia D. Crude fiber modulates the fecal microbiome and steroid hormones in pregnant Meishan sows. Gen Comp Endocrinol 2019; 277:141-147. [PMID: 30951727 DOI: 10.1016/j.ygcen.2019.04.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [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: 10/11/2018] [Revised: 03/11/2019] [Accepted: 04/01/2019] [Indexed: 01/22/2023]
Abstract
The beneficial effects of dietary fiber on the reproductive performance and welfare of sows have been discussed broadly, but few researches examined the causal changes and the association of gut microbiota and the steroid hormones, the main regulators of reproductive function. To shed light on this, thirty-six Meishan sows were allocated into 2.5% crude fiber (CF) group and 7.5% CF group respectively for an entire farrowing interval. On the 90th day of gestation, the saliva and fresh stool of sows were individually collected in the morning (06:00-07:00) for steroid hormones, short-chain fatty acids (SCFAs) and microbiome analysis. In addition, the parameter of pregnant behavioral and farrowing performance was recorded and evaluated. We observed that, as compared with the 2.5% CF treatment, 7.5% CF significantly increased the litter size (p = 0.01), reduced the stereotypic behaviors including sham chewing, rolling tongue and licking ground (p = 0.02, 0.04, 0.01) at later gestation stage, but increased lying time (p = 0.00). In coincide with this, 7.5% CF diet increased the salivary progesterone (p = 0.00), fecal estradiol and progesterone (p = 0.01, 0.02) level, fecal water and SCFAs content (p = 0.02, 0.03), decreased the salivary and fecal cortisol (p = 0.01, 0.00) level. Further, 7.5% CF diet increased the fecal microbiota richness (ACE, p = 0.04; Chao, p = 0.07) and diversity (Shannon, p = 0.01; Simpson, p = 0.04), the proportion of genus Ruminococcus, Butyrivibrio, Lactobacillus and Fibrobacter (p = 0.02, 0.05, 0.04, 0.00), whereas reduced the proportion of genus Clostridium, Streptococcus, Bacteroides and Escherichia-Shigella (p = 0.00, 0.00, 0.04, 0.04). These results indicate that, fibrous diet can regulate the steroid hormones secretion and modulate the gut with more cellulose-degrading and probiotic bacterium, but less opportunistic pathogens, and this may contribute to the improvement of reproductive performance and welfare in sows.
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Affiliation(s)
- Xueyuan Jiang
- Shanghai Engineering Research Center of Breeding Pig, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Naisheng Lu
- Shanghai Engineering Research Center of Breeding Pig, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Yun Xue
- Shanghai Engineering Research Center of Breeding Pig, Shanghai Academy of Agricultural Sciences, Shanghai, PR China; Shanghai Animal Disease Control Center, Shanghai, PR China
| | - Suli Liu
- Shanghai Engineering Research Center of Breeding Pig, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Hulong Lei
- Shanghai Engineering Research Center of Breeding Pig, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Weilong Tu
- Shanghai Engineering Research Center of Breeding Pig, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Yang Lu
- Shanghai Engineering Research Center of Breeding Pig, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Dong Xia
- Shanghai Engineering Research Center of Breeding Pig, Shanghai Academy of Agricultural Sciences, Shanghai, PR China.
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Westreich ST, Ardeshir A, Alkan Z, Kable ME, Korf I, Lemay DG. Fecal metatranscriptomics of macaques with idiopathic chronic diarrhea reveals altered mucin degradation and fucose utilization. Microbiome 2019; 7:41. [PMID: 30885266 PMCID: PMC6423747 DOI: 10.1186/s40168-019-0664-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 03/11/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND Idiopathic chronic diarrhea (ICD) is a common cause of morbidity and mortality among juvenile rhesus macaques. Characterized by chronic inflammation of the colon and repeated bouts of diarrhea, ICD is largely unresponsive to medical interventions, including corticosteroid, antiparasitic, and antibiotic treatments. Although ICD is accompanied by large disruptions in the composition of the commensal gut microbiome, no single pathogen has been concretely identified as responsible for the onset and continuation of the disease. RESULTS Fecal samples were collected from 12 ICD-diagnosed macaques and 12 age- and sex-matched controls. RNA was extracted for metatranscriptomic analysis of organisms and functional annotations associated with the gut microbiome. Bacterial, fungal, archaeal, protozoan, and macaque (host) transcripts were simultaneously assessed. ICD-afflicted animals were characterized by increased expression of host-derived genes involved in inflammation and increased transcripts from bacterial pathogens such as Campylobacter and Helicobacter and the protozoan Trichomonas. Transcripts associated with known mucin-degrading organisms and mucin-degrading enzymes were elevated in the fecal microbiomes of ICD-afflicted animals. Assessment of colon sections using immunohistochemistry and of the host transcriptome suggests differential fucosylation of mucins between control and ICD-afflicted animals. Interrogation of the metatranscriptome for fucose utilization genes reveals possible mechanisms by which opportunists persist in ICD. Bacteroides sp. potentially cross-fed fucose to Haemophilus whereas Campylobacter expressed a mucosa-associated transcriptome with increased expression of adherence genes. CONCLUSIONS The simultaneous profiling of bacterial, fungal, archaeal, protozoan, and macaque transcripts from stool samples reveals that ICD of rhesus macaques is associated with increased gene expression by pathogens, increased mucin degradation, and altered fucose utilization. The data suggest that the ICD-afflicted host produces fucosylated mucins that are leveraged by potentially pathogenic microbes as a carbon source or as adhesion sites.
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Affiliation(s)
| | - Amir Ardeshir
- California National Primate Research Center, University of California, Davis, California USA
| | - Zeynep Alkan
- USDA ARS Western Human Nutrition Research Center, Davis, California USA
| | - Mary E. Kable
- USDA ARS Western Human Nutrition Research Center, Davis, California USA
- Department of Nutrition, University of California, Davis, California USA
| | - Ian Korf
- Genome Center, University of California, Davis, California USA
| | - Danielle G. Lemay
- Genome Center, University of California, Davis, California USA
- USDA ARS Western Human Nutrition Research Center, Davis, California USA
- Department of Nutrition, University of California, Davis, California USA
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Best of the 2019 AUA Annual Meeting: Highlights From the 2019 American Urological Association Annual Meeting, May 3-6, 2019, Chicago, IL. Rev Urol 2019; 21:109-17. [PMID: 31768138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
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Bever CS, Rand AA, Nording M, Taft D, Kalanetra KM, Mills DA, Breck MA, Smilowitz JT, German JB, Hammock BD. Effects of triclosan in breast milk on the infant fecal microbiome. Chemosphere 2018; 203:467-473. [PMID: 29635158 PMCID: PMC5915298 DOI: 10.1016/j.chemosphere.2018.03.186] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 03/14/2018] [Accepted: 03/26/2018] [Indexed: 05/05/2023]
Abstract
Triclosan is frequently used for its antimicrobial properties and has been detected in human serum, urine, and breast milk. Animal and molecular studies have shown that triclosan exerts a wide range of adverse health effects at both high (ppm) and low (ppb) concentrations. Since triclosan is of growing concern to human and environmental health, there is a need to improve extraction procedures and to study additional effects from triclosan exposure. In this study, we have improved triclosan extraction from breast milk by using salt (MgSO4) to reduce emulsion formation and increase water polarity and water (∼80%) to enhance the overall extraction efficiency (∼3.5 fold). This extraction method was applied to breast milk samples collected from donors who i) recorded their use of triclosan-containing personal care products and ii) provided matching infant stool samples. Of the participants who had detectable amounts of triclosan in their breast milk, nine (75%) of them reported daily use of triclosan-containing personal care products. Levels of triclosan in breast milk were compared to the donor's infant's fecal microbiome. We found that the bacterial diversity in the fecal microbiome of the infants exposed to breast milk with detectable triclosan levels differed compared to their peers exposed to milk containing non-detectable amounts. This finding implies that exogenous chemicals are impacting microbiome diversity.
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Affiliation(s)
- Candace S Bever
- Department of Entomology and Nematology, and UCD Comprehensive Cancer Center, University of California Davis, Davis, CA 95616, USA.
| | - Amy A Rand
- Department of Entomology and Nematology, and UCD Comprehensive Cancer Center, University of California Davis, Davis, CA 95616, USA
| | - Malin Nording
- Department of Entomology and Nematology, and UCD Comprehensive Cancer Center, University of California Davis, Davis, CA 95616, USA
| | - Diana Taft
- Department of Food Science and Technology, University of California Davis, Davis, CA 95616, USA
| | - Karen M Kalanetra
- Department of Food Science and Technology, University of California Davis, Davis, CA 95616, USA; Department of Viticulture and Enology, University of California Davis, Davis, CA 95616, USA
| | - David A Mills
- Department of Food Science and Technology, University of California Davis, Davis, CA 95616, USA; Department of Viticulture and Enology, University of California Davis, Davis, CA 95616, USA
| | - Melissa A Breck
- Department of Food Science and Technology, University of California Davis, Davis, CA 95616, USA
| | - Jennifer T Smilowitz
- Department of Food Science and Technology, University of California Davis, Davis, CA 95616, USA; Foods for Health Institute, University of California Davis, Davis, CA 95616, USA
| | - J Bruce German
- Department of Food Science and Technology, University of California Davis, Davis, CA 95616, USA; Foods for Health Institute, University of California Davis, Davis, CA 95616, USA
| | - Bruce D Hammock
- Department of Entomology and Nematology, and UCD Comprehensive Cancer Center, University of California Davis, Davis, CA 95616, USA.
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Fieten KB, Totté JEE, Levin E, Reyman M, Meijer Y, Knulst A, Schuren F, Pasmans SGMA. Fecal Microbiome and Food Allergy in Pediatric Atopic Dermatitis: A Cross-Sectional Pilot Study. Int Arch Allergy Immunol 2018; 175:77-84. [PMID: 29393195 DOI: 10.1159/000484897] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 10/31/2017] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Exposure to microbes may be important in the development of atopic disease. Atopic diseases have been associated with specific characteristics of the intestinal microbiome. The link between intestinal microbiota and food allergy has rarely been studied, and the gold standard for diagnosing food allergy (double-blind placebo-controlled food challenge [DBPCFC]) has seldom been used. We aimed to distinguish fecal microbial signatures for food allergy in children with atopic dermatitis (AD). METHODS Pediatric patients with AD, with and without food allergy, were included in this cross-sectional observational pilot study. AD was diagnosed according to the UK Working Party criteria. Food allergy was defined as a positive DBPCFC or a convincing clinical history, in combination with sensitization to the relevant food allergen. Fecal samples were analyzed using 16S rRNA microbial analysis. Microbial signature species, discriminating between the presence and absence food allergy, were selected by elastic net regression. RESULTS Eighty-two children with AD (39 girls) with a median age of 2.5 years, and 20 of whom were diagnosed with food allergy, provided fecal samples. Food allergy to peanut and cow's milk was the most common. Six bacterial species from the fecal microbiome were identified, that, when combined, distinguished between children with and without food allergy: Bifidobacterium breve, Bifidobacterium pseudocatenulatum, Bifidobacterium adolescentis, Escherichia coli, Faecalibacterium prausnitzii, and Akkermansia muciniphila (AUC 0.83, sensitivity 0.77, specificity 0.80). CONCLUSIONS In this pilot study, we identified a microbial signature in children with AD that discriminates between the absence and presence of food allergy. Future studies are needed to confirm our findings.
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Lu D, Tiezzi F, Schillebeeckx C, McNulty NP, Schwab C, Shull C, Maltecca C. Host contributes to longitudinal diversity of fecal microbiota in swine selected for lean growth. Microbiome 2018; 6:4. [PMID: 29301569 PMCID: PMC5755158 DOI: 10.1186/s40168-017-0384-1] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 12/14/2017] [Indexed: 05/16/2023]
Abstract
BACKGROUND In pigs, gut bacteria have been shown to play important roles in nutritional, physiological, and immunological processes in the host. However, the contribution of their metagenomes or part of them, which are normally reflected by fragments of 16S rRNA-encoding genes, has yet to be fully investigated. RESULTS Fecal samples, collected from a population of crossbred pigs at three time points, including weaning, week 15 post weaning (hereafter "week 15"), and end-of-feeding test (hereafter "off-test"), were used to evaluate changes in the composition of the fecal microbiome of each animal over time. This study used 1205, 1295, and 1283 samples collected at weaning, week 15, and off-test, respectively. There were 1039 animals that had samples collected at all three time points and also had phenotypic records on back fat thickness (BF) and average daily body weight gain (ADG). Firmicutes and Bacteroidetes were the most abundant phyla at all three time points. The most abundant genera at all three time points included Clostridium, Escherichia, Bacteroides, Prevotella, Ruminococcus, Fusobacterium, Campylobacter, Eubacterium, and Lactobacillus. Two enterotypes were identified at each time point. However, only enterotypes at week 15 and off-test were significantly associated with BF. We report herein two novel findings: (i) alpha diversity and operational taxonomic unit (OTU) richness were moderately heritable at week 15, h2 of 0.15 ± 0.06 to 0.16 ± 0.07 and 0.23 ± 0.09 to 0.26 ± 0.08, respectively, as well as at off-test, h2 of 0.20 ± 0.09 to 0.33 ± 0.10 and 0.17 ± 0.08 to 0.24 ± 0.08, respectively, whereas very low heritability estimates for both measures were detected at weaning; and (ii) alpha diversity at week 15 had strong and negative genetic correlations with BF, - 0.53 ± 0.23 to - 0.45 ± 0.25, as well as with ADG, - 0.53 ± 0.32 to - 0.53 ± 0.29. CONCLUSIONS These results are important for efforts to genetically improve the domesticated pig because they suggest fecal microbiota diversity can be used as an indicator trait to improve traits that are expensive to measure.
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Affiliation(s)
- Duc Lu
- Department of Animal Science, North Carolina State University, Raleigh, 27606 NC USA
| | - Francesco Tiezzi
- Department of Animal Science, North Carolina State University, Raleigh, 27606 NC USA
| | | | - Nathan P. McNulty
- Matatu Inc., 4320 Forest Park Ave., Suite 321, Saint Louis, 63108 MO USA
| | | | | | - Christian Maltecca
- Department of Animal Science, North Carolina State University, Raleigh, 27606 NC USA
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Nash AK, Auchtung TA, Wong MC, Smith DP, Gesell JR, Ross MC, Stewart CJ, Metcalf GA, Muzny DM, Gibbs RA, Ajami NJ, Petrosino JF. The gut mycobiome of the Human Microbiome Project healthy cohort. Microbiome 2017; 5:153. [PMID: 29178920 PMCID: PMC5702186 DOI: 10.1186/s40168-017-0373-4] [Citation(s) in RCA: 484] [Impact Index Per Article: 69.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Accepted: 11/14/2017] [Indexed: 05/02/2023]
Abstract
BACKGROUND Most studies describing the human gut microbiome in healthy and diseased states have emphasized the bacterial component, but the fungal microbiome (i.e., the mycobiome) is beginning to gain recognition as a fundamental part of our microbiome. To date, human gut mycobiome studies have primarily been disease centric or in small cohorts of healthy individuals. To contribute to existing knowledge of the human mycobiome, we investigated the gut mycobiome of the Human Microbiome Project (HMP) cohort by sequencing the Internal Transcribed Spacer 2 (ITS2) region as well as the 18S rRNA gene. RESULTS Three hundred seventeen HMP stool samples were analyzed by ITS2 sequencing. Fecal fungal diversity was significantly lower in comparison to bacterial diversity. Yeast dominated the samples, comprising eight of the top 15 most abundant genera. Specifically, fungal communities were characterized by a high prevalence of Saccharomyces, Malassezia, and Candida, with S. cerevisiae, M. restricta, and C. albicans operational taxonomic units (OTUs) present in 96.8, 88.3, and 80.8% of samples, respectively. There was a high degree of inter- and intra-volunteer variability in fungal communities. However, S. cerevisiae, M. restricta, and C. albicans OTUs were found in 92.2, 78.3, and 63.6% of volunteers, respectively, in all samples donated over an approximately 1-year period. Metagenomic and 18S rRNA gene sequencing data agreed with ITS2 results; however, ITS2 sequencing provided greater resolution of the relatively low abundance mycobiome constituents. CONCLUSIONS Compared to bacterial communities, the human gut mycobiome is low in diversity and dominated by yeast including Saccharomyces, Malassezia, and Candida. Both inter- and intra-volunteer variability in the HMP cohort were high, revealing that unlike bacterial communities, an individual's mycobiome is no more similar to itself over time than to another person's. Nonetheless, several fungal species persisted across a majority of samples, evidence that a core gut mycobiome may exist. ITS2 sequencing data provided greater resolution of the mycobiome membership compared to metagenomic and 18S rRNA gene sequencing data, suggesting that it is a more sensitive method for studying the mycobiome of stool samples.
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Affiliation(s)
- Andrea K. Nash
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX USA
| | - Thomas A. Auchtung
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX USA
| | - Matthew C. Wong
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX USA
| | - Daniel P. Smith
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX USA
| | - Jonathan R. Gesell
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX USA
| | - Matthew C. Ross
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX USA
| | - Christopher J. Stewart
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX USA
| | - Ginger A. Metcalf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - Donna M. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - Nadim J. Ajami
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX USA
| | - Joseph F. Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX USA
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Oetama VSP, Hennersdorf P, Abdul-Aziz MA, Mrotzek G, Haryanti H, Saluz HP. Microbiome analysis and detection of pathogenic bacteria of Penaeus monodon from Jakarta Bay and Bali. Mar Pollut Bull 2016; 110:718-725. [PMID: 27090886 DOI: 10.1016/j.marpolbul.2016.03.043] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 03/09/2016] [Accepted: 03/20/2016] [Indexed: 06/05/2023]
Abstract
Penaeus monodon, the Asian black tiger shrimp is one of the most widely consumed marine crustaceans worldwide. In this study, we examine and compare the fecal microbiota of P. monodon from highly polluted waters around Jakarta Bay, with those of less polluted waters of Bali. Using next generation sequencing techniques, we identified potential bacterial pathogens and common viral diseases of shrimp. Proteobacteria (96.08%) was found to be the most predominant phylum, followed by Bacteriodetes (2.32%), Fusobacteria (0.96%), and Firmicutes (0.53%). On the order level, Vibrionales (66.20%) and Pseudoaltermonadales (24.81%) were detected as predominant taxa. qPCR profiling was used as a confirmatory step and further revealed Vibrio alginolyticus and Photobacterium damselae as two potential pathogenic species present in most of the samples. In addition, viral diseases for shrimp were discovered among the samples, WSSV in Jakarta free-living samples, YHV in Bali free-living samples and IHHNV in both.
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Affiliation(s)
- Vincensius S P Oetama
- Leibniz-Institute for Natural Product Research and Infection Biology, Beutenbergstr. 11a, D-07745 Jena, Germany; Friedrich Schiller University of Jena, Fürstengraben 1, D-07743 Jena, Germany
| | - Philipp Hennersdorf
- Leibniz-Institute for Natural Product Research and Infection Biology, Beutenbergstr. 11a, D-07745 Jena, Germany; Friedrich Schiller University of Jena, Fürstengraben 1, D-07743 Jena, Germany
| | - Muslihudeen A Abdul-Aziz
- Friedrich Schiller University of Jena, Fürstengraben 1, D-07743 Jena, Germany; Australian Centre for Ancient DNA, University of Adelaide, Adelaide, South Australia, Australia
| | - Grit Mrotzek
- Leibniz-Institute for Natural Product Research and Infection Biology, Beutenbergstr. 11a, D-07745 Jena, Germany
| | - Haryanti Haryanti
- Gondol Research Institute for Mariculture GRIM, ds Penyabangan, Br. Gondol, PO. Box 140, Singaraja 81101, Bali, Indonesia
| | - Hans Peter Saluz
- Leibniz-Institute for Natural Product Research and Infection Biology, Beutenbergstr. 11a, D-07745 Jena, Germany; Friedrich Schiller University of Jena, Fürstengraben 1, D-07743 Jena, Germany
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Beaumont M, Goodrich JK, Jackson MA, Yet I, Davenport ER, Vieira-Silva S, Debelius J, Pallister T, Mangino M, Raes J, Knight R, Clark AG, Ley RE, Spector TD, Bell JT. Heritable components of the human fecal microbiome are associated with visceral fat. Genome Biol 2016; 17:189. [PMID: 27666579 PMCID: PMC5036307 DOI: 10.1186/s13059-016-1052-7] [Citation(s) in RCA: 149] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 08/31/2016] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Variation in the human fecal microbiota has previously been associated with body mass index (BMI). Although obesity is a global health burden, the accumulation of abdominal visceral fat is the specific cardio-metabolic disease risk factor. Here, we explore links between the fecal microbiota and abdominal adiposity using body composition as measured by dual-energy X-ray absorptiometry in a large sample of twins from the TwinsUK cohort, comparing fecal 16S rRNA diversity profiles with six adiposity measures. RESULTS We profile six adiposity measures in 3666 twins and estimate their heritability, finding novel evidence for strong genetic effects underlying visceral fat and android/gynoid ratio. We confirm the association of lower diversity of the fecal microbiome with obesity and adiposity measures, and then compare the association between fecal microbial composition and the adiposity phenotypes in a discovery subsample of twins. We identify associations between the relative abundances of fecal microbial operational taxonomic units (OTUs) and abdominal adiposity measures. Most of these results involve visceral fat associations, with the strongest associations between visceral fat and Oscillospira members. Using BMI as a surrogate phenotype, we pursue replication in independent samples from three population-based cohorts including American Gut, Flemish Gut Flora Project and the extended TwinsUK cohort. Meta-analyses across the replication samples indicate that 8 OTUs replicate at a stringent threshold across all cohorts, while 49 OTUs achieve nominal significance in at least one replication sample. Heritability analysis of the adiposity-associated microbial OTUs prompted us to assess host genetic-microbe interactions at obesity-associated human candidate loci. We observe significant associations of adiposity-OTU abundances with host genetic variants in the FHIT, TDRG1 and ELAVL4 genes, suggesting a potential role for host genes to mediate the link between the fecal microbiome and obesity. CONCLUSIONS Our results provide novel insights into the role of the fecal microbiota in cardio-metabolic disease with clear potential for prevention and novel therapies.
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Affiliation(s)
- Michelle Beaumont
- Department of Twin Research & Genetic Epidemiology, King's College London, St Thomas' Hospital, 3rd Floor, South Wing, Block D, London, SE1 7EH, UK
| | - Julia K Goodrich
- Department of Microbiology, Cornell University, Ithaca, NY, 14853, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Matthew A Jackson
- Department of Twin Research & Genetic Epidemiology, King's College London, St Thomas' Hospital, 3rd Floor, South Wing, Block D, London, SE1 7EH, UK
| | - Idil Yet
- Department of Twin Research & Genetic Epidemiology, King's College London, St Thomas' Hospital, 3rd Floor, South Wing, Block D, London, SE1 7EH, UK
| | - Emily R Davenport
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Sara Vieira-Silva
- Department of Microbiology and Immunology, KU Leuven - University of Leuven, Leuven, Belgium
- VIB lab for Bioinformatics and (eco-)systems biology, Leuven, Belgium
| | - Justine Debelius
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO, 80309, USA
- Present address: Departments of Pediatrics and Computer Science and Engineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Tess Pallister
- Department of Twin Research & Genetic Epidemiology, King's College London, St Thomas' Hospital, 3rd Floor, South Wing, Block D, London, SE1 7EH, UK
| | - Massimo Mangino
- Department of Twin Research & Genetic Epidemiology, King's College London, St Thomas' Hospital, 3rd Floor, South Wing, Block D, London, SE1 7EH, UK
| | - Jeroen Raes
- Department of Microbiology and Immunology, KU Leuven - University of Leuven, Leuven, Belgium
- VIB lab for Bioinformatics and (eco-)systems biology, Leuven, Belgium
| | - Rob Knight
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO, 80309, USA
- Biofrontiers Institute, University of Colorado, Boulder, CO, 80309, USA
- Howard Hughes Medical Institute, Boulder, CO, 80309, USA
- Present address: Departments of Pediatrics and Computer Science and Engineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Andrew G Clark
- Department of Microbiology, Cornell University, Ithaca, NY, 14853, USA
| | - Ruth E Ley
- Department of Microbiology, Cornell University, Ithaca, NY, 14853, USA
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Tim D Spector
- Department of Twin Research & Genetic Epidemiology, King's College London, St Thomas' Hospital, 3rd Floor, South Wing, Block D, London, SE1 7EH, UK.
| | - Jordana T Bell
- Department of Twin Research & Genetic Epidemiology, King's College London, St Thomas' Hospital, 3rd Floor, South Wing, Block D, London, SE1 7EH, UK.
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Eichmiller JJ, Hamilton MJ, Staley C, Sadowsky MJ, Sorensen PW. Environment shapes the fecal microbiome of invasive carp species. Microbiome 2016; 4:44. [PMID: 27514729 PMCID: PMC4981970 DOI: 10.1186/s40168-016-0190-1] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 08/02/2016] [Indexed: 05/20/2023]
Abstract
BACKGROUND Although the common, silver, and bighead carps are native and sparsely distributed in Eurasia, these fish have become abundant and invasive in North America. An understanding of the biology of these species may provide insights into sustainable control methods. The animal-associated microbiome plays an important role in host health. Characterization of the carp microbiome and the factors that affect its composition is an important step toward understanding the biology and interrelationships between these species and their environments. RESULTS We compared the fecal microbiomes of common, silver, and bighead carps from wild and laboratory environments using Illumina sequencing of bacterial 16S ribosomal RNA (rRNA). The fecal bacterial communities of fish were diverse, with Shannon indices ranging from 2.3 to 4.5. The phyla Proteobacteria, Firmicutes, and Fusobacteria dominated carp guts, comprising 76.7 % of total reads. Environment played a large role in shaping fecal microbial community composition, and microbiomes among captive fishes were more similar than among wild fishes. Although differences among wild fishes could be attributed to feeding preferences, diet did not strongly affect microbial community structure in laboratory-housed fishes. Comparison of wild- and lab-invasive carps revealed five shared OTUs that comprised approximately 40 % of the core fecal microbiome. CONCLUSIONS The environment is a dominant factor shaping the fecal bacterial communities of invasive carps. Captivity alters the microbiome community structure relative to wild fish, while species differences are pronounced within habitats. Despite the absence of a true stomach, invasive carp species exhibited a core microbiota that warrants future study.
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Affiliation(s)
- Jessica J. Eichmiller
- Department of Fisheries, Wildlife, and Conservation Biology, Minnesota Aquatic Invasive Species Research Center, University of Minnesota, Twin Cities, Saint Paul, MN 55108 USA
| | - Matthew J. Hamilton
- Department of Soil, Water and Climate, Biotechnology Institute, University of Minnesota, Saint Paul, MN 55108 USA
| | - Christopher Staley
- Department of Soil, Water and Climate, Biotechnology Institute, University of Minnesota, Saint Paul, MN 55108 USA
| | - Michael J. Sadowsky
- Department of Fisheries, Wildlife, and Conservation Biology, Minnesota Aquatic Invasive Species Research Center, University of Minnesota, Twin Cities, Saint Paul, MN 55108 USA
- Department of Soil, Water and Climate, Biotechnology Institute, University of Minnesota, Saint Paul, MN 55108 USA
| | - Peter W. Sorensen
- Department of Fisheries, Wildlife, and Conservation Biology, Minnesota Aquatic Invasive Species Research Center, University of Minnesota, Twin Cities, Saint Paul, MN 55108 USA
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Janabi AHD, Kerkhof LJ, McGuinness LR, Biddle AS, McKeever KH. Comparison of a modified phenol/chloroform and commercial-kit methods for extracting DNA from horse fecal material. J Microbiol Methods 2016; 129:14-19. [PMID: 27460337 DOI: 10.1016/j.mimet.2016.07.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [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: 07/19/2016] [Revised: 07/22/2016] [Accepted: 07/22/2016] [Indexed: 02/08/2023]
Abstract
There are many choices for methods of extracting bacterial DNA for Next Generation Sequencing (NGS) from fecal samples. Here, we compare our modifications of a phenol/chloroform extraction method plus an inhibitor removal solution (C3) (ph/Chl+C3) to the PowerFecal® DNA Isolation Kit (MoBio-K). DNA quality and quantity coupled to NGS results were used to assess differences in relative abundance, Shannon diversity index, unique species, and principle coordinate analysis (PCoA) between biological replicates. Six replicate samples, taken from a single ball of horse feces manually collected from the rectum, were subjected to each extraction method. The Ph/Chl+C3 method produced 100× higher DNA yields with less shearing than the MoBio-K method. To assess the methods, the two method samples were sent for sequencing of the bacterial V3-V4 region of 16S rRNA gene using the Illumina MiSeq platform. The relative abundance of Bacteroidetes was greater and there were more unique species assigned to this group in MoBio-K than in Ph/Chl+C3 (P<0.05). In contrast, Firmicutes had greater relative abundance and more unique species in Ph/Chl+C3 extracts than in MoBio-K (P<0.05). The other major bacterial phyla were equally abundant in samples using both extraction methods. Alpha diversity and Shannon Weaver indices showed greater evenness of bacterial distribution in Ph/Chl+C3 compared with MoBio-K (P<0.05), but there was no difference in the OTU richness. Principle coordinate analysis (PCoA) indicated a distinct separation between the two methods (P<0.05) and tighter clustering (less variability) in Ph/Chl+C3 than in MoBio-K. These results suggest that the Ph/Chl+C3 may be preferred for research to identify specific Firmicutes taxa such as Clostridium, and Bacillus. However; MoBio-K may be a better choice for projects focusing on Bacteroidetes abundance. The Ph/Chl+C3 method required less time, but has some safety concerns associated with exposure and disposal of phenol and chloroform. While the MoBio-K may be better choice for researchers with less access to safety equipment like a fume hood.
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Affiliation(s)
- Ali H D Janabi
- Microbial Biology Graduate Program, Rutgers-The State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Lee J Kerkhof
- Department of Marine and Coastal Sciences, Rutgers-The State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Lora R McGuinness
- Department of Marine and Coastal Sciences, Rutgers-The State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Amy S Biddle
- Department of Animal and Food Sciences, University of Delaware, Newark, DE 19716, USA
| | - Kenneth H McKeever
- Microbial Biology Graduate Program, Rutgers-The State University of New Jersey, New Brunswick, NJ 08901, USA; Department of Animal Science, Rutgers-The State University of New Jersey, New Brunswick, NJ 08901, USA.
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Lewis ZT, Davis JCC, Smilowitz JT, German JB, Lebrilla CB, Mills DA. The impact of freeze-drying infant fecal samples on measures of their bacterial community profiles and milk-derived oligosaccharide content. PeerJ 2016; 4:e1612. [PMID: 26819854 PMCID: PMC4727960 DOI: 10.7717/peerj.1612] [Citation(s) in RCA: 12] [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: 09/11/2015] [Accepted: 12/29/2015] [Indexed: 12/13/2022] Open
Abstract
Infant fecal samples are commonly studied to investigate the impacts of breastfeeding on the development of the microbiota and subsequent health effects. Comparisons of infants living in different geographic regions and environmental contexts are needed to aid our understanding of evolutionarily-selected milk adaptations. However, the preservation of fecal samples from individuals in remote locales until they can be processed can be a challenge. Freeze-drying (lyophilization) offers a cost-effective way to preserve some biological samples for transport and analysis at a later date. Currently, it is unknown what, if any, biases are introduced into various analyses by the freeze-drying process. Here, we investigated how freeze-drying affected analysis of two relevant and intertwined aspects of infant fecal samples, marker gene amplicon sequencing of the bacterial community and the fecal oligosaccharide profile (undigested human milk oligosaccharides). No differences were discovered between the fecal oligosaccharide profiles of wet and freeze-dried samples. The marker gene sequencing data showed an increase in proportional representation of Bacteriodes and a decrease in detection of bifidobacteria and members of class Bacilli after freeze-drying. This sample treatment bias may possibly be related to the cell morphology of these different taxa (Gram status). However, these effects did not overwhelm the natural variation among individuals, as the community data still strongly grouped by subject and not by freeze-drying status. We also found that compensating for sample concentration during freeze-drying, while not necessary, was also not detrimental. Freeze-drying may therefore be an acceptable method of sample preservation and mass reduction for some studies of microbial ecology and milk glycan analysis.
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Affiliation(s)
- Zachery T Lewis
- Department of Food Science and Technology, University of California, Davis, CA, United States; Foods For Health Institute, University of California, Davis, CA, United States
| | - Jasmine C C Davis
- Foods For Health Institute, University of California, Davis, CA, United States; Department of Chemistry, University of California, Davis, CA, United States
| | - Jennifer T Smilowitz
- Department of Food Science and Technology, University of California, Davis, CA, United States; Foods For Health Institute, University of California, Davis, CA, United States
| | - J Bruce German
- Department of Food Science and Technology, University of California, Davis, CA, United States; Foods For Health Institute, University of California, Davis, CA, United States
| | - Carlito B Lebrilla
- Foods For Health Institute, University of California, Davis, CA, United States; Department of Chemistry, University of California, Davis, CA, United States
| | - David A Mills
- Department of Food Science and Technology, University of California, Davis, CA, United States; Foods For Health Institute, University of California, Davis, CA, United States; Department of Viticulture and Enology, University of California, Davis, CA, United States
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40
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Moore AM, Ahmadi S, Patel S, Gibson MK, Wang B, Ndao MI, Deych E, Shannon W, Tarr PI, Warner BB, Dantas G. Gut resistome development in healthy twin pairs in the first year of life. Microbiome 2015; 3:27. [PMID: 26113976 PMCID: PMC4480905 DOI: 10.1186/s40168-015-0090-9] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 06/05/2015] [Indexed: 05/24/2023]
Abstract
BACKGROUND The early life of the human host marks a critically important time for establishment of the gut microbial community, yet the developmental trajectory of gut community-encoded resistance genes (resistome) is unknown. We present a longitudinal study of the fecal antibiotic resistome of healthy amoxicillin-exposed and antibiotic-naive twins and their mothers during the first year of life. RESULTS We extracted metagenomic DNA (mgDNA) from fecal samples collected from three healthy twin pairs at three timepoints (1 or 2 months, 6 or 7 months, and 11 months) and from their mothers (collected at delivery). The mgDNA was used to construct metagenomic expression libraries in an Escherichia coli host. These libraries were screened for antibiotic resistance, and functionally selected resistance genes were sequenced and annotated. A diverse fecal resistome distinct from the maternal resistome was apparent by 2 months of age, and infants' fecal resistomes included resistance to clinically important broad-spectrum beta-lactam antibiotics (e.g., piperacillin-tazobactam, aztreonam, cefepime) not found in their mothers. Dissemination of resistance genes among members of a given family was positively correlated with sharing of those same resistance genes between unrelated families, potentially identifying within-family sharing as a marker of resistance genes emerging in the human community at large. Finally, we found a distinct developmental trajectory for a community-encoded function: chloramphenicol resistance. All study subjects at all timepoints harbored chloramphenicol resistance determinants, but multidrug efflux pumps (rarely found in mothers) were the primary effectors of chloramphenicol resistance in young infants. Chloramphenicol acetyltransferases were more common in mothers than in infants and were found in nearly all the infants at later timepoints. CONCLUSIONS Our results suggest that healthy 1-2-month-old infants' gut microbes harbor clinically relevant resistance genes distinct from those of their mothers, and that family-specific shared environmental factors early in life shape resistome development.
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Affiliation(s)
- Aimee M. Moore
- />Department of Pediatrics, Washington University in St Louis School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110 USA
- />Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, 4444 Forest Park Boulevard, St. Louis, MO 63108 USA
| | - Sara Ahmadi
- />Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110 USA
- />Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, 4444 Forest Park Boulevard, St. Louis, MO 63108 USA
| | - Sanket Patel
- />Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110 USA
- />Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, 4444 Forest Park Boulevard, St. Louis, MO 63108 USA
| | - Molly K. Gibson
- />Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, 4444 Forest Park Boulevard, St. Louis, MO 63108 USA
| | - Bin Wang
- />Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110 USA
- />Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, 4444 Forest Park Boulevard, St. Louis, MO 63108 USA
| | - Malick I. Ndao
- />Department of Pediatrics, Washington University in St Louis School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110 USA
| | - Elena Deych
- />Department of Biostatistics, Washington University in St. Louis School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110 USA
| | - William Shannon
- />Department of Biostatistics, Washington University in St. Louis School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110 USA
| | - Phillip I. Tarr
- />Department of Pediatrics, Washington University in St Louis School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110 USA
- />Department of Molecular Microbiology, Washington University in St. School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110 USA
| | - Barbara B. Warner
- />Department of Pediatrics, Washington University in St Louis School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110 USA
| | - Gautam Dantas
- />Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110 USA
- />Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, 4444 Forest Park Boulevard, St. Louis, MO 63108 USA
- />Department of Biomedical Engineering, Washington University in St. Louis, One Brookings Drive, St. Louis, MO 63130 USA
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Walters SS, Quiros A, Rolston M, Grishina I, Li J, Fenton A, DeSantis TZ, Thai A, Andersen GL, Papathakis P, Nieves R, Prindiville T, Dandekar S. Analysis of Gut Microbiome and Diet Modification in Patients with Crohn's Disease. ACTA ACUST UNITED AC 2014; 2:1-13. [PMID: 29756026 DOI: 10.15226/sojmid/2/3/00122] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Objective The human intestine harbors trillions of commensal microbes that live in homeostasis with the host immune system. Changes in the composition and complexity of gut microbial communities are seen in inflammatory bowel disease (IBD), indicating disruption in host-microbe interactions. Multiple factors including diet and inflammatory conditions alter the microbial complexity. The goal of this study was to develop an optimized methodology for fecal sample processing and to detect changes in the gut microbiota of patients with Crohn's disease receiving specialized diets. Design Fecal samples were obtained from patients with Crohn's disease in a pilot diet crossover trial comparing the effects of a specific carbohydrate diet (SCD) versus a low residue diet (LRD) on the composition and complexity of the gut microbiota and resolution of IBD symptoms. The gut microbiota composition was assessed using a high-density DNA microarray PhyloChip. Results DNA extraction from fecal samples using a column based method provided consistent results. The complexity of the gut microbiome was lower in IBD patients compared to healthy controls. An increased abundance of Bacteroides fragilis (B. fragilis) was observed in fecal samples from IBD positive patients. The temporal response of gut microbiome to the SCD resulted in an increased microbial diversity while the LRD diet was associated with reduced diversity of the microbial communities. Conclusion Changes in the composition and complexity of the gut microbiome were identified in response to specialized carbohydrate diet. The SCD was associated with restructuring of the gut microbial communities.
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Affiliation(s)
| | - Antonio Quiros
- Department of Internal Medicine, University of CA Davis, Sacramento, USA.,Division of Pediatric Gastroenterology MUSC Children's Hospital, Charleston, SC
| | - Matthew Rolston
- Department of Medical Microbiology and Immunology, University of CA Davis, USA
| | - Irina Grishina
- Department of Medical Microbiology and Immunology, University of CA Davis, USA
| | - Jay Li
- Department of Medical Microbiology and Immunology, University of CA Davis, USA
| | - Anne Fenton
- Department of Medical Microbiology and Immunology, University of CA Davis, USA
| | - Todd Z DeSantis
- Department of Bioinformatics, Second Genome, San Bruno, CA 94066
| | - Anne Thai
- Department of Internal Medicine, University of CA Davis, Sacramento, USA
| | - Gary L Andersen
- Ecology Department, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Peggy Papathakis
- Department of Nutrition, California Polytechnic State University, San Luis Obispo, CA, USA
| | - Raquel Nieves
- Department of Pediatrics, David Grant Medical Center, Travis Air Force Base, California, 94535
| | - Thomas Prindiville
- Department of Internal Medicine, University of CA Davis, Sacramento, USA
| | - Satya Dandekar
- Department of Medical Microbiology and Immunology, University of CA Davis, USA
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