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Nenciarini S, Renzi S, di Paola M, Meriggi N, Cavalieri D. The yeast-human coevolution: Fungal transition from passengers, colonizers, and invaders. WIREs Mech Dis 2024; 16:e1639. [PMID: 38146626 DOI: 10.1002/wsbm.1639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 12/27/2023]
Abstract
Fungi are the cause of more than a billion infections in humans every year, although their interactions with the host are still neglected compared to bacteria. Major systemic fungal infections are very unusual in the healthy population, due to the long history of coevolution with the human host. Humans are routinely exposed to environmental fungi and can host a commensal mycobiota, which is increasingly considered as a key player in health and disease. Here, we review the current knowledge on host-fungi coevolution and the factors that regulate their interaction. On one hand, fungi have learned to survive and inhabit the host organisms as a natural ecosystem, on the other hand, the host immune system finely tunes the response toward fungi. In turn, recognition of fungi as commensals or pathogens regulates the host immune balance in health and disease. In the human gut ecosystem, yeasts provide a fingerprint of the transient microbiota. Their status as passengers or colonizers is related to the integrity of the gut barrier and the risk of multiple disorders. Thus, the study of this less known component of the microbiota could unravel the rules of the transition from passengers to colonizers and invaders, as well as their dependence on the innate component of the host's immune response. This article is categorized under: Infectious Diseases > Environmental Factors Immune System Diseases > Environmental Factors Infectious Diseases > Molecular and Cellular Physiology.
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Affiliation(s)
| | - Sonia Renzi
- Department of Biology, University of Florence, Florence, Italy
| | - Monica di Paola
- Department of Biology, University of Florence, Florence, Italy
| | - Niccolò Meriggi
- Department of Biology, University of Florence, Florence, Italy
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Liu X, Jia Q, Sun D, Zhang J, Zheng H, Chen Y. Influence of nitrogen substitution at an equivalent total nitrogen level on bacterial and fungal communities, as well as enzyme activities of the ditch bottom soil in a rice-fish coculture system. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:4206-4217. [PMID: 38436513 DOI: 10.1002/jsfa.13302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 12/23/2023] [Accepted: 12/26/2023] [Indexed: 03/05/2024]
Abstract
BACKGROUND Rice-fish coculture system (RFS) operates through effectively utilizing water and land resources in a complementary form, but it requires more efficient utilization of fertilizer and feed without compromising rice yield. However, the knowledge of how to regulate the proportion of nitrogen (N) supplied from fertilizer and feed at an equivalent total N level to improve the benefits of RFS remains limited. Therefore, four treatments (S0: RFS with 0% N from fertilizer and 100% N from feed; S25: RFS with 25% N from fertilizer and 75% N from feed; S50: RFS with 50% N from fertilizer and 50% N from feed; S75: RFS with 75% N from fertilizer and 25% N from feed) were conducted to assess the variation of ditch bottom soil properties, microbial communities and enzyme activities, as well as to obtain the optimal ratio of N supplied from fish feed and fertilizer. RESULTS The experiments showed that the contents of soil organic matter, total carbon and total N, and the activities of urease, N-acetyl-β-D-glucosaminidase, protease, β-1,4-glucosidase and catalase in the ditch bottom soil significantly reduced in S25 treatment, compared with the other three treatments. Ammonium N content decreased with increasing percentage of the basal fertilizer, whereas nitrate N content and pH value showed an adverse trend. However, the bacterial and fungal communities were unaffected by the ratio shifts between fertilizer-N and feed-N, but their dominant phyla were influenced by the ditch bottom soil N level. Moreover, the bacterial community composition was positively related to nitrate N, whereas fungal diversity was positively correlated with pH, ammonium N and nitrate N, and urease. We also found that the treatment of N input with 25% N from fertilizer and 75% N from feed can reduce N deposition in the ditch bottom soil in the rice-fish coculture system. CONCLUSION Our findings indicate that under the equivalent total N input level, the relative higher ratio of N from fish feed increased (S0 treatment) or reduced (S25 treatment) the deposition of N in the ditch bottom soil, and improved fish production, but decreased rice yield; while the higher ratio of N from basal fertilizer increased the transportation of nutrients into the ditch bottom soil and rice yield, but reduced fish production. So when considering multi-balance and multiple benefits, we recommend that a selective substitution ratio within 50% ~ 75% from fish feed to substitute for the basal fertilizer under the equivalent total N input may achieve a good balance of rice and fish production improvement, and reduce nutrients wastage to the ditch bottom, as well as alleviate the potential of non-point source pollution. This study also provides an evidence for regulating and optimizing the ratio of N supplied from fertilizer and fish feed at an equivalent total N level through monitoring the nutrient accumulation in ditch bottom soil in the rice-fish coculture system. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Xing Liu
- Guangdong Engineering Technology Research Center of Modern Eco-agriculture and Circular Agriculture, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Eco-circular Agriculture, South China Agricultural University, Guangzhou, China
- Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Qi Jia
- Guangdong Engineering Technology Research Center of Modern Eco-agriculture and Circular Agriculture, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Eco-circular Agriculture, South China Agricultural University, Guangzhou, China
- Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Daolin Sun
- Guangdong Engineering Technology Research Center of Modern Eco-agriculture and Circular Agriculture, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Eco-circular Agriculture, South China Agricultural University, Guangzhou, China
- Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Jiaen Zhang
- Guangdong Engineering Technology Research Center of Modern Eco-agriculture and Circular Agriculture, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Eco-circular Agriculture, South China Agricultural University, Guangzhou, China
- Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, China
| | - Hongjun Zheng
- Guangdong Engineering Technology Research Center of Modern Eco-agriculture and Circular Agriculture, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Eco-circular Agriculture, South China Agricultural University, Guangzhou, China
- Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Yuting Chen
- Guangdong Engineering Technology Research Center of Modern Eco-agriculture and Circular Agriculture, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Eco-circular Agriculture, South China Agricultural University, Guangzhou, China
- Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
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Nenciarini S, Renzi S, di Paola M, Meriggi N, Cavalieri D. Ascomycetes yeasts: The hidden part of human microbiome. WIREs Mech Dis 2024; 16:e1641. [PMID: 38228159 DOI: 10.1002/wsbm.1641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 12/17/2023] [Accepted: 12/19/2023] [Indexed: 01/18/2024]
Abstract
The fungal component of the microbiota, the mycobiota, has been neglected for a long time due to its poor richness compared to bacteria. Limitations in fungal detection and taxonomic identification arise from using metagenomic approaches, often borrowed from bacteriome analyses. However, the relatively recent discoveries of the ability of fungi to modulate the host immune response and their involvement in human diseases have made mycobiota a fundamental component of the microbial communities inhabiting the human host, deserving some consideration in host-microbe interaction studies and in metagenomics. Here, we reviewed recent data on the identification of yeasts of the Ascomycota phylum across human body districts, focusing on the most representative genera, that is, Saccharomyces and Candida. Then, we explored the key factors involved in shaping the human mycobiota across the lifespan, ranging from host genetics to environment, diet, and lifestyle habits. Finally, we discussed the strengths and weaknesses of culture-dependent and independent methods for mycobiota characterization. Overall, there is still room for some improvements, especially regarding fungal-specific methodological approaches and bioinformatics challenges, which are still critical steps in mycobiota analysis, and to advance our knowledge on the role of the gut mycobiota in human health and disease. This article is categorized under: Immune System Diseases > Genetics/Genomics/Epigenetics Immune System Diseases > Environmental Factors Infectious Diseases > Environmental Factors.
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Affiliation(s)
| | - Sonia Renzi
- Department of Biology, University of Florence, Florence, Italy
| | - Monica di Paola
- Department of Biology, University of Florence, Florence, Italy
| | - Niccolò Meriggi
- Department of Biology, University of Florence, Florence, Italy
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Wang T, Liu J, Luo Y, Yu B, Kong X, Zheng P, Huang Z, Mao X, Yu J, Luo J, Yan H, He J. Combined effects of host genetics and diet on porcine intestinal fungi and their pathogenic genes. Front Microbiol 2023; 14:1192288. [PMID: 37822749 PMCID: PMC10563851 DOI: 10.3389/fmicb.2023.1192288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 09/11/2023] [Indexed: 10/13/2023] Open
Abstract
As research on gut microbes progresses, it becomes increasingly clear that a small family of microbiota--fungi, plays a crucial role in animal health. However, little is known about the fungal composition in the pig intestine, especially after a dietary fiber diet and hybrid genetics, and the changes in host pathogenicity-associated genes they carry. The purpose of this study is to investigate the effects of diet and genetics on the diversity and structure of porcine intestinal fungi and to describe, for the first time, the host pathogenicity-related genes carried by porcine intestinal fungi. Samples of colonic contents were collected for metagenomic analysis using a 3 × 2 parsing design, where three pig breeds (Taoyuan, Duroc, and crossbred Xiangcun) were fed high or low fiber diets (n = 10). In all samples, we identified a total of 281 identifiable fungal genera, with Ascomycota and Microsporidia being the most abundant fungi. Compared to Duroc pigs, Taoyuan and Xiangcun pigs had higher fungal richness. Interestingly, the fiber diet significantly reduced the abundance of the pathogenic fungus Mucor and significantly increased the abundance of the fiber digestion-associated fungus Neocallimastix. Pathogenic fungi exert their pathogenicity through the genes they carry that are associated with host pathogenicity. Therefore, we obtained 839 pathogenicity genes carried by the spectrum of fungi in the pig intestine by comparing the PHI-base database. Our results showed that fungi in the colon of Taoyuan pigs carried the highest abundance of different classes of host pathogenicity-related genes, and the lowest in Duroc pigs. Specifically, Taoyuan pigs carried high abundance of animal pathogenicity-related genes (CaTUP1, CPAR2_106400, CaCDC35, Tfp1, CaMNT2), and CaTUP1 was the key gene for Candida pathogenicity. The intestinal fungal composition of crossbred Xiangcun pigs and the abundance of host pathogenicity-associated genes they carried exhibited a mixture of characteristics of Taoyuan and Duroc pigs. In conclusion, our results provide the first comprehensive report on the effects of dietary fiber and genetics on the composition of intestinal fungi and the host-associated pathogenicity genes they carry in pigs. These findings provide a reference for subsequent pig breeding and development of anti-pathogenic fungal drugs.
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Affiliation(s)
- Tao Wang
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease-resistant Nutrition, Chengdu, China
| | - Jiahao Liu
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease-resistant Nutrition, Chengdu, China
| | - Yuheng Luo
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease-resistant Nutrition, Chengdu, China
| | - Bing Yu
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease-resistant Nutrition, Chengdu, China
| | - Xiangfeng Kong
- Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Ping Zheng
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease-resistant Nutrition, Chengdu, China
| | - Zhiqing Huang
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease-resistant Nutrition, Chengdu, China
| | - Xiangbing Mao
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease-resistant Nutrition, Chengdu, China
| | - Jie Yu
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease-resistant Nutrition, Chengdu, China
| | - Junqiu Luo
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease-resistant Nutrition, Chengdu, China
| | - Hui Yan
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease-resistant Nutrition, Chengdu, China
| | - Jun He
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease-resistant Nutrition, Chengdu, China
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Li F, Gao Y, Cheng W, Su X, Yang R. Gut fungal mycobiome: A significant factor of tumor occurrence and development. Cancer Lett 2023; 569:216302. [PMID: 37451425 DOI: 10.1016/j.canlet.2023.216302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 06/28/2023] [Accepted: 07/01/2023] [Indexed: 07/18/2023]
Abstract
A variety of bacteria, viruses, fungi, protists, archaea and protozoa coexists within the mammalian gastrointestinal (GI) tract such as that fungi are detectable in all intestinal and colon segments in almost all healthy adults. Although fungi can cause infectious diseases, they are also related to gut and systemic homeostasis. Importantly, through transformation of different forms such as from yeast to hyphae, interaction among gut microbiota such as fungal and bacterial interaction, host factors such as immune and host derived factors, and fungus genetic and epigenetic factors, fungi can be transformed from commensal into pathogenic lifestyles. Recent studies have shown that fungi play a significant role in the occurrence and development of tumors such as colorectal cancer. Indeed, evidences have shown that multiple species of different fungi exist in different tumors. Studies have also demonstrated that fungi are related to the occurrence and development of tumors, and also survival of patients. Here we summarize recent advances in the transformation of fungi from commensal into pathogenic lifestyles, and the effects of gut pathogenic fungi on the occurrence and development of tumors such as colorectal and pancreatic cancers.
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Affiliation(s)
- Fan Li
- Translational Medicine Institute, Affiliated Tianjin Union Medical Center of Nankai University, Nankai University, Tianjin, 300071, China; Department of Immunology, Nankai University School of Medicine, Nankai University, Tianjin, 300071, China; State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China
| | - Yunhuan Gao
- Translational Medicine Institute, Affiliated Tianjin Union Medical Center of Nankai University, Nankai University, Tianjin, 300071, China; Department of Immunology, Nankai University School of Medicine, Nankai University, Tianjin, 300071, China; State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China
| | - Wenyue Cheng
- Translational Medicine Institute, Affiliated Tianjin Union Medical Center of Nankai University, Nankai University, Tianjin, 300071, China; Department of Immunology, Nankai University School of Medicine, Nankai University, Tianjin, 300071, China; State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China
| | - Xiaomin Su
- Translational Medicine Institute, Affiliated Tianjin Union Medical Center of Nankai University, Nankai University, Tianjin, 300071, China; Department of Immunology, Nankai University School of Medicine, Nankai University, Tianjin, 300071, China; State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China
| | - Rongcun Yang
- Translational Medicine Institute, Affiliated Tianjin Union Medical Center of Nankai University, Nankai University, Tianjin, 300071, China; Department of Immunology, Nankai University School of Medicine, Nankai University, Tianjin, 300071, China; State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China.
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Sun M, Ju J, Xu H, Wang Y. Intestinal fungi and antifungal secretory immunoglobulin A in Crohn's disease. Front Immunol 2023; 14:1177504. [PMID: 37359518 PMCID: PMC10285161 DOI: 10.3389/fimmu.2023.1177504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 05/30/2023] [Indexed: 06/28/2023] Open
Abstract
The human gastrointestinal tract harbors trillions of commensal microorganisms. Emerging evidence points to a possible link between intestinal fungal dysbiosis and antifungal mucosal immunity in inflammatory bowel disease, especially in Crohn's disease (CD). As a protective factor for the gut mucosa, secretory immunoglobulin A (SIgA) prevents bacteria from invading the intestinal epithelium and maintains a healthy microbiota community. In recent years, the roles of antifungal SIgA antibodies in mucosal immunity, including the regulation of intestinal immunity binding to hyphae-associated virulence factors, are becoming increasingly recognized. Here we review the current knowledge on intestinal fungal dysbiosis and antifungal mucosal immunity in healthy individuals and in patients with CD, discuss the factors governing antifungal SIgA responses in the intestinal mucosa in the latter group, and highlight potential antifungal vaccines targeting SIgA to prevent CD.
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Lv QB, Meng JX, Ma H, Liu R, Qin Y, Qin YF, Geng HL, Ni HB, Zhang XX. Description of Gut Mycobiota Composition and Diversity of Caprinae Animals. Microbiol Spectr 2023; 11:e0242422. [PMID: 36625628 PMCID: PMC9927506 DOI: 10.1128/spectrum.02424-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 12/20/2022] [Indexed: 01/11/2023] Open
Abstract
The fungal community, also known as mycobiota, plays pivotal roles in host nutrition and metabolism and has potential to cause disease. However, knowledge of the gut fungal structure in Caprinae is quite limited. In this study, the composition and diversity of the gut mycobiota of Caprinae animals from different geographical locations (Anhui, Jilin, Guangxi, Shandong, Shanxi, and Tibet) were comprehensively characterized by analyzing the internal transcribed spacer 2 (ITS-2) sequences of the fungal community. The results showed that Ascomycota and Basidiomycota were the dominant phyla, which, respectively, accounted for 90.86 to 95.27% and 2.58 to 7.62% of sequences in samples from each region. Nonetheless, the structure of the gut mycobiota was largely different in Caprinae animals in the different provinces. Therein, Sporormiaceae and Thelebolaceae were the dominant fungal families in the samples from Tibet, whereas their abundance was generally low in other regions. The intestinal diversity of individuals from Guangxi was higher than that in other regions. In addition, there were 114 differential genera among all regions. Finally, the co-occurrence network revealed 285 significant correlations in cross-family pairs in the guts of Caprinae animals, which contained 149 positive and 136 negative relationships, with 96 bacterial and 86 fungal participants at the family level. This study has improved the understanding of the mycobiota of ruminants and provided support for the improvement in animal health and productivity. IMPORTANCE In this study, we elucidated and analyzed the structure of the gut mycobiota of Caprinae animals from different regions. This study revealed differences in the structure of the gut mycobiota among Caprinae animals from different geographical environments. Based on previous findings, correlations between fungal and bacterial communities were analyzed. This study adds to previous research that has expanded the present understanding of the gut microbiome of Caprinae animals.
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Affiliation(s)
- Qing-Bo Lv
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, People’s Republic of China
- College of Veterinary Medicine, Jilin University, Changchun, Jilin Province, People’s Republic of China
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People's Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Jin-Xin Meng
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, People’s Republic of China
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People's Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - He Ma
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, People’s Republic of China
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People's Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Rui Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, People’s Republic of China
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People's Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Ya Qin
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, People’s Republic of China
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People's Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin Province, People’s Republic of China
| | - Yi-Feng Qin
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, People’s Republic of China
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People's Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin Province, People’s Republic of China
| | - Hong-Li Geng
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, People’s Republic of China
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People's Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin Province, People’s Republic of China
| | - Hong-Bo Ni
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, People’s Republic of China
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People's Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Xiao-Xuan Zhang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, People’s Republic of China
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Fungal-Bacterial Interactions in the Human Gut of Healthy Individuals. J Fungi (Basel) 2023; 9:jof9020139. [PMID: 36836254 PMCID: PMC9965947 DOI: 10.3390/jof9020139] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 01/07/2023] [Accepted: 01/17/2023] [Indexed: 01/21/2023] Open
Abstract
Most studies of the microbiota in the human gut focus on the bacterial part, but increasing information shows that intestinal fungi are also important for maintaining health. This can be either by directly influencing the host or by indirectly influencing the gut bacteria that link to host health. Studies of fungal communities in large cohorts are scarce; therefore, this study aims at obtaining more insight into the mycobiome of healthy individuals and how this mycobiome interacts with the bacterial component of the microbiome. For this purpose, ITS2 and 16S rRNA gene amplicon sequencing was performed on fecal samples from 163 individuals which were available from two separate studies to analyze the fungal and bacterial microbiome, respectively, as well as the cross-kingdom interactions. The results showed a much lower fungal, as compared to bacterial, diversity. Ascomycota and Basidiomycota were the dominant fungal phyla across all the samples, but levels varied enormously between individuals. The ten most abundant fungal genera were Saccharomyces, Candida, Dipodascus, Aureobasidium, Penicillium, Hanseniaspora, Agaricus, Debaryomyces, Aspergillus, and Pichia, and here also extensive inter-individual variation was observed. Correlations were made between bacteria and fungi, and only positive correlations were observed. One of the correlations was between Malassezia restricta and the genus Bacteroides, which have both been previously described as alleviated in IBD. Most of the other correlations found were with fungi that are not known as gut colonizers but originate from food and the environment. To further investigate the importance of the observed correlations found, more research is needed to discriminate between gut colonizers and transient species.
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Rao WQ, Lin Z, Jiang J, Wang JW, Lin ZF, Fu R, Chen WL, Chen YM, Peng XE, Hu ZJ. Esophageal mycobiome landscape and interkingdom interactions in esophageal squamous cell carcinoma. Gastroenterol Rep (Oxf) 2023; 11:goad022. [PMID: 37124071 PMCID: PMC10147516 DOI: 10.1093/gastro/goad022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 03/06/2023] [Accepted: 04/02/2023] [Indexed: 05/02/2023] Open
Abstract
Background The study purpose was to characterize the mycobiome and its associations with the expression of pathogenic genes in esophageal squamous cell carcinoma (ESCC). Methods Patients with primary ESCC were recruited from two central hospitals. We performed internal transcribed spacer 1 (ITS1) ribosomal DNA sequencing analysis. We compared differential fungi and explored the ecology of fungi and the interaction of bacteria and fungi. Results The mycobiota diversity was significantly different between tumors and tumor-adjacent samples. We further analysed the differences between the two groups, at the species level, confirming that Rhodotorula toruloides, Malassezia dermatis, Hanseniaspora lachancei, and Spegazzinia tessarthra were excessively colonized in the tumor samples, whereas Preussia persica, Fusarium solani, Nigrospora oryzae, Acremonium furcatum, Golovinomyces artemisiae, and Tausonia pullulans were significantly more abundant in tumor-adjacent samples. The fungal co-occurrence network in tumor-adjacent samples was larger and denser than that in tumors. Similarly, the more complex bacterial-fungal interactions in tumor-adjacent samples were also detected. The expression of mechanistic target of rapamycin kinase was positively correlated with the abundance of N. oryzae and T. pullulans in tumor-adjacent samples. In tumors, the expression of MET proto-oncogene, receptor tyrosine kinase (MET) had a negative correlation and a positive correlation with the abundance of R. toruloides and S. tessarthra, respectively. Conclusion This study revealed the landscape of the esophageal mycobiome characterized by an altered fungal composition and bacterial and fungal ecology in ESCC.
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Affiliation(s)
| | | | - Jian Jiang
- Department of Epidemiology and Health Statistics, Fujian Medical University Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, Fujian, P. R. China
- Department of Medical Services, Fujian Provincial Hospital, Fuzhou, Fujian, P. R. China
| | - Jian-Wen Wang
- Department of Digestive Endoscopy, Anxi County Hospital, Anxi, Fujian, P. R. China
| | - Zhi-Feng Lin
- Department of Epidemiology and Health Statistics, Fujian Medical University Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, Fujian, P. R. China
| | - Rong Fu
- Department of Epidemiology and Health Statistics, Fujian Medical University Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, Fujian, P. R. China
| | - Wei-Lin Chen
- Department of Radiation Oncology, Zhangzhou Affiliated Hospital of Fujian Medical University, Zhangzhou, Fujian, P. R. China
| | - Yuan-Mei Chen
- Department of Thoracic Surgery, Fujian Provincial Cancer Hospital Affiliation to Fujian Medical University, Fuzhou, Fujian, P. R. China
| | - Xian-E Peng
- Department of Epidemiology and Health Statistics, Fujian Medical University Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, Fujian, P. R. China
| | - Zhi-Jian Hu
- Corresponding author. Department of Epidemiology and Health Statistics, Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, Fujian 350122, China. Tel: +86-591-83383362; Fax: +86-591-22862510;
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10
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Santus W, Rana AP, Devlin JR, Kiernan KA, Jacob CC, Tjokrosurjo J, Underhill DM, Behnsen J. Mycobiota and diet-derived fungal xenosiderophores promote Salmonella gastrointestinal colonization. Nat Microbiol 2022; 7:2025-2038. [PMID: 36411353 DOI: 10.1038/s41564-022-01267-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 10/11/2022] [Indexed: 11/22/2022]
Abstract
The fungal gut microbiota (mycobiota) has been implicated in diseases that disturb gut homeostasis, such as inflammatory bowel disease. However, little is known about functional relationships between bacteria and fungi in the gut during infectious colitis. Here we investigated the role of fungal metabolites during infection with the intestinal pathogen Salmonella enterica serovar Typhimurium, a major cause of gastroenteritis worldwide. We found that, in the gut lumen, both the mycobiota and fungi present in the diet can be a source of siderophores, small molecules that scavenge iron from the host. The ability to use fungal siderophores, such as ferrichrome and coprogen, conferred a competitive growth advantage to Salmonella strains expressing the fungal siderophore receptors FhuA or FhuE in vitro and in a mouse model. Our study highlights the role of inter-kingdom cross-feeding between fungi and Salmonella and elucidates an additional function of the gut mycobiota, revealing the importance of these understudied members of the gut ecosystem during bacterial infection.
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Affiliation(s)
- William Santus
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, IL, USA
| | - Amisha P Rana
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, IL, USA
| | - Jason R Devlin
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, IL, USA
| | - Kaitlyn A Kiernan
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, IL, USA
| | - Carol C Jacob
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, IL, USA
| | - Joshua Tjokrosurjo
- Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, CA, USA
| | - David M Underhill
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA.,F. Widjaja Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Judith Behnsen
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, IL, USA.
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11
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McKnight DT, Huerlimann R, Bower DS, Schwarzkopf L, Alford RA, Zenger KR. The interplay of fungal and bacterial microbiomes on rainforest frogs following a disease outbreak. Ecosphere 2022. [DOI: 10.1002/ecs2.4037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- Donald T. McKnight
- College of Science and Engineering James Cook University Townsville Queensland Australia
| | - Roger Huerlimann
- College of Science and Engineering James Cook University Townsville Queensland Australia
- Marine Climate Change Unit Okinawa Institute of Science and Technology Onnason Okinawa Japan
| | - Deborah S. Bower
- College of Science and Engineering James Cook University Townsville Queensland Australia
- School of Environmental and Rural Science University of New England Armidale New South Wales Australia
| | - Lin Schwarzkopf
- College of Science and Engineering James Cook University Townsville Queensland Australia
| | - Ross A. Alford
- College of Science and Engineering James Cook University Townsville Queensland Australia
| | - Kyall R. Zenger
- College of Science and Engineering James Cook University Townsville Queensland Australia
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12
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Xiong X, Rao Y, Tu X, Wang Z, Gong J, Yang Y, Wu H, Liu X. Gut archaea associated with bacteria colonization and succession during piglet weaning transitions. BMC Vet Res 2022; 18:243. [PMID: 35751084 PMCID: PMC9229118 DOI: 10.1186/s12917-022-03330-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 05/27/2022] [Indexed: 11/10/2022] Open
Abstract
Background Host-associated gut microbial communities are key players in shaping the fitness and health of animals. However, most current studies have focused on the gut bacteria, neglecting important gut fungal and archaeal components of these communities. Here, we investigated the gut fungi and archaea community composition in Large White piglets using shotgun metagenomic sequencing, and systematically evaluated how community composition association with gut microbiome, functional capacity, and serum metabolites varied across three weaning periods. Results We found that Mucoromycota, Ascomycota and Basidiomycota were the most common fungi phyla and Euryarchaeota was the most common archaea phyla across individuals. We identified that Methanosarcina siciliae was the most significantly different archaea species among three weaning periods, while Parasitella parasitica, the only differential fungi species, was significantly and positively correlated with Methanosarcina siciliae enriched in day 28 group. The random forest analysis also identified Methanosarcina siciliae and Parasitella parasitica as weaning-biased archaea and fungi at the species level. Additionally, Methanosarcina siciliae was significantly correlated with P. copri and the shifts of functional capacities of the gut microbiome and several CAZymes in day 28 group. Furthermore, characteristic successional alterations in gut archaea, fungi, bacteria, and serum metabolites with each weaning step revealed a weaning transition coexpression network, e.g., Methanosarcina siciliae and P. copri were positively and significantly correlated with 15-HEPE, 8-O-Methyloblongine, and Troxilin B3. Conclusion Our findings provide a deep insight into the interactions among gut archaea, fungi, bacteria, and serum metabolites and will present a theoretical framework for understanding gut bacterial colonization and succession association with archaea during piglet weaning transitions. Supplementary Information The online version contains supplementary material available at 10.1186/s12917-022-03330-4.
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Affiliation(s)
- Xinwei Xiong
- Institute of Biological Technology, Nanchang Normal University, Nanchang, Jiangxi, 330032, People's Republic of China.
| | - Yousheng Rao
- Institute of Biological Technology, Nanchang Normal University, Nanchang, Jiangxi, 330032, People's Republic of China
| | - Xutang Tu
- Institute of Biological Technology, Nanchang Normal University, Nanchang, Jiangxi, 330032, People's Republic of China
| | - Zhangfeng Wang
- Institute of Biological Technology, Nanchang Normal University, Nanchang, Jiangxi, 330032, People's Republic of China
| | - Jishang Gong
- Institute of Biological Technology, Nanchang Normal University, Nanchang, Jiangxi, 330032, People's Republic of China
| | - Yanbei Yang
- Institute of Biological Technology, Nanchang Normal University, Nanchang, Jiangxi, 330032, People's Republic of China
| | - Haobin Wu
- Institute of Biological Technology, Nanchang Normal University, Nanchang, Jiangxi, 330032, People's Republic of China
| | - Xianxian Liu
- Key Laboratory of Women's Reproductive Health of Jiangxi, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi, 330006, People's Republic of China.
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13
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Robinson K, Yang Q, Stewart S, Whitmore MA, Zhang G. Biogeography, succession, and origin of the chicken intestinal mycobiome. MICROBIOME 2022; 10:55. [PMID: 35365230 PMCID: PMC8976367 DOI: 10.1186/s40168-022-01252-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 02/24/2022] [Indexed: 05/15/2023]
Abstract
BACKGROUND Extensive work has been accomplished to characterize the intestinal bacterial community, known as the microbiota, and its association with host health and disease. However, very little is known about the spatiotemporal development and the origin of a minor intestinal fungal community, known as the mycobiota, in humans and animals, particularly in avian species. RESULTS In this study, we comprehensively characterized the biogeography and succession of the gastrointestinal (GI) mycobiota of broiler chickens and further revealed the fungal sources that are responsible for initial and long-term establishment of the mycobiota in the GI tract. Using Illumina sequencing of the internal transcribed spacer 2 (ITS2) region of fungal rRNA genes, we detected significant spatial and temporal differences in the mycobiota along the GI tract. In contrary to the microbiota, the mycobiota was more diverse in the upper than the lower GI tract with no apparent trend of succession up to 42 days of age. The intestinal mycobiota was dominated by the phyla Ascomycota and Basidiomycota with Gibberella, Aspergillus, and Candida being the most abundant genera. Although the chicken mycobiota was highly dynamic, Fusarium pseudonygamai was dominant throughout the GI tract regardless of age in this study. The core chicken mycobiome consisted of 26 fungal taxa accounting for greater than 85% of the fungal population in each GI location. However, we observed high variations of the intestinal mycobiota among different studies. We also showed that the total fungal population varied greatly from 1.0 × 104 to 1.1 × 106 /g digesta along the GI tract and only accounted for less than 0.06% of the bacteria in day-42 broilers. Finally, we revealed that the mycobiota from the hatchery environment was responsible for initial colonization in the GI tract of newly hatched chickens, but was quickly replaced by the fungi in the diet within 3 days. CONCLUSIONS Relative to the intestinal microbiota that consists of trillions of bacteria in hundreds of different species and becomes relatively stabilized as animals age, the chicken intestinal mycobiota is a minor microbial community that is temporally dynamic with limited diversity and no obvious pattern of successive changes. However, similar to the microbiota, the chicken mycobiota is spatially different along the GI tract, although it is more diverse in the upper than the lower GI tract. Dietary fungi are the major source of the intestinal mycobiota in growing chickens. Video abstract.
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Affiliation(s)
- Kelsy Robinson
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, Oklahoma USA
- Present Address: Poultry Research Unit, USDA–Agricultural Research Service, Mississippi State, MS USA
| | - Qing Yang
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, Oklahoma USA
| | - Sydney Stewart
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, Oklahoma USA
- Present Address: Safety and Security Division, Institute for Public Research, CNA, Arlington, VA USA
| | - Melanie A. Whitmore
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, Oklahoma USA
| | - Guolong Zhang
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, Oklahoma USA
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14
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Xu SS, Zhang XL, Liu SS, Feng ST, Xiang GM, Xu CJ, Fan ZY, Xu K, Wang N, Wang Y, Che JJ, Liu ZG, Mu YL, Li K. Multi-Omic Analysis in a Metabolic Syndrome Porcine Model Implicates Arachidonic Acid Metabolism Disorder as a Risk Factor for Atherosclerosis. Front Nutr 2022; 9:807118. [PMID: 35284467 PMCID: PMC8906569 DOI: 10.3389/fnut.2022.807118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 01/10/2022] [Indexed: 11/25/2022] Open
Abstract
Background The diet-induced gut microbiota dysbiosis has been suggested as a major risk factor for atherothrombosis, however, the detailed mechanism linking these conditions is yet to be fully understood. Methods We established a long-term excessive-energy diet-induced metabolic syndrome (MetS) inbred Wuzhishan minipig model, which is characterized by its genetic stability, small size, and human-like physiology. The metabolic parameters, atherosclerotic lesions, gut microbiome, and host transcriptome were analyzed. Metabolomics profiling revealed a linkage between gut microbiota and atherothrombosis. Results We showed that white atheromatous plaque was clearly visible on abdominal aorta in the MetS model. Furthermore, using metagenome and metatranscriptome sequencing, we discovered that the long-term excessive energy intake altered the local intestinal microbiota composition and transcriptional profile, which was most dramatically illustrated by the reduced abundance of SCFAs-producing bacteria including Bacteroides, Lachnospiraceae, and Ruminococcaceae in the MetS model. Liver and abdominal aorta transcriptomes in the MetS model indicate that the diet-induced gut microbiota dysbiosis activated host chronic inflammatory responses and significantly upregulated the expression of genes related to arachidonic acid-dependent signaling pathways. Notably, metabolomics profiling further revealed an intimate linkage between arachidonic acid metabolism and atherothrombosis in the host-gut microbial metabolism axis. Conclusions These findings provide new insights into the relationship between atherothrombosis and regulation of gut microbiota via host metabolomes and will be of potential value for the treatment of cardiovascular diseases in MetS.
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Affiliation(s)
- Song-Song Xu
- State Key Laboratory of Animal Nutrition and Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xiu-Ling Zhang
- State Key Laboratory of Animal Nutrition and Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Sha-Sha Liu
- State Key Laboratory of Animal Nutrition and Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Animal Husbandry and Veterinary Department, Beijing Vocational College of Agriculture, Beijing, China
| | - Shu-Tang Feng
- State Key Laboratory of Animal Nutrition and Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guang-Ming Xiang
- State Key Laboratory of Animal Nutrition and Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chang-Jiang Xu
- State Key Laboratory of Animal Nutrition and Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zi-Yao Fan
- State Key Laboratory of Animal Nutrition and Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Kui Xu
- State Key Laboratory of Animal Nutrition and Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Nan Wang
- State Key Laboratory of Animal Nutrition and Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yue Wang
- State Key Laboratory of Animal Nutrition and Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jing-Jing Che
- State Key Laboratory of Animal Nutrition and Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhi-Guo Liu
- State Key Laboratory of Animal Nutrition and Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yu-Lian Mu
- State Key Laboratory of Animal Nutrition and Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Yu-Lian Mu
| | - Kui Li
- State Key Laboratory of Animal Nutrition and Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Kui Li
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15
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Mohamed Qadir R, Assafi MS. The association between body mass index and the oral Firmicutes and Bacteroidetes profiles of healthy individuals. MALAYSIAN FAMILY PHYSICIAN : THE OFFICIAL JOURNAL OF THE ACADEMY OF FAMILY PHYSICIANS OF MALAYSIA 2021; 16:36-43. [PMID: 34938391 PMCID: PMC8680938 DOI: 10.51866/oa1129] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
INTRODUCTION Microbiome status is considered an important factor that contributes to obesity. Investigations have shown that the oral microbiome comprises a vast array of bacterial species that can influence human health. OBJECTIVE To determine the association between the presence of the bacterial phyla Firmicutes and Bacteroidetes and the body mass index (BMI) status of normal, overweight and obese subjects in Duhok, Iraq. Additionally, to investigate the composition of oral Firmicutes and Bacteroidetes profiles for individuals with different BMI statuses. METHODS A total of 155 saliva samples were collected from participants in Duhok, Iraq. Bacterial genomic DNA was then extracted from the collected saliva. The presence of Firmicutes and Bacteroidetes phyla was detected via polymerase chain reaction. RESULTS Firmicutes and Bacteroidetes were detected in 63.2 and 37.4% of the population, respectively. Differences in the carriage rates of oral Firmicutes in overweight (78%) and obese individuals (83%) were statistically significant when compared to normal weight individuals (36%) (P<0.0001). The percentage rates of Bacteroidetes in obese individuals (26.4%) was statistically significant when compared to normal weight individuals (50.8%) (P=0.0078). The Firmicutes/ Bacteroidetes ratios (obese=3.1, overweight= 2.5 and normal weight=0.7) were higher with increasing BMI. CONCLUSION This study provides evidence of the Firmicutes/Bacteroidetes ratio growing with increasing BMI. High rates of Firmicutes could serve a role in the development of obesity. Further studies are required to clarify the exact relationship between oral bacteria and obesity, which could lead to a promising therapeutic method for improving the physical health of humans.
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Affiliation(s)
- Roshna Mohamed Qadir
- MSc, Department of Biology, College of Science, University of Duhok, Duhok Kurdistan Region, Iraq
| | - Mahde Saleh Assafi
- PhD, Department of Biology, College of Science, University of Duhok, Duhok Kurdistan Region, Iraq,
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16
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Mishra K, Bukavina L, Ghannoum M. Symbiosis and Dysbiosis of the Human Mycobiome. Front Microbiol 2021; 12:636131. [PMID: 34630340 PMCID: PMC8493257 DOI: 10.3389/fmicb.2021.636131] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 08/04/2021] [Indexed: 12/13/2022] Open
Abstract
The influence of microbiological species has gained increased visibility and traction in the medical domain with major revelations about the role of bacteria on symbiosis and dysbiosis. A large reason for these revelations can be attributed to advances in deep-sequencing technologies. However, the research on the role of fungi has lagged. With the continued utilization of sequencing technologies in conjunction with traditional culture assays, we have the opportunity to shed light on the complex interplay between the bacteriome and the mycobiome as they relate to human health. In this review, we aim to offer a comprehensive overview of the human mycobiome in healthy and diseased states in a systematic way. The authors hope that the reader will utilize this review as a scaffolding to formulate their understanding of the mycobiome and pursue further research.
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Affiliation(s)
- Kirtishri Mishra
- University Hospitals Cleveland Medical Center, Urology Institute, Cleveland, OH, United States.,Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland, OH, United States
| | - Laura Bukavina
- University Hospitals Cleveland Medical Center, Urology Institute, Cleveland, OH, United States.,Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland, OH, United States
| | - Mahmoud Ghannoum
- Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland, OH, United States.,Center for Medical Mycology, and Integrated Microbiome Core, Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland, OH, United States.,Department of Dermatology, Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland, OH, United States
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17
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Effect of Microgravity Environment on Gut Microbiome and Angiogenesis. Life (Basel) 2021; 11:life11101008. [PMID: 34685381 PMCID: PMC8541308 DOI: 10.3390/life11101008] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 09/08/2021] [Accepted: 09/10/2021] [Indexed: 12/24/2022] Open
Abstract
Microgravity environments are known to cause a plethora of stressors to astronauts. Recently, it has become apparent that gut microbiome composition of astronauts is altered following space travel, and this is of significance given the important role of the gut microbiome in human health. Other changes observed in astronauts comprise reduced muscle strength and bone fragility, visual impairment, endothelial dysfunction, metabolic changes, behavior changes due to fatigue or stress and effects on mental well-being. However, the effects of microgravity on angiogenesis, as well as the connection with the gut microbiome are incompletely understood. Here, the potential association of angiogenesis with visual impairment, skeletal muscle and gut microbiome is proposed and explored. Furthermore, metabolites that are effectors of angiogenesis are deliberated upon along with their connection with gut bacterial metabolites. Targeting and modulating the gut microbiome may potentially have a profound influence on astronaut health, given its impact on overall human health, which is thus warranted given the likelihood of increased human activity in the solar system, and the determination to travel to Mars in future missions.
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18
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You N, Zhuo L, Zhou J, Song Y, Shi J. The Role of Intestinal Fungi and Its Metabolites in Chronic Liver Diseases. Gut Liver 2021; 14:291-296. [PMID: 31554391 PMCID: PMC7234879 DOI: 10.5009/gnl18579] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 03/27/2019] [Accepted: 04/15/2019] [Indexed: 12/12/2022] Open
Abstract
Current studies have confirmed that liver diseases are closely related to intestinal microorganisms; however, those studies have mainly concentrated on bacteria. Although the proportion of intestinal microorganisms accounted for by colonizing fungi is very small, these fungi do have a significant effect on the homeostasis of the intestinal microecosystem. In this paper, the characteristics of intestinal fungi in patients with chronic liver diseases such as alcoholic liver disease, nonalcoholic fatty liver disease and cirrhosis are summarized, and the effects of intestinal fungi and their metabolites are analyzed and discussed. It is important to realize that not only bacteria but also intestinal fungi play important roles in liver diseases.
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Affiliation(s)
- Ningning You
- Department of Liver Diseases, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
| | - Lili Zhuo
- Department of Liver Diseases, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
| | - Jingxin Zhou
- Department of Liver Diseases, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
| | - Yu Song
- Department of Liver Diseases, Zhejiang Chinese Medical University, Hangzhou, China
| | - Junping Shi
- Department of Liver Diseases, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
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19
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Isnard S, Lin J, Bu S, Fombuena B, Royston L, Routy JP. Gut Leakage of Fungal-Related Products: Turning Up the Heat for HIV Infection. Front Immunol 2021; 12:656414. [PMID: 33912183 PMCID: PMC8071945 DOI: 10.3389/fimmu.2021.656414] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 03/22/2021] [Indexed: 12/13/2022] Open
Abstract
The intestinal epithelial layer serves as a physical and functional barrier between the microbiota in the lumen and immunologically active submucosa. Th17 T-cell function protects the gut epithelium from aggression from microbes and their by-products. Loss of barrier function has been associated with enhanced translocation of microbial products which act as endotoxins, leading to local and systemic immune activation. Whereas the inflammatory role of LPS produced by Gram-negative bacteria has been extensively studied, the role of fungal products such as β-D-glucan remains only partially understood. As HIV infection is characterized by impaired gut Th17 function and increased gut permeability, we critically review mechanisms of immune activation related to fungal translocation in this viral infection. Additionally, we discuss markers of fungal translocation for diagnosis and monitoring of experimental treatment responses. Targeting gut barrier dysfunction and reducing fungal translocation are emerging strategies for the prevention and treatment of HIV-associated inflammation and may prove useful in other inflammatory chronic diseases.
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Affiliation(s)
- Stéphane Isnard
- Infectious Diseases and Immunity in Global Health Program, Research Institute, McGill University Health Centre, Montreal, QC, Canada
- Chronic Viral Illness Service, McGill University Health Centre, Montreal, QC, Canada
- CIHR Canadian HIV Trials Network, Vancouver, BC, Canada
| | - John Lin
- Infectious Diseases and Immunity in Global Health Program, Research Institute, McGill University Health Centre, Montreal, QC, Canada
- Chronic Viral Illness Service, McGill University Health Centre, Montreal, QC, Canada
| | - Simeng Bu
- Infectious Diseases and Immunity in Global Health Program, Research Institute, McGill University Health Centre, Montreal, QC, Canada
- Chronic Viral Illness Service, McGill University Health Centre, Montreal, QC, Canada
| | - Brandon Fombuena
- Infectious Diseases and Immunity in Global Health Program, Research Institute, McGill University Health Centre, Montreal, QC, Canada
- Chronic Viral Illness Service, McGill University Health Centre, Montreal, QC, Canada
| | - Léna Royston
- Infectious Diseases and Immunity in Global Health Program, Research Institute, McGill University Health Centre, Montreal, QC, Canada
- Chronic Viral Illness Service, McGill University Health Centre, Montreal, QC, Canada
| | - Jean-Pierre Routy
- Infectious Diseases and Immunity in Global Health Program, Research Institute, McGill University Health Centre, Montreal, QC, Canada
- Chronic Viral Illness Service, McGill University Health Centre, Montreal, QC, Canada
- Division of Hematology, McGill University Health Centre, Montreal, QC, Canada
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20
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Haelewaters D, Urbina H, Brown S, Newerth-Henson S, Aime MC. Isolation and Molecular Characterization of the Romaine Lettuce Phylloplane Mycobiome. J Fungi (Basel) 2021; 7:277. [PMID: 33917072 PMCID: PMC8067711 DOI: 10.3390/jof7040277] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 03/27/2021] [Accepted: 04/05/2021] [Indexed: 02/06/2023] Open
Abstract
Romaine lettuce (Lactuca sativa) is an important staple of American agriculture. Unlike many vegetables, romaine lettuce is typically consumed raw. Phylloplane microbes occur naturally on plant leaves; consumption of uncooked leaves includes consumption of phylloplane microbes. Despite this fact, the microbes that naturally occur on produce such as romaine lettuce are for the most part uncharacterized. In this study, we conducted culture-based studies of the fungal romaine lettuce phylloplane community from organic and conventionally grown samples. In addition to an enumeration of all such microbes, we define and provide a discussion of the genera that form the "core" romaine lettuce mycobiome, which represent 85.5% of all obtained isolates: Alternaria, Aureobasidium, Cladosporium, Filobasidium, Naganishia, Papiliotrema, Rhodotorula, Sampaiozyma, Sporobolomyces, Symmetrospora and Vishniacozyma. We highlight the need for additional mycological expertise in that 23% of species in these core genera appear to be new to science and resolve some taxonomic issues we encountered during our work with new combinations for Aureobasidiumbupleuri and Curvibasidium nothofagi. Finally, our work lays the ground for future studies that seek to understand the effect these communities may have on preventing or facilitating establishment of exogenous microbes, such as food spoilage microbes and plant or human pathogens.
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Affiliation(s)
- Danny Haelewaters
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA; (H.U.); (S.B.); (S.N.-H.)
| | - Hector Urbina
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA; (H.U.); (S.B.); (S.N.-H.)
- Division of Plant Industry, Florida Department of Agriculture and Consumer Services, Gainesville, FL 32608, USA
| | - Samuel Brown
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA; (H.U.); (S.B.); (S.N.-H.)
| | - Shannon Newerth-Henson
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA; (H.U.); (S.B.); (S.N.-H.)
| | - M. Catherine Aime
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA; (H.U.); (S.B.); (S.N.-H.)
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Crossing Kingdoms: How the Mycobiota and Fungal-Bacterial Interactions Impact Host Health and Disease. Infect Immun 2021; 89:IAI.00648-20. [PMID: 33526565 PMCID: PMC8090948 DOI: 10.1128/iai.00648-20] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The term “microbiota” invokes images of mucosal surfaces densely populated with bacteria. These surfaces and the luminal compartments they form indeed predominantly harbor bacteria. The term “microbiota” invokes images of mucosal surfaces densely populated with bacteria. These surfaces and the luminal compartments they form indeed predominantly harbor bacteria. However, research from this past decade has started to complete the picture by focusing on important but largely neglected constituents of the microbiota: fungi, viruses, and archaea. The community of commensal fungi, also called the mycobiota, interacts with commensal bacteria and the host. It is thus not surprising that changes in the mycobiota have significant impact on host health and are associated with pathological conditions such as inflammatory bowel disease (IBD). In this review we will give an overview of why the mycobiota is an important research area and different mycobiota research tools. We will specifically focus on distinguishing transient and actively colonizing fungi of the oral and gut mycobiota and their roles in health and disease. In addition to correlative and observational studies, we will discuss mechanistic studies on specific cross-kingdom interactions of fungi, bacteria, and the host.
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22
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Wu X, Xia Y, He F, Zhu C, Ren W. Intestinal mycobiota in health and diseases: from a disrupted equilibrium to clinical opportunities. MICROBIOME 2021; 9:60. [PMID: 33715629 PMCID: PMC7958491 DOI: 10.1186/s40168-021-01024-x] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 02/04/2021] [Indexed: 05/08/2023]
Abstract
Bacteria, viruses, protozoa, and fungi establish a complex ecosystem in the gut. Like other microbiota, gut mycobiota plays an indispensable role in modulating intestinal physiology. Notably, the most striking characteristics of intestinal fungi are their extraintestinal functions. Here, we provide a comprehensive review of the importance of gut fungi in the regulation of intestinal, pulmonary, hepatic, renal, pancreatic, and brain functions, and we present possible opportunities for the application of gut mycobiota to alleviate/treat human diseases. Video Abstract.
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Affiliation(s)
- Xiaoyan Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Animal Nutrition Control, College of Animal Science, South China Agricultural University, Guangzhou, 510642 China
| | - Yaoyao Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Animal Nutrition Control, College of Animal Science, South China Agricultural University, Guangzhou, 510642 China
| | - Fang He
- College of Animal Science and Technology, Southwest University, Chongqing, 400716 China
| | - Congrui Zhu
- College of Veterinary Medicine, Kansas State University, Manhattan, KS USA
| | - Wenkai Ren
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Animal Nutrition Control, College of Animal Science, South China Agricultural University, Guangzhou, 510642 China
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23
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Guo L, Dou X, Zou R, Guo X, Liu X, Tang H. The mycobiome in murine intestine is more perturbed by food arsenic exposure than in excreted feces. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 753:141871. [PMID: 32891997 DOI: 10.1016/j.scitotenv.2020.141871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 08/19/2020] [Accepted: 08/19/2020] [Indexed: 06/11/2023]
Abstract
Arsenic is a global pollutant that can accumulate in rice and has been confirmed to disturb the gut microbiome. By contrast, the influence on the gut mycobiome is seldom concerned because fungi comprise a numerically small proportion of the whole gut microcommunity. To expand the detection of the mycobiome in different gut sections of mammals and investigate the influence of food arsenic on the gut mycobiome in the digestive tract, we treated mice with feeds containing different compositions of arsenic species (7.3% sodium arsenate, 72.7% sodium arsenite, 1.0% sodium monomethylarsonate, and 19.0% sodium dimethylarsinate) in rice at a total arsenic dose of 30 mg/kg. After 60 days of exposure, the feces of four different sites, the ileum, cecum, colon, and excreted feces, were collected and analyzed by internal transcribed spacer gene sequencing. Among the samples, the major fungal phyla were Ascomycota, Basidiomycota, and Zygomycota; the top 10 fungal genera were Aspergillus, Verticillium, Penicillium, Cladosporium, Alternaria, Fusarium, Ophiocordyceps, Trametes, Mucor, and Nigrospora. In control mice, along the murine digestive tract, the mycobial richness and composition were significantly changed; Aspergillus and Penicillium possessed the higher ability to be stabilized in the murine gut, and larger proportions of positive correlations were observed among the major fungi. After arsenic exposure, the fungal composition was more disturbed in the intestinal tract than in feces. Along the digestive tract, arsenic can trigger larger mycobial variations, and the sensitivities of major fungi to arsenic were changed. Thus, the murine intestinal spatial mycobiota are more perturbed than excreted fecal mycobiota after food arsenic exposure. Feces are insufficient to be selected as a representative of the gut mycobiota in arsenic exposure studies.
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Affiliation(s)
- Lianxian Guo
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan 523808, China
| | - Xinghao Dou
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan 523808, China
| | - Rong Zou
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan 523808, China
| | - Xuming Guo
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan 523808, China
| | - Xiaoshan Liu
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan 523808, China.
| | - Huanwen Tang
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan 523808, China.
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25
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van Tilburg Bernardes E, Gutierrez MW, Arrieta MC. The Fungal Microbiome and Asthma. Front Cell Infect Microbiol 2020; 10:583418. [PMID: 33324573 PMCID: PMC7726317 DOI: 10.3389/fcimb.2020.583418] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/29/2020] [Indexed: 12/14/2022] Open
Abstract
Asthma is a group of inflammatory conditions that compromises the airways of a continuously increasing number of people around the globe. Its complex etiology comprises both genetic and environmental aspects, with the intestinal and lung microbiomes emerging as newly implicated factors that can drive and aggravate asthma. Longitudinal infant cohort studies combined with mechanistic studies in animal models have identified microbial signatures causally associated with subsequent asthma risk. The recent inclusion of fungi in human microbiome surveys has revealed that microbiome signatures associated with asthma risk are not limited to bacteria, and that fungi are also implicated in asthma development in susceptible individuals. In this review, we examine the unique properties of human-associated and environmental fungi, which confer them the ability to influence immune development and allergic responses. The important contribution of fungi to asthma development and exacerbations prompts for their inclusion in current and future asthma studies in humans and animal models.
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Affiliation(s)
- Erik van Tilburg Bernardes
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada.,Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| | - Mackenzie W Gutierrez
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada.,Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| | - Marie-Claire Arrieta
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada.,Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
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26
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Sae-Khow K, Charoensappakit A, Visitchanakun P, Saisorn W, Svasti S, Fucharoen S, Leelahavanichkul A. Pathogen-Associated Molecules from Gut Translocation Enhance Severity of Cecal Ligation and Puncture Sepsis in Iron-Overload β-Thalassemia Mice. J Inflamm Res 2020; 13:719-735. [PMID: 33116751 PMCID: PMC7569041 DOI: 10.2147/jir.s273329] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 09/12/2020] [Indexed: 12/15/2022] Open
Abstract
Introduction Systemic inflammation induced by gut translocation of lipopolysaccharide (LPS), a major component of Gram-negative bacteria, in thalassemia with iron-overload worsens sepsis. However, the impact of (1→3)-β-D-glucan (BG), a major fungal molecule, in iron-overload thalassemia is still unclear. Hence, the influence of BG was explored in 1) iron-overload mice with sepsis induced by cecal ligation and puncture (CLP) surgery; and 2) in bone marrow-derived macrophages (BMMs). Methods The heterozygous β-globin-deficient mice, Hbbth3/+ mice, were used as representative thalassemia (TH) mice. Iron overload was generated by 6 months of oral iron administration before CLP surgery- induced sepsis in TH mice and wild-type (WT) mice. Additionally, BMMs from both mouse strains were used to explore the impact of BG. Results Without sepsis, iron-overload TH mice demonstrated more severe intestinal mucosal injury (gut leakage) with higher LPS and BG in serum, from gut translocation, when compared with WT mice. With CLP in iron-overload mice, sepsis severity in TH mice was more severe than WT as determined by survival analysis, organ injury (kidney and liver), bacteremia, endotoxemia, gut leakage (FITC-dextran) and serum BG. Activation by LPS plus BG (LPS+BG) in BMMs and in peripheral blood-derived neutrophils (both WT and TH cells) demonstrated more prominent cytokine production when compared with LPS activation alone. In parallel, LPS+BG also prominently induced genes expression of M1 macrophage polarization (iNOS, TNF-α and IL-1β) in both WT and TH cells in comparison with LPS activation alone. In addition, LPS+BG activated macrophage cytokine production was enhanced by a high dose of ferric ion (800 mM), more predominantly in TH macrophages compared with WT cells. Moreover, LPS+BG induced higher glycolysis activity with similar respiratory capacity in RAW264.7 (a macrophage cell line) compared with LPS activation alone. These data support an additive pro-inflammatory effect of BG upon LPS. Conclusion The enhanced-severity of sepsis in iron-overload TH mice was due to 1) increased LPS and BG in serum from iron-induced gut-mucosal injury; and 2) the pro-inflammatory amplification by ferric ion on LPS+BG activation.
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Affiliation(s)
- Kritsanawan Sae-Khow
- Medical Microbiology, Interdisciplinary and International Program, Graduate School, Chulalongkorn University, Bangkok, Thailand
| | - Awirut Charoensappakit
- Translational Research in Inflammation and Immunology Research Unit (TRIRU), Department of Microbiology, Chulalongkorn University, Bangkok, Thailand
| | - Peerapat Visitchanakun
- Medical Microbiology, Interdisciplinary and International Program, Graduate School, Chulalongkorn University, Bangkok, Thailand
| | - Wilasinee Saisorn
- Translational Research in Inflammation and Immunology Research Unit (TRIRU), Department of Microbiology, Chulalongkorn University, Bangkok, Thailand
| | - Saovaros Svasti
- Thalassemia Research Center, Institute of Molecular Biosciences, Mahidol University, Nakornpathom, Thailand
| | - Suthat Fucharoen
- Thalassemia Research Center, Institute of Molecular Biosciences, Mahidol University, Nakornpathom, Thailand
| | - Asada Leelahavanichkul
- Translational Research in Inflammation and Immunology Research Unit (TRIRU), Department of Microbiology, Chulalongkorn University, Bangkok, Thailand.,Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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27
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Chikina AS, Nadalin F, Maurin M, San-Roman M, Thomas-Bonafos T, Li XV, Lameiras S, Baulande S, Henri S, Malissen B, Lacerda Mariano L, Barbazan J, Blander JM, Iliev ID, Matic Vignjevic D, Lennon-Duménil AM. Macrophages Maintain Epithelium Integrity by Limiting Fungal Product Absorption. Cell 2020; 183:411-428.e16. [PMID: 32970988 PMCID: PMC7646275 DOI: 10.1016/j.cell.2020.08.048] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/27/2020] [Accepted: 08/26/2020] [Indexed: 12/14/2022]
Abstract
The colon is primarily responsible for absorbing fluids. It contains a large number of microorganisms including fungi, which are enriched in its distal segment. The colonic mucosa must therefore tightly regulate fluid influx to control absorption of fungal metabolites, which can be toxic to epithelial cells and lead to barrier dysfunction. How this is achieved remains unknown. Here, we describe a mechanism by which the innate immune system allows rapid quality check of absorbed fluids to avoid intoxication of colonocytes. This mechanism relies on a population of distal colon macrophages that are equipped with "balloon-like" protrusions (BLPs) inserted in the epithelium, which sample absorbed fluids. In the absence of macrophages or BLPs, epithelial cells keep absorbing fluids containing fungal products, leading to their death and subsequent loss of epithelial barrier integrity. These results reveal an unexpected and essential role of macrophages in the maintenance of colon-microbiota interactions in homeostasis. VIDEO ABSTRACT.
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Affiliation(s)
- Aleksandra S Chikina
- Institut Curie, PSL Research University, CNRS UMR 144, F-75005 Paris, France; Institut Curie, PSL Research University, INSERM U932, F-75005 Paris, France
| | - Francesca Nadalin
- Institut Curie, PSL Research University, INSERM U932, F-75005 Paris, France
| | - Mathieu Maurin
- Institut Curie, PSL Research University, INSERM U932, F-75005 Paris, France
| | - Mabel San-Roman
- Institut Curie, PSL Research University, INSERM U932, F-75005 Paris, France
| | | | - Xin V Li
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Sonia Lameiras
- Institut Curie, PSL Research University, Next Generation Sequencing Facility, F-75005 Paris, France
| | - Sylvain Baulande
- Institut Curie, PSL Research University, Next Generation Sequencing Facility, F-75005 Paris, France
| | - Sandrine Henri
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, 13288 Marseille, France
| | - Bernard Malissen
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, 13288 Marseille, France; Centre d'Immunophénomique, Aix Marseille Université, INSERM, CNRS, 13288 Marseille, France
| | | | - Jorge Barbazan
- Institut Curie, PSL Research University, CNRS UMR 144, F-75005 Paris, France
| | - J Magarian Blander
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Iliyan D Iliev
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
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28
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29
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Vinzelj J, Joshi A, Insam H, Podmirseg SM. Employing anaerobic fungi in biogas production: challenges & opportunities. BIORESOURCE TECHNOLOGY 2020; 300:122687. [PMID: 31926794 DOI: 10.1016/j.biortech.2019.122687] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 12/21/2019] [Accepted: 12/23/2019] [Indexed: 05/24/2023]
Abstract
Anaerobic fungi (AF, phylum Neocallimastigomycota) are best known for their ability to efficiently break down lignocellulosic biomass. Their unique combination of mechanical and enzymatic attacks on recalcitrant plant structures bears great potential for enhancement of the anaerobic digestion (AD) process. Although scientists in this field have long agreed upon the potential of AF for biotechnology, research is only recently gaining traction. This delay was largely due to difficulties in culture-dependent and culture-independent analysis of those high-maintenance organisms with their still unknown complex growth requirements. In this review, we will summarize current research efforts on bioaugmentation with AF and further point out, how the lack of basic knowledge on AF nutritional needs hampers their implementation on an industrial scale. Through this, we hope to further kindle interest into basic research on AF in order to advance their stable integration into biotechnological processes.
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Affiliation(s)
- Julia Vinzelj
- Institute of Microbiology, University of Innsbruck, Technikerstraße 25d, A-6020 Innsbruck, Austria
| | - Akshay Joshi
- ZHAW School of Life Sciences and Facility Management, Einsiedlerstrasse 31, CH-8820 Wädenswil, Switzerland
| | - Heribert Insam
- Institute of Microbiology, University of Innsbruck, Technikerstraße 25d, A-6020 Innsbruck, Austria
| | - Sabine Marie Podmirseg
- Institute of Microbiology, University of Innsbruck, Technikerstraße 25d, A-6020 Innsbruck, Austria
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30
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Li J, Luo Y, Chen D, Yu B, He J, Huang Z, Mao X, Zheng P, Yu J, Luo J, Tian G, Yan H, Wang Q, Wang H. The fungal community and its interaction with the concentration of short-chain fatty acids in the caecum and colon of weaned piglets. J Anim Physiol Anim Nutr (Berl) 2020; 104:616-628. [PMID: 31943421 DOI: 10.1111/jpn.13300] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 12/03/2019] [Accepted: 12/07/2019] [Indexed: 12/17/2022]
Abstract
In sharp contrast to the numerous studies on bacteria, very little is known about the fungal community in mammalian gut. Recent studies on human and mice highlighted the importance of "mycobiota" in the metabolism and gut health of host, but our knowledge on the fungal composition and distribution in swine gut is very limited. In the current study, the fungal community in the caecal and colonic digesta from five weaned piglets was analysed based on an Illumina HiSeq 2500 platform targeting the internal transcribed spacer 1 region, and its relationship with the concentration of short-chain fatty acids was also investigated. Results revealed that the fungal profile in the caecal and colonic digesta of the piglets was distinct, and the caecal fungal diversity was significantly higher (p < .05). Basidiomycota and Ascomycota were the two predominant fungal phyla in the caecum and colon of the piglets. Comparing with that in colon, the abundance of Saccharomycopsis, Wallemia and Mrakia showed significantly higher (p < .05), and the abundance of Scheffersomyces, Aspergillus, Penicillium and Mucor was significantly lower in the caecum (p < .05). Canonical correspondence analysis showed a correlation between the fungal community and the concentration of isobutyrate, isovalerate, propionate and acetate in the digesta samples. Spearman's correlation indicated that the low-abundance genera, Fusarium, Plectosphaerella and Metarhizium, were positively correlated with of isobutyrate (p < .05), while Xeromyces were negatively correlated with acetate (p < .05), and Cornuvesica was negatively correlated with both acetate and propionate (p < .05). Results illuminated a probable interaction between the fungal composition and the bacterial degradation of protein and complex carbohydrates in the diet. These findings would be helpful to enhance our understanding of fungi in swine gut and provide a foundation for future work on the function of mycobiota in pigs.
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Affiliation(s)
- Jiayan Li
- Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education of China, Chengdu, China.,Key Laboratory for Animal Disease-Resistance Nutrition and Feed of Ministry of Agriculture of China, Chengdu, China.,Key laboratory of Animal Disease-resistant Nutrition of Sichuan Province, Chengdu, China.,Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Yuheng Luo
- Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education of China, Chengdu, China.,Key Laboratory for Animal Disease-Resistance Nutrition and Feed of Ministry of Agriculture of China, Chengdu, China.,Key laboratory of Animal Disease-resistant Nutrition of Sichuan Province, Chengdu, China.,Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Daiwen Chen
- Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education of China, Chengdu, China.,Key Laboratory for Animal Disease-Resistance Nutrition and Feed of Ministry of Agriculture of China, Chengdu, China.,Key laboratory of Animal Disease-resistant Nutrition of Sichuan Province, Chengdu, China.,Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Bing Yu
- Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education of China, Chengdu, China.,Key Laboratory for Animal Disease-Resistance Nutrition and Feed of Ministry of Agriculture of China, Chengdu, China.,Key laboratory of Animal Disease-resistant Nutrition of Sichuan Province, Chengdu, China.,Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Jun He
- Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education of China, Chengdu, China.,Key Laboratory for Animal Disease-Resistance Nutrition and Feed of Ministry of Agriculture of China, Chengdu, China.,Key laboratory of Animal Disease-resistant Nutrition of Sichuan Province, Chengdu, China.,Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Zhiqing Huang
- Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education of China, Chengdu, China.,Key Laboratory for Animal Disease-Resistance Nutrition and Feed of Ministry of Agriculture of China, Chengdu, China.,Key laboratory of Animal Disease-resistant Nutrition of Sichuan Province, Chengdu, China.,Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Xiangbing Mao
- Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education of China, Chengdu, China.,Key Laboratory for Animal Disease-Resistance Nutrition and Feed of Ministry of Agriculture of China, Chengdu, China.,Key laboratory of Animal Disease-resistant Nutrition of Sichuan Province, Chengdu, China.,Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Ping Zheng
- Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education of China, Chengdu, China.,Key Laboratory for Animal Disease-Resistance Nutrition and Feed of Ministry of Agriculture of China, Chengdu, China.,Key laboratory of Animal Disease-resistant Nutrition of Sichuan Province, Chengdu, China.,Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Jie Yu
- Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education of China, Chengdu, China.,Key Laboratory for Animal Disease-Resistance Nutrition and Feed of Ministry of Agriculture of China, Chengdu, China.,Key laboratory of Animal Disease-resistant Nutrition of Sichuan Province, Chengdu, China.,Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Junqiu Luo
- Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education of China, Chengdu, China.,Key Laboratory for Animal Disease-Resistance Nutrition and Feed of Ministry of Agriculture of China, Chengdu, China.,Key laboratory of Animal Disease-resistant Nutrition of Sichuan Province, Chengdu, China.,Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Gang Tian
- Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education of China, Chengdu, China.,Key Laboratory for Animal Disease-Resistance Nutrition and Feed of Ministry of Agriculture of China, Chengdu, China.,Key laboratory of Animal Disease-resistant Nutrition of Sichuan Province, Chengdu, China.,Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Hui Yan
- Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education of China, Chengdu, China.,Key Laboratory for Animal Disease-Resistance Nutrition and Feed of Ministry of Agriculture of China, Chengdu, China.,Key laboratory of Animal Disease-resistant Nutrition of Sichuan Province, Chengdu, China.,Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Quyuan Wang
- Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education of China, Chengdu, China.,Key Laboratory for Animal Disease-Resistance Nutrition and Feed of Ministry of Agriculture of China, Chengdu, China.,Key laboratory of Animal Disease-resistant Nutrition of Sichuan Province, Chengdu, China.,Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Huifen Wang
- Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education of China, Chengdu, China.,Key Laboratory for Animal Disease-Resistance Nutrition and Feed of Ministry of Agriculture of China, Chengdu, China.,Key laboratory of Animal Disease-resistant Nutrition of Sichuan Province, Chengdu, China.,Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
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van Tilburg Bernardes E, Gutierrez MW, Arrieta MC. The Fungal Microbiome and Asthma. Front Cell Infect Microbiol 2020. [PMID: 33324573 DOI: 10.3389/fcimb.2020.583418/full] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
Asthma is a group of inflammatory conditions that compromises the airways of a continuously increasing number of people around the globe. Its complex etiology comprises both genetic and environmental aspects, with the intestinal and lung microbiomes emerging as newly implicated factors that can drive and aggravate asthma. Longitudinal infant cohort studies combined with mechanistic studies in animal models have identified microbial signatures causally associated with subsequent asthma risk. The recent inclusion of fungi in human microbiome surveys has revealed that microbiome signatures associated with asthma risk are not limited to bacteria, and that fungi are also implicated in asthma development in susceptible individuals. In this review, we examine the unique properties of human-associated and environmental fungi, which confer them the ability to influence immune development and allergic responses. The important contribution of fungi to asthma development and exacerbations prompts for their inclusion in current and future asthma studies in humans and animal models.
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Affiliation(s)
- Erik van Tilburg Bernardes
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada
- Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| | - Mackenzie W Gutierrez
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada
- Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| | - Marie-Claire Arrieta
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada
- Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
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32
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Ahern PP, Maloy KJ. Understanding immune-microbiota interactions in the intestine. Immunology 2020; 159:4-14. [PMID: 31777071 PMCID: PMC6904641 DOI: 10.1111/imm.13150] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 10/01/2019] [Accepted: 10/07/2019] [Indexed: 12/13/2022] Open
Abstract
The past two decades have seen an explosion in research that aims to understand how the dynamic interplay with the gut microbiota impacts host health and disease, establishing a role for the gut microbiota in a plethora of pathologies. Understanding how health-promoting microbiota are established and how beneficial host-microbiota interactions are maintained is of immense biomedical importance. Despite the enormous progress that has been made, our knowledge of the specific microbiota members that mediate these effects and the mechanisms underlying these interactions is rudimentary. The dearth of information regarding the nature of advantageous host-microbiota interactions, and the factors that cause these relationships to go awry, has hampered our ability to realize the therapeutic potential of the microbiota. Here we discuss key issues that limit current knowledge and describe a path forwards to improving our understanding of the contributions of the microbiota to host health.
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Affiliation(s)
- Philip P. Ahern
- Department of Cardiovascular and Metabolic SciencesCleveland Clinic Lerner Research InstituteClevelandOHUSA
| | - Kevin J. Maloy
- Institute of Infection, Immunity and InflammationCollege of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowUK
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33
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Song Y, Gyarmati P. Microbiota changes in a pediatric acute lymphocytic leukemia mouse model. Microbiologyopen 2019; 9:e982. [PMID: 31884727 PMCID: PMC7066458 DOI: 10.1002/mbo3.982] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 12/02/2019] [Accepted: 12/03/2019] [Indexed: 01/01/2023] Open
Abstract
Hematological malignancies are the most common type of pediatric cancers, and acute lymphocytic leukemia (ALL) is the most frequently occurring hematological malignancy during childhood. A major cause of mortality in leukemia is bloodstream infection (BSI). The aim of the current study was to explore the gut microbiota in ALL and its potential functional alterations. High-throughput sequencing was used to characterize the bacterial and fungal microbiota in feces and their predicted functional characteristics in a xenotransplant pediatric ALL mouse model. Our work shows that gut microbiota significantly changes in leukemia, which may result in functional alterations. This study may provide potential therapeutic or preventive strategies of BSI in ALL.
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Affiliation(s)
- Yajing Song
- Department of Cancer Biology and Pharmacology, University of Illinois College of Medicine at Peoria, Peoria, IL, USA
| | - Peter Gyarmati
- Department of Cancer Biology and Pharmacology, University of Illinois College of Medicine at Peoria, Peoria, IL, USA
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Li J, Chen D, Yu B, He J, Huang Z, Mao X, Zheng P, Yu J, Luo J, Tian G, Luo Y. The fungal community and its interaction with the concentration of short-chain fatty acids in the faeces of Chenghua, Yorkshire and Tibetan pigs. Microb Biotechnol 2019; 13:509-521. [PMID: 31691493 PMCID: PMC7017814 DOI: 10.1111/1751-7915.13507] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 10/08/2019] [Accepted: 10/18/2019] [Indexed: 12/12/2022] Open
Abstract
Despite their important roles in host nutrition and metabolism, and potential to cause disease, our knowledge of the fungal community in the mammalian gut is quite limited. To date, diversity and composition of fungi in swine gut still remains unknown. Therefore, the first internal transcribed spacer of fungi in faecal samples from three breeds of pigs (10 pigs for each breed) was sequenced based on an Illumina HiSeq 2500 platform, and the relationship between the fungal community and the concentrations of main short‐chain fatty acids (SCFAs) was also analysed. Results indicated that Chenghua (local, higher body fat rate), Yorkshire (foreign, higher lean meat and growth rate) and Tibetan (plateau, stronger disease resistance) pigs harboured distinct fungal community. The Basidiomycota and Ascomycota presented as the two predominant phyla, with Loreleia, Russula and Candida as the top three genera in all samples. Network analysis revealed a total of 35 correlations among different fungal genera, with 27 (77.14%) positive and 8 (22.86%) negative pairwise interactions. Canonical correspondence analysis suggested that fungi in the faeces of pigs were more correlated to the concentration of acetate and butyrate rather than propionate. Spearman’s correlation further showed that Tomentella was positively correlated to both acetate and butyrate, and Loreleia was positively correlated to propionate (P < 0.05), while Nephroma and Taiwanofungus were negatively correlated to acetate and propionate (P < 0.05). These findings expanded our knowledge on the intestinal fungi in pigs with different genotypes and phenotypes, indicating that fungi may play an indispensable role during the metabolism of host and the maintenance of intestinal health. The cross‐feeding between fungi and other microorganisms may be crucial during the digestion of dietary carbohydrates and the associated physiological processes, which is worthy to be further studied.
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Affiliation(s)
- Jiayan Li
- Key Laboratory for Animal Disease-Resistance Nutrition, Ministry of Education of China, Chengdu, China.,Key Laboratory for Animal Disease-Resistance Nutrition and Feed, Ministry of Agriculture of China, Chengdu, China.,Key Laboratory of Animal Disease-Resistant Nutrition, Sichuan Province, China.,Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Daiwen Chen
- Key Laboratory for Animal Disease-Resistance Nutrition, Ministry of Education of China, Chengdu, China.,Key Laboratory for Animal Disease-Resistance Nutrition and Feed, Ministry of Agriculture of China, Chengdu, China.,Key Laboratory of Animal Disease-Resistant Nutrition, Sichuan Province, China.,Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Bing Yu
- Key Laboratory for Animal Disease-Resistance Nutrition, Ministry of Education of China, Chengdu, China.,Key Laboratory for Animal Disease-Resistance Nutrition and Feed, Ministry of Agriculture of China, Chengdu, China.,Key Laboratory of Animal Disease-Resistant Nutrition, Sichuan Province, China.,Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Jun He
- Key Laboratory for Animal Disease-Resistance Nutrition, Ministry of Education of China, Chengdu, China.,Key Laboratory for Animal Disease-Resistance Nutrition and Feed, Ministry of Agriculture of China, Chengdu, China.,Key Laboratory of Animal Disease-Resistant Nutrition, Sichuan Province, China.,Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Zhiqing Huang
- Key Laboratory for Animal Disease-Resistance Nutrition, Ministry of Education of China, Chengdu, China.,Key Laboratory for Animal Disease-Resistance Nutrition and Feed, Ministry of Agriculture of China, Chengdu, China.,Key Laboratory of Animal Disease-Resistant Nutrition, Sichuan Province, China.,Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Xiangbing Mao
- Key Laboratory for Animal Disease-Resistance Nutrition, Ministry of Education of China, Chengdu, China.,Key Laboratory for Animal Disease-Resistance Nutrition and Feed, Ministry of Agriculture of China, Chengdu, China.,Key Laboratory of Animal Disease-Resistant Nutrition, Sichuan Province, China.,Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Ping Zheng
- Key Laboratory for Animal Disease-Resistance Nutrition, Ministry of Education of China, Chengdu, China.,Key Laboratory for Animal Disease-Resistance Nutrition and Feed, Ministry of Agriculture of China, Chengdu, China.,Key Laboratory of Animal Disease-Resistant Nutrition, Sichuan Province, China.,Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Jie Yu
- Key Laboratory for Animal Disease-Resistance Nutrition, Ministry of Education of China, Chengdu, China.,Key Laboratory for Animal Disease-Resistance Nutrition and Feed, Ministry of Agriculture of China, Chengdu, China.,Key Laboratory of Animal Disease-Resistant Nutrition, Sichuan Province, China.,Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Junqiu Luo
- Key Laboratory for Animal Disease-Resistance Nutrition, Ministry of Education of China, Chengdu, China.,Key Laboratory for Animal Disease-Resistance Nutrition and Feed, Ministry of Agriculture of China, Chengdu, China.,Key Laboratory of Animal Disease-Resistant Nutrition, Sichuan Province, China.,Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Gang Tian
- Key Laboratory for Animal Disease-Resistance Nutrition, Ministry of Education of China, Chengdu, China.,Key Laboratory for Animal Disease-Resistance Nutrition and Feed, Ministry of Agriculture of China, Chengdu, China.,Key Laboratory of Animal Disease-Resistant Nutrition, Sichuan Province, China.,Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Yuheng Luo
- Key Laboratory for Animal Disease-Resistance Nutrition, Ministry of Education of China, Chengdu, China.,Key Laboratory for Animal Disease-Resistance Nutrition and Feed, Ministry of Agriculture of China, Chengdu, China.,Key Laboratory of Animal Disease-Resistant Nutrition, Sichuan Province, China.,Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
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35
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The gut mycobiota: insights into analysis, environmental interactions and role in gastrointestinal diseases. Nat Rev Gastroenterol Hepatol 2019; 16:331-345. [PMID: 30824884 DOI: 10.1038/s41575-019-0121-2] [Citation(s) in RCA: 139] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The gut microbiota is a dense and diverse ecosystem that is involved in many physiological functions as well as in disease pathogenesis. It is dominated by bacteria, which have been extensively studied in the past 15 years; however, other microorganisms, such as fungi, phages, archaea and protists, are also present in the gut microbiota. Exploration of the fungal component, namely, the mycobiota, is at an early stage, and several specific technical challenges are associated with mycobiota analysis. The number of fungi in the lower gastrointestinal tract is far lower than that of bacteria, but fungal cells are much larger and much more complex than bacterial cells. In addition, a role of the mycobiota in disease, notably in IBD, is indicated by both descriptive data in humans and mechanistic data in mice. Interactions between bacteria and fungi within the gut, their functional roles and their interplay with the host and its immune system are fascinating areas that researchers are just beginning to investigate. In this Review, we discuss the newest data on the gut mycobiota and explore both the technical aspects of its study and its role in health and gastrointestinal diseases.
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36
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Krüger W, Vielreicher S, Kapitan M, Jacobsen ID, Niemiec MJ. Fungal-Bacterial Interactions in Health and Disease. Pathogens 2019; 8:E70. [PMID: 31117285 PMCID: PMC6630686 DOI: 10.3390/pathogens8020070] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 05/02/2019] [Accepted: 05/16/2019] [Indexed: 12/28/2022] Open
Abstract
Fungi and bacteria encounter each other in various niches of the human body. There, they interact directly with one another or indirectly via the host response. In both cases, interactions can affect host health and disease. In the present review, we summarized current knowledge on fungal-bacterial interactions during their commensal and pathogenic lifestyle. We focus on distinct mucosal niches: the oral cavity, lung, gut, and vagina. In addition, we describe interactions during bloodstream and wound infections and the possible consequences for the human host.
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Affiliation(s)
- Wibke Krüger
- Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Jena 07745, Germany.
| | - Sarah Vielreicher
- Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Jena 07745, Germany.
| | - Mario Kapitan
- Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Jena 07745, Germany.
- Center for Sepsis Control and Care, Jena 07747, Germany.
| | - Ilse D Jacobsen
- Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Jena 07745, Germany.
- Center for Sepsis Control and Care, Jena 07747, Germany.
- Institute of Microbiology, Friedrich Schiller University, Jena 07743, Germany.
| | - Maria Joanna Niemiec
- Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Jena 07745, Germany.
- Center for Sepsis Control and Care, Jena 07747, Germany.
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37
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Wang T, Fan C, Yao A, Xu X, Zheng G, You Y, Jiang C, Zhao X, Hou Y, Hung MC, Lin X. The Adaptor Protein CARD9 Protects against Colon Cancer by Restricting Mycobiota-Mediated Expansion of Myeloid-Derived Suppressor Cells. Immunity 2019; 49:504-514.e4. [PMID: 30231984 DOI: 10.1016/j.immuni.2018.08.018] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Revised: 03/29/2018] [Accepted: 07/06/2018] [Indexed: 01/19/2023]
Abstract
The adaptor protein CARD9 links detection of fungi by surface receptors to the activation of the NF-κB pathway. Mice deficient in CARD9 exhibit dysbiosis and are more susceptible to colitis. Here we examined the impact of Card9 deficiency in the development of colitis-associated colon cancer (CAC). Treatment of Card9-/- mice with AOM-DSS resulted in increased tumor loads as compared to WT mice and in the accumulation of myeloid-derived suppressor cells (MDSCs) in tumor tissue. The impaired fungicidal functions of Card9-/- macrophages led to increased fungal loads and variation in the overall composition of the intestinal mycobiota, with a notable increase in C. tropicalis. Bone marrow cells incubated with C. tropicalis exhibited MDSC features and suppressive functions. Fluconazole treatment suppressed CAC in Card9-/- mice and was associated with decreased MDSC accumulation. The frequency of MDSCs in tumor tissues of colon cancer patients correlated positively with fungal burden, pointing to the relevance of this regulatory axis in human disease.
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Affiliation(s)
- Tingting Wang
- The State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Key Laboratory of Molecular Medicine, Division of Immunology, Medical School, Nanjing University, Nanjing 210093, China; Department of Molecular and Cellular Oncology, The University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Chaogang Fan
- General Surgery, Jinling Hospital affiliated Medical School, Nanjing University, Nanjing 210093, China
| | - Anran Yao
- The State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Key Laboratory of Molecular Medicine, Division of Immunology, Medical School, Nanjing University, Nanjing 210093, China
| | - Xingwei Xu
- General Surgery, Jinling Hospital affiliated Medical School, Nanjing University, Nanjing 210093, China
| | - Guoxing Zheng
- Institute for Immunology, Tsinghua University School of Medicine, Tsinghua, Beijing 100084, China; Tsinghua University-Peking University Joint Center for Life Sciences, Beijing 100084, China
| | - Yun You
- Department of Molecular and Cellular Oncology, The University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Changying Jiang
- Department of Molecular and Cellular Oncology, The University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xueqiang Zhao
- Institute for Immunology, Tsinghua University School of Medicine, Tsinghua, Beijing 100084, China
| | - Yayi Hou
- The State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Key Laboratory of Molecular Medicine, Division of Immunology, Medical School, Nanjing University, Nanjing 210093, China
| | - Mien-Chie Hung
- Department of Molecular and Cellular Oncology, The University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xin Lin
- Institute for Immunology, Tsinghua University School of Medicine, Tsinghua, Beijing 100084, China; Tsinghua University-Peking University Joint Center for Life Sciences, Beijing 100084, China.
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38
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Jayasudha R, Chakravarthy SK, Prashanthi GS, Sharma S, Garg P, Murthy SI, Shivaji S. Alterations in gut bacterial and fungal microbiomes are associated with bacterial Keratitis, an inflammatory disease of the human eye. J Biosci 2018; 43:835-856. [PMID: 30541945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Dysbiosis, or imbalance in the gut microbiome, has been implicated in auto-immune, inflammatory, neurological diseases as well as in cancers. More recently it has also been shown to be associated with ocular diseases. In the present study, the association of gut microbiome dysbiosis with bacterial Keratitis, an inflammatory eye disease which significantly contributes to corneal blindness, was investigated. Bacterial and fungal gut microbiomes were analysed using fecal samples of healthy controls (HC, n = 21) and bacterial Keratitis patients (BK, n = 19). An increase in abundance of several antiinflammatory organisms including Dialister, Megasphaera, Faecalibacterium, Lachnospira, Ruminococcus and Mitsuokella and members of Firmicutes, Veillonellaceae, Ruminococcaceae and Lachnospiraceae was observed in HC compared to BK patients in the bacterial microbiome. In the fungal microbiome, a decrease in the abundance of Mortierella, Rhizopus, Kluyveromyces, Embellisia and Haematonectria and an increase in the abundance of pathogenic fungi Aspergillus and Malassezia were observed in BK patients compared to HC. In addition, heatmaps, PCoA plots and inferred functional profiles also indicated significant variations between the HC and BK microbiomes, which strongly suggest dysbiosis in the gut microbiome of BK patients. This is the first study demonstrating the association of gut microbiome with the pathophysiology of BK and thus supports the gut-eye axis hypothesis. Considering that Keratitis affects about 1 million people annually across the globe, the data could be the basis for developing alternate strategies for treatment like use of probiotics or fecal transplantation to restore the healthy microbiome as a treatment protocol for Keratitis.
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Affiliation(s)
- Rajagopalaboopathi Jayasudha
- Jhaveri Microbiology Centre, Prof. Brien Holden Eye Research Centre, L. V. Prasad Eye Institute, Kallam Anji Reddy campus, Hyderabad 500 034, India
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39
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Alterations in gut bacterial and fungal microbiomes are associated with bacterial Keratitis, an inflammatory disease of the human eye. J Biosci 2018. [DOI: 10.1007/s12038-018-9798-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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40
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Li J, Chen D, Yu B, He J, Zheng P, Mao X, Yu J, Luo J, Tian G, Huang Z, Luo Y. Fungi in Gastrointestinal Tracts of Human and Mice: from Community to Functions. MICROBIAL ECOLOGY 2018; 75:821-829. [PMID: 29110065 DOI: 10.1007/s00248-017-1105-9] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 10/30/2017] [Indexed: 05/10/2023]
Abstract
Fungi are often ignored in studies on gut microbes because of their low level of presence (making up only 0.1% of the total microorganisms) in the gastrointestinal tract (GIT) of monogastric animals. Recent studies using novel technologies such as next generation sequencing have expanded our understanding on the importance of intestinal fungi in humans and animals. Here, we provide a comprehensive review on the fungal community, the so-called mycobiome, and their functions from recent studies in humans and mice. In the GIT of humans, fungi belonging to the phyla Ascomycota, Basidiomycota and Chytridiomycota are predominant. The murine intestines harbor a more diverse assemblage of fungi. Diet is one of the major factors influencing colonization of fungi in the GIT. Presence of the genus Candida is positively associated with dietary carbohydrates, but are negatively correlated with dietary amino acids, proteins, and fatty acids. However, the relationship between diet and the fungal community (and functions), as well as the underlying mechanisms remains unclear. Dysbiosis of intestinal fungi can cause invasive infections and inflammatory bowel diseases (IBD). However, it is not clear whether dysbiosis of the mycobiome is a cause, or a result of IBD. Compared to non-inflamed intestinal mucosa, the abundance and diversity of fungi is significantly increased in the inflamed mucosa. The commonly observed commensal fungal species Candida albicans might contribute to occurrence and development of IBD. Limited studies show that Candida albicans might interact with immune cells of the host intestines through the pathways associated with Dectin-1, Toll-like receptor 2 (TLR2), and TLR4. This review is expected to provide new thoughts for future studies on intestinal fungi and for new therapies to fungal infections in the GIT of human and animals.
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Affiliation(s)
- Jiayan Li
- Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Daiwen Chen
- Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Bing Yu
- Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Jun He
- Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Ping Zheng
- Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Xiangbing Mao
- Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Jie Yu
- Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Junqiu Luo
- Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Gang Tian
- Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Zhiqing Huang
- Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Yuheng Luo
- Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China.
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Leonardi I, Li X, Semon A, Li D, Doron I, Putzel G, Bar A, Prieto D, Rescigno M, McGovern DPB, Pla J, Iliev ID. CX3CR1 + mononuclear phagocytes control immunity to intestinal fungi. Science 2018; 359:232-236. [PMID: 29326275 DOI: 10.1126/science.aao1503] [Citation(s) in RCA: 190] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 11/15/2017] [Accepted: 12/09/2017] [Indexed: 12/23/2022]
Abstract
Intestinal fungi are an important component of the microbiota, and recent studies have unveiled their potential in modulating host immune homeostasis and inflammatory disease. Nonetheless, the mechanisms governing immunity to gut fungal communities (mycobiota) remain unknown. We identified CX3CR1+ mononuclear phagocytes (MNPs) as being essential for the initiation of innate and adaptive immune responses to intestinal fungi. CX3CR1+ MNPs express antifungal receptors and activate antifungal responses in a Syk-dependent manner. Genetic ablation of CX3CR1+ MNPs in mice led to changes in gut fungal communities and to severe colitis that was rescued by antifungal treatment. In Crohn's disease patients, a missense mutation in the gene encoding CX3CR1 was identified and found to be associated with impaired antifungal responses. These results unravel a role of CX3CR1+ MNPs in mediating interactions between intestinal mycobiota and host immunity at steady state and during inflammatory disease.
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Affiliation(s)
- Irina Leonardi
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA.,The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Xin Li
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA.,The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Alexa Semon
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA.,The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Dalin Li
- The F. Widjaja Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Itai Doron
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA.,The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Gregory Putzel
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Agnieszka Bar
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA.,The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Daniel Prieto
- Faculty of Pharmacy, Department of Microbiology II, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Maria Rescigno
- Department of Experimental Oncology, European Institute of Oncology, I-20141 Milan, Italy
| | - Dermot P B McGovern
- The F. Widjaja Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jesus Pla
- Faculty of Pharmacy, Department of Microbiology II, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Iliyan D Iliev
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA.,The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA.,Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
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42
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Borges FM, de Paula TO, Sarmiento MRA, de Oliveira MG, Pereira MLM, Toledo IV, Nascimento TC, Ferreira-Machado AB, Silva VL, Diniz CG. Fungal Diversity of Human Gut Microbiota Among Eutrophic, Overweight, and Obese Individuals Based on Aerobic Culture-Dependent Approach. Curr Microbiol 2018; 75:726-735. [PMID: 29368026 DOI: 10.1007/s00284-018-1438-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 01/16/2018] [Indexed: 12/14/2022]
Abstract
Fungi have a complex role in the intestinal tract, influencing health and disease, with dysbiosis contributing to obesity. Our objectives were to investigate fungal diversity in human gut microbiota among eutrophic, overweight, and obese. Epidemiological and nutritional information were collected from adult individuals, as well as stool samples processed for selective fungi isolation and identification by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (yeasts) or microculture (filamentous fungi). Further 18S rDNA sequencing was performed to confirm identification. The mean count of fungi was 241 CFU/g of feces. Differences in the population level of the filamentous fungi were observed within eutrophic and obese groups. Overall, 34 genera were identified. The predominant phylum was Ascomycota with 20 different genera, followed by Basidiomycota and Zygomycota. As for Ascomycota, the most prevalent species were Paecilomyces sp., Penicillium sp., Candida sp., Aspergillus sp., Fonsecaea sp., and Geotrichum sp. (76.39, 65.28, 59.72, 58.33, 12.50, and 9.72%, respectively). As for Basidiomycota, Trichosporon sp. and Rhodotorula sp. were the most prevalent (30.56 and 15.28%, respectively), and for Zygomycota, Rhizopus sp. and Mucor sp. were the most numerous (15.28 and 9.72%, respectively). As expected there is a mycobiota shift towards obesity, with slightly higher diversity associated to eutrophic individuals. This mycobiota shift seems also to be related to the nutritional behavior of the individuals, as observed that the macronutrients intake may be positively related to the different fungi occurrences. Other studies are needed to better understand relationships between mycobiota and obesity, which could be used in future obesity treatments.
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Affiliation(s)
- Francis M Borges
- Department of Parasitology, Microbiology and Immunology, Institute of Biological Sciences, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, 36036-900, Brazil
| | - Thaís O de Paula
- Department of Parasitology, Microbiology and Immunology, Institute of Biological Sciences, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, 36036-900, Brazil
| | - Marjorie R A Sarmiento
- Department of Parasitology, Microbiology and Immunology, Institute of Biological Sciences, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, 36036-900, Brazil
| | - Maycon G de Oliveira
- Department of Parasitology, Microbiology and Immunology, Institute of Biological Sciences, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, 36036-900, Brazil
| | - Maria L M Pereira
- Department of Parasitology, Microbiology and Immunology, Institute of Biological Sciences, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, 36036-900, Brazil
| | - Isabela V Toledo
- Department of Parasitology, Microbiology and Immunology, Institute of Biological Sciences, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, 36036-900, Brazil
| | - Thiago C Nascimento
- Department of Parasitology, Microbiology and Immunology, Institute of Biological Sciences, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, 36036-900, Brazil
| | - Alessandra B Ferreira-Machado
- Department of Parasitology, Microbiology and Immunology, Institute of Biological Sciences, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, 36036-900, Brazil
| | - Vânia L Silva
- Department of Parasitology, Microbiology and Immunology, Institute of Biological Sciences, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, 36036-900, Brazil
| | - Cláudio G Diniz
- Department of Parasitology, Microbiology and Immunology, Institute of Biological Sciences, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, 36036-900, Brazil.
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43
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Hillman ET, Lu H, Yao T, Nakatsu CH. Microbial Ecology along the Gastrointestinal Tract. Microbes Environ 2017; 32:300-313. [PMID: 29129876 PMCID: PMC5745014 DOI: 10.1264/jsme2.me17017] [Citation(s) in RCA: 296] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 08/19/2017] [Indexed: 02/06/2023] Open
Abstract
The ecosystem of the human gastrointestinal (GI) tract traverses a number of environmental, chemical, and physical conditions because it runs from the oral cavity to the anus. These differences in conditions along with food or other ingested substrates affect the composition and density of the microbiota as well as their functional roles by selecting those that are the most suitable for that environment. Previous studies have mostly focused on Bacteria, with the number of studies conducted on Archaea, Eukarya, and Viruses being limited despite their important roles in this ecosystem. Furthermore, due to the challenges associated with collecting samples directly from the inside of humans, many studies are still exploratory, with a primary focus on the composition of microbiomes. Thus, mechanistic studies to investigate functions are conducted using animal models. However, differences in physiology and microbiomes need to be clarified in order to aid in the translation of animal model findings into the context of humans. This review will highlight Bacteria, Archaea, Fungi, and Viruses, discuss differences along the GI tract of healthy humans, and perform comparisons with three common animal models: rats, mice, and pigs.
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Affiliation(s)
- Ethan T. Hillman
- Department of Agricultural and Biological Engineering, Purdue UniversityWest Lafayette, Indiana 47907USA
| | - Hang Lu
- Department of Animal Science, Purdue UniversityWest Lafayette, Indiana 47907USA
| | - Tianming Yao
- Department of Food Science, Purdue UniversityWest Lafayette, Indiana 47907USA
| | - Cindy H. Nakatsu
- Department of Agronomy, Purdue UniversityWest Lafayette, Indiana 47907USA
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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: 506] [Impact Index Per Article: 72.3] [Reference Citation Analysis] [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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45
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Huseyin CE, O'Toole PW, Cotter PD, Scanlan PD. Forgotten fungi-the gut mycobiome in human health and disease. FEMS Microbiol Rev 2017; 41:479-511. [PMID: 28430946 DOI: 10.1093/femsre/fuw047] [Citation(s) in RCA: 154] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 01/04/2017] [Indexed: 12/11/2022] Open
Abstract
The human body is home to a complex and diverse microbial ecosystem that plays a central role in host health. This includes a diversity of fungal species that is collectively referred to as our 'mycobiome'. Although research into the mycobiome is still in its infancy, its potential role in human disease is increasingly recognised. Here we review the existing literature available on the human mycobiota with an emphasis on the gut mycobiome, including how fungi interact with the human host and other microbes. In doing so, we provide a comprehensive critique of the methodologies available to research the human mycobiota as well as highlighting the latest research findings from mycological surveys of different groups of interest including infants, obese and inflammatory bowel disease cohorts. This in turn provides new insights and directions for future studies in this burgeoning research area.
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Affiliation(s)
- Chloe E Huseyin
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork P61 C996, Ireland.,APC Microbiome Institute, Biosciences Institute, University College Cork, Cork T12 YT20 Ireland.,School of Microbiology, University College Cork, Cork T12 YT20, Ireland
| | - Paul W O'Toole
- APC Microbiome Institute, Biosciences Institute, University College Cork, Cork T12 YT20 Ireland.,School of Microbiology, University College Cork, Cork T12 YT20, Ireland
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork P61 C996, Ireland.,APC Microbiome Institute, Biosciences Institute, University College Cork, Cork T12 YT20 Ireland
| | - Pauline D Scanlan
- APC Microbiome Institute, Biosciences Institute, University College Cork, Cork T12 YT20 Ireland
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Abstract
The diversity and abundance of zoosporic true fungi have been analyzed recently using fungal sequence libraries and advances in molecular methods, such as high-throughput sequencing. This review focuses on four evolutionary primitive true fungal phyla: the Aphelidea, Chytridiomycota, Neocallimastigomycota, and Rosellida (Cryptomycota), most species of which are not polycentric or mycelial (filamentous), rather they tend to be primarily monocentric (unicellular). Zoosporic fungi appear to be both abundant and diverse in many aquatic habitats around the world, with abundance often exceeding other fungal phyla in these habitats, and numerous novel genetic sequences identified. Zoosporic fungi are able to survive extreme conditions, such as high and extremely low pH; however, more work remains to be done. They appear to have important ecological roles as saprobes in decomposition of particulate organic substrates, pollen, plant litter, and dead animals; as parasites of zooplankton and algae; as parasites of vertebrate animals (such as frogs); and as symbionts in the digestive tracts of mammals. Some chytrids cause economically important diseases of plants and animals. They regulate sizes of phytoplankton populations. Further metagenomics surveys of aquatic ecosystems are expected to enlarge our knowledge of the diversity of true zoosporic fungi. Coupled with studies on their functional ecology, we are moving closer to unraveling the role of zoosporic fungi in carbon cycling and the impact of climate change on zoosporic fungal populations.
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Chiaro TR, Soto R, Zac Stephens W, Kubinak JL, Petersen C, Gogokhia L, Bell R, Delgado JC, Cox J, Voth W, Brown J, Stillman DJ, O'Connell RM, Tebo AE, Round JL. A member of the gut mycobiota modulates host purine metabolism exacerbating colitis in mice. Sci Transl Med 2017; 9:eaaf9044. [PMID: 28275154 PMCID: PMC5994919 DOI: 10.1126/scitranslmed.aaf9044] [Citation(s) in RCA: 153] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 04/17/2016] [Accepted: 02/10/2017] [Indexed: 12/20/2022]
Abstract
The commensal microbiota has an important impact on host health, which is only beginning to be elucidated. Despite the presence of fungal, archaeal, and viral members, most studies have focused solely on the bacterial microbiota. Antibodies against the yeast Saccharomyces cerevisiae are found in some patients with Crohn's disease (CD), suggesting that the mycobiota may contribute to disease severity. We report that S. cerevisiae exacerbated intestinal disease in a mouse model of colitis and increased gut barrier permeability. Transcriptome analysis of colon tissue from germ-free mice inoculated with S. cerevisiae or another fungus, Rhodotorula aurantiaca, revealed that S. cerevisiae colonization affected the intestinal barrier and host metabolism. A fecal metabolomics screen of germ-free animals demonstrated that S. cerevisiae colonization enhanced host purine metabolism, leading to an increase in uric acid production. Treatment with uric acid alone worsened disease and increased gut permeability. Allopurinol, a clinical drug used to reduce uric acid, ameliorated colitis induced by S. cerevisiae in mice. In addition, we found a positive correlation between elevated uric acid and anti-yeast antibodies in human sera. Thus, yeast in the gut may be able to potentiate metabolite production that negatively affects the course of inflammatory bowel disease.
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Affiliation(s)
- Tyson R Chiaro
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Ray Soto
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - W Zac Stephens
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Jason L Kubinak
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Charisse Petersen
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Lasha Gogokhia
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Rickesha Bell
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Julio C Delgado
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
- ARUP Laboratories, 500 Chipeta Way, Salt Lake City, UT 84108, USA
| | - James Cox
- Metabolomics Core, University of Utah Health Sciences Center, Salt Lake City, UT 84112, USA
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Warren Voth
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Jessica Brown
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - David J Stillman
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Ryan M O'Connell
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Anne E Tebo
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
- ARUP Laboratories, 500 Chipeta Way, Salt Lake City, UT 84108, USA
| | - June L Round
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
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Ackerman AL, Underhill DM. The mycobiome of the human urinary tract: potential roles for fungi in urology. ANNALS OF TRANSLATIONAL MEDICINE 2017; 5:31. [PMID: 28217696 DOI: 10.21037/atm.2016.12.69] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The mycobiome, defined as the fungal microbiota within a host environment, is an important but understudied component of the human microbial ecosystem. New culture-independent approaches to determine microbial diversity, such as next-generation sequencing methods, have discovered specific, characteristic, commensal fungal populations present in different body sites. These studies have also identified diverse patterns in fungal communities associated with various diseases. While alterations in urinary bacterial communities have been noted in disease states, a comprehensive description of the urinary mycobiome has been lacking. Early evidence suggests the urinary mycobiome is a diverse community with high intraindividual variability. In other disease systems, the mycobiome is thought to interact with other biomes and the host to play a role in organ homeostasis and pathology; further study will be needed to elucidate the role fungi play in bladder health and disease.
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Affiliation(s)
- A Lenore Ackerman
- Division of Urology, Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - David M Underhill
- Department of Medicine and Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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Abstract
PURPOSE OF REVIEW Asthma is a complex and heterogeneous disease with strong genetic and environmental components that manifests within a variety of clinical features and diverse patterns of immune responses. Asthma prevalence has dramatically increased over the last decade in Westernized societies, thereby suggesting a key function of environmental factors in disease promotion and development. RECENT FINDINGS 'Early-life' microbial exposure and bacterial colonization are crucial for the maturation and the education of the immune system. The commensal flora is also critical in order to maintain immune homeostasis at the mucosal surfaces and may consequently play an important function in allergic disease development. Recent evidence demonstrates that asthma influences and is also impacted by the composition and function of the human intestinal and respiratory microbiome. SUMMARY In this review, we summarize the most recent findings on how asthma development is connected with respiratory and intestinal microbial dysbiosis. We highlight and discuss recent research that reveals the existence of a 'gut-lung' microbial axis and its impact on asthma development. We also analyze how 'early-life' microbial exposure affects the immune response and the consequences for asthma development.
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50
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The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota. Nat Microbiol 2016; 1:16131. [PMID: 27670113 DOI: 10.1038/nmicrobiol.2016.131] [Citation(s) in RCA: 268] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 07/05/2016] [Indexed: 01/14/2023]
Abstract
Intestinal bacteria influence mammalian physiology, but many types of bacteria are still uncharacterized. Moreover, reference strains of mouse gut bacteria are not easily available, although mouse models are extensively used in medical research. These are major limitations for the investigation of intestinal microbiomes and their interactions with diet and host. It is thus important to study in detail the diversity and functions of gut microbiota members, including those colonizing the mouse intestine. To address these issues, we aimed at establishing the Mouse Intestinal Bacterial Collection (miBC), a public repository of bacterial strains and associated genomes from the mouse gut, and studied host-specificity of colonization and sequence-based relevance of the resource. The collection includes several strains representing novel species, genera and even one family. Genomic analyses showed that certain species are specific to the mouse intestine and that a minimal consortium of 18 strains covered 50-75% of the known functional potential of metagenomes. The present work will sustain future research on microbiota-host interactions in health and disease, as it will facilitate targeted colonization and molecular studies. The resource is available at www.dsmz.de/miBC.
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