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Gerrick ER, DeSchepper LB, Mechler CM, Joubert LM, Dunker F, Colston TJ, Howitt MR. Commensal protists in reptiles display flexible host range and adaptation to ectothermic hosts. mBio 2023; 14:e0227323. [PMID: 37962346 PMCID: PMC10746265 DOI: 10.1128/mbio.02273-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 10/04/2023] [Indexed: 11/15/2023] Open
Abstract
IMPORTANCE Environmental factors like climate change and captive breeding can impact the gut microbiota and host health. Therefore, conservation efforts for threatened species may benefit from understanding how these factors influence animal microbiomes. Parabasalid protists are members of the mammalian microbiota that can modulate the immune system and impact susceptibility to infections. However, little is known about parabasalids in reptiles. Here, we profile reptile-associated parabasalids in wild and captive reptiles and find that captivity has minimal impact on parabasalid prevalence or diversity. However, because reptiles are cold-blooded (ectothermic), their microbiotas experience wider temperature fluctuation than microbes in warm-blooded animals. To investigate whether extreme weather patterns affect parabasalid-host interactions, we analyzed the gene expression in reptile-associated parabasalids and found that temperature differences significantly alter genes associated with host health. These results expand our understanding of parabasalids in this vulnerable vertebrate group and highlight important factors to be taken into consideration for conservation efforts.
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Affiliation(s)
- Elias R. Gerrick
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Leila B. DeSchepper
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Claire M. Mechler
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Lydia-Marie Joubert
- Cell Sciences Imaging Facility (CSIF), Stanford University, Stanford, California, USA
| | - Freeland Dunker
- Steinhart Aquarium, California Academy of Sciences, San Francisco, California, USA
| | | | - Michael R. Howitt
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
- Department of Microbiology, Stanford University School of Medicine, Stanford, California, USA
- Program in Immunology, Stanford University School of Medicine, Stanford, California, USA
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2
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Renzi S, Nenciarini S, Bacci G, Cavalieri D. Yeast metagenomics: analytical challenges in the analysis of the eukaryotic microbiome. Microbiome Res Rep 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] [What about the content of this article? (0)] [Affiliation(s)] [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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3
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Markussen Bjorbaekmo MF, Brodie J, Krabberød AK, Logares R, Fuss J, Fredriksen S, Wold-Dobbe A, Shalchian-Tabrizi K, Bass D. 18S rDNA gene metabarcoding of microeukaryotes and epi-endophytes in the holobiome of seven species of large brown algae. J Phycol 2023; 59:859-878. [PMID: 37726938 DOI: 10.1111/jpy.13377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 06/29/2023] [Accepted: 06/29/2023] [Indexed: 09/21/2023]
Abstract
Brown algae (Phaeophyceae) are habitat-forming species in coastal ecosystems and include kelp forests and seaweed beds that support a wide diversity of marine life. Host-associated microbial communities are an integral part of phaeophyte biology, and whereas the bacterial microbial partners have received considerable attention, the microbial eukaryotes associated with brown algae have hardly been studied. Here, we used broadly targeted "pan-eukaryotic" primers (metabarcoding) to investigate brown algal-associated eukaryotes (the eukaryome). Using this approach, we aimed to investigate the eukaryome of seven large brown algae that are important and common species in coastal ecosystems. We also aimed to assess whether these macroalgae harbor novel eukaryotic diversity and to ascribe putative functional roles to the host-associated eukaryome based on taxonomic affiliation and phylogenetic placement. We detected a significant diversity of microeukaryotic and algal lineages associated with the brown algal species investigated. The operational taxonomic units (OTUs) were taxonomically assigned to 10 of the eukaryotic major supergroups, including taxonomic groups known to be associated with seaweeds as epibionts, endobionts, parasites, and commensals. Additionally, we revealed previously unrecorded sequence types, including novel phaeophyte OTUs, particularly in the Fucus spp. samples, that may represent fucoid genomic variants, sequencing artifacts, or undescribed epi-/endophytes. Our results provide baseline data and technical insights that will be useful for more comprehensive seaweed eukaryome studies investigating the evidently lineage-rich and functionally diverse symbionts of brown algae.
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Affiliation(s)
- Marit F Markussen Bjorbaekmo
- Norwegian Institute for Water Research (NIVA), Section for Marine Biology, Oslo, Norway
- Natural History Museum (NHM), Science, London, UK
- Department of Biosciences, Section for Genetics and Evolutionary Biology (EVOGENE) and Centre for Integrative Microbial Evolution (CIME), University of Oslo, Oslo, Norway
| | | | - Anders K Krabberød
- Department of Biosciences, Section for Genetics and Evolutionary Biology (EVOGENE) and Centre for Integrative Microbial Evolution (CIME), University of Oslo, Oslo, Norway
| | - Ramiro Logares
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Catalonia, Spain
| | - Janina Fuss
- Department of Biosciences, Section for Genetics and Evolutionary Biology (EVOGENE) and Centre for Integrative Microbial Evolution (CIME), University of Oslo, Oslo, Norway
| | - Stein Fredriksen
- Department of Biosciences, Section for Aquatic Biology and Toxicology (AQUA), University of Oslo, Oslo, Norway
| | - Anders Wold-Dobbe
- Department of Biosciences, Section for Genetics and Evolutionary Biology (EVOGENE) and Centre for Integrative Microbial Evolution (CIME), University of Oslo, Oslo, Norway
| | - Kamran Shalchian-Tabrizi
- Department of Biosciences, Section for Genetics and Evolutionary Biology (EVOGENE) and Centre for Integrative Microbial Evolution (CIME), University of Oslo, Oslo, Norway
| | - David Bass
- Natural History Museum (NHM), Science, London, UK
- Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Dorset, UK
- Sustainable Aquaculture Futures, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
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4
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Godny L, Reshef L, Sharar Fischler T, Elial-Fatal S, Pfeffer-Gik T, Raykhel B, Rabinowitz K, Levi-Barda A, Perets TT, Barkan R, Goren I, Ollech JE, Yanai H, Gophna U, Dotan I. Increasing adherence to the Mediterranean diet and lifestyle is associated with reduced fecal calprotectin and intra-individual changes in microbial composition of healthy subjects. Gut Microbes 2022; 14:2120749. [PMID: 36226673 PMCID: PMC9578447 DOI: 10.1080/19490976.2022.2120749] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The Mediterranean diet (MED) is associated with the modification of gut microbial composition. In this pilot study, we investigate the feasibility of a microbiota-targeted MED-based lifestyle intervention in healthy subjects. MED intervention integrating dietary counseling, a supporting mobile application, and daily physical activity measurement using step trackers was prospectively applied for 4 weeks. Blood and fecal samples were collected at baseline, after the 4-week intervention, and at 6 and 12 months. Blood counts, inflammatory markers, microbial and eukaryotic composition were analyzed. Dietary adherence was assessed using daily questionnaires. All 20 healthy participants (females 65%, median age 37), completed the 4-week intervention. Adherence to MED increased from 15.6 ± 4.1 (baseline) to 23.2 ± 3.6 points (4 weeks), p < .01, reflected by increased dietary fiber and decreased saturated fat intake (both p < .05). MED intervention modestly reduced fecal calprotectin, white blood cell, neutrophil, and lymphocyte counts, within the normal ranges (P < .05). Levels of butyrate producers including Faecalibacterium and Lachnospira were positively correlated with adherence to MED and the number of daily steps. Bacterial composition was associated with plant-based food intake, while fungal composition with animal-based food as well as olive oil and sweets. Increasing adherence to MED correlated with increased absolute abundances of multiple beneficial gut symbionts. Therefore, increasing adherence to MED is associated with reduction of fecal calprotectin and beneficial microbial alterations in healthy subjects. Microbiota targeted lifestyle interventions may be used to modify the intestinal ecosystem with potential implications for microbiome-mediated diseases.
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Affiliation(s)
- L. Godny
- Division of Gastroenterology, Rabin Medical Center, Petah-Tikva, Israel, Affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - L. Reshef
- The Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - T. Sharar Fischler
- Division of Gastroenterology, Rabin Medical Center, Petah-Tikva, Israel, Affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - S. Elial-Fatal
- Division of Gastroenterology, Rabin Medical Center, Petah-Tikva, Israel, Affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - T. Pfeffer-Gik
- Division of Gastroenterology, Rabin Medical Center, Petah-Tikva, Israel, Affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - B. Raykhel
- Division of Gastroenterology, Rabin Medical Center, Petah-Tikva, Israel, Affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - K. Rabinowitz
- Division of Gastroenterology, Rabin Medical Center, Petah-Tikva, Israel, Affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - A. Levi-Barda
- Biobank, Department of Pathology, Rabin Medical Center, Petah Tikva, Israel
| | - TT. Perets
- Gastroenterology Laboratory, Division of Gastroenterology, Rabin Medical Center, Petah Tikva, Israel,Adelson School of Medicine, Ariel University, Ariel, Israel
| | - R. Barkan
- Division of Gastroenterology, Rabin Medical Center, Petah-Tikva, Israel, Affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - I. Goren
- Division of Gastroenterology, Rabin Medical Center, Petah-Tikva, Israel, Affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel,Department of inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Ohio, USA
| | - JE. Ollech
- Division of Gastroenterology, Rabin Medical Center, Petah-Tikva, Israel, Affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - H. Yanai
- Division of Gastroenterology, Rabin Medical Center, Petah-Tikva, Israel, Affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - U. Gophna
- The Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - I. Dotan
- Division of Gastroenterology, Rabin Medical Center, Petah-Tikva, Israel, Affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel,CONTACT I. Dotan Division of Gastroenterology, Rabin Medical Center, Petah-Tikva, Israel, Affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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5
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Chabé M, Certad G, Caccio SM. Editorial: Enteric Unicellular Eukaryotic Parasites and Gut Microbiota: Mechanisms and Ecology. Front Microbiol 2021; 12:779412. [PMID: 34759914 PMCID: PMC8573350 DOI: 10.3389/fmicb.2021.779412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 10/04/2021] [Indexed: 11/24/2022] Open
Affiliation(s)
- Magali Chabé
- University Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Centre d'Infection et d'Immunité de Lille, Lille, France
| | - Gabriela Certad
- University Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Centre d'Infection et d'Immunité de Lille, Lille, France.,Délégation à la Recherche Clinique et à l'Innovation, Groupement des Hôpitaux de l'Institut Catholique de Lille, Lille, France
| | - Simone Mario Caccio
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
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Nourrisson C, Scanzi J, Brunet J, Delbac F, Dapoigny M, Poirier P. Prokaryotic and Eukaryotic Fecal Microbiota in Irritable Bowel Syndrome Patients and Healthy Individuals Colonized With Blastocystis. Front Microbiol 2021; 12:713347. [PMID: 34603241 PMCID: PMC8486285 DOI: 10.3389/fmicb.2021.713347] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 08/26/2021] [Indexed: 12/30/2022] Open
Abstract
Blastocystis is the most frequently isolated protozoan from human stool. Its role in human health is still debated, and a high prevalence was reported in irritable bowel syndrome (IBS) subjects, suggesting a potential link with microbiota. In the present study, we aimed to investigate prokaryotic and eukaryotic microbiota in both IBS-C (constipated) and healthy individuals. We recruited 35 IBS-C patients and 23 healthy subjects, from which 12 and 11 carried Blastocystis, respectively. We performed 16S and 18S rRNA high-throughput sequencing on feces. Whereas we did not observe differences between infected and non-infected controls, several phyla were significantly modified in IBS-C patients according to the presence of Blastocystis. Tenericutes phylum and Ruminococcaceae family were especially increased in Blastocystis carriers. Furthermore, colonization with Blastocystis was associated with discrete changes in the microbial eukaryome, particularly among the Fungi taxa. Depending on the group of patients considered, the mycobiota changes do not go in the same direction and seem more deleterious in the IBS-C group. These results encourage further in vivo and in vitro investigations concerning the role of Blastocystis in the gut environment.
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Affiliation(s)
- Céline Nourrisson
- Service de Parasitologie-Mycologie, CHU de Clermont-Ferrand, 3IHP, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Julien Scanzi
- Service de Médecine Digestive et Hépatobiliaire, CHU de Clermont-Ferrand, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Julie Brunet
- Service de Parasitologie-Mycologie, CHU de Clermont-Ferrand, 3IHP, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | | | - Michel Dapoigny
- Service de Médecine Digestive et Hépatobiliaire, CHU de Clermont-Ferrand, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Philippe Poirier
- Service de Parasitologie-Mycologie, CHU de Clermont-Ferrand, 3IHP, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
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Minardi D, Ryder D, Del Campo J, Garcia Fonseca V, Kerr R, Mortensen S, Pallavicini A, Bass D. Improved high throughput protocol for targeting eukaryotic symbionts in metazoan and eDNA samples. Mol Ecol Resour 2021; 22:664-678. [PMID: 34549891 PMCID: PMC9292944 DOI: 10.1111/1755-0998.13509] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 08/23/2021] [Accepted: 09/01/2021] [Indexed: 01/04/2023]
Abstract
Eukaryote symbionts of animals are major drivers of ecosystems not only because of their diversity and host interactions from variable pathogenicity but also through different key roles such as commensalism and to different types of interdependence. However, molecular investigations of metazoan eukaryomes require minimising coamplification of homologous host genes. In this study we (1) identified a previously published “antimetazoan” reverse primer to theoretically enable amplification of a wider range of microeukaryotic symbionts, including more evolutionarily divergent sequence types, (2) evaluated in silico several antimetazoan primer combinations, and (3) optimised the application of the best performing primer pair for high throughput sequencing (HTS) by comparing one‐step and two‐step PCR amplification approaches, testing different annealing temperatures and evaluating the taxonomic profiles produced by HTS and data analysis. The primer combination 574*F – UNonMet_DB tested in silico showed the largest diversity of nonmetazoan sequence types in the SILVA database and was also the shortest available primer combination for broadly‐targeting antimetazoan amplification across the 18S rRNA gene V4 region. We demonstrate that the one‐step PCR approach used for library preparation produces significantly lower proportions of metazoan reads, and a more comprehensive coverage of host‐associated microeukaryote reads than the two‐step approach. Using higher PCR annealing temperatures further increased the proportion of nonmetazoan reads in all sample types tested. The resulting V4 region amplicons were taxonomically informative even when only the forward read is analysed. This region also revealed a diversity of known and putatively parasitic lineages and a wider diversity of host‐associated eukaryotes.
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Affiliation(s)
- Diana Minardi
- Centre for Environment, Fisheries and Aquaculture Research, Weymouth, Dorset, UK.,Cefas, International Centre for Aquatic Animal Health, Weymouth, Dorset, UK
| | - David Ryder
- Centre for Environment, Fisheries and Aquaculture Research, Weymouth, Dorset, UK.,Cefas, International Centre for Aquatic Animal Health, Weymouth, Dorset, UK
| | - Javier Del Campo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Catalonia, Spain
| | - Vera Garcia Fonseca
- Centre for Environment, Fisheries and Aquaculture Research, Weymouth, Dorset, UK.,Cefas, International Centre for Aquatic Animal Health, Weymouth, Dorset, UK
| | - Rose Kerr
- Centre for Environment, Fisheries and Aquaculture Research, Weymouth, Dorset, UK.,Cefas, International Centre for Aquatic Animal Health, Weymouth, Dorset, UK
| | | | | | - David Bass
- Centre for Environment, Fisheries and Aquaculture Research, Weymouth, Dorset, UK.,Cefas, International Centre for Aquatic Animal Health, Weymouth, Dorset, UK.,Department of Life Sciences, The Natural History Museum, London, UK
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8
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Stensvold CR. Pinning down the role of common luminal intestinal parasitic protists in human health and disease - status and challenges. Parasitology 2019; 146:695-701. [PMID: 30732665 DOI: 10.1017/S0031182019000039] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
While some single-celled intestinal parasites are direct causes of diarrhoea and other types of intestinal pathology, the impact of other gut micro-eukaryotes on human health remains elusive. The fact that some common luminal intestinal parasitic protists (CLIPPs) have lately been found more often in healthy than in diseased individuals has fuelled the hypothesis that some parasites might in fact be protective against disease. To this end, the use of new DNA technologies has helped us investigate trans-kingdom relationships in the gut. However, research into these relationships is currently hampered by the limited data available on the genetic diversity within the CLIPPs genera, which results in limited efficacy of publicly available DNA sequence databases for taxonomic annotation of sequences belonging to the eukaryotic component of the gut microbiota. In this paper, I give a brief overview of the status on CLIPPs in human health and disease and challenges related to the mapping of intestinal eukaryotic diversity of the human gut.
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9
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Nieves-Ramírez ME, Partida-Rodríguez O, Laforest-Lapointe I, Reynolds LA, Brown EM, Valdez-Salazar A, Morán-Silva P, Rojas-Velázquez L, Morien E, Parfrey LW, Jin M, Walter J, Torres J, Arrieta MC, Ximénez-García C, Finlay BB. Asymptomatic Intestinal Colonization with Protist Blastocystis Is Strongly Associated with Distinct Microbiome Ecological Patterns. mSystems 2018; 3:e00007-18. [PMID: 29963639 DOI: 10.1128/mSystems.00007-18] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 05/02/2018] [Indexed: 12/25/2022] Open
Abstract
Given the results of our study and other reports of the effects of the most common human gut protist on the diversity and composition of the bacterial microbiome, Blastocystis and, possibly, other gut protists should be studied as ecosystem engineers that drive community diversity and composition. Blastocystis is the most prevalent protist of the human intestine, colonizing approximately 20% of the North American population and up to 100% in some nonindustrialized settings. Blastocystis is associated with gastrointestinal and systemic disease but can also be an asymptomatic colonizer in large populations. While recent findings in humans have shown bacterial microbiota changes associated with this protist, it is unknown whether these occur due to the presence of Blastocystis or as a result of inflammation. To explore this, we evaluated the fecal bacterial and eukaryotic microbiota in 156 asymptomatic adult subjects from a rural population in Xoxocotla, Mexico. Colonization with Blastocystis was strongly associated with an increase in bacterial alpha diversity and broad changes in beta diversity and with more discrete changes to the microbial eukaryome. More than 230 operational taxonomic units (OTUs), including those of dominant species Prevotella copri and Ruminococcus bromii, were differentially abundant in Blastocystis-colonized individuals. Large functional changes accompanied these observations, with differential abundances of 202 (out of 266) predicted metabolic pathways (PICRUSt), as well as lower fecal concentrations of acetate, butyrate, and propionate in colonized individuals. Fecal calprotectin was markedly decreased in association with Blastocystis colonization, suggesting that this ecological shift induces subclinical immune consequences to the asymptomatic host. This work is the first to show a direct association between the presence of Blastocystis and shifts in the gut bacterial and eukaryotic microbiome in the absence of gastrointestinal disease or inflammation. These results prompt further investigation of the role Blastocystis and other eukaryotes play within the human microbiome. IMPORTANCE Given the results of our study and other reports of the effects of the most common human gut protist on the diversity and composition of the bacterial microbiome, Blastocystis and, possibly, other gut protists should be studied as ecosystem engineers that drive community diversity and composition.
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10
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Heitlinger E, Ferreira SCM, Thierer D, Hofer H, East ML. The Intestinal Eukaryotic and Bacterial Biome of Spotted Hyenas: The Impact of Social Status and Age on Diversity and Composition. Front Cell Infect Microbiol 2017; 7:262. [PMID: 28670573 PMCID: PMC5472691 DOI: 10.3389/fcimb.2017.00262] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 06/02/2017] [Indexed: 01/24/2023] Open
Abstract
In mammals, two factors likely to affect the diversity and composition of intestinal bacteria (bacterial microbiome) and eukaryotes (eukaryome) are social status and age. In species in which social status determines access to resources, socially dominant animals maintain better immune processes and health status than subordinates. As high species diversity is an index of ecosystem health, the intestinal biome of healthier, socially dominant animals should be more diverse than those of subordinates. Gradual colonization of the juvenile intestine after birth predicts lower intestinal biome diversity in juveniles than adults. We tested these predictions on the effect of: (1) age (juvenile/adult) and (2) social status (low/high) on bacterial microbiome and eukaryome diversity and composition in the spotted hyena (Crocuta crocuta), a highly social, female-dominated carnivore in which social status determines access to resources. We comprehensively screened feces from 35 individually known adult females and 7 juveniles in the Serengeti ecosystem for bacteria and eukaryotes, using a set of 48 different amplicons (4 for bacterial 16S, 44 for eukaryote 18S) in a multi-amplicon sequencing approach. We compared sequence abundances to classical coprological egg or oocyst counts. For all parasite taxa detected in more than six samples, the number of sequence reads significantly predicted the number of eggs or oocysts counted, underscoring the value of an amplicon sequencing approach for quantitative measurements of parasite load. In line with our predictions, our results revealed a significantly less diverse microbiome in juveniles than adults and a significantly higher diversity of eukaryotes in high-ranking than low-ranking animals. We propose that free-ranging wildlife can provide an intriguing model system to assess the adaptive value of intestinal biome diversity for both bacteria and eukaryotes.
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Affiliation(s)
- Emanuel Heitlinger
- Research Group Ecology and Evolution of Molecular Parasite Host Interactions, Leibniz Institute for Zoo and Wildlife ResearchBerlin, Germany.,Institute for Biology, Molecular Parasitology, Humboldt UniversityBerlin, Germany
| | - Susana C M Ferreira
- Department of Evolutionary Ecology, Leibniz Institute for Zoo and Wildlife ResearchBerlin, Germany
| | - Dagmar Thierer
- Department of Evolutionary Ecology, Leibniz Institute for Zoo and Wildlife ResearchBerlin, Germany
| | - Heribert Hofer
- Department of Evolutionary Ecology, Leibniz Institute for Zoo and Wildlife ResearchBerlin, Germany
| | - Marion L East
- Department of Evolutionary Ecology, Leibniz Institute for Zoo and Wildlife ResearchBerlin, Germany
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