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Geyer JK, Grunberg RL, Wang J, Mitchell CE. Leaf age structures phyllosphere microbial communities in the field and greenhouse. Front Microbiol 2024; 15:1429166. [PMID: 39206365 PMCID: PMC11349622 DOI: 10.3389/fmicb.2024.1429166] [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: 05/07/2024] [Accepted: 07/25/2024] [Indexed: 09/04/2024] Open
Abstract
The structure of the leaf microbiome can alter host fitness and change in response to abiotic and biotic factors, like seasonality, climate, and leaf age. However, relatively few studies consider the influence of host age on microbial communities at a time scale of a few days, a short time scale relevant to microbes. To understand how host age modulates changes in the fungal and bacterial leaf microbiome on a short time scale, we ran independent field and greenhouse-based studies and characterized phyllosphere communities using next-generation sequencing approaches. Our field study characterized changes in the fungal and bacterial phyllosphere by examining leaves of different relative ages across individuals, whereas the greenhouse study examined changes in the fungal microbiome by absolute leaf age across individuals. Together, these results indicate that fungal communities are susceptible to change as a leaf ages as evidenced by shifts in the diversity of fungal taxa both in the field and the greenhouse. Similarly, there were increases in the diversity of fungal taxa by leaf age in the greenhouse. In bacterial communities in the field, we observed changes in the diversity, composition, and relative abundance of common taxa. These findings build upon previous literature characterizing host-associated communities at longer time scales and provide a foundation for targeted work examining how specific microbial taxa might interact with each other, such as fine-scale interactions between pathogenic and non-pathogenic species.
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Affiliation(s)
- Julie K. Geyer
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Rita L. Grunberg
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Wilson Center for Science and Justice at Duke Law, Durham, NC, United States
| | - Jeremy Wang
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Charles E. Mitchell
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Environment, Ecology, and Energy Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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Ilík V, Schwarz EM, Nosková E, Pafčo B. Hookworm genomics: dusk or dawn? Trends Parasitol 2024; 40:452-465. [PMID: 38677925 DOI: 10.1016/j.pt.2024.04.003] [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: 02/27/2024] [Revised: 03/28/2024] [Accepted: 04/04/2024] [Indexed: 04/29/2024]
Abstract
Hookworms are parasites, closely related to the model nematode Caenorhabditis elegans, that are a major economic and health burden worldwide. Primarily three hookworm species (Necator americanus, Ancylostoma duodenale, and Ancylostoma ceylanicum) infect humans. Another 100 hookworm species from 19 genera infect primates, ruminants, and carnivores. Genetic data exist for only seven of these species. Genome sequences are available from only four of these species in two genera, leaving 96 others (particularly those parasitizing wildlife) without any genomic data. The most recent hookworm genomes were published 5 years ago, leaving the field in a dusk. However, assembling genomes from single hookworms may bring a new dawn. Here we summarize advances, challenges, and opportunities for studying these neglected but important parasitic nematodes.
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Affiliation(s)
- Vladislav Ilík
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic; Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic.
| | - Erich M Schwarz
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Eva Nosková
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic; Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Barbora Pafčo
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic.
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Mason B, Cervena B, Frias L, Goossens B, Hasegawa H, Keuk K, Langgeng A, Majewski K, Matsumoto T, Matsuura K, Mendonça R, Okamoto M, Peter S, Petrzelkova KJ, Sipangkui S, Xu Z, Pafco B, MacIntosh AJ. Novel insight into the genetic diversity of strongylid nematodes infecting South-East and East Asian primates. Parasitology 2024; 151:514-522. [PMID: 38629119 PMCID: PMC11106507 DOI: 10.1017/s0031182024000386] [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: 01/12/2024] [Revised: 03/21/2024] [Accepted: 03/21/2024] [Indexed: 05/18/2024]
Abstract
With many non-human primates (NHPs) showing continued population decline, there is an ongoing need to better understand their ecology and conservation threats. One such threat is the risk of disease, with various bacterial, viral and parasitic infections previously reported to have damaging consequences for NHP hosts. Strongylid nematodes are one of the most commonly reported parasitic infections in NHPs. Current knowledge of NHP strongylid infections is restricted by their typical occurrence as mixed infections of multiple genera, which are indistinguishable through traditional microscopic approaches. Here, modern metagenomics approaches were applied for insight into the genetic diversity of strongylid infections in South-East and East Asian NHPs. We hypothesized that strongylid nematodes occur in mixed communities of multiple taxa, dominated by Oesophagostomum, matching previous findings using single-specimen genetics. Utilizing the Illumina MiSeq platform, ITS-2 strongylid metabarcoding was applied to 90 samples from various wild NHPs occurring in Malaysian Borneo and Japan. A clear dominance of Oesophagostomum aculeatum was found, with almost all sequences assigned to this species. This study suggests that strongylid communities of Asian NHPs may be less species-rich than those in African NHPs, where multi-genera communities are reported. Such knowledge contributes baseline data, assisting with ongoing monitoring of health threats to NHPs.
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Affiliation(s)
- Bethan Mason
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Barbora Cervena
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Liesbeth Frias
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Benoit Goossens
- Danau Girang Field Centre, c/o Sabah Wildlife Department, Kota Kinabalu, Sabah, Malaysia
- Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Cardiff, UK
| | - Hideo Hasegawa
- Department of Biomedicine, Faculty of Medicine, Oita University, Oita, Japan
| | - Kenneth Keuk
- Wildlife Research Center, Kyoto University, Inuyama Campus, Inuyama, Japan
| | - Abdullah Langgeng
- Wildlife Research Center, Kyoto University, Inuyama Campus, Inuyama, Japan
| | - Kasia Majewski
- Wildlife Research Center, Kyoto University, Inuyama Campus, Inuyama, Japan
| | - Takashi Matsumoto
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Japan
| | - Keiko Matsuura
- Department of Biomedicine, Faculty of Medicine, Oita University, Oita, Japan
| | - Renata Mendonça
- Wildlife Research Center, Kyoto University, Kyoto, Japan
- Centre for Functional Ecology – Science for People & the Planet, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Munehiro Okamoto
- Center for the Evolutionary Origins of Human Behavior (EHUB), Kyoto University, Kyoto, Japan
| | - Steve Peter
- Kulliyah of Science, Department of Biotechnology, International Islamic University of Malaysia, Kuantan, Pahang, Malaysia
| | - Klara J. Petrzelkova
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Liberec Zoo, Liberec, Czech Republic
| | | | - Zhihong Xu
- Wildlife Research Center, Kyoto University, Inuyama Campus, Inuyama, Japan
| | - Barbora Pafco
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
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Ilík V, Kreisinger J, Modrý D, Schwarz EM, Tagg N, Mbohli D, Nkombou IC, Petrželková KJ, Pafčo B. High diversity and sharing of strongylid nematodes in humans and great apes co-habiting an unprotected area in Cameroon. PLoS Negl Trop Dis 2023; 17:e0011499. [PMID: 37624869 PMCID: PMC10484444 DOI: 10.1371/journal.pntd.0011499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 09/07/2023] [Accepted: 07/03/2023] [Indexed: 08/27/2023] Open
Abstract
Rapid increases in human populations and environmental changes of past decades have led to changes in rates of contact and spatial overlap with wildlife. Together with other historical, social and environmental processes, this has significantly contributed to pathogen transmission in both directions, especially between humans and non-human primates, whose close phylogenetic relationship facilitates cross-infections. Using high-throughput amplicon sequencing, we studied strongylid communities in sympatric western lowland gorillas, central chimpanzees and humans co-occurring in an unprotected area in the northern periphery of the Dja Faunal Reserve, Cameroon. At the genus level, we classified 65 strongylid ITS-2 amplicon sequencing variants (ASVs) in humans and great apes. Great apes exhibited higher strongylid diversity than humans. Necator and Oesophagostomum were the most prevalent genera, and we commonly observed mixed infections of more than one strongylid species. Human strongylid communities were dominated by the human hookworm N. americanus, while great apes were mainly infected with N. gorillae, O. stephanostomum and trichostrongylids. We were also able to detect rare strongylid taxa (such as Ancylostoma and Ternidens). We detected eight ASVs shared between humans and great apes (four N. americanus variants, two N. gorillae variants, one O. stephanostomum type I and one Trichostrongylus sp. type II variant). Our results show that knowledge of strongylid communities in primates, including humans, is still limited. Sharing the same habitat, especially outside protected areas (where access to the forest is not restricted), can enable mutual parasite exchange and can even override host phylogeny or conserved patterns. Such studies are critical for assessing the threats posed to all hosts by increasing human-wildlife spatial overlap. In this study, the term "contact" refers to physical contact, while "spatial overlap" refers to environmental contact.
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Affiliation(s)
- Vladislav Ilík
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Jakub Kreisinger
- Department of Zoology, Faculty of Science, Charles University, Praha, Czech Republic
| | - David Modrý
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czech Republic
- Department of Veterinary Sciences, Faculty of Agrobiology, Food and Natural Resources/CINeZ, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Erich Marquard Schwarz
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Nikki Tagg
- Centre for Research and Conservation/KMDA, Antwerp, Belgium
| | - Donald Mbohli
- Association de la Protection des Grands Singes, Yaoundé, Cameroon
| | | | - Klára Judita Petrželková
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | - Barbora Pafčo
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
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