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Miller ML, Rota C, Welsh A. Transforming gastrointestinal helminth parasite identification in vertebrate hosts with metabarcoding: a systematic review. Parasit Vectors 2024; 17:311. [PMID: 39030625 PMCID: PMC11265005 DOI: 10.1186/s13071-024-06388-1] [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: 02/24/2024] [Accepted: 07/03/2024] [Indexed: 07/21/2024] Open
Abstract
BACKGROUND Gastrointestinal helminths are a very widespread group of intestinal parasites that can cause major health issues in their hosts, including severe illness or death. Traditional methods of helminth parasite identification using microscopy are time-consuming and poor in terms of taxonomic resolution, and require skilled observers. DNA metabarcoding has emerged as a powerful alternative for assessing community composition in a variety of sample types over the last few decades. While metabarcoding approaches have been reviewed for use in other research areas, the use of metabarcoding for parasites has only recently become widespread. As such, there is a need to synthesize parasite metabarcoding methodology and highlight the considerations to be taken into account when developing a protocol. METHODS We reviewed published literature that utilized DNA metabarcoding to identify gastrointestinal helminth parasites in vertebrate hosts. We extracted information from 62 peer-reviewed papers published between 2014 and 2023 and created a stepwise guide to the metabarcoding process. RESULTS We found that studies in our review varied in technique and methodology, such as the sample type utilized, genetic marker regions targeted and bioinformatic databases used. The main limitations of metabarcoding are that parasite abundance data may not be reliably attained from sequence read numbers, metabarcoding data may not be representative of the species present in the host and the cost and bioinformatic expertise required to utilize this method may be prohibitive to some groups. CONCLUSIONS Overall, using metabarcoding to assess gastrointestinal parasite communities is preferable to traditional methods, yielding higher taxonomic resolution, higher throughput and increased versatility due to its utility in any geographical location, with a variety of sample types, and with virtually any vertebrate host species. Additionally, metabarcoding has the potential for exciting new discoveries regarding host and parasite evolution.
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Affiliation(s)
- Madison L Miller
- Division of Forestry and Natural Resources, West Virginia University, Morgantown, WV, USA.
| | - Christopher Rota
- Division of Forestry and Natural Resources, West Virginia University, Morgantown, WV, USA
| | - Amy Welsh
- Division of Forestry and Natural Resources, West Virginia University, Morgantown, WV, USA
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Donohue ME, Hert ZL, Karrick CE, Rowe AK, Wright PC, Randriamanandaza LJ, Zakamanana F, Nomenjanahary ES, Everson KM, Weisrock DW. Lemur Gut Microeukaryotic Community Variation Is Not Associated with Host Phylogeny, Diet, or Habitat. MICROBIAL ECOLOGY 2023; 86:2149-2160. [PMID: 37133496 DOI: 10.1007/s00248-023-02233-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 04/26/2023] [Indexed: 05/04/2023]
Abstract
Identifying the major forces driving variation in gut microbiomes enhances our understanding of how and why symbioses between hosts and microbes evolved. Gut prokaryotic community variation is often closely associated with host evolutionary and ecological variables. Whether these same factors drive variation in other microbial taxa occupying the animal gut remains largely untested. Here, we present a one-to-one comparison of gut prokaryotic (16S rRNA metabarcoding) and microeukaryotic (18S rRNA metabarcoding) community patterning among 12 species of wild lemurs. Lemurs were sampled from dry forests and rainforests of southeastern Madagascar and display a range of phylogenetic and ecological niche diversity. We found that while lemur gut prokaryotic community diversity and composition vary with host taxonomy, diet, and habitat, gut microeukaryotic communities have no detectable association with any of these factors. We conclude that gut microeukaryotic community composition is largely random, while gut prokaryotic communities are conserved among host species. It is likely that a greater proportion of gut microeukaryotic communities comprise taxa with commensal, transient, and/or parasitic symbioses compared with gut prokaryotes, many of which form long-term relationships with the host and perform important biological functions. Our study highlights the importance of greater specificity in microbiome research; the gut microbiome contains many "omes" (e.g., prokaryome, eukaryome), each comprising different microbial taxa shaped by unique selective pressures.
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Affiliation(s)
- Mariah E Donohue
- Department of Biology, University of Kentucky, 101 T.H.M. Building, Lexington, KY, 40506, USA.
| | - Zoe L Hert
- Department of Biology, University of Kentucky, 101 T.H.M. Building, Lexington, KY, 40506, USA
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Carly E Karrick
- Department of Biology, University of Kentucky, 101 T.H.M. Building, Lexington, KY, 40506, USA
- Department of BioSciences, Rice University, Houston, TX, USA
| | - Amanda K Rowe
- Interdepartmental Doctoral Program in Anthropological Sciences, Stony Brook University, Stony Brook, New York, USA
| | - Patricia C Wright
- Department of Anthropology, Stony Brook University, Stony Brook, NY, USA
- Centre ValBio Research Station, Ranomafana, MD, USA
| | | | | | | | - Kathryn M Everson
- Department of Biology, University of Kentucky, 101 T.H.M. Building, Lexington, KY, 40506, USA
| | - David W Weisrock
- Department of Biology, University of Kentucky, 101 T.H.M. Building, Lexington, KY, 40506, USA
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Zhao J, Yao Y, Li D, Zhu W, Xiao H, Xie M, Xiong Y, Wu J, Ni Q, Zhang M, Xu H. Metagenome and metabolome insights into the energy compensation and exogenous toxin degradation of gut microbiota in high-altitude rhesus macaques (Macaca mulatta). NPJ Biofilms Microbiomes 2023; 9:20. [PMID: 37081021 PMCID: PMC10119431 DOI: 10.1038/s41522-023-00387-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 03/29/2023] [Indexed: 04/22/2023] Open
Abstract
There have been many reports on the genetic mechanism in rhesus macaques (RMs) for environmental adaptation to high altitudes, but the synergistic involvement of gut microbiota in this adaptation remains unclear. Here we performed fecal metagenomic and metabolomic studies on samples from high- and low-altitude populations to assess the synergistic role of gut microbiota in the adaptation of RMs to high-altitude environments. Microbiota taxonomic annotation yielded 7471 microbiota species. There were 37 bacterial species whose abundance was significantly enriched in the high-altitude populations, 16 of which were previously reported to be related to the host's dietary digestion and energy metabolism. Further functional gene enrichment found a stronger potential for gut microbiota to synthesize energy substrate acetyl-CoA using CO2 and energy substrate pyruvate using oxaloacetate, as well as a stronger potential to transform acetyl-CoA to energy substrate acetate in high-altitude populations. Interestingly, there were no apparent differences between low-altitude and high-altitude populations in terms of genes enriched in the main pathways by which the microbiota consumed the three energy substrates, and none of the three energy substrates were detected in the fecal metabolites. These results strongly suggest that gut microbiota plays an important energy compensatory role that helps RMs to adapt to high-altitude environments. Further functional enrichment after metabolite source analysis indicated the abundance of metabolites related to the degradation of exogenous toxins was also significantly higher in high-altitude populations, which suggested a contributory role of gut microbiota to the degradation of exogenous toxins in wild RMs adapted to high-altitude environments.
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Affiliation(s)
- Junsong Zhao
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
- College of Agronomy and Life Sciences, Zhaotong University, Zhaotong, 657000, China
| | - Yongfang Yao
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Diyan Li
- School of Pharmacy, Chengdu University, Chengdu, 610106, China
| | - Wei Zhu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hongtao Xiao
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Meng Xie
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Ying Xiong
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Jiayun Wu
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Qingyong Ni
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Mingwang Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Huailiang Xu
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China.
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Kapsetaki SE, Marquez Alcaraz G, Maley CC, Whisner CM, Aktipis A. Diet, Microbes, and Cancer Across the Tree of Life: a Systematic Review. Curr Nutr Rep 2022; 11:508-525. [PMID: 35704266 PMCID: PMC9197725 DOI: 10.1007/s13668-022-00420-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2022] [Indexed: 11/09/2022]
Abstract
PURPOSE OF REVIEW Cancers are a leading cause of death in humans and for many other species. Diet has often been associated with cancers, and the microbiome is an essential mediator between diet and cancers. Here, we review the work on cancer and the microbiome across species to search for broad patterns of susceptibility associated with different microbial species. RECENT FINDINGS Some microbes, such as Helicobacter bacteria, papillomaviruses, and the carnivore-associated Fusobacteria, consistently induce tumorigenesis in humans and other species. Other microbes, such as the milk-associated Lactobacillus, consistently inhibit tumorigenesis in humans and other species. We systematically reviewed over a thousand published articles and identified links between diet, microbes, and cancers in several species of mammals, birds, and flies. Future work should examine a larger variety of host species to discover new model organisms for human preclinical trials, to better understand the observed variance in cancer prevalence across species, and to discover which microbes and diets are associated with cancers across species. Ultimately, this could help identify microbial and dietary interventions to diagnose, prevent, and treat cancers in humans as well as other animals.
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Affiliation(s)
- Stefania E Kapsetaki
- Arizona Cancer Evolution Center, Biodesign Institute and School of Life Sciences, Arizona State University, Tempe, AZ, USA.
- Biodesign Center for Biocomputing, Security and Society, Arizona State University, Tempe, USA.
| | - Gissel Marquez Alcaraz
- Arizona Cancer Evolution Center, Biodesign Institute and School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Biodesign Center for Biocomputing, Security and Society, Arizona State University, Tempe, USA
| | - Carlo C Maley
- Arizona Cancer Evolution Center, Biodesign Institute and School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Biodesign Center for Biocomputing, Security and Society, Arizona State University, Tempe, USA
| | - Corrie M Whisner
- College of Health Solutions, Arizona State University, Phoenix, AZ, USA
- Biodesign Center for Health Through Microbiomes, Arizona State University, Tempe, AZ, USA
| | - Athena Aktipis
- Arizona Cancer Evolution Center, Biodesign Institute and School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Department of Psychology, Arizona State University, Tempe, AZ, USA
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Gohar D, Põldmaa K, Tedersoo L, Aslani F, Furneaux B, Henkel TW, Saar I, Smith ME, Bahram M. Global diversity and distribution of mushroom-inhabiting bacteria. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:254-264. [PMID: 35102713 DOI: 10.1111/1758-2229.13045] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 01/11/2022] [Accepted: 01/14/2022] [Indexed: 06/14/2023]
Abstract
Mushroom-forming fungi are important sources of food and medicine in many regions of the world, and their development and health are known to depend on various microbes. Recent studies have examined the structure of mushroom-inhabiting bacterial (MIB) communities and their association with local environmental variables, but global-scale diversity and determinants of these communities remain poorly understood. Here we examined the MIB global diversity and community composition in relation to climate, soil and host factors. We found a core global mushroom microbiome, accounting for 30% of sequence reads, while comprising a few bacterial genera such as Halomonas, Serratia, Bacillus, Cutibacterium, Bradyrhizobium and Burkholderia. Our analysis further revealed an important role of host phylogeny in shaping the communities of MIB, whereas the effects of climate and soil factors remained negligible. The results suggest that the communities of MIB and free-living bacteria are structured by contrasting community assembly processes and that fungal-bacterial interactions are an important determinant of MIB community structure.
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Affiliation(s)
- Daniyal Gohar
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi St. 2, Tartu, 50409, Estonia
| | - Kadri Põldmaa
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi St. 2, Tartu, 50409, Estonia
- Natural History Museum and Botanical Garden, University of Tartu, Vanemuise 46, Tartu, 51003, Estonia
| | - Leho Tedersoo
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi St. 2, Tartu, 50409, Estonia
| | - Farzad Aslani
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi St. 2, Tartu, 50409, Estonia
- School of Environmental and Rural Sciences, University of New England, Armidale, NSW, Australia
| | - Brendan Furneaux
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, Uppsala, 75236, Sweden
| | - Terry W Henkel
- Department of Biological Sciences, Humboldt State University, Arcata, CA, USA
| | - Irja Saar
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi St. 2, Tartu, 50409, Estonia
| | - Matthew E Smith
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls väg 16, Uppsala, 756 51, Sweden
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