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Hill JH, Round JL. Intestinal fungal-host interactions in promoting and maintaining health. Cell Host Microbe 2024; 32:1668-1680. [PMID: 39389031 DOI: 10.1016/j.chom.2024.09.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2024] [Revised: 09/05/2024] [Accepted: 09/14/2024] [Indexed: 10/12/2024]
Abstract
The resident microbiota are a key component of a healthy organism. The vast majority of microbiome studies have focused on bacterial members, which constitute a significant portion of resident microbial biomass. Recent studies have demonstrated how the fungal component of the microbiota, or the mycobiome, influences mammalian biology despite its low abundance compared to other microbes. Fungi are known for their pathogenic potential, yet fungi are also prominent colonizers in healthy states, highlighting their duality. We summarize the characteristics that define the gut mycobiome across life, the factors that can impact its composition, and studies that identify mechanisms of how fungi confer health benefits. The goal of this review is to synthesize our knowledge regarding the composition and function of a healthy mycobiome with a view to inspiring future therapeutic advances.
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Affiliation(s)
- Jennifer H Hill
- University of Colorado Boulder, BioFrontiers Institute, Department of Molecular, Cellular & Developmental Biology, Boulder, CO 80303, USA.
| | - June L Round
- University of Utah, School of Medicine, Department of Pathology, Huntsman Cancer Institute, Salt Lake City, UT 84112, USA.
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2
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Katsoulis O, Pitts OR, Singanayagam A. The airway mycobiome and interactions with immunity in health and chronic lung disease. OXFORD OPEN IMMUNOLOGY 2024; 5:iqae009. [PMID: 39206335 PMCID: PMC11357796 DOI: 10.1093/oxfimm/iqae009] [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: 01/30/2024] [Revised: 07/07/2024] [Accepted: 07/15/2024] [Indexed: 09/04/2024] Open
Abstract
The existence of commensal fungi that reside within the respiratory tract, termed the airway mycobiome, has only recently been discovered. Studies are beginning to characterize the spectrum of fungi that inhabit the human upper and lower respiratory tract but heterogeneous sampling and analysis techniques have limited the generalizability of findings to date. In this review, we discuss existing studies that have examined the respiratory mycobiota in healthy individuals and in those with inflammatory lung conditions such as asthma, chronic obstructive pulmonary disease and cystic fibrosis. Associations between specific fungi and features of disease pathogenesis are emerging but the precise functional consequences imparted by mycobiota upon the immune system remain poorly understood. It is imperative that further research is conducted in this important area as a more detailed understanding could facilitate the development of novel approaches to manipulating the mycobiome for therapeutic benefit.
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Affiliation(s)
- Orestis Katsoulis
- Centre for Bacterial Resistance Biology, Department of Infectious Disease, Imperial College London, London SW7 2DD, UK
| | - Oliver R Pitts
- Centre for Bacterial Resistance Biology, Department of Infectious Disease, Imperial College London, London SW7 2DD, UK
| | - Aran Singanayagam
- Centre for Bacterial Resistance Biology, Department of Infectious Disease, Imperial College London, London SW7 2DD, UK
- National Heart and Lung Institute, Imperial College London, London SW7 2DD, UK
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3
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Pu L, Pang S, Mu W, Chen X, Zou Y, Wang Y, Ding Y, Yan Q, Huang Y, Chen X, Peng T, Luo W, Wang S. The gut mycobiome signatures in long-lived populations. iScience 2024; 27:110412. [PMID: 39081291 PMCID: PMC11284699 DOI: 10.1016/j.isci.2024.110412] [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: 02/22/2024] [Revised: 04/22/2024] [Accepted: 06/26/2024] [Indexed: 08/02/2024] Open
Abstract
Long-lived individuals have been extensively studied as a model to investigate the role of the gut microbiota in aging, but their gut fungi remain almost unexplored. Here, we recruited a community-dwelling cohort of 251 participants (24-108 years, including 47 centenarians) from Guangxi in China to characterize the gut mycobiome signatures. We found gut mycobiome markedly varied during aging and determined aging as a predominant factor driving these variations. For long-lived individuals, core taxa, including Penicillium and Aspergillus, were maintained and Candida enterotype was enriched when compared with old counterparts. Individuals with this enterotype were more likely to possess Bacteroides enterotype enriched in young and centenarians. Moreover, the drivers from Candida enterotype were positively linked with the bacteria components dominated in Bacteroides enterotype. We also identified potentially beneficial yeasts-enriched features to differentiate long-lived individuals from others. Our findings suggest that the gut mycobiome develops with aging, and long-lived individuals possess unique fungal signatures.
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Affiliation(s)
- Lixia Pu
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Shifu Pang
- AIage Life Science Corporation Ltd., Guangxi Free Trade Zone Aisheng Biotechnology Corporation Ltd., Nanning, Guangxi, China
| | - Wenjie Mu
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Xiaodong Chen
- AIage Life Science Corporation Ltd., Guangxi Free Trade Zone Aisheng Biotechnology Corporation Ltd., Nanning, Guangxi, China
- Guangxi Key Laboratory of Longevity Science and Technology, AIage Life Science Corporation Ltd., Nanning, Guangxi, China
| | - Yang Zou
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Yugui Wang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Yingying Ding
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Qi Yan
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Yu Huang
- AIage Life Science Corporation Ltd., Guangxi Free Trade Zone Aisheng Biotechnology Corporation Ltd., Nanning, Guangxi, China
| | - Xiaochun Chen
- AIage Life Science Corporation Ltd., Guangxi Free Trade Zone Aisheng Biotechnology Corporation Ltd., Nanning, Guangxi, China
- Guangxi Key Laboratory of Longevity Science and Technology, AIage Life Science Corporation Ltd., Nanning, Guangxi, China
| | - Tao Peng
- Guangxi Key Laboratory of Enhanced Recovery After Surgery for Gastrointestinal Cancer, Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Weifei Luo
- AIage Life Science Corporation Ltd., Guangxi Free Trade Zone Aisheng Biotechnology Corporation Ltd., Nanning, Guangxi, China
- Guangxi Key Laboratory of Longevity Science and Technology, AIage Life Science Corporation Ltd., Nanning, Guangxi, China
| | - Shuai Wang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
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Mpakosi A, Sokou R, Theodoraki M, Kaliouli-Antonopoulou C. Neonatal Gut Mycobiome: Immunity, Diversity of Fungal Strains, and Individual and Non-Individual Factors. Life (Basel) 2024; 14:902. [PMID: 39063655 PMCID: PMC11278438 DOI: 10.3390/life14070902] [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: 06/11/2024] [Revised: 07/11/2024] [Accepted: 07/18/2024] [Indexed: 07/28/2024] Open
Abstract
The human gastrointestinal ecosystem, or microbiome (comprising the total bacterial genome in an environment), plays a crucial role in influencing host physiology, immune function, metabolism, and the gut-brain axis. While bacteria, fungi, viruses, and archaea are all present in the gastrointestinal ecosystem, research on the human microbiome has predominantly focused on the bacterial component. The colonization of the human intestine by microbes during the first two years of life significantly impacts subsequent composition and diversity, influencing immune system development and long-term health. Early-life exposure to pathogens is crucial for establishing immunological memory and acquired immunity. Factors such as maternal health habits, delivery mode, and breastfeeding duration contribute to gut dysbiosis. Despite fungi's critical role in health, particularly for vulnerable newborns, research on the gut mycobiome in infants and children remains limited. Understanding early-life factors shaping the gut mycobiome and its interactions with other microbial communities is a significant research challenge. This review explores potential factors influencing the gut mycobiome, microbial kingdom interactions, and their connections to health outcomes from childhood to adulthood. We identify gaps in current knowledge and propose future research directions in this complex field.
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Affiliation(s)
- Alexandra Mpakosi
- Department of Microbiology, General Hospital of Nikaia “Agios Panteleimon”, 18454 Piraeus, Greece
| | - Rozeta Sokou
- Neonatal Intensive Care Unit, General Hospital of Nikaia “Agios Panteleimon”, 18454 Piraeus, Greece;
- Neonatal Department, National and Kapodistrian University of Athens, Aretaieio Hospital, 11528 Athens, Greece
| | - Martha Theodoraki
- Neonatal Intensive Care Unit, General Hospital of Nikaia “Agios Panteleimon”, 18454 Piraeus, Greece;
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Pereira H, Chakarov N, Hoffman JI, Rinaud T, Ottensmann M, Gladow KP, Tobias B, Caspers BA, Maraci Ö, Krüger O. Early-life factors shaping the gut microbiota of Common buzzard nestlings. Anim Microbiome 2024; 6:27. [PMID: 38745254 DOI: 10.1186/s42523-024-00313-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 05/01/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Exploring the dynamics of gut microbiome colonisation during early-life stages is important for understanding the potential impact of microbes on host development and fitness. Evidence from model organisms suggests a crucial early-life phase when shifts in gut microbiota can lead to immune dysregulation and reduced host condition. However, our understanding of gut microbiota colonisation in long-lived vertebrates, especially during early development, remains limited. We therefore used a wild population of common buzzard nestlings (Buteo buteo) to investigate connections between the early-life gut microbiota colonisation, environmental and host factors. RESULTS We targeted both bacterial and eukaryotic microbiota using the 16S and 28S rRNA genes. We sampled the individuals during early developmental stages in a longitudinal design. Our data revealed that age significantly affected microbial diversity and composition. Nest environment was a notable predictor of microbiota composition, with particularly eukaryotic communities differing between habitats occupied by the hosts. Nestling condition and infection with the blood parasite Leucocytozoon predicted microbial community composition. CONCLUSION Our findings emphasise the importance of studying microbiome dynamics to capture changes occurring during ontogeny. They highlight the role of microbial communities in reflecting host health and the importance of the nest environment for the developing nestling microbiome. Overall, this study contributes to understanding the complex interplay between microbial communities, host factors, and environmental variables, and sheds light on the ecological processes governing gut microbial colonisation during early-life stages.
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Affiliation(s)
- Hugo Pereira
- Department of Animal Behaviour, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany.
| | - Nayden Chakarov
- Department of Animal Behaviour, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany
- Joint Institute for Individualisation in a Changing Environment (JICE), Bielefeld University and University of Münster, Konsequenz 45, 33615, Bielefeld, NRW, Germany
| | - Joseph I Hoffman
- Department of Animal Behaviour, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany
- Department of Evolutionary Population Genetics, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany
- Joint Institute for Individualisation in a Changing Environment (JICE), Bielefeld University and University of Münster, Konsequenz 45, 33615, Bielefeld, NRW, Germany
- British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 OET, UK
| | - Tony Rinaud
- Department of Animal Behaviour, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany
| | - Meinolf Ottensmann
- Department of Animal Behaviour, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany
| | - Kai-Philipp Gladow
- Department of Animal Behaviour, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany
| | - Busche Tobias
- Medical School East Westphalia-Lippe & Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, NRW, Germany
| | - Barbara A Caspers
- Department of Behavioural Ecology, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany
- Joint Institute for Individualisation in a Changing Environment (JICE), Bielefeld University and University of Münster, Konsequenz 45, 33615, Bielefeld, NRW, Germany
| | - Öncü Maraci
- Department of Behavioural Ecology, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany
- Joint Institute for Individualisation in a Changing Environment (JICE), Bielefeld University and University of Münster, Konsequenz 45, 33615, Bielefeld, NRW, Germany
| | - Oliver Krüger
- Department of Animal Behaviour, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany
- Joint Institute for Individualisation in a Changing Environment (JICE), Bielefeld University and University of Münster, Konsequenz 45, 33615, Bielefeld, NRW, Germany
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Yuu EY, Bührer C, Eckmanns T, Fulde M, Herz M, Kurzai O, Lindstedt C, Panagiotou G, Piro VC, Radonic A, Renard BY, Reuss A, Siliceo SL, Thielemann N, Thürmer A, Vorst KV, Wieler LH, Haller S. The gut microbiome, resistome, and mycobiome in preterm newborn infants and mouse pups: lack of lasting effects by antimicrobial therapy or probiotic prophylaxis. Gut Pathog 2024; 16:27. [PMID: 38735967 PMCID: PMC11089716 DOI: 10.1186/s13099-024-00616-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 04/13/2024] [Indexed: 05/14/2024] Open
Abstract
BACKGROUND Enhancing our understanding of the underlying influences of medical interventions on the microbiome, resistome and mycobiome of preterm born infants holds significant potential for advancing infection prevention and treatment strategies. We conducted a prospective quasi-intervention study to better understand how antibiotics, and probiotics, and other medical factors influence the gut development of preterm infants. A controlled neonatal mice model was conducted in parallel, designed to closely reflect and predict exposures. Preterm infants and neonatal mice were stratified into four groups: antibiotics only, probiotics only, antibiotics followed by probiotics, and none of these interventions. Stool samples from both preterm infants and neonatal mice were collected at varying time points and analyzed by 16 S rRNA amplicon sequencing, ITS amplicon sequencing and whole genome shotgun sequencing. RESULTS The human infant microbiomes showed an unexpectedly high degree of heterogeneity. Little impact from medical exposure (antibiotics/probiotics) was observed on the strain patterns, however, Bifidobacterium bifidum was found more abundant after exposure to probiotics, regardless of prior antibiotic administration. Twenty-seven antibiotic resistant genes were identified in the resistome. High intra-variability was evident within the different treatment groups. Lastly, we found significant effects of antibiotics and probiotics on the mycobiome but not on the microbiome and resistome of preterm infants. CONCLUSIONS Although our analyses showed transient effects, these results provide positive motivation to continue the research on the effects of medical interventions on the microbiome, resistome and mycobiome of preterm infants.
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Affiliation(s)
- Elizabeth Y Yuu
- Data Analytics & Computational Statistics, Hasso Plattner Institute, University of Potsdam, Prof.-Dr.-Helmert-Straße 2-3, 14482 , Potsdam, Germany
| | | | | | - Marcus Fulde
- Department of Mathematics and Computer Science, Freie Universität Berlin, 14195, Berlin, Germany
| | - Michaela Herz
- Institute for Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | - Oliver Kurzai
- Institute for Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
- Department of Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Beutenbergstraße 11A, 07745 , Jena, Germany
| | | | - Gianni Panagiotou
- Department of Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Beutenbergstraße 11A, 07745 , Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University, 07745, Jena, Germany
- Department of Medicine, The University of Hong Kong, Hong Kong, China
| | - Vitor C Piro
- Data Analytics & Computational Statistics, Hasso Plattner Institute, University of Potsdam, Prof.-Dr.-Helmert-Straße 2-3, 14482 , Potsdam, Germany
- Department of Mathematics and Computer Science, Freie Universität Berlin, 14195, Berlin, Germany
| | | | - Bernhard Y Renard
- Data Analytics & Computational Statistics, Hasso Plattner Institute, University of Potsdam, Prof.-Dr.-Helmert-Straße 2-3, 14482 , Potsdam, Germany
| | - Annicka Reuss
- Robert Koch Institute, Berlin, Germany
- Ministry of Justice and Health, Schleswig-Holstein, Kiel , Germany
| | - Sara Leal Siliceo
- Department of Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Beutenbergstraße 11A, 07745 , Jena, Germany
| | - Nadja Thielemann
- Institute for Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | | | - Kira van Vorst
- Department of Mathematics and Computer Science, Freie Universität Berlin, 14195, Berlin, Germany
| | - Lothar H Wieler
- Data Analytics & Computational Statistics, Hasso Plattner Institute, University of Potsdam, Prof.-Dr.-Helmert-Straße 2-3, 14482 , Potsdam, Germany
- Robert Koch Institute, Berlin, Germany
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7
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Li Y, Xiao P, Cao R, Le J, Xu Q, Xiao F, Ye L, Wang X, Wang Y, Zhang T. Effects and microbiota changes following oral lyophilized fecal microbiota transplantation in children with autism spectrum disorder. Front Pediatr 2024; 12:1369823. [PMID: 38783921 PMCID: PMC11112010 DOI: 10.3389/fped.2024.1369823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 04/23/2024] [Indexed: 05/25/2024] Open
Abstract
Background and purpose Autism spectrum disorder (ASD) is a group of heterogeneous neurodevelopmental disorders that is characterized by core features in social communication impairment and restricted, repetitive sensory-motor behaviors. This study aimed to further investigate the utilization of fecal microbiota transplantation (FMT) in children with ASD, both with and without gastrointestinal (GI) symptoms, evaluate the effect of FMT and analyze the alterations in bacterial and fungal composition within the gut microbiota. Methods A total of 38 children diagnosed with ASD participated in the study and underwent oral lyophilized FMT treatment. The dosage of the FMT treatment was determined based on a ratio of 1 g of donor stool per 1 kg of recipient body weight, with a frequency of once every 4 weeks for a total of 12 weeks. In addition, 30 healthy controls (HC) were included in the analysis. The clinical efficacy of FMT was evaluated, while the composition of fecal bacteria and fungi was determined using 16S rRNA and ITS gene sequencing methods. Results Median age of the 38 children with ASD was 7 years. Among these children, 84.2% (32 of 38) were boys and 81.6% (31 of 38) exhibited GI symptoms, with indigestion, constipation and diarrhea being the most common symptoms. Sample collections and assessments were conducted at baseline (week 0), post-treatment (week 12) and follow-up (week 20). At the end of the follow-up phase after FMT treatment, the autism behavior checklist (ABC) scores decreased by 23% from baseline, and there was a 10% reduction in scores on the childhood autism rating scale (CARS), a 6% reduction in scores on the social responsiveness scale (SRS) and a 10% reduction in scores on the sleep disturbance scale for children (SDSC). In addition, short-term adverse events observed included vomiting and fever in 2 participants, which were self-limiting and resolved within 24 h, and no long-term adverse events were observed. Although there was no significant difference in alpha and beta diversity in children with ASD before and after FMT therapy, the FMT treatment resulted in alterations in the relative abundances of various bacterial and fungal genera in the samples of ASD patients. Comparisons between children with ASD and healthy controls (HC) revealed statistically significant differences in microbial abundance before and after FMT. Blautia, Sellimonas, Saccharomycopsis and Cystobasidium were more abundant in children with ASD than in HC, while Dorea were less abundant. After FMT treatment, levels of Blautia, Sellimonas, Saccharomycopsis and Cystobasidium decreased, while levels of Dorea increased. Moreover, the increased abundances of Fusicatenibacter, Erysipelotrichaceae_UCG-003, Saccharomyces, Rhodotorula, Cutaneotrichosporon and Zygosaccharomyces were negatively correlated with the scores of ASD core symptoms. Conclusions Oral lyophilized FMT could improve GI and ASD related symptoms, as well as sleep disturbances, and alter the gut bacterial and fungal microbiota composition in children with ASD. Clinical Trial Registration Chinese Clinical Trial Registry, ChiCTR2200055943. Registered 28 January 2022, www.chictr.org.cn.
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Affiliation(s)
- Youran Li
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Pei Xiao
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Rong Cao
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jun Le
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Qiao Xu
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Fangfei Xiao
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lin Ye
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xufei Wang
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yizhong Wang
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Institute of Pediatric Infection, Immunity and Critical Care Medicine, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ting Zhang
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Institute of Pediatric Infection, Immunity and Critical Care Medicine, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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Dombrowska-Pali A, Wiktorczyk-Kapischke N, Chrustek A, Olszewska-Słonina D, Gospodarek-Komkowska E, Socha MW. Human Milk Microbiome-A Review of Scientific Reports. Nutrients 2024; 16:1420. [PMID: 38794658 PMCID: PMC11124344 DOI: 10.3390/nu16101420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 05/01/2024] [Accepted: 05/06/2024] [Indexed: 05/26/2024] Open
Abstract
One of the most important bioactive components of breast milk are free breast milk oligosaccharides, which are a source of energy for commensal intestinal microorganisms, stimulating the growth of Bifidobacterium, Lactobacillus, and Bacteroides in a child's digestive tract. There is some evidence that maternal, perinatal, and environmental-cultural factors influence the modulation of the breast milk microbiome. This review summarizes research that has examined the composition of the breast milk microbiome and the factors that may influence it. The manuscript highlights the potential importance of the breast milk microbiome for the future development and health of children. The origin of bacteria in breast milk is thought to include the mother's digestive tract (entero-mammary tract), bacterial exposure to the breast during breastfeeding, and the retrograde flow of breast milk from the infant's mouth to the woman's milk ducts. Unfortunately, despite increasingly more precise methods for assessing microorganisms in human milk, the topic of the human milk microbiome is still quite limited and requires scientific research that takes into account various conditions.
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Affiliation(s)
- Agnieszka Dombrowska-Pali
- Department of Perinatology, Gynecology and Gynecologic Oncology, Faculty of Health Sciences, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, Łukasiewicza 1, 85-821 Bydgoszcz, Poland;
| | - Natalia Wiktorczyk-Kapischke
- Department of Microbiology, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, M. Curie-Skłodowskiej 9, 85-094 Bydgoszcz, Poland; (N.W.-K.); (E.G.-K.)
| | - Agnieszka Chrustek
- Department of Pathobiochemistry and Clinical Chemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, M. Curie-Skłodowskiej 9, 85-094 Bydgoszcz, Poland; (A.C.); (D.O.-S.)
| | - Dorota Olszewska-Słonina
- Department of Pathobiochemistry and Clinical Chemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, M. Curie-Skłodowskiej 9, 85-094 Bydgoszcz, Poland; (A.C.); (D.O.-S.)
| | - Eugenia Gospodarek-Komkowska
- Department of Microbiology, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, M. Curie-Skłodowskiej 9, 85-094 Bydgoszcz, Poland; (N.W.-K.); (E.G.-K.)
| | - Maciej W. Socha
- Department of Perinatology, Gynecology and Gynecologic Oncology, Faculty of Health Sciences, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, Łukasiewicza 1, 85-821 Bydgoszcz, Poland;
- Department of Obstetrics and Gynecology, St. Adalberts’s Hospital in Gdańsk, Copernicus Healthcare Entity LLC, Jana Pawła II 50, 80-462 Gdańsk, Poland
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9
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Abdillah A, Kodio A, Ranque S. Malian Children's Core Gut Mycobiome. Microorganisms 2024; 12:926. [PMID: 38792756 PMCID: PMC11124064 DOI: 10.3390/microorganisms12050926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/26/2024] [Accepted: 04/29/2024] [Indexed: 05/26/2024] Open
Abstract
Because data on the fungal gut community structure of African children are scarce, we aimed to describe it by reanalysing rRNA ITS1 and ITS2 metabarcoding data from a study designed to assess the influence of microbiota in malaria susceptibility in Malian children from the Dogon country. More specifically, we aimed to establish the core gut mycobiome and compare the gut fungal community structure of breastfed children, aged 0-2 years, with other age groups. Briefly, DNA was extracted from 296 children's stool samples. Both rRNA ITS1 and ITS2 genomic barcodes were amplified and subjected to Illumina MiSeq sequencing. The ITS2 barcode generated 1,975,320 reads and 532 operational taxonomic units (OTUs), while the ITS1 barcode generated 647,816 reads and 532 OTUs. The alpha diversity was significantly higher by using the ITS1 compared to the ITS2 barcode (p < 0.05); but, regardless of the ITS barcode, we found no significant difference between breastfed children, aged 0-2 years, compared to the other age groups. The core gut mycobiome of the Malian children included Saccharomyces cerevisiae, Candida albicans, Pichia kudriavzevii, Malassezia restricta, Candida tropicalis and Aspergillus section Aspergillus, which were present in at least 50% of the 296 children. Further studies in other African countries are warranted to reach a global view of African children's core gut mycobiome.
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Affiliation(s)
| | - Aly Kodio
- IHU-Méditerranée Infection, 13385 Marseille, France; (A.A.); (A.K.)
- Malaria Research and Training Centre-International Center for Excellence in Research (MRTC-ICER), Department of Epidemiology of Parasitic Diseases, Faculty of Medicine and Dentistry, Université des Sciences des Techniques et des Technologies de Bamako, Point G, Bamako BP 1805, Mali
| | - Stéphane Ranque
- IHU-Méditerranée Infection, 13385 Marseille, France; (A.A.); (A.K.)
- AP-HM, RITMES, Aix-Marseille Université, 13005 Marseille, France
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10
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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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11
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Gorostidi-Aicua M, Reparaz I, Otaegui-Chivite A, García K, Romarate L, Álvarez de Arcaya A, Mendiburu I, Arruti M, Castillo-Triviño T, Moles L, Otaegui D. Bacteria-Fungi Interactions in Multiple Sclerosis. Microorganisms 2024; 12:872. [PMID: 38792701 PMCID: PMC11124083 DOI: 10.3390/microorganisms12050872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 04/12/2024] [Accepted: 04/18/2024] [Indexed: 05/26/2024] Open
Abstract
Multiple sclerosis (MS) arises from a complex interplay between host genetic factors and environmental components, with the gut microbiota emerging as a key area of investigation. In the current study, we used ion torrent sequencing to delve into the bacteriome (bacterial microbiota) and mycobiome (fungal microbiota) of people with MS (pwMS), and compared them to healthy controls (HC). Through principal coordinate, diversity, and abundance analyses, as well as clustering and cross-kingdom microbial correlation assessments, we uncovered significant differences in the microbial profiles between pwMS and HC. Elevated levels of the fungus Torulaspora and the bacterial family Enterobacteriaceae were observed in pwMS, whereas beneficial bacterial taxa, such as Prevotelladaceae and Dialister, were reduced. Notably, clustering analysis revealed overlapping patterns in the bacteriome and mycobiome data for 74% of the participants, with weakened cross-kingdom interactions evident in the altered microbiota of pwMS. Our findings highlight the dysbiosis of both bacterial and fungal microbiota in MS, characterized by shifts in biodiversity and composition. Furthermore, the distinct disease-associated pattern of fungi-bacteria interactions suggests that fungi, in addition to bacteria, contribute to the pathogenesis of MS. Overall, our study sheds light on the intricate microbial dynamics underlying MS, paving the way for further investigation into the potential therapeutic targeting of the gut microbiota in MS management.
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Affiliation(s)
- Miriam Gorostidi-Aicua
- Biogipuzkoa Health Research Institute, Neuroimmunology Group, 20014 San Sebastián, Spain; (M.G.-A.); (I.R.); (A.O.-C.); (K.G.); (L.R.); (I.M.); (M.A.); (T.C.-T.)
- Center for Biomedical Research Network in Neurodegenerative Diseases (CIBER-CIBERNED-ISCIII), 28029 Madrid, Spain
| | - Iraia Reparaz
- Biogipuzkoa Health Research Institute, Neuroimmunology Group, 20014 San Sebastián, Spain; (M.G.-A.); (I.R.); (A.O.-C.); (K.G.); (L.R.); (I.M.); (M.A.); (T.C.-T.)
| | - Ane Otaegui-Chivite
- Biogipuzkoa Health Research Institute, Neuroimmunology Group, 20014 San Sebastián, Spain; (M.G.-A.); (I.R.); (A.O.-C.); (K.G.); (L.R.); (I.M.); (M.A.); (T.C.-T.)
- Center for Biomedical Research Network in Neurodegenerative Diseases (CIBER-CIBERNED-ISCIII), 28029 Madrid, Spain
| | - Koldo García
- Biogipuzkoa Health Research Institute, Neuroimmunology Group, 20014 San Sebastián, Spain; (M.G.-A.); (I.R.); (A.O.-C.); (K.G.); (L.R.); (I.M.); (M.A.); (T.C.-T.)
| | - Leire Romarate
- Biogipuzkoa Health Research Institute, Neuroimmunology Group, 20014 San Sebastián, Spain; (M.G.-A.); (I.R.); (A.O.-C.); (K.G.); (L.R.); (I.M.); (M.A.); (T.C.-T.)
| | - Amaya Álvarez de Arcaya
- Neurology Department, Osakidetza Basque Health Service, Hospital Universitario Araba, 01009 Vitoria-Gasteiz, Spain;
| | - Idoia Mendiburu
- Biogipuzkoa Health Research Institute, Neuroimmunology Group, 20014 San Sebastián, Spain; (M.G.-A.); (I.R.); (A.O.-C.); (K.G.); (L.R.); (I.M.); (M.A.); (T.C.-T.)
- Neurology Department, Osakidetza Basque Health Service, Hospital Universitario Donostia, 20014 San Sebastián, Spain
| | - Maialen Arruti
- Biogipuzkoa Health Research Institute, Neuroimmunology Group, 20014 San Sebastián, Spain; (M.G.-A.); (I.R.); (A.O.-C.); (K.G.); (L.R.); (I.M.); (M.A.); (T.C.-T.)
- Neurology Department, Osakidetza Basque Health Service, Hospital Universitario Donostia, 20014 San Sebastián, Spain
| | - Tamara Castillo-Triviño
- Biogipuzkoa Health Research Institute, Neuroimmunology Group, 20014 San Sebastián, Spain; (M.G.-A.); (I.R.); (A.O.-C.); (K.G.); (L.R.); (I.M.); (M.A.); (T.C.-T.)
- Center for Biomedical Research Network in Neurodegenerative Diseases (CIBER-CIBERNED-ISCIII), 28029 Madrid, Spain
- Neurology Department, Osakidetza Basque Health Service, Hospital Universitario Donostia, 20014 San Sebastián, Spain
| | - Laura Moles
- Biogipuzkoa Health Research Institute, Neuroimmunology Group, 20014 San Sebastián, Spain; (M.G.-A.); (I.R.); (A.O.-C.); (K.G.); (L.R.); (I.M.); (M.A.); (T.C.-T.)
- Center for Biomedical Research Network in Neurodegenerative Diseases (CIBER-CIBERNED-ISCIII), 28029 Madrid, Spain
| | - David Otaegui
- Biogipuzkoa Health Research Institute, Neuroimmunology Group, 20014 San Sebastián, Spain; (M.G.-A.); (I.R.); (A.O.-C.); (K.G.); (L.R.); (I.M.); (M.A.); (T.C.-T.)
- Center for Biomedical Research Network in Neurodegenerative Diseases (CIBER-CIBERNED-ISCIII), 28029 Madrid, Spain
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12
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Sun X, Sitters J, Ruytinx J, Wassen MJ, Olde Venterink H. Microbial community composition in the dung of five sympatric European herbivore species. Ecol Evol 2024; 14:e11071. [PMID: 38481755 PMCID: PMC10933625 DOI: 10.1002/ece3.11071] [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: 06/27/2023] [Revised: 01/29/2024] [Accepted: 02/09/2024] [Indexed: 06/21/2024] Open
Abstract
The dung microbiome is a complex system that is highly influenced by species and diet. This study characterized the dung bacterial and fungal communities of five herbivore species inhabiting the National Park Zuid-Kennemerland, the Netherlands. The five selected herbivore species were rabbit (Oryctolagus cuniculus L.), cow (Bos taurus L.), horse (Equus ferus caballus L.), fallow deer (Dama dama L.), and European bison (Bison bonasus L.). We explored the effects of distinct digestive physiology (ruminants vs. non-ruminants) and diverse dietary preferences on the microbial community composition of herbivore dung. Firmicutes and Bacteroidetes were dominant bacterial phyla in the dung of all five herbivore species, and Ascomycota was the predominant fungal phylum. Verrucomicrobiota and Mucoromycota were more present in horse dung and Proteobacteria were more abundant in rabbit dung than the three ruminant dung types. There were few significant differences in the microbial community structure among the three ruminant dung types. The alpha and beta diversity of dung microbial communities significantly differed between ruminants and non-ruminants, especially in bacterial communities. Based on MetaCyc pathways, we found that the primary functions of bacteria in herbivore dung were focused on biosynthesis, various super pathways, and degradation, with a few differences between ruminant and non-ruminant dung. FUNGuild analysis showed that horse dung had more saprotrophic fungi, while the fungi in fallow deer dung had more symbiotrophic properties, with the fungal functions of bison, cow, and rabbit dung somewhere in between. There was also a correlation between microbial community and nutrient composition of the substrate in herbivore dung. Understanding the dung microbial community composition of these herbivore species can enrich the database of mammalian gut microbiomes for studying the mechanisms of microbial community variation while preparing for exploring a new perspective to study the impact of herbivores on ecosystems through dung deposition.
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Affiliation(s)
- Xingzhao Sun
- Research Group WILDVrije Universiteit BrusselBrusselsBelgium
| | - Judith Sitters
- Research Group WILDVrije Universiteit BrusselBrusselsBelgium
- B‐WARE Research CentreNijmegenThe Netherlands
| | - Joske Ruytinx
- Research Groups Microbiology and Plant GeneticsVrije Universiteit BrusselBrusselsBelgium
| | - Martin J. Wassen
- Environmental Sciences, Copernicus Institute of Sustainable DevelopmentUtrecht UniversityUtrechtThe Netherlands
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13
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Claypool DJ, Zhang YG, Xia Y, Sun J. Conditional Vitamin D Receptor Deletion Induces Fungal and Archaeal Dysbiosis and Altered Metabolites. Metabolites 2024; 14:32. [PMID: 38248835 PMCID: PMC10819266 DOI: 10.3390/metabo14010032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 12/24/2023] [Accepted: 12/28/2023] [Indexed: 01/23/2024] Open
Abstract
A vitamin D receptor (VDR) deficiency leads to the dysbiosis of intestinal bacteria and is associated with various diseases, including cancer, infections, and inflammatory bowel disease. However, the impact of a VDR deficiency on fungi and archaea is unknown. We conditionally deleted the VDR in Paneth cells (VDRΔPC), intestinal epithelial cells (VDRΔIEC), or myeloid cells (VDRΔLyz) in mice and collected feces for shotgun metagenomic sequencing and untargeted metabolomics. We found that fungi were significantly altered in each knockout (KO) group compared to the VDRLoxp control. The VDRΔLyz mice had the most altered fungi species (three depleted and seven enriched), followed by the VDRΔPC mice (six depleted and two enriched), and the VDRΔIEC mice (one depleted and one enriched). The methanogen Methanofollis liminatans was enriched in the VDRΔPC and VDRΔLyz mice and two further archaeal species (Thermococcus piezophilus and Sulfolobus acidocaldarius) were enriched in the VDRΔLyz mice compared to the Loxp group. Significant correlations existed among altered fungi, archaea, bacteria, and viruses in the KO mice. Functional metagenomics showed changes in several biologic functions, including decreased sulfate reduction and increased biosynthesis of cobalamin (vitamin B12) in VDRΔLyz mice relative to VDRLoxp mice. Fecal metabolites were analyzed to examine the involvement of sulfate reduction and other pathways. In conclusion, a VDR deficiency caused the formation of altered fungi and archaea in a tissue- and sex-dependent manner. These results provide a foundation about the impact of a host factor (e.g., VDR deficiency) on fungi and archaea. It opens the door for further studies to determine how mycobiome and cross-kingdom interactions in the microbiome community and metabolites contribute to the risk of certain diseases.
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Affiliation(s)
- Duncan J. Claypool
- Department of Medicine, University of Illinois Chicago, Chicago, IL 60612, USA; (D.J.C.); (Y.-G.Z.)
- Department of Bioengineering, University of Illinois Chicago, Chicago, IL 60607, USA
| | - Yong-Guo Zhang
- Department of Medicine, University of Illinois Chicago, Chicago, IL 60612, USA; (D.J.C.); (Y.-G.Z.)
| | - Yinglin Xia
- Department of Medicine, University of Illinois Chicago, Chicago, IL 60612, USA; (D.J.C.); (Y.-G.Z.)
- Jesse Brown VA Medical Center, Chicago, IL 60612, USA
| | - Jun Sun
- Department of Medicine, University of Illinois Chicago, Chicago, IL 60612, USA; (D.J.C.); (Y.-G.Z.)
- Department of Bioengineering, University of Illinois Chicago, Chicago, IL 60607, USA
- Jesse Brown VA Medical Center, Chicago, IL 60612, USA
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, IL 60612, USA
- UIC Cancer Center, University of Illinois Chicago, Chicago, IL 60612, USA
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14
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Kreulen IAM, de Jonge WJ, van den Wijngaard RM, van Thiel IAM. Candida spp. in Human Intestinal Health and Disease: More than a Gut Feeling. Mycopathologia 2023; 188:845-862. [PMID: 37294505 PMCID: PMC10687130 DOI: 10.1007/s11046-023-00743-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/09/2023] [Indexed: 06/10/2023]
Abstract
Fungi are an essential part of the normal collection of intestinal microorganisms, even though their collective abundance comprises only 0.1-1% of all fecal microbes. The composition and role of the fungal population is often studied in relation to early-life microbial colonization and development of the (mucosal) immune system. The genus Candida is frequently described as one of the most abundant genera, and altered fungal compositions (including elevated abundance of Candida spp.) have been linked with intestinal diseases such as inflammatory bowel disease and irritable bowel syndrome. These studies are performed using both culture-dependent and genomic (metabarcoding) techniques. In this review, we aimed to summarize existing data on intestinal Candida spp. colonization in relation to intestinal disease and provide a brief overview of the biological and technical challenges in this field, including the recently described role of sub-species strain variation of intestinal Candida albicans. Together, the evidence for a contributing role of Candida spp. in pediatric and adult intestinal disease is quickly expanding, even though technical and biological challenges may limit full understanding of host-microbe interactions.
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Affiliation(s)
- Irini A M Kreulen
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology, Endocrinology and Metabolism, Amsterdam UMC, Location Academic Medical Center, Meibergdreef 69-71, 1105 BK, Amsterdam, the Netherlands
| | - Wouter J de Jonge
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology, Endocrinology and Metabolism, Amsterdam UMC, Location Academic Medical Center, Meibergdreef 69-71, 1105 BK, Amsterdam, the Netherlands
- Department of Gastroenterology and Hepatology, Amsterdam UMC, Location Academic Medical Center, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands
- Department of General, Visceral, Thoracic and Vascular Surgery, University Hospital Bonn, 53127, Bonn, Germany
| | - René M van den Wijngaard
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology, Endocrinology and Metabolism, Amsterdam UMC, Location Academic Medical Center, Meibergdreef 69-71, 1105 BK, Amsterdam, the Netherlands
- Department of Gastroenterology and Hepatology, Amsterdam UMC, Location Academic Medical Center, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands
| | - Isabelle A M van Thiel
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology, Endocrinology and Metabolism, Amsterdam UMC, Location Academic Medical Center, Meibergdreef 69-71, 1105 BK, Amsterdam, the Netherlands.
- Royal Netherlands Academy of Arts and Sciences, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, the Netherlands.
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15
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Renzi S, Nenciarini S, Bacci G, Cavalieri D. Yeast metagenomics: analytical challenges in the analysis of the eukaryotic microbiome. MICROBIOME RESEARCH REPORTS 2023; 3:2. [PMID: 38455081 PMCID: PMC10917621 DOI: 10.20517/mrr.2023.27] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 10/09/2023] [Accepted: 10/17/2023] [Indexed: 03/09/2024]
Abstract
Even if their impact is often underestimated, yeasts and yeast-like fungi represent the most prevalent eukaryotic members of microbial communities on Earth. They play numerous roles in natural ecosystems and in association with their hosts. They are involved in the food industry and pharmaceutical production, but they can also cause diseases in other organisms, making the understanding of their biology mandatory. The ongoing loss of biodiversity due to overexploitation of environmental resources is a growing concern in many countries. Therefore, it becomes crucial to understand the ecology and evolutionary history of these organisms to systematically classify them. To achieve this, it is essential that our knowledge of the mycobiota reaches a level similar to that of the bacterial communities. To overcome the existing challenges in the study of fungal communities, the first step should be the establishment of standardized techniques for the correct identification of species, even from complex matrices, both in wet lab practices and in bioinformatic tools.
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Affiliation(s)
| | | | | | - Duccio Cavalieri
- Correspondence to: Prof. Duccio Cavalieri, Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino 50019, Italy. E-mail:
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16
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Garcia-Bonete MJ, Rajan A, Suriano F, Layunta E. The Underrated Gut Microbiota Helminths, Bacteriophages, Fungi, and Archaea. Life (Basel) 2023; 13:1765. [PMID: 37629622 PMCID: PMC10455619 DOI: 10.3390/life13081765] [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: 06/30/2023] [Revised: 08/12/2023] [Accepted: 08/13/2023] [Indexed: 08/27/2023] Open
Abstract
The microbiota inhabits the gastrointestinal tract, providing essential capacities to the host. The microbiota is a crucial factor in intestinal health and regulates intestinal physiology. However, microbiota disturbances, named dysbiosis, can disrupt intestinal homeostasis, leading to the development of diseases. Classically, the microbiota has been referred to as bacteria, though other organisms form this complex group, including viruses, archaea, and eukaryotes such as fungi and protozoa. This review aims to clarify the role of helminths, bacteriophages, fungi, and archaea in intestinal homeostasis and diseases, their interaction with bacteria, and their use as therapeutic targets in intestinal maladies.
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Affiliation(s)
- Maria Jose Garcia-Bonete
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Anandi Rajan
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Francesco Suriano
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Elena Layunta
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, SE-405 30 Gothenburg, Sweden
- Instituto de Investigación Sanitaria de Aragón (IIS Aragón), 50009 Zaragoza, Spain
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17
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Balderramo DC, Romagnoli PA, Granlund AVB, Catalan-Serra I. Fecal Fungal Microbiota (Mycobiome) Study as a Potential Tool for Precision Medicine in Inflammatory Bowel Disease. Gut Liver 2023; 17:505-515. [PMID: 37305948 PMCID: PMC10352062 DOI: 10.5009/gnl220537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/06/2023] [Accepted: 02/15/2023] [Indexed: 06/13/2023] Open
Abstract
There is growing evidence of the role of fungal microbiota in the pathogenesis of inflammatory bowel disease (IBD). Fungi can exert direct pro-inflammatory effects or modify the bacterial composition via interkingdom interactions. Although several studies have demonstrated alterations in the fecal fungal microbiota composition in IBD, there is a wide variation in the mycobiome in different populations, with no definite pattern that can define the mycobiome in IBD having yet been identified. Recent work has suggested that characterizing the fecal fungal composition may influence therapeutic decisions and help to predict outcomes in a subset of IBD patients. In this study, we review the current literature on the emerging role of the fecal mycobiome as a potential tool for precision medicine in IBD.
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Affiliation(s)
- Domingo C. Balderramo
- Department of Gastroenterology, Private Hospital Medical Center of Cordoba S.A., Cordoba, Argentina
| | - Pablo Alberto Romagnoli
- Universitarian Institute for Biomedical Sciences of Cordoba (IUCBC), Translational Medicine Research Center "Severo R. Amuchastegui" (CIMETSA). G.V. Medical Research Institute "Mercedes and Martin Ferreyra" (INIMEC-CONICET-UNC), Cordoba, Argentina
| | - Atle van Beelen Granlund
- Department of Gastroenterology and Hepatology, Clinic of Medicine, St. Olav’s University Hospital, Trondheim, Norway
- Department of Clinical and Molecular Medicine (IKOM), NTNU-Norwegian University of Science and Technology, Trondheim, Norway
- Centre of Molecular Inflammation Research, NTNU-Norwegian University of Science and Technology, Trondheim, Norway
| | - Ignacio Catalan-Serra
- Department of Clinical and Molecular Medicine (IKOM), NTNU-Norwegian University of Science and Technology, Trondheim, Norway
- Centre of Molecular Inflammation Research, NTNU-Norwegian University of Science and Technology, Trondheim, Norway
- Department of Medicine, Gastroenterology, Levanger Hospital, Nord-Trøndelag Hospital Trust, Levanger, Norway
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18
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Yue R, Chen H, Xu X, Xia Y, Sun Y, Xia M, Xia D, Sun B. Maternal and infantile gut mycobiome during the weaning period in free ranging Tibetan macaques ( Macaca thibetana). Ecol Evol 2023; 13:e10108. [PMID: 37214608 PMCID: PMC10196218 DOI: 10.1002/ece3.10108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 05/02/2023] [Accepted: 05/05/2023] [Indexed: 05/24/2023] Open
Abstract
Gut microbiome is critical to the health of mammals. Many previous studies have revealed the gut bacterial microbiomes of mother and infant changed significantly during the weaning period. However, little is known concerning the gut mycobiome of wild primates. Here, we examined the variations on gut mycobiome between weaning and post-weaning for both mother and infant in wild-living Tibetan macaques (Macaca thibetana). Our results showed that the gut mycobiomes of mother and infant were dominated by two phyla Ascomycota and Basidiomycota. For both mother and infant, the ASV richness of gut mycobiome remained relatively steady from weaning to post-weaning periods, while the Shannon indexes increased significant in weaning compared to post-weaning periods. However, no significant difference between mother and infant ASV richness and Shannon indexes during weaning and post-weaning periods respectively. Compared to mothers, we found that much more known taxa of gut fungi were enriched in weaning or post-weaning periods of infants. In particular, we found that the dominant genus Aspergillus was enriched in infants during weaning period. Furthermore, we found that the relative abundance of plant pathogens were significantly higher in the post-weaning period than in the weaning period for infants. Our results indicated that weaning events could affect the gut mycobiome significantly for both mothers and infant in Tibetan macaques, which had a stronger effect on the gut mycobiome of infant monkeys than on their mothers.
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Affiliation(s)
- Ran Yue
- School of Resource and Environmental EngineeringAnhui UniversityHefeiChina
- International Collaborative Research Center for Huangshan Biodiversity and Tibetan Macaque Behavioral EcologyAnhui UniversityHefeiChina
| | - Huijuan Chen
- School of Resource and Environmental EngineeringAnhui UniversityHefeiChina
- International Collaborative Research Center for Huangshan Biodiversity and Tibetan Macaque Behavioral EcologyAnhui UniversityHefeiChina
| | - Xiaojuan Xu
- School of Life SciencesHefei Normal UniversityHefeiChina
| | - Yingna Xia
- School of Resource and Environmental EngineeringAnhui UniversityHefeiChina
- International Collaborative Research Center for Huangshan Biodiversity and Tibetan Macaque Behavioral EcologyAnhui UniversityHefeiChina
| | - Yu Sun
- School of Resource and Environmental EngineeringAnhui UniversityHefeiChina
- International Collaborative Research Center for Huangshan Biodiversity and Tibetan Macaque Behavioral EcologyAnhui UniversityHefeiChina
| | - Mengyi Xia
- School of Resource and Environmental EngineeringAnhui UniversityHefeiChina
- International Collaborative Research Center for Huangshan Biodiversity and Tibetan Macaque Behavioral EcologyAnhui UniversityHefeiChina
| | - Dongpo Xia
- School of Life SciencesAnhui UniversityHefeiChina
| | - Binghua Sun
- School of Resource and Environmental EngineeringAnhui UniversityHefeiChina
- International Collaborative Research Center for Huangshan Biodiversity and Tibetan Macaque Behavioral EcologyAnhui UniversityHefeiChina
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19
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Tian Y, Gou W, Ma Y, Shuai M, Liang X, Fu Y, Zheng JS. The Short-Term Variation of Human Gut Mycobiome in Response to Dietary Intervention of Different Macronutrient Distributions. Nutrients 2023; 15:2152. [PMID: 37432284 DOI: 10.3390/nu15092152] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/10/2023] [Accepted: 04/27/2023] [Indexed: 07/12/2023] Open
Abstract
While the human gut is home to a complex and diverse community of microbes, including bacteria and fungi, research on the gut microbiome has largely focused on bacteria, with relatively little attention given to the gut mycobiome. This study aims to investigate how diets with different dietary macronutrient distributions impact the gut mycobiome. We investigated gut mycobiome response to high-carbohydrate, low-fat (HC) and low-carbohydrate high-fat (LC) diet interventions based on a series of 72-day feeding-based n-of-1 clinical trials. A total of 30 participants were enrolled and underwent three sets of HC and LC dietary interventions in a randomized sequence. Each set lasted for 24 days with a 6-day washout period between dietary interventions. We collected and analyzed the fungal composition of 317 stool samples before and after each intervention period. To account for intra-individual variation across the three sets, we averaged the mycobiome data from the repeated sets for analysis. Of the 30 participants, 28 (aged 22-34 years) completed the entire intervention. Our results revealed a significant increase in gut fungal alpha diversity (p < 0.05) and significant changes in fungal composition (beta diversity, p < 0.05) after the HC dietary intervention. Specifically, we observed the enrichment of five fungal genera (Pleurotus, Kazachstania, Auricularia, Paraphaeosphaeria, Ustilaginaceae sp.; FDR < 0.052) and depletion of one fungal genus (Blumeria; FDR = 0.03) after the HC intervention. After the LC dietary intervention, one fungal genus was enriched (Ustilaginaceae sp.; FDR = 0.003), and five fungal genera were depleted (Blumeria, Agaricomycetes spp., Malassezia, Rhizopus, and Penicillium; FDR < 0.1). This study provides novel evidence on how the gut mycobiome structure and composition change in response to the HC and LC dietary interventions and reveals diet-specific changes in the fungal genera.
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Affiliation(s)
- Yunyi Tian
- School of Medicine, Zhejiang University, Hangzhou 310058, China
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310030, China
| | - Wanglong Gou
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310030, China
- Westlake Intelligent Biomarker Discovery Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310030, China
| | - Yue Ma
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310030, China
- Westlake Intelligent Biomarker Discovery Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310030, China
| | - Menglei Shuai
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310030, China
- Westlake Intelligent Biomarker Discovery Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310030, China
| | - Xinxiu Liang
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310030, China
- Westlake Intelligent Biomarker Discovery Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310030, China
| | - Yuanqing Fu
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310030, China
- Westlake Intelligent Biomarker Discovery Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310030, China
| | - Ju-Sheng Zheng
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310030, China
- Westlake Intelligent Biomarker Discovery Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310030, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310030, China
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20
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Wilson A, Bogie B, Chaaban H, Burge K. The Nonbacterial Microbiome: Fungal and Viral Contributions to the Preterm Infant Gut in Health and Disease. Microorganisms 2023; 11:909. [PMID: 37110332 PMCID: PMC10144239 DOI: 10.3390/microorganisms11040909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 03/27/2023] [Accepted: 03/30/2023] [Indexed: 04/29/2023] Open
Abstract
The intestinal microbiome is frequently implicated in necrotizing enterocolitis (NEC) pathogenesis. While no particular organism has been associated with NEC development, a general reduction in bacterial diversity and increase in pathobiont abundance has been noted preceding disease onset. However, nearly all evaluations of the preterm infant microbiome focus exclusively on the bacterial constituents, completely ignoring any fungi, protozoa, archaea, and viruses present. The abundance, diversity, and function of these nonbacterial microbes within the preterm intestinal ecosystem are largely unknown. Here, we review findings on the role of fungi and viruses, including bacteriophages, in preterm intestinal development and neonatal intestinal inflammation, with potential roles in NEC pathogenesis yet to be determined. In addition, we highlight the importance of host and environmental influences, interkingdom interactions, and the role of human milk in shaping fungal and viral abundance, diversity, and function within the preterm intestinal ecosystem.
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Affiliation(s)
| | | | - Hala Chaaban
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Kathryn Burge
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
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21
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James SA, Telatin A, Baker D, Evans R, Clarke P, Hall LJ, Carding SR. Draft Genome Sequence of a Preterm Infant-Derived Isolate of Candida parapsilosis. Microbiol Resour Announc 2023; 12:e0127322. [PMID: 36847565 PMCID: PMC10019213 DOI: 10.1128/mra.01273-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 02/10/2023] [Indexed: 03/01/2023] Open
Abstract
Candida parapsilosis is a human fungal pathogen of increasing incidence and causes invasive candidiasis, notably in preterm or low-birthweight neonates. Here, we present the genome sequence of C. parapsilosis NCYC 4289, a fecal isolate from a preterm male infant.
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Affiliation(s)
- Steve A. James
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Andrea Telatin
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, United Kingdom
| | - David Baker
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Rhiannon Evans
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Paul Clarke
- Neonatal Intensive Care Unit, Norfolk and Norwich University Hospitals NHS Foundation Trust, Norwich, United Kingdom
- Norwich Medical School, University of East Anglia, Norwich, United Kingdom
| | - Lindsay J. Hall
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, United Kingdom
- Ziel–Institute for Food and Health, Technical University of Munich, Freising, Germany
| | - Simon R. Carding
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, United Kingdom
- Norwich Medical School, University of East Anglia, Norwich, United Kingdom
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22
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Mediator Subunit Med15 Regulates Cell Morphology and Mating in Candida lusitaniae. J Fungi (Basel) 2023; 9:jof9030333. [PMID: 36983501 PMCID: PMC10053558 DOI: 10.3390/jof9030333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/26/2023] [Accepted: 02/27/2023] [Indexed: 03/12/2023] Open
Abstract
Candida lusitaniae is an emerging opportunistic pathogenic yeast capable of shifting from yeast to pseudohyphae form, and it is one of the few Candida species with the ability to reproduce sexually. In this study, we showed that a dpp3Δ mutant, inactivated for a putative pyrophosphatase, is impaired in cell separation, pseudohyphal growth and mating. The defective phenotypes were not restored after the reconstruction of a wild-type DPP3 locus, reinforcing the hypothesis of the presence of an additional mutation that we suspected in our previous study. Genetic crosses and genome sequencing identified an additional mutation in MED15, encoding a subunit of the mediator complex that functions as a general transcriptional co-activator in Eukaryotes. We confirmed that inactivation of MED15 was responsible for the defective phenotypes by rescuing the dpp3Δ mutant with a wild-type copy of MED15 and constructing a med15Δ knockout mutant that mimics the phenotypes of dpp3Δ in vitro. Proteomic analyses revealed the biological processes under the control of Med15 and involved in hyphal growth, cell separation and mating. This is the first description of the functions of MED15 in the regulation of hyphal growth, cell separation and mating, and the pathways involved in C. lusitaniae.
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23
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Gutierrez MW, Mercer EM, Moossavi S, Laforest-Lapointe I, Reyna ME, Becker AB, Simons E, Mandhane PJ, Turvey SE, Moraes TJ, Sears MR, Subbarao P, Azad MB, Arrieta MC. Maturational patterns of the infant gut mycobiome are associated with early-life body mass index. Cell Rep Med 2023; 4:100928. [PMID: 36736319 PMCID: PMC9975311 DOI: 10.1016/j.xcrm.2023.100928] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 10/24/2022] [Accepted: 01/06/2023] [Indexed: 02/05/2023]
Abstract
Unlike the bacterial microbiome, the role of early-life gut fungi in host metabolism and childhood obesity development remains poorly characterized. To address this, we investigate the relationship between the gut mycobiome of 100 infants from the Canadian Healthy Infant Longitudinal Development (CHILD) Cohort Study and body mass index Z scores (BMIz) in the first 5 years of life. An increase in fungal richness during the first year of life is linked to parental and infant BMI. The relationship between richness pattern and early-life BMIz is modified by maternal BMI, maternal diet, infant antibiotic exposure, and bacterial beta diversity. Further, the abundances of Saccharomyces, Rhodotorula, and Malassezia are differentially associated with early-life BMIz. Using structural equation modeling, we determine that the mycobiome's contribution to BMIz is likely mediated by the bacterial microbiome. This demonstrates that mycobiome maturation and infant growth trajectories are distinctly linked, advocating for inclusion of fungi in larger pediatric microbiome studies.
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Affiliation(s)
- Mackenzie W Gutierrez
- Department of Physiology and Pharmacology, University of Calgary, Calgary, AB T2N 1N4, Canada; Department of Pediatrics, University of Calgary, Calgary, AB T2N 1N4, Canada; International Microbiome Center, University of Calgary, Calgary, AB T2N 1N4, Canada; Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Emily M Mercer
- Department of Physiology and Pharmacology, University of Calgary, Calgary, AB T2N 1N4, Canada; Department of Pediatrics, University of Calgary, Calgary, AB T2N 1N4, Canada; International Microbiome Center, University of Calgary, Calgary, AB T2N 1N4, Canada; Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Shirin Moossavi
- Department of Physiology and Pharmacology, University of Calgary, Calgary, AB T2N 1N4, Canada; Department of Pediatrics, University of Calgary, Calgary, AB T2N 1N4, Canada; International Microbiome Center, University of Calgary, Calgary, AB T2N 1N4, Canada; Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB T2N 1N4, Canada
| | | | - Myrtha E Reyna
- Department of Pediatrics, Hospital for Sick Children, University of Toronto, Toronto, ON M5G 1X8, Canada
| | - Allan B Becker
- Children's Hospital Research Institute of Manitoba, Winnipeg, MB R3E 3P4, Canada; Developmental Origins of Chronic Diseases in Children Network (DEVOTION), Winnipeg, MB, Canada; Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
| | - Elinor Simons
- Children's Hospital Research Institute of Manitoba, Winnipeg, MB R3E 3P4, Canada; Developmental Origins of Chronic Diseases in Children Network (DEVOTION), Winnipeg, MB, Canada; Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
| | - Piush J Mandhane
- Department of Pediatrics, University of Alberta, Edmonton, AB T6G 2R7, Canada
| | - Stuart E Turvey
- Department of Pediatrics, BC Children's Hospital, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Theo J Moraes
- Department of Pediatrics, Hospital for Sick Children, University of Toronto, Toronto, ON M5G 1X8, Canada
| | - Malcolm R Sears
- Department of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Padmaja Subbarao
- Department of Pediatrics, Hospital for Sick Children, University of Toronto, Toronto, ON M5G 1X8, Canada; Department of Physiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Meghan B Azad
- Children's Hospital Research Institute of Manitoba, Winnipeg, MB R3E 3P4, Canada; Developmental Origins of Chronic Diseases in Children Network (DEVOTION), Winnipeg, MB, Canada; Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
| | - Marie-Claire Arrieta
- Department of Physiology and Pharmacology, University of Calgary, Calgary, AB T2N 1N4, Canada; Department of Pediatrics, University of Calgary, Calgary, AB T2N 1N4, Canada; International Microbiome Center, University of Calgary, Calgary, AB T2N 1N4, Canada; Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB T2N 1N4, Canada.
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24
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Gupta Y, Ernst AL, Vorobyev A, Beltsiou F, Zillikens D, Bieber K, Sanna-Cherchi S, Christiano AM, Sadik CD, Ludwig RJ, Sezin T. Impact of diet and host genetics on the murine intestinal mycobiome. Nat Commun 2023; 14:834. [PMID: 36788222 PMCID: PMC9929102 DOI: 10.1038/s41467-023-36479-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 02/01/2023] [Indexed: 02/16/2023] Open
Abstract
The mammalian gut is home to a diverse microbial ecosystem, whose composition affects various physiological traits of the host. Next-generation sequencing-based metagenomic approaches demonstrated how the interplay of host genetics, bacteria, and environmental factors shape complex traits and clinical outcomes. However, the role of fungi in these complex interactions remains understudied. Here, using 228 males and 363 females from an advanced-intercross mouse line, we provide evidence that fungi are regulated by host genetics. In addition, we map quantitative trait loci associated with various fungal species to single genes in mice using whole genome sequencing and genotyping. Moreover, we show that diet and its' interaction with host genetics alter the composition of fungi in outbred mice, and identify fungal indicator species associated with different dietary regimes. Collectively, in this work, we uncover an association of the intestinal fungal community with host genetics and a regulatory role of diet in this ecological niche.
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Affiliation(s)
- Yask Gupta
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
- Division of Nephrology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Anna Lara Ernst
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Artem Vorobyev
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
- Department of Dermatology, University of Lübeck, Lübeck, Germany
| | - Foteini Beltsiou
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Detlef Zillikens
- Department of Dermatology, University of Lübeck, Lübeck, Germany
| | - Katja Bieber
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Simone Sanna-Cherchi
- Division of Nephrology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Angela M Christiano
- Department of Dermatology, Columbia University Irving Medical Center, New York, NY, USA
| | | | - Ralf J Ludwig
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany.
- Department of Dermatology, University of Lübeck, Lübeck, Germany.
| | - Tanya Sezin
- Department of Dermatology, University of Lübeck, Lübeck, Germany.
- Department of Dermatology, Columbia University Irving Medical Center, New York, NY, USA.
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25
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Abstract
Recent studies revealed a significant role of the gut fungal community in human health. Here, we investigated the content and variation of gut mycobiota among subjects from the European population. We explored the interplay between gut fungi and various host-related sociodemographic, lifestyle, health, and dietary factors. The study included 923 participants. Fecal DNA samples were analyzed by whole-metagenome high-throughput sequencing. Subsequently, fungi taxonomic profiles were determined and accompanied by computational and statistical analyses of the association with 53 host-related factors. Fungal communities were characterized by a high prevalence of Saccharomyces, Candida, and Sporisorium. Ten factors were found to correlate significantly with the overall mycobiota variation. Most were diet related, including the consumption of chips, meat, sodas, sweetening, processed food, and alcohol, followed by age and marital status. Differences in α- and/or β-diversity were also reported for other factors such as body mass index (BMI), job type, autoimmunological diseases, and probiotics. Differential abundance analysis revealed fungal species that exhibited different patterns of changes under specific conditions. The human gut mycobiota is dominated by yeast, including Saccharomyces, Malassezia, and Candida. Although intervolunteer variability was high, several fungal species persisted across most samples, which may be evidence that a core gut mycobiota exists. Moreover, we showed that host-related factors such as diet, age, and marital status influence the variability of gut mycobiota. To our knowledge, this is the first large and comprehensive study of the European cohort in terms of gut mycobiota associations with such an extensive and differentiated host-related set of factors. IMPORTANCE The human gut is inhabited by many organisms, including bacteria and fungi, that may affect human health. However, research on human gut mycobiome is still rare. Moreover, the large European-based cohort study is missing. Here, we analyzed the first large European cohort in terms of gut mycobiota associations with a differentiated host-related set of factors. Our results showed that chips, meat, sodas, sweetening, processed food, beer, alcohol consumption, age, and marital status were associated with the variability of gut mycobiota. Moreover, our analysis revealed changes in abundances at the fungal species level for many investigated factors. Our results can suggest potentially valuable paths for further, narrowly focused research on gut mycobiome and its impact on human health. In the coming era of gut microbiome-based precision medicine, further research into the relationship between different mycobial structures and host-related factors may result in new preventive approaches or therapeutic procedures.
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26
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Mishima R, Tanaka M, Momoda R, Sanefuji M, Morokuma S, Ogawa M, Kato K, Nakayama J. Longitudinal gut mycobiota changes in Japanese infants during first three years of life. J Biosci Bioeng 2023; 135:266-273. [PMID: 36740519 DOI: 10.1016/j.jbiosc.2023.01.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/19/2022] [Accepted: 01/13/2023] [Indexed: 02/06/2023]
Abstract
Although fungi can have a large impact on host health through the stimulation of the immune system and toxin production, few studies have investigated the gut mycobiota during infancy, a period during which sensitivity to internal and external stimuli is high. To capture the trend in fungal colonization during infancy, we evaluated the gut mycobiota of ten Japanese infants during the first 3 years of life. Infants had two major phyla, Ascomycota (68.9%) and Basidiomycota (29.6%), and the most abundant genus was Saccharomyces (26.8%), followed by Malassezia (18.5%), Candida (12.3%), Meyerozyma (8.5%), and Penicillium (8.3%). Alpha diversity analysis revealed a significant decrease in fungal richness and evenness with age, suggesting adaptive selection of the colonizing species in the gut environment. Beta diversity analysis divided infant mycobiota into age-related clusters and showed discrete separation before and after weaning, suggesting shift in microenvironment via weaning. In the initial stage, a variety of fungal species that likely originated from an environment, such as Malassezia spp., was highly colonized and were replaced by yeasts, such as Saccharomyces, after weaning. Further studies are needed to shed light on how the passage of the series of fungal colonizations in infancy affects the development of the host immune system and the other homeostasis involved in health later in life.
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Affiliation(s)
- Riko Mishima
- Laboratory of Microbial Technology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka-shi, Fukuoka 819-0395, Japan
| | - Masaru Tanaka
- Laboratory of Microbial Technology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka-shi, Fukuoka 819-0395, Japan
| | - Rie Momoda
- Laboratory of Microbial Technology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka-shi, Fukuoka 819-0395, Japan
| | - Masafumi Sanefuji
- Department of Pediatrics, Faculty of Medicine, Saga University, 5-1-1 Nabeshima, Saga-shi, Saga 849-8501, Japan; Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan
| | - Seiichi Morokuma
- Department of Health Sciences, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan
| | - Masanobu Ogawa
- Department of Obstetrics and Gynecology, Faculty of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan
| | - Kiyoko Kato
- Department of Obstetrics and Gynecology, Faculty of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan
| | - Jiro Nakayama
- Laboratory of Microbial Technology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka-shi, Fukuoka 819-0395, Japan.
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27
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West AG, Digby A, Taylor MW. The mycobiota of faeces from the critically endangered kākāpō and associated nest litter. NEW ZEALAND JOURNAL OF ZOOLOGY 2023. [DOI: 10.1080/03014223.2023.2170428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Annie G. West
- Te Kura Mātauranga Koiora School of Biological Sciences, Waipapa Taumata Rau University of Auckland, Auckland, New Zealand
| | - Andrew Digby
- Te Papa Atawhai Department of Conservation, Kākāpō Recovery Programme, Invercargill, New Zealand
| | - Michael W. Taylor
- Te Kura Mātauranga Koiora School of Biological Sciences, Waipapa Taumata Rau University of Auckland, Auckland, New Zealand
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28
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Wang H, Wu H, Li KD, Wang YY, Huang RG, Du YJ, Jin X, Zhang QR, Li XB, Li BZ. Intestinal fungi and systemic autoimmune diseases. Autoimmun Rev 2023; 22:103234. [PMID: 36423833 DOI: 10.1016/j.autrev.2022.103234] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 11/17/2022] [Indexed: 11/23/2022]
Abstract
Nearly 20 years of studies have shown that fungi and the human immune system (non-specific immunity and specific immunity) and bacterial--fungal interactions maintain a balance that can't lead to diseases. Fungi--microorganism that lives in human intestine--may play an important role in human health and disease. Population studies and animal models in some diseases have found the changes in the diversity and composition of fungi. The dysregulation of the fungi can disrupt the normal "running" of the immune system and bacteria, which triggers the development of inflammatory diseases. The latest studies of fungi in inflammatory bowel disease, systemic lupus erythematosus, ankylosing spondylitis and type 1 diabetes mellitus were summarized. This review considers how the healthy host protect against the potential harm of intestinal fungi through the immune system and how fungal dysregulation alters host immunity.
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Affiliation(s)
- Hua Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Hong Wu
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Kai-Di Li
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Yi-Yu Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Rong-Gui Huang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Yu-Jie Du
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Xue Jin
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Qian-Ru Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China; Department of Cardiovascular Surgery, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Xian-Bao Li
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Bao-Zhu Li
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China.
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29
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McCoubrey LE, Favaron A, Awad A, Orlu M, Gaisford S, Basit AW. Colonic drug delivery: Formulating the next generation of colon-targeted therapeutics. J Control Release 2023; 353:1107-1126. [PMID: 36528195 DOI: 10.1016/j.jconrel.2022.12.029] [Citation(s) in RCA: 45] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/08/2022] [Accepted: 12/10/2022] [Indexed: 12/26/2022]
Abstract
Colonic drug delivery can facilitate access to unique therapeutic targets and has the potential to enhance drug bioavailability whilst reducing off-target effects. Delivering drugs to the colon requires considered formulation development, as both oral and rectal dosage forms can encounter challenges if the colon's distinct physiological environment is not appreciated. As the therapeutic opportunities surrounding colonic drug delivery multiply, the success of novel pharmaceuticals lies in their design. This review provides a modern insight into the key parameters determining the effective design and development of colon-targeted medicines. Influential physiological features governing the release, dissolution, stability, and absorption of drugs in the colon are first discussed, followed by an overview of the most reliable colon-targeted formulation strategies. Finally, the most appropriate in vitro, in vivo, and in silico preclinical investigations are presented, with the goal of inspiring strategic development of new colon-targeted therapeutics.
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Affiliation(s)
- Laura E McCoubrey
- 29 - 39 Brunswick Square, UCL School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Alessia Favaron
- 29 - 39 Brunswick Square, UCL School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Atheer Awad
- 29 - 39 Brunswick Square, UCL School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Mine Orlu
- 29 - 39 Brunswick Square, UCL School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Simon Gaisford
- 29 - 39 Brunswick Square, UCL School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Abdul W Basit
- 29 - 39 Brunswick Square, UCL School of Pharmacy, University College London, London, WC1N 1AX, UK.
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30
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S Forster C, Liu H, Kurs-Lasky M, Ullmer W, Krumbeck JA, Shaikh N. Uromycobiome in infants and toddlers with and without urinary tract infections. Pediatr Nephrol 2022:10.1007/s00467-022-05844-3. [PMID: 36547733 DOI: 10.1007/s00467-022-05844-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 11/23/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND The bacterial components of the urobiome have been described in children, both with and without urinary tract infections (UTI). However, less is known about the pediatric uromycobiome: the community of fungi in the urine. The objectives of this study were to describe the uromycobiome in children and determine whether the uromycobiome differs between children with and without UTI. METHODS This was a cross-sectional study of febrile children less than 3 years of age who presented to the Emergency Department and had a catheterized urine sample sent as part of clinical care. We obtained residual urine for use in this study and identified components of the uromyobiome through amplification and sequencing of the fungal ITS2 region. We then compared the uromycobiome between those with and without UTI. RESULTS We included 374 children in this study (UTI = 50, no UTI = 324). Fungi were isolated from urine samples of 310 (83%) children. Fungi were identified in a higher proportion of children with UTI, compared to those without UTI (96% vs. 81%, p = 0.01). Shannon diversity index was higher in children with UTI, compared to those without (p = 0.04). Although there were differences in the most abundant taxa between children with and without UTI, there was no significant difference in beta diversity between groups. CONCLUSIONS Fungi were detected in the majority of catheterized urine samples from children. While a higher proportion of children with UTI had fungi in their urine, compared to children without UTI, there was no difference in the composition of these groups. A higher resolution version of the Graphical abstract is available as Supplementary information.
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Affiliation(s)
- Catherine S Forster
- Department of Pediatrics School of Medicine, University of Pittsburgh, 4401 Penn Ave, Pittsburgh, PA, 15224, USA.
| | - Hui Liu
- Department of Pediatrics School of Medicine, University of Pittsburgh, 4401 Penn Ave, Pittsburgh, PA, 15224, USA
| | - Marcia Kurs-Lasky
- Department of Pediatrics School of Medicine, University of Pittsburgh, 4401 Penn Ave, Pittsburgh, PA, 15224, USA
| | - Wendy Ullmer
- Zymo Research Corporation, Irvine, CA, USA.,Pangea Laboratory, Tustin, CA, USA
| | - Janina A Krumbeck
- Zymo Research Corporation, Irvine, CA, USA.,Pangea Laboratory, Tustin, CA, USA
| | - Nader Shaikh
- Department of Pediatrics School of Medicine, University of Pittsburgh, 4401 Penn Ave, Pittsburgh, PA, 15224, USA
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31
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Davies CP, Summers KL, Arfken AM, Darwish N, Chaudhari A, Frey JF, Schreier L, Proszkowiec-Weglarz M. Temporal dynamics of the chicken mycobiome. Front Physiol 2022; 13:1057810. [PMID: 36589448 PMCID: PMC9799259 DOI: 10.3389/fphys.2022.1057810] [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: 09/30/2022] [Accepted: 11/30/2022] [Indexed: 12/23/2022] Open
Abstract
The microbiome is an integral part of chicken health and can affect immunity, nutrient utilization, and performance. The role of bacterial microbiota members in host health is relatively well established, but less attention has been paid to fungal members of the gastrointestinal tract (GIT) community. However, human studies indicate that fungi play a critical role in health. Here, we described fungal communities, or mycobiomes, in both the lumen and mucosa of the chicken ileum and cecum from hatch through 14 days of age. We also assessed the effects of delayed access to feed immediately post-hatch (PH) on mycobiome composition, as PH feed delay is commonly associated with poor health performance. Chicken mycobiomes in each of the populations were distinct and changed over time. All mycobiomes were dominated by Gibberella, but Aspergillus, Cladosporium, Sarocladium, Meyerozyma, and Penicillium were also abundant. Relative abundances of some taxa differed significantly over time. In the cecal and ileal lumens, Penicillium was present in extremely low quantities or absent during days one and two and then increased over time. Meyerozyma and Wickerhamomyces also increased over time in luminal sites. In contrast, several highly abundant unclassified fungi decreased after days one and two, highlighting the need for improved understanding of fungal gut biology. Mycobiomes from chicks fed during the first 2 days PH versus those not fed during the first 2 days did not significantly differ, except during days one and two. Similarities observed among mycobiomes of fed and unfed chicks at later timepoints suggest that delays in PH feeding do not have long lasting effects on mycobiome composition. Together, these results provide a foundation for future mycobiome studies, and suggest that negative health and production impacts of delayed feeding are not likely related to the development of fungal populations in the GIT.
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Affiliation(s)
- Cary Pirone Davies
- Animal Biosciences and Biotechnology Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States,*Correspondence: Cary Pirone Davies,
| | - Katie Lynn Summers
- Animal Biosciences and Biotechnology Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Ann M. Arfken
- Animal Biosciences and Biotechnology Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States,Oak Ridge Institute for Science and Education through an interagency Agreement between the U.S., Department of Energy and the USDA, Atlanta, GA, United States,Oak Ridge Institute for Science and Education, Center for Disease Control, Atlanta, GA, United States
| | - Nadia Darwish
- Animal Biosciences and Biotechnology Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States,Oak Ridge Institute for Science and Education through an interagency Agreement between the U.S., Department of Energy and the USDA, Atlanta, GA, United States,University of Arkansas for Medical Sciences, Little Rock, AK, United States
| | - Atul Chaudhari
- Animal Biosciences and Biotechnology Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States,Oak Ridge Institute for Science and Education through an interagency Agreement between the U.S., Department of Energy and the USDA, Atlanta, GA, United States,Pharmaceuticals Product Development, Wilmington, NC, United States
| | - Juli Foster Frey
- Animal Biosciences and Biotechnology Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States,Northeast Area, United States Department of Agriculture, Beltsville, MD, United States
| | - Lori Schreier
- Animal Biosciences and Biotechnology Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Monika Proszkowiec-Weglarz
- Animal Biosciences and Biotechnology Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
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32
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Shuai M, Fu Y, Zhong HL, Gou W, Jiang Z, Liang Y, Miao Z, Xu JJ, Huynh T, Wahlqvist ML, Chen YM, Zheng JS. Mapping the human gut mycobiome in middle-aged and elderly adults: multiomics insights and implications for host metabolic health. Gut 2022; 71:1812-1820. [PMID: 35017200 PMCID: PMC9380515 DOI: 10.1136/gutjnl-2021-326298] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 12/26/2021] [Indexed: 12/20/2022]
Abstract
OBJECTIVE The human gut fungal community, known as the mycobiome, plays a fundamental role in the gut ecosystem and health. Here we aimed to investigate the determinants and long-term stability of gut mycobiome among middle-aged and elderly adults. We further explored the interplay between gut fungi and bacteria on metabolic health. DESIGN The present study included 1244 participants from the Guangzhou Nutrition and Health Study. We characterised the long-term stability and determinants of the human gut mycobiome, especially long-term habitual dietary consumption. The comprehensive multiomics analyses were performed to investigate the ecological links between gut bacteria, fungi and faecal metabolome. Finally, we examined whether the interaction between gut bacteria and fungi could modulate the metabolic risk. RESULTS The gut fungal composition was temporally stable and mainly determined by age, long-term habitual diet and host physiological states. Specifically, compared with middle-aged individuals, Blastobotrys and Agaricomycetes spp were depleted, while Malassezia was enriched in the elderly. Dairy consumption was positively associated with Saccharomyces but inversely associated with Candida. Notably, Saccharomycetales spp interacted with gut bacterial diversity to influence insulin resistance. Bidirectional mediation analyses indicated that bacterial function or faecal histidine might causally mediate an impact of Pichia on blood cholesterol. CONCLUSION We depict the sociodemographic and dietary determinants of human gut mycobiome in middle-aged and elderly individuals, and further reveal that the gut mycobiome may be closely associated with the host metabolic health through regulating gut bacterial functions and metabolites.
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Affiliation(s)
- Menglei Shuai
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Yuanqing Fu
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Hai-li Zhong
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health; Department of Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Wanglong Gou
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China,Westlake Intelligent Biomarker Discovery Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
| | - Zengliang Jiang
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China,Westlake Intelligent Biomarker Discovery Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
| | - Yuhui Liang
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Zelei Miao
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Jin-Jian Xu
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health; Department of Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Tien Huynh
- School of Science, RMIT University, Melbourne, Victoria, Australia
| | - Mark L Wahlqvist
- Monash Asia Institute, Monash University, Clayton, Victoria, Australia .,Institute of Nutrition and Health, Qingdao University, Qingdao, Shandong, China.,Institute of Population Health, National Health Research Institutes, Zhunan, Taiwan, China
| | - Yu-ming Chen
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health; Department of Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Ju-Sheng Zheng
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China .,Westlake Intelligent Biomarker Discovery Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
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33
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Nel Van Zyl K, Whitelaw AC, Hesseling AC, Seddon JA, Demers AM, Newton-Foot M. Fungal diversity in the gut microbiome of young South African children. BMC Microbiol 2022; 22:201. [PMID: 35978282 PMCID: PMC9387017 DOI: 10.1186/s12866-022-02615-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 08/01/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The fungal microbiome, or mycobiome, is a poorly described component of the gut ecosystem and little is known about its structure and development in children. In South Africa, there have been no culture-independent evaluations of the child gut mycobiota. This study aimed to characterise the gut mycobiota and explore the relationships between fungi and bacteria in the gut microbiome of children from Cape Town communities. METHODS Stool samples were collected from children enrolled in the TB-CHAMP clinical trial. Internal transcribed spacer 1 (ITS1) gene sequencing was performed on a total of 115 stool samples using the Illumina MiSeq platform. Differences in fungal diversity and composition in relation to demographic, clinical, and environmental factors were investigated, and correlations between fungi and previously described bacterial populations in the same samples were described. RESULTS Taxa from the genera Candida and Saccharomyces were detected in all participants. Differential abundance analysis showed that Candida spp. were significantly more abundant in children younger than 2 years compared to older children. The gut mycobiota was less diverse than the bacterial microbiota of the same participants, consistent with the findings of other human microbiome studies. The variation in richness and evenness of fungi was substantial, even between individuals of the same age. There was significant association between vitamin A supplementation and higher fungal alpha diversity (p = 0.047), and girls were shown to have lower fungal alpha diversity (p = 0.003). Co-occurrence between several bacterial taxa and Candida albicans was observed. CONCLUSIONS The dominant fungal taxa in our study population were similar to those reported in other paediatric studies; however, it remains difficult to identify the true core gut mycobiota due to the challenges set by the low abundance of gut fungi and the lack of true gut colonising species. The connection between the microbiota, vitamin A supplementation, and growth and immunity warrants exploration, especially in populations at risk for micronutrient deficiencies. While we were able to provide insight into the gut mycobiota of young South African children, further functional studies are necessary to explain the role of the mycobiota and the correlations between bacteria and fungi in human health.
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Affiliation(s)
- K Nel Van Zyl
- Division of Medical Microbiology, Department of Pathology, Stellenbosch University, Stellenbosch, South Africa.
| | - A C Whitelaw
- Division of Medical Microbiology, Department of Pathology, Stellenbosch University, Stellenbosch, South Africa
- National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
- African Microbiome Institute, Stellenbosch University, Stellenbosch, South Africa
| | - A C Hesseling
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Stellenbosch University, Stellenbosch, South Africa
| | - J A Seddon
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Stellenbosch University, Stellenbosch, South Africa
- Department of Infectious Diseases, Imperial College London, London, UK
| | - A-M Demers
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Stellenbosch University, Stellenbosch, South Africa
- Service de Microbiologie, Département Clinique de Médecine de Laboratoire, Centre Hospitalier Universitaire Sainte-Justine, Montréal, Canada
| | - M Newton-Foot
- Division of Medical Microbiology, Department of Pathology, Stellenbosch University, Stellenbosch, South Africa
- National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
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34
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Gang J, Wang H, Xue X, Zhang S. Microbiota and COVID-19: Long-term and complex influencing factors. Front Microbiol 2022; 13:963488. [PMID: 36033885 PMCID: PMC9417543 DOI: 10.3389/fmicb.2022.963488] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 07/25/2022] [Indexed: 01/08/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). According to the World Health Organization statistics, more than 500 million individuals have been infected and more than 6 million deaths have resulted worldwide. Although COVID-19 mainly affects the respiratory system, considerable evidence shows that the digestive, cardiovascular, nervous, and reproductive systems can all be involved. Angiotensin-converting enzyme 2 (AEC2), the target of SARS-CoV-2 invasion of the host is mainly distributed in the respiratory and gastrointestinal tract. Studies found that microbiota contributes to the onset and progression of many diseases, including COVID-19. Here, we firstly conclude the characterization of respiratory, gut, and oral microbial dysbiosis, including bacteria, fungi, and viruses. Then we explore the potential mechanisms of microbial involvement in COVID-19. Microbial dysbiosis could influence COVID-19 by complex interactions with SARS-CoV-2 and host immunity. Moreover, microbiota may have an impact on COVID-19 through their metabolites or modulation of ACE2 expression. Subsequently, we generalize the potential of microbiota as diagnostic markers for COVID-19 patients and its possible association with post-acute COVID-19 syndrome (PACS) and relapse after recovery. Finally, we proposed directed microbiota-targeted treatments from the perspective of gut microecology such as probiotics and prebiotics, fecal transplantation and antibiotics, and other interventions such as traditional Chinese medicine, COVID-19 vaccines, and ACE2-based treatments.
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Affiliation(s)
- Jiaqi Gang
- Department of Emergency, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Department of Oncology, Xiuwu County People’s Hospital, Jiaozuo, China
| | - Haiyu Wang
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiangsheng Xue
- Department of Oncology, Xiuwu County People’s Hospital, Jiaozuo, China
| | - Shu Zhang
- Department of Emergency, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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35
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Microbiota succession throughout life from the cradle to the grave. Nat Rev Microbiol 2022; 20:707-720. [PMID: 35906422 DOI: 10.1038/s41579-022-00768-z] [Citation(s) in RCA: 73] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2022] [Indexed: 11/08/2022]
Abstract
Associations between age and the human microbiota are robust and reproducible. The microbial composition at several body sites can predict human chronological age relatively accurately. Although it is largely unknown why specific microorganisms are more abundant at certain ages, human microbiota research has elucidated a series of microbial community transformations that occur between birth and death. In this Review, we explore microbial succession in the healthy human microbiota from the cradle to the grave. We discuss the stages from primary succession at birth, to disruptions by disease or antibiotic use, to microbial expansion at death. We address how these successions differ by body site and by domain (bacteria, fungi or viruses). We also review experimental tools that microbiota researchers use to conduct this work. Finally, we discuss future directions for studying the microbiota's relationship with age, including designing consistent, well-powered, longitudinal studies, performing robust statistical analyses and improving characterization of non-bacterial microorganisms.
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36
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Gargano F, Guerrera G, Piras E, Serafini B, Di Paola M, Rizzetto L, Buscarinu MC, Annibali V, Vuotto C, De Bardi M, D’Orso S, Ruggieri S, Gasperini C, Pavarini L, Ristori G, Picozza M, Rosicarelli B, Ballerini C, Mechelli R, Vitali F, Cavalieri D, Salvetti M, Angelini DF, Borsellino G, De Filippo C, Battistini L. Proinflammatory mucosal-associated invariant CD8+ T cells react to gut flora yeasts and infiltrate multiple sclerosis brain. Front Immunol 2022; 13:890298. [PMID: 35979352 PMCID: PMC9376942 DOI: 10.3389/fimmu.2022.890298] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 06/28/2022] [Indexed: 11/17/2022] Open
Abstract
The composition of the intestinal microbiota plays a critical role in shaping the immune system. Modern lifestyle, the inappropriate use of antibiotics, and exposure to pollution have significantly affected the composition of commensal microorganisms. The intestinal microbiota has been shown to sustain inappropriate autoimmune responses at distant sites in animal models of disease, and may also have a role in immune-mediated central nervous system (CNS) diseases such as multiple sclerosis (MS). We studied the composition of the gut mycobiota in fecal samples from 27 persons with MS (pwMS) and in 18 healthy donors (HD), including 5 pairs of homozygous twins discordant for MS. We found a tendency towards higher fungal abundance and richness in the MS group, and we observed that MS twins showed a higher rate of food-associated strains, such as Saccharomyces cerevisiae. We then found that in pwMS, a distinct population of cells with antibacterial and antifungal activity is expanded during the remitting phase and markedly decreases during clinically and/or radiologically active disease. These cells, named MAIT (mucosal-associated invariant T cells) lymphocytes, were significantly more activated in pwMS compared to HD in response to S. cerevisiae and Candida albicans strains isolated from fecal samples. This activation was also mediated by fungal-induced IL-23 secretion by innate immune cells. Finally, immunofluorescent stainings of MS post-mortem brain tissues from persons with the secondary progressive form of the disease showed that MAIT cells cross the blood–brain barrier (BBB) and produce pro-inflammatory cytokines in the brain. These results were in agreement with the hypothesis that dysbiosis of the gut microbiota might determine the inappropriate response of a subset of pathogenic mucosal T cells and favor the development of systemic inflammatory and autoimmune diseases.
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Affiliation(s)
- Francesca Gargano
- Neuroimmunology Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Santa Lucia Foundation, Rome, Italy
| | - Gisella Guerrera
- Neuroimmunology Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Santa Lucia Foundation, Rome, Italy
| | - Eleonora Piras
- Neuroimmunology Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Santa Lucia Foundation, Rome, Italy
| | - Barbara Serafini
- Istituto Superiore di Sanità, Department of Neuroscience, Rome, Italy
| | - Monica Di Paola
- University of Florence, Department of Biology, Florence, Italy
| | - Lisa Rizzetto
- Research and Innovation Centre – Fondazione Edmund Mach, S. Michele all’Adige (TN), Italy
| | - Maria Chiara Buscarinu
- Neurology and Centre for Experimental Neurological therapies (CENTERS), S. Andrea Hospital, Sapienza University, Rome, Italy
| | - Viviana Annibali
- Neurology and Centre for Experimental Neurological therapies (CENTERS), S. Andrea Hospital, Sapienza University, Rome, Italy
| | - Claudia Vuotto
- Neuroimmunology Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Santa Lucia Foundation, Rome, Italy
| | - Marco De Bardi
- Neuroimmunology Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Santa Lucia Foundation, Rome, Italy
| | - Silvia D’Orso
- Neuroimmunology Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Santa Lucia Foundation, Rome, Italy
| | - Serena Ruggieri
- Department of Neuroscience “Lancisi”, S. Camillo Hospital, Rome, Italy
| | - Claudio Gasperini
- Department of Neuroscience “Lancisi”, S. Camillo Hospital, Rome, Italy
| | - Lorenzo Pavarini
- Neuroimmunology Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Santa Lucia Foundation, Rome, Italy
- University of Florence, Department of Biology, Florence, Italy
| | - Giovanni Ristori
- Neuroimmunology Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Santa Lucia Foundation, Rome, Italy
- Neurology and Centre for Experimental Neurological therapies (CENTERS), S. Andrea Hospital, Sapienza University, Rome, Italy
| | - Mario Picozza
- Neuroimmunology Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Santa Lucia Foundation, Rome, Italy
| | | | - Clara Ballerini
- University of Florence, Clinical and Experimental Medicine, Florence, Italy
| | - Rosella Mechelli
- Neurology and Centre for Experimental Neurological therapies (CENTERS), S. Andrea Hospital, Sapienza University, Rome, Italy
| | - Francesco Vitali
- National Research Council, Institute of Agricultural Biology and Biotechnology, Pisa, Italy
| | | | - Marco Salvetti
- Neurology and Centre for Experimental Neurological therapies (CENTERS), S. Andrea Hospital, Sapienza University, Rome, Italy
| | - Daniela F. Angelini
- Neuroimmunology Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Santa Lucia Foundation, Rome, Italy
| | - Giovanna Borsellino
- Neuroimmunology Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Santa Lucia Foundation, Rome, Italy
- *Correspondence: Giovanna Borsellino, ; Luca Battistini,
| | - Carlotta De Filippo
- National Research Council, Institute of Agricultural Biology and Biotechnology, Pisa, Italy
| | - Luca Battistini
- Neuroimmunology Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Santa Lucia Foundation, Rome, Italy
- *Correspondence: Giovanna Borsellino, ; Luca Battistini,
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37
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Auchtung TA, Stewart CJ, Smith DP, Triplett EW, Agardh D, Hagopian WA, Ziegler AG, Rewers MJ, She JX, Toppari J, Lernmark Å, Akolkar B, Krischer JP, Vehik K, Auchtung JM, Ajami NJ, Petrosino JF. Temporal changes in gastrointestinal fungi and the risk of autoimmunity during early childhood: the TEDDY study. Nat Commun 2022; 13:3151. [PMID: 35672407 PMCID: PMC9174155 DOI: 10.1038/s41467-022-30686-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 05/09/2022] [Indexed: 12/11/2022] Open
Abstract
Fungal infections are a major health problem that often begin in the gastrointestinal tract. Gut microbe interactions in early childhood are critical for proper immune responses, yet there is little known about the development of the fungal population from infancy into childhood. Here, as part of the TEDDY (The Environmental Determinants of Diabetes in the Young) study, we examine stool samples of 888 children from 3 to 48 months and find considerable differences between fungi and bacteria. The metagenomic relative abundance of fungi was extremely low but increased while weaning from milk and formula. Overall fungal diversity remained constant over time, in contrast with the increase in bacterial diversity. Fungal profiles had high temporal variation, but there was less variation from month-to-month in an individual than among different children of the same age. Fungal composition varied with geography, diet, and the use of probiotics. Multiple Candida spp. were at higher relative abundance in children than adults, while Malassezia and certain food-associated fungi were lower in children. There were only subtle fungal differences associated with the subset of children that developed islet autoimmunity or type 1 diabetes. Having proper fungal exposures may be crucial for children to establish appropriate responses to fungi and limit the risk of infection: the data here suggests those gastrointestinal exposures are limited and variable.
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Grants
- U01 DK063821 NIDDK NIH HHS
- UC4 DK063863 NIDDK NIH HHS
- UL1 TR002535 NCATS NIH HHS
- U01 DK063790 NIDDK NIH HHS
- UL1 TR000064 NCATS NIH HHS
- HHSN267200700014C NLM NIH HHS
- U01 DK063836 NIDDK NIH HHS
- U01 DK063829 NIDDK NIH HHS
- U01 DK063865 NIDDK NIH HHS
- UC4 DK095300 NIDDK NIH HHS
- UC4 DK063861 NIDDK NIH HHS
- UC4 DK063829 NIDDK NIH HHS
- UC4 DK063821 NIDDK NIH HHS
- UC4 DK117483 NIDDK NIH HHS
- UC4 DK063836 NIDDK NIH HHS
- UC4 DK112243 NIDDK NIH HHS
- U01 DK124166 NIDDK NIH HHS
- U01 DK063861 NIDDK NIH HHS
- P30 ES030285 NIEHS NIH HHS
- U01 DK128847 NIDDK NIH HHS
- UC4 DK063865 NIDDK NIH HHS
- U01 DK063863 NIDDK NIH HHS
- UC4 DK106955 NIDDK NIH HHS
- UC4 DK100238 NIDDK NIH HHS
- This research was performed on behalf of the TEDDY Study Group, which is funded by U01 DK63829, U01 DK63861, U01 DK63821, U01 DK63865, U01 DK63863, U01 DK63836, U01 DK63790, UC4 DK63829, UC4 DK63861, UC4 DK63821, UC4 DK63865, UC4 DK63863, UC4 DK63836, UC4 DK95300, UC4 DK100238, UC4 DK106955, UC4 DK112243, UC4 DK117483, U01 DK124166, U01 DK128847, and Contract No. HHSN267200700014C from the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institute of Allergy and Infectious Diseases (NIAID), Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institute of Environmental Health Sciences (NIEHS), Centers for Disease Control and Prevention (CDC), and JDRF. This work is supported in part by the NIH/NCATS Clinical and Translational Science Awards to the University of Florida (UL1 TR000064) and the University of Colorado (UL1 TR002535).
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Affiliation(s)
- Thomas A Auchtung
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA.
| | - Christopher J Stewart
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Daniel P Smith
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Eric W Triplett
- Microbiology and Cell Science Department, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| | - Daniel Agardh
- Department of Clinical Sciences, Lund University Clinical Research Center, Skåne University Hospital, Malmö, Sweden
| | | | - Anette G Ziegler
- Institute of Diabetes Research, Helmholtz Zentrum München, Munich, Germany
- Forschergruppe Diabetes, Technische Universität München, Klinikum Rechts der Isar, Munich, Germany
- Forschergruppe Diabetes e.V. at Helmholtz Zentrum München, Munich, Germany
| | - Marian J Rewers
- Barbara Davis Center for Childhood Diabetes, University of Colorado, Aurora, CO, USA
| | - Jin-Xiong She
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, Augusta, GA, USA
- Jinfiniti Precision Medicine, Inc, Augusta, GA, USA
| | - Jorma Toppari
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, University of Turku, Turku, Finland
- Department of Pediatrics, Turku University Hospital, Turku, Finland
| | - Åke Lernmark
- Department of Clinical Sciences, Lund University/CRC, Skane University Hospital, Malmö, Sweden
| | - Beena Akolkar
- National Institute of Diabetes & Digestive & Kidney Diseases, Bethesda, MD, USA
| | - Jeffrey P Krischer
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Kendra Vehik
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Jennifer M Auchtung
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Nadim J Ajami
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Program for Innovative Microbiome and Translational Research, Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 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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38
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Mycobiota composition and changes across pregnancy in patients with gestational diabetes mellitus (GDM). Sci Rep 2022; 12:9192. [PMID: 35654937 PMCID: PMC9163055 DOI: 10.1038/s41598-022-13438-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 05/12/2022] [Indexed: 01/09/2023] Open
Abstract
The gut mycobiota has never been studied either during pregnancy or in patients with gestational diabetes (GDM). This study aimed to analyze the fecal mycobiota of GDM patients during the second (T2) and third (T3) trimester of pregnancy and to compare it with the mycobiota of pregnant normoglycemic women (controls). Forty-one GDM patients and 121 normoglycemic women were studied. GDM mycobiota was composed almost exclusively by the Ascomycota phylum; Basidiomicota accounted for 43% of the relative frequency of the controls. Kluyveromyces (p < 0.001), Metschnikowia (p < 0.001), and Pichia (p < 0.001) showed a significantly higher frequency in GDM patients, while Saccharomyces (p = 0.019), were more prevalent in controls. From T2 to T3, a reduction in fungal alpha diversity was found in GDM patients, with an increase of the relative frequency of Candida, and the reduction of some pro-inflammatory taxa. Many associations between fungi and foods and nutrients were detected. Finally, several fungi and bacteria showed competition or co-occurrence. Patients with GDM showed a predominance of fungal taxa with potential inflammatory effects when compared to normoglycemic pregnant women, with a marked shift in their mycobiota during pregnancy, and complex bacteria-fungi interactions.
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Reinold J, Farahpour F, Schoerding AK, Fehring C, Dolff S, Konik M, Korth J, van Baal L, Buer J, Witzke O, Westendorf AM, Kehrmann J. The Fungal Gut Microbiome Exhibits Reduced Diversity and Increased Relative Abundance of Ascomycota in Severe COVID-19 Illness and Distinct Interconnected Communities in SARS-CoV-2 Positive Patients. Front Cell Infect Microbiol 2022; 12:848650. [PMID: 35521219 PMCID: PMC9062042 DOI: 10.3389/fcimb.2022.848650] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 03/25/2022] [Indexed: 12/31/2022] Open
Abstract
Clinical and experimental studies indicate that the bacterial and fungal gut microbiota modulates immune responses in distant organs including the lungs. Immune dysregulation is associated with severe SARS-CoV-2 infection, and several groups have observed gut bacterial dysbiosis in SARS-CoV-2 infected patients, while the fungal gut microbiota remains poorly defined in these patients. We analyzed the fungal gut microbiome from rectal swabs taken prior to anti-infective treatment in 30 SARS-CoV-2 positive (21 non-severe COVID-19 and 9 developing severe/critical COVID-19 patients) and 23 SARS-CoV-2 negative patients by ITS2-sequencing. Pronounced but distinct interconnected fungal communities distinguished SARS-CoV-2 positive and negative patients. Fungal gut microbiota in severe/critical COVID-19 illness was characterized by a reduced diversity, richness and evenness and by an increase of the relative abundance of the Ascomycota phylum compared with non-severe COVID-19 illness. A dominance of a single fungal species with a relative abundance of >75% was a frequent feature in severe/critical COVID-19. The dominating fungal species were highly variable between patients even within the groups. Several fungal taxa were depleted in patients with severe/critical COVID-19.The distinct compositional changes of the fungal gut microbiome in SARS-CoV-2 infection, especially in severe COVID-19 illness, illuminate the necessity of a broader approach to investigate whether the differences in the fungal gut microbiome are consequences of SARS-CoV-2 infection or a predisposing factor for critical illness.
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Affiliation(s)
- Johanna Reinold
- Department of Infectious Diseases, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Farnoush Farahpour
- Bioinformatics and Computational Biophysics, University of Duisburg-Essen, Essen, Germany
| | - Ann-Kathrin Schoerding
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Christian Fehring
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Sebastian Dolff
- Department of Infectious Diseases, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Margarethe Konik
- Department of Infectious Diseases, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Johannes Korth
- Department of Nephrology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Lukas van Baal
- Department of Endocrinology, Diabetes and Metabolism, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Jan Buer
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Oliver Witzke
- Department of Infectious Diseases, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Astrid M. Westendorf
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Jan Kehrmann
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
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40
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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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41
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Gutierrez MW, van Tilburg Bernardes E, Changirwa D, McDonald B, Arrieta MC. "Molding" immunity-modulation of mucosal and systemic immunity by the intestinal mycobiome in health and disease. Mucosal Immunol 2022; 15:573-583. [PMID: 35474360 DOI: 10.1038/s41385-022-00515-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/24/2022] [Accepted: 04/04/2022] [Indexed: 02/04/2023]
Abstract
Fungi are important yet understudied contributors to the microbial communities of the gastrointestinal tract. Starting at birth, the intestinal mycobiome undergoes a period of dynamic maturation under the influence of microbial, host, and extrinsic influences, with profound functional implications for immune development in early life, and regulation of immune homeostasis throughout life. Candida albicans serves as a model organism for understanding the cross-talk between fungal colonization dynamics and immunity, and exemplifies unique mechanisms of fungal-immune interactions, including fungal dimorphism, though our understanding of other intestinal fungi is growing. Given the prominent role of the gut mycobiome in promoting immune homeostasis, emerging evidence points to fungal dysbiosis as an influential contributor to immune dysregulation in a variety of inflammatory and infectious diseases. Here we review current knowledge on the factors that govern host-fungi interactions in the intestinal tract and immunological outcomes in both mucosal and systemic compartments.
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Affiliation(s)
- Mackenzie W Gutierrez
- Immunology Research Group, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada.,Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,International Microbiome Centre, University of Calgary, Calgary, AB, Canada
| | - Erik van Tilburg Bernardes
- Immunology Research Group, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada.,Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,International Microbiome Centre, University of Calgary, Calgary, AB, Canada
| | - Diana Changirwa
- Immunology Research Group, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,International Microbiome Centre, University of Calgary, Calgary, AB, Canada.,Department of Critical Care Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Braedon McDonald
- Immunology Research Group, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,International Microbiome Centre, University of Calgary, Calgary, AB, Canada.,Department of Critical Care Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Marie-Claire Arrieta
- Immunology Research Group, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada. .,Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada. .,Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada. .,International Microbiome Centre, University of Calgary, Calgary, AB, Canada.
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42
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Reynoso-García J, Narganes-Storde Y, Santiago-Rodriguez TM, Toranzos GA. Mycobiome-Host Coevolution? The Mycobiome of Ancestral Human Populations Seems to Be Different and Less Diverse Than Those of Extant Native and Urban-Industrialized Populations. Microorganisms 2022; 10:microorganisms10020459. [PMID: 35208912 PMCID: PMC8877467 DOI: 10.3390/microorganisms10020459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/24/2021] [Accepted: 12/07/2021] [Indexed: 02/06/2023] Open
Abstract
Few data exist on the human gut mycobiome in relation to lifestyle, ethnicity, and dietary habits. To understand the effect of these factors on the structure of the human gut mycobiome, we analyzed sequences belonging to two extinct pre-Columbian cultures inhabiting Puerto Rico (the Huecoid and Saladoid) and compared them to coprolite samples found in Mexico and Ötzi, the Iceman’s large intestine. Stool mycobiome samples from extant populations in Peru and urban cultures from the United States were also included. The ancient Puerto Rican cultures exhibited a lower fungal diversity in comparison to the extant populations. Dissimilarity distances showed that the Huecoid gut mycobiome resembled that from ancient Mexico. Fungal genera including Aspergillus spp., Penicillium spp., Rasamsonia spp., Byssochlamys spp., Talaromyces spp., Blastomyces spp., Monascus spp., and Penicilliopsis spp. were differentially abundant in the ancient and extant populations. Despite cultural differences, certain fungal taxa were present in all samples. These results suggest that culture and diet may impact the gut mycobiome and emphasize that modern lifestyles could be associated with the alteration of gut mycobiome diversity. The present study presents data on ancient and extant human gut mycobiomes in terms of lifestyle, ethnicity, and diet in the Americas.
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Affiliation(s)
- Jelissa Reynoso-García
- Environmental Microbiology Laboratory, Biology Department, University of Puerto Rico, San Juan 00931, Puerto Rico;
- Correspondence:
| | - Yvonne Narganes-Storde
- Center for Archaeological Research, Río Piedras Campus, University of Puerto Rico, San Juan 00931, Puerto Rico;
| | | | - Gary A. Toranzos
- Environmental Microbiology Laboratory, Biology Department, University of Puerto Rico, San Juan 00931, Puerto Rico;
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43
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Guzzo GL, Andrews JM, Weyrich LS. The Neglected Gut Microbiome: Fungi, Protozoa, and Bacteriophages in Inflammatory Bowel Disease. Inflamm Bowel Dis 2022; 28:1112-1122. [PMID: 35092426 PMCID: PMC9247841 DOI: 10.1093/ibd/izab343] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Indexed: 12/14/2022]
Abstract
The gut microbiome has been implicated in the pathogenesis of inflammatory bowel disease (IBD). Studies suggest that the IBD gut microbiome is less diverse than that of the unaffected population, a phenomenon often referred to as dysbiosis. However, these studies have heavily focused on bacteria, while other intestinal microorganisms-fungi, protozoa, and bacteriophages-have been neglected. Of the nonbacterial microbes that have been studied in relation to IBD, most are thought to be pathogens, although there is evidence that some of these species may instead be harmless commensals. In this review, we discuss the nonbacterial gut microbiome of IBD, highlighting the current biases, limitations, and outstanding questions that can be addressed with high-throughput DNA sequencing methods. Further, we highlight the importance of studying nonbacterial microorganisms alongside bacteria for a comprehensive view of the whole IBD biome and to provide a more precise definition of dysbiosis in patients. With the rise in popularity of microbiome-altering therapies for the treatment of IBD, such as fecal microbiota transplantation, it is important that we address these knowledge gaps to ensure safe and effective treatment of patients.
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Affiliation(s)
- Gina L Guzzo
- Address correspondence to: Gina L. Guzzo, The University of Adelaide, Adelaide, South Australia, Australia ()
| | - Jane M Andrews
- Inflammatory Bowel Disease Service, Department of Gastroenterology and Hepatology, Royal Adelaide Hospital and School of Medicine, Faculty of Health Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Laura S Weyrich
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia,Department of Anthropology and Huck Institutes of the Life Sciences, Pennsylvania State University, State College, PA, USA
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44
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Henderickx JGE, de Weerd H, Groot Jebbink LJ, van Zoeren-Grobben D, Hemels MAC, van Lingen RA, Knol J, Belzer C. The first fungi: mode of delivery determines early life fungal colonization in the intestine of preterm infants. MICROBIOME RESEARCH REPORTS 2022; 1:7. [PMID: 38089064 PMCID: PMC10714301 DOI: 10.20517/mrr.2021.03] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/06/2021] [Accepted: 01/15/2022] [Indexed: 06/26/2024]
Abstract
Aim: The role of intestinal fungi in human health and disease is becoming more evident. The mycobiota composition and diversity of preterm infants is affected by interactions with bacteria and clinical variables. In this study, we aimed to characterize the composition and the diversity of the preterm infant mycobiota and the effect of clinical variables on it in the first six postnatal weeks. Methods: Preterm infants (n = 50) and full-term infants (n = 6) admitted to Isala Women and Children's hospital (Zwolle, The Netherlands) who were born during 24-36 or 37-40 weeks of gestation, respectively, were included in this study. Feces were collected during the first six postnatal weeks (n = 109) and their mycobiota composition and diversity were characterized by ITS2 amplicon sequencing. Results: Composition analyses identified fungi and other eukaryotic kingdoms, of which Viridiplantae was most abundant. Of the fungal kingdom, Ascomycota and Basidiomycota were the first and second most prominent phyla in early life of all infants. Candida was the most abundant genus in the first six weeks of life and increased with gestational and postnatal age. Fungal phylogenetic diversity remained stable in the first six postnatal weeks. The individuality and the mode of delivery were identified as significant predictors for the variation in the mycobiota composition. Vaginally delivered infants were enriched in Candida spp., whereas infants delivered through emergency C-section were characterized by Malassezia spp. Conclusion: These results indicate that fungi and other eukaryotic kingdoms are detected in the intestine of preterm and full-term infants in the first six postnatal weeks. Similar to the microbiota, colonization of the preterm intestine with fungi is determined by clinical variables including individuality and mode of delivery.
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Affiliation(s)
- Jannie G. E. Henderickx
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, Wageningen 6708 WE, The Netherlands
| | - Heleen de Weerd
- Danone Nutricia Research, Uppsalalaan 12, Utrecht 3584 CT, The Netherlands
| | - Liesbeth J. Groot Jebbink
- Isala Women and Children’s Hospital, Department of Neonatology, Dokter van Heesweg 2, Zwolle 8025 AB, The Netherlands
| | - Diny van Zoeren-Grobben
- Isala Women and Children’s Hospital, Department of Neonatology, Dokter van Heesweg 2, Zwolle 8025 AB, The Netherlands
| | - Marieke A. C. Hemels
- Isala Women and Children’s Hospital, Department of Neonatology, Dokter van Heesweg 2, Zwolle 8025 AB, The Netherlands
| | - Richard A. van Lingen
- Isala Women and Children’s Hospital, Department of Neonatology, Dokter van Heesweg 2, Zwolle 8025 AB, The Netherlands
| | - Jan Knol
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, Wageningen 6708 WE, The Netherlands
- Danone Nutricia Research, Uppsalalaan 12, Utrecht 3584 CT, The Netherlands
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, Wageningen 6708 WE, The Netherlands
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45
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George S, Aguilera X, Gallardo P, Farfán M, Lucero Y, Torres JP, Vidal R, O'Ryan M. Bacterial Gut Microbiota and Infections During Early Childhood. Front Microbiol 2022; 12:793050. [PMID: 35069488 PMCID: PMC8767011 DOI: 10.3389/fmicb.2021.793050] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 12/10/2021] [Indexed: 12/12/2022] Open
Abstract
Gut microbiota composition during the first years of life is variable, dynamic and influenced by both prenatal and postnatal factors, such as maternal antibiotics administered during labor, delivery mode, maternal diet, breastfeeding, and/or antibiotic consumption during infancy. Furthermore, the microbiota displays bidirectional interactions with infectious agents, either through direct microbiota-microorganism interactions or indirectly through various stimuli of the host immune system. Here we review these interactions during childhood until 5 years of life, focusing on bacterial microbiota, the most common gastrointestinal and respiratory infections and two well characterized gastrointestinal diseases related to dysbiosis (necrotizing enterocolitis and Clostridioides difficile infection). To date, most peer-reviewed studies on the bacterial microbiota in childhood have been cross-sectional and have reported patterns of gut dysbiosis during infections as compared to healthy controls; prospective studies suggest that most children progressively return to a "healthy microbiota status" following infection. Animal models and/or studies focusing on specific preventive and therapeutic interventions, such as probiotic administration and fecal transplantation, support the role of the bacterial gut microbiota in modulating both enteric and respiratory infections. A more in depth understanding of the mechanisms involved in the establishment and maintenance of the early bacterial microbiota, focusing on specific components of the microbiota-immunity-infectious agent axis is necessary in order to better define potential preventive or therapeutic tools against significant infections in children.
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Affiliation(s)
- Sergio George
- Host-Pathogen Interaction Laboratory, Microbiology and Mycology Program, ICBM, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Ximena Aguilera
- School of Medicine, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Pablo Gallardo
- Department of Pediatrics and Pediatric Surgery, Dr. Luis Calvo Mackenna Hospital, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Mauricio Farfán
- Department of Pediatrics and Pediatric Surgery, Dr. Luis Calvo Mackenna Hospital, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Yalda Lucero
- Host-Pathogen Interaction Laboratory, Microbiology and Mycology Program, ICBM, Faculty of Medicine, University of Chile, Santiago, Chile.,Department of Pediatrics and Pediatric Surgery, Dr. Roberto del Río Hospital, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Juan Pablo Torres
- Host-Pathogen Interaction Laboratory, Microbiology and Mycology Program, ICBM, Faculty of Medicine, University of Chile, Santiago, Chile.,Department of Pediatrics and Pediatric Surgery, Dr. Luis Calvo Mackenna Hospital, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Roberto Vidal
- Microbiology and Mycology Program, ICBM, Faculty of Medicine, University of Chile, Santiago, Chile.,Millennium Institute on Immunology and Immunotherapy, Faculty of Medicine, University of Chile, Santiago, Chile.,ANID - Millennium Science Initiative Program - Millennium Nucleus in the Biology of Intestinal Microbiota, Santiago, Chile
| | - Miguel O'Ryan
- Host-Pathogen Interaction Laboratory, Microbiology and Mycology Program, ICBM, Faculty of Medicine, University of Chile, Santiago, Chile.,Millennium Institute on Immunology and Immunotherapy, Faculty of Medicine, University of Chile, Santiago, Chile
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46
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Phuna ZX, Madhavan P. A CLOSER LOOK AT THE MYCOBIOME IN ALZHEIMER'S DISEASE: FUNGAL SPECIES, PATHOGENESIS AND TRANSMISSION. Eur J Neurosci 2022; 55:1291-1321. [DOI: 10.1111/ejn.15599] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Zhi Xin Phuna
- School of Medicine, Faculty of Health & Medical Sciences, Taylor’s University Malaysia Subang Jaya Selangor
| | - Priya Madhavan
- School of Medicine, Faculty of Health & Medical Sciences, Taylor’s University Malaysia Subang Jaya Selangor
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Fungal allergic sensitisation in young rural Zimbabwean children: Gut mycobiome and seroreactivity characteristics. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 2:100082. [PMID: 35028627 PMCID: PMC8714770 DOI: 10.1016/j.crmicr.2021.100082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 11/09/2021] [Accepted: 11/12/2021] [Indexed: 11/20/2022] Open
Abstract
Background The prevalence of allergic diseases has increased over the last few decades, with sensitisation to fungal allergens and gut microbiome dysbiosis implicated in this trend. The fungal community in the gut (mycobiome) has yet to be characterised and related to fungal allergic sensitisation. Thus, we characterised the gut mycobiome and related it to fungal sensitisation and seroreactivity among Zimbabwean children. We further determined the effect of host age, sex, Schistosoma haematobium infection and mycobiome composition on fungal sensitisation and seroreactivity. Methods Using shotgun metagenomic sequencing, we characterised the gut microbiome of stool samples of 116 preschool aged children (PSAC) (≤5 years old, 57(49.1%) male and 59 (50.9%) female). Sensitisation to common fungi in Zimbabwe was assessed using skin prick tests (SPTs). Allergen-specific IgM, IgA, IgG, IgE and IgG4 antibodies were quantified by ELISA. We analysed the relationship between fungal genera and SPT reactivity by ANOVA; fungal genera and IgE antibody reactivity by linear regression; variation in mycobiome abundance with host and environmental factors by PERMANOVA; SPT reactivity and host and environmental factors by logistic regression; seroreactivity and host and environmental factors by ANOVA. Results The mycobiome formed <1% of the sequenced gut microbiome and 228 fungal genera were identified. The most abundant genera detected were Protomyces, Taphrina, and Aspergillus. S.haematobium infection had a significant effect on fungal genera. Prevalence of SPT sensitisation to ≥1 fungal species was 96%, and individuals were frequently sensitised to Saccharomyces cerevisiae. Antibodies were detected in 100% of the population. There was no relationship between mycobiome abundance and IgE titres or IgE/IgG4 ratios for each fungal species; no significant differences between SPT reactivity and abundance of fungal species except for S. cerevisiae; and fungal seroreactivity did not significantly differ with age. There were some sex (m>f for, Epicoccum nigrum and Penicillium chrysogenum) and SPT reactivity -related differences in seroreactivity. Conclusion This is the first comprehensive characterisation of gut mycobiome and fungal allergic sensitisation of rural children in Zimbabwe. Although reported allergic disease is low there is a high percentage of sensitisation. Further studies with larger populations are required to understand the role of the mycobiome in allergic diseases.
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Analyzing the human gut mycobiome – a short guide for beginners. Comput Struct Biotechnol J 2022; 20:608-614. [PMID: 35116136 PMCID: PMC8790610 DOI: 10.1016/j.csbj.2022.01.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 01/04/2022] [Accepted: 01/08/2022] [Indexed: 12/30/2022] Open
Abstract
The human body is a dynamic ecosystem consisting of millions of microbes which are often comprised under the term microbiome. Compared to bacteria, which count for the overwhelming majority of the microbiome, the number of human-associated fungi is small and often underestimated. Nonetheless, they can be found in different host niches such as the gut, the oral cavity and the skin. The fungal community has several potential roles in health and disease of the human host. In this review we will focus on intestinal fungi and their interaction with the host as well as bacteria. We also summarize technical challenges and possible biases researchers must be aware of when conducting mycobiome analysis.
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Begum N, Harzandi A, Lee S, Uhlen M, Moyes DL, Shoaie S. Host-mycobiome metabolic interactions in health and disease. Gut Microbes 2022; 14:2121576. [PMID: 36151873 PMCID: PMC9519009 DOI: 10.1080/19490976.2022.2121576] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/31/2022] [Accepted: 08/31/2022] [Indexed: 02/04/2023] Open
Abstract
Fungal communities (mycobiome) have an important role in sustaining the resilience of complex microbial communities and maintenance of homeostasis. The mycobiome remains relatively unexplored compared to the bacteriome despite increasing evidence highlighting their contribution to host-microbiome interactions in health and disease. Despite being a small proportion of the total species, fungi constitute a large proportion of the biomass within the human microbiome and thus serve as a potential target for metabolic reprogramming in pathogenesis and disease mechanism. Metabolites produced by fungi shape host niches, induce immune tolerance and changes in their levels prelude changes associated with metabolic diseases and cancer. Given the complexity of microbial interactions, studying the metabolic interplay of the mycobiome with both host and microbiome is a demanding but crucial task. However, genome-scale modelling and synthetic biology can provide an integrative platform that allows elucidation of the multifaceted interactions between mycobiome, microbiome and host. The inferences gained from understanding mycobiome interplay with other organisms can delineate the key role of the mycobiome in pathophysiology and reveal its role in human disease.
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Affiliation(s)
- Neelu Begum
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, London, UK
| | - Azadeh Harzandi
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, London, UK
| | - Sunjae Lee
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, London, UK
| | - Mathias Uhlen
- Science for Life Laboratory, KTH–Royal Institute of Technology, Stockholm, Sweden
| | - David L. Moyes
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, London, UK
| | - Saeed Shoaie
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, London, UK
- Science for Life Laboratory, KTH–Royal Institute of Technology, Stockholm, Sweden
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Yalcin SS, Aksu T, Kuskonmaz B, Ozbek NY, Pérez-Brocal V, Celik M, Uckan Cetinkaya D, Moya A, Dinleyici EC. Intestinal mycobiota composition and changes in children with thalassemia who underwent allogeneic hematopoietic stem cell transplantation. Pediatr Blood Cancer 2022; 69:e29411. [PMID: 34699120 DOI: 10.1002/pbc.29411] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/03/2021] [Accepted: 09/27/2021] [Indexed: 12/16/2022]
Abstract
BACKGROUND Allogeneic hematopoietic stem cell transplantation (HSCT) alters the diversity of the intestinal bacterial microbiota. This study aimed to evaluate human mycobiota composition pre-HSCT and post-HSCT in children with thalassemia. METHOD Ten children with thalassemia undergoing allogeneic HSCT were enrolled. The stool samples were collected before the transplantation regimen, before the transplant day, and +15, +30 days, and three months after transplantation. Stool samples were also collected from the donor and the patient's caregivers. Gut mycobiota composition was evaluated with metagenomic analysis. RESULTS Pretransplant mycobiota of children with thalassemia (the predominant genus was Saccharomyces, 64.1%) has been shown to approximate the diverse mycobiota compositions of healthy adult donors but becomes altered (lower diversity) following transplant procedures. Three months after HSCT, phyla Ascomycota and Basidiomycota were 83.4% and 15.6%, respectively. The predominant species were Saccaharomyces_uc and Saccharomyces cerevisiae (phylum Ascomycota); we also observed Malassezia restricta and Malassezia globosa (phylum Basidiomycota) (∼13%). On day 90 after HSCT, we observed 65.3% M. restricta and 18.4% M. globosa predominance at the species level in a four-year-old boy with acute graft-versus-host disease (GVHD) (skin and gut involvement) 19 days after transplantation included. CONCLUSION The mycobiota composition of children with thalassemia altered after HSCT. We observed Malassezia predominance in a child with GVHD. Further studies in children with GVHD will identify this situation.
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Affiliation(s)
- Siddika Songul Yalcin
- Department of Social Pediatrics, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Tekin Aksu
- Department of Pediatric Hematology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Baris Kuskonmaz
- Department of Pediatric Hematology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Namık Yasar Ozbek
- Ankara City Hospital, Department of Pediatric Hematology, Health Science University Faculty of Medicine, Ankara, Turkey
| | - Vicente Pérez-Brocal
- Area of Genomics and Health, Foundation for the Promotion of Sanitary and Biomedical Research of Valencia Region (FISABIO-Public Health), Valencia, Spain.,CIBER in Epidemiology and Public Health (CIBEResp), Madrid, Spain
| | - Melda Celik
- Department of Social Pediatrics, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Duygu Uckan Cetinkaya
- Department of Pediatric Hematology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Andrés Moya
- Area of Genomics and Health, Foundation for the Promotion of Sanitary and Biomedical Research of Valencia Region (FISABIO-Public Health), Valencia, Spain.,CIBER in Epidemiology and Public Health (CIBEResp), Madrid, Spain.,Institute for Integrative Systems Biology (I2SysBio), University of Valencia and Spanish National Research Council (CSIC), Valencia, Spain
| | - Ener Cagri Dinleyici
- Department of Pediatrics, Eskisehir Osmangazi University Faculty of Medicine, Eskisehir, Turkey
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